Re: [ECOLOG-L] Faculty Job Postings for UNB Saint John

[Jeff Houlahan]

Dear ECOLOGers, please find two job ads for assistant professor listed below.  
We will begin reviewing applications this week but the preliminaries will take 
a few weeks so there is still time to get applications in.   Jeff Houlahan


DEPARTMENT OF BIOLOGICAL SCIENCES
FACULTY OF SCIENCE, APPLIED SCIENCE & ENGINEERING
The Department of Biological Sciences at the University of New Brunswick Saint 
John invites applications for a tenure-track appointment at the Assistant 
Professor level, beginning preferably July 1, 2018. The position is subject to 
final budgetary approval.
The successful candidate will be a Marine Microbiologist with research 
interests in the evolution, ecology, physiology, biodiversity and/or 
biochemistry of marine micro-organisms including bacteria, archaea, viruses, 
fungi and/or protists.
Qualifications include a PhD degree and clear evidence of strong research 
ability, as the successful candidate will be expected to establish an 
externally funded research program and be involved in supervision of BSc 
(Honors) and graduate (MSc and PhD) students. She/he will also be expected to 
contribute to the development and activity of a new regional research 
initiative in Coastal Studies, which is led by the Department. The successful 
candidate will be responsible for teaching three undergraduate courses 
annually, two Introductory Microbiology courses (to Biology and Nursing 
students) and one upper-level course in their area of expertise, potentially 
during our Marine Semester at the Huntsman Marine Science Centre in St. 
Andrews, NB. UNB Saint John has a strong commitment to teaching, and a 
demonstrated excellence in teaching will be an asset.
The Department of Biological Sciences offers 4-year BSc degrees in Marine 
Biology, Biology, Environmental Biology, and Biology-Psychology. It has 17 
faculty members with research expertise in marine biology, evolution, ecology, 
physiology, geology, natural products chemistry, aquaculture, fisheries, 
environmental biology and biodiversity. For more information, visit the 
Departmental website: http://bit.ly/2Fmu0TB. The candidate will also have the 
opportunity to develop collaborations with the Canadian Rivers Institute, the 
DFO St. Andrews Biological Station, and the Huntsman Marine Science Centre.

Applicants are requested to submit electronically (preferably as a single PDF) 
a curriculum vitae, the names and addresses (e-mail and telephone number) of 
three referees, a statement of research interests, a statement of teaching 
philosophy, and up to three reprints of recent publications to:
Dr. Rémy Rochette, Chair of Biological Sciences
Email: sjb...@unb.ca<mailto:sjb...@unb.ca>
Review of applications will begin on March 1, 2018 and will continue until the 
position is filled.
All qualified candidates are encouraged to apply; however, Canadians and 
permanent residents will be given priority.  Applicants should indicate their 
current citizenship status.





DEPARTMENT OF BIOLOGICAL SCIENCES
FACULTY OF SCIENCE, APPLIED SCIENCE & ENGINEERING
The Department of Biological Sciences at the University of New Brunswick Saint 
John invites applications for a tenure-track appointment at the Assistant 
Professor level, beginning preferably July 1, 2018. The position is subject to 
final budgetary approval.
The successful candidate will be a Marine Biochemist or Marine Biogeochemist 
with research interests at the chemistry-biology interface of marine organisms 
and environments, such as marine ecotoxicology, marine chemical pollution and 
eutrophication, natural products chemistry, chemical oceanography, as well as 
carbon sequestration and climate change.
Qualifications include a PhD degree and clear evidence of strong research 
ability, as the successful candidate will be expected to establish an 
externally funded research program and be involved in supervision of BSc 
(Honors) and graduate (MSc and PhD) students. She/he will also be expected to 
contribute to the development and activity of a new regional research 
initiative in Coastal Studies, which is led by the Department. The successful 
candidate will be responsible for teaching three undergraduate courses 
annually, Introductory Biochemistry, Organic Chemistry, and an upper-level 
courses in their area of expertise, potentially during our Marine Semester at 
the Huntsman Marine Science Centre in St. Andrews, NB. UNB Saint John has a 
strong commitment to teaching, and a demonstrated excellence in teaching will 
be an asset.
The Department of Biological Sciences offers 4-year BSc degrees in Marine 
Biology, Biology, Environmental Biology, and Biology-Psychology. It has 17 
faculty members with research expertise in marine biology, evolution, ecology, 
physiology, geology, natural products chemistry, aquaculture, fisheries, 
environmental biology and biodiversity. For more information, visit the 
Departmental website: http://bit.ly/2Fmu0TB. The candidate 

[ECOLOG-L] Houlahan Ph. D. position

[Jeff Houlahan]

Ph. D. position with Jeff Houlahan's lab in the Department of Biological 
Sciences/The Canadian Rivers Institute, University of New Brunswick Saint John 
(UNB Saint John).


 The Houlahan lab is looking for a Ph.D. student interested in fundamental 
questions in population and/or community ecology to begin in the fall of 2017 
(although later start dates could be negotiated).  We are happy to hear from 
students with a wide range of interests -  some examples of topics include (i) 
the relationship between diversity and stability, (ii) the relative importance 
of density dependent effects on population dynamics, and (iii) the stability of 
competitive hierarchies in nature but we are less concerned about the question 
than the approach.  The approach would involve developing theoretical and/or 
statistical models that would then be tested on new data (see Houlahan et al. 
2017 in Oikos) to assess the predictive ability of those models and how 
predictive ability changes over time and space.


The successful applicant will have strong quantitative skills, and more 
particularly, be somebody who is comfortable analyzing data and modeling in 
something like R or Python.  Students will have an opportunity to improve their 
analytical and modeling skills, become better grounded in basic ecology theory, 
and improve writing, logical thinking and problem-solving abilities.  We are 
interested in ecology, environmental science, computer science and/or 
mathematics students.  Funding of at least $21,000/year is guaranteed for 4 
years and comes from TA'ships, RA'ships and scholarships.


The University of New Brunswick is a comprehensive university with campuses in 
Saint John and Fredericton, New Brunswick, Canada with approximately 10,000 
students.  The Houlahan lab is part of the Department of Biological Sciences 
and The Canadian Rivers Institute at the Saint John campus.  This is a vibrant 
department with a focus on aquatic and marine biology and more than 50 graduate 
students.  Saint John is a small (pop - 68,000) attractive, coastal city in 
southern New Brunswick.


If you are interested in the position drop me a note  at 
jeffh...@unb.ca  and attach your cv, transcripts 
(unofficial or official) and 3 references with contact info.


Expiry date: July 1, 2017.?

[ECOLOG-L] Houlahan Ph. D. position

[Jeff Houlahan]

Ph. D. position with Jeff Houlahan's lab in the Department of Biological 
Sciences/The Canadian Rivers Institute, University of New Brunswick Saint John 
(UNB Saint John).


 The Houlahan lab is looking for a Ph.D. student interested in fundamental 
questions in population and/or community ecology to begin in the fall of 2017 
(although later start dates could be negotiated).  We are happy to hear from 
students with a wide range of interests -  some examples of topics include (i) 
the relationship between diversity and stability, (ii) the relative importance 
of density dependent effects on population dynamics, and (iii) the stability of 
competitive hierarchies in nature but we are less concerned about the question 
than the approach.  The approach would involve developing theoretical and/or 
statistical models that would then be tested on new data (see Houlahan et al. 
2017 in Oikos) to assess the predictive ability of those models and how 
predictive ability changes over time and space.


The successful applicant will have strong quantitative skills, and more 
particularly, be somebody who is comfortable analyzing data and modeling in 
something like R or Python.  Students will have an opportunity to improve their 
analytical and modeling skills, become better grounded in basic ecology theory, 
and improve writing, logical thinking and problem-solving abilities.  We are 
interested in ecology, environmental science, computer science and/or 
mathematics students.  Funding of at least $21,000/year is guaranteed for 4 
years and comes from TA'ships, RA'ships and scholarships.


The University of New Brunswick is a comprehensive university with campuses in 
Saint John and Fredericton, New Brunswick, Canada with approximately 10,000 
students.  The Houlahan lab is part of the Department of Biological Sciences 
and The Canadian Rivers Institute at the Saint John campus.  This is a vibrant 
department with a focus on aquatic and marine biology and more than 50 graduate 
students.  Saint John is a small (pop - 68,000) attractive, coastal city in 
southern New Brunswick.


If you are interested in the position drop me a note  at 
jeffh...@unb.ca  and attach your cv, transcripts 
(unofficial or official) and 3 references with contact info.


Expiry date: July 1, 2017.

Re: [ECOLOG-L] Query on authorship

[Jeff Houlahan]

Hi Gary and all, this one's an interesting one.  Your position is one I have a 
lot of sympathy for - it's generous and gives credit where it's due.  What 
makes this tricky is that it also gives responsibility that somebody might not 
want to accept.  I know it's unlikely and not that common but there may be 
instances where somebody would prefer not to have their name on a paper where 
they've done enough work to warrant authorship.  If my name showed up on a 
paper without me ever being aware that it had been submitted I would be a 
little bothered.  If I read the paper and didn't agree with the interpretation 
I would be very unhappy.  That said, the idea of not giving credit to somebody 
who deserves it just seems wrong.  This is a rock and a hard place. Best, Jeff 
Houlahan


From: Ecological Society of America: grants, jobs, news 
<ECOLOG-L@LISTSERV.UMD.EDU> on behalf of Gary Grossman <gdgross...@gmail.com>
Sent: August 20, 2016 12:04 PM
To: ECOLOG-L@LISTSERV.UMD.EDU
Subject: Re: [ECOLOG-L] Query on authorship

Querido Jorge, this is a murky area of co-authorship except for one point. 
Coauthorship is *earned* and should not be taken away because of some other 
circumstance outside of the project responsibilities. Given that the second 
student completed the work while they were at your institution, the simple 
solution, given that they did indeed earn coauthorship, is to put them on the 
paper with your institutional address. If you're worried about someone 
contacting them then just asterisk their name and in the footnote put "current 
address unknown". !Eso!  g2

On Fri, Aug 19, 2016 at 3:24 PM, Jorge A. Santiago-Blay 
<blayjo...@gmail.com<mailto:blayjo...@gmail.com>> wrote:
Query on authorship

Dear Colleagues:

I am writing a small paper resulting from research done with two undergraduates 
many years ago (and, later on, involving several other colleagues using 
cutting-edge technology). As the results became obvious, both of the students 
agreed (orally, in person) with me that we should get the research published. 
As far as I remember, there was no email or letter documenting that and, there 
was no manuscript, only the data and the methods we were using.

The problem: I have located one of the former students (now a researcher at a 
major research institution), who is excited about getting the research 
published, but not the second student.

Question: How to handle the contribution (including authorship) of the other 
person? Here are some options I see.

a. Omit the name of the person that has not been located and indicate that 
another person was involved in the data collection but we were hot able to 
locate him/her to get his/her approval to use his/her name as an author.  Under 
these circumstances, would it be OK to name the person in the Acknowledgments? 
Lately, I am asking permission to do that because sometimes some people prefer 
to remain anonymous.

b. Include the name of the person I cannot locate as an author, an act of 
fairness and good faith on my part. If the person does not like the idea (and 
the paper is published) retract the name of the person in an erratum, later on, 
and assume responsibility for my error. A kind colleague did that to me once 
and, subsequently, it has resulted a long standing collaboration (and 
co-authorship in many papers, with my knowledge) :)

c. Nor use the data garnered by the person I cannot locate. Although I am 
pretty sure I am authorized by the institution to use the data, as a general 
personal; preference, I like to ask permission.

If you have something constructive to comment, kindly direct your comments to 
me, blayjo...@gmail.com<mailto:blayjo...@gmail.com> ,

Apologies for potential duplicate emails.

Sincerely,

Jorge

Jorge A. Santiago-Blay, PhD
blaypublishers.com<http://blaypublishers.com>


1. Positive experiences for authors of papers published in LEB 
http://blaypublishers.com/testimonials/

2. Free examples of papers published in LEB: 
http://blaypublishers.com/category/previous-issues/.

3. Guidelines for Authors and page charges of LEB: 
http://blaypublishers.com/archives/ .

4. Want to subscribe to LEB? http://blaypublishers.com/subscriptions/

http://blayjorge.wordpress.com/
http://paleobiology.si.edu/staff/individuals/santiagoblay.cfm



--
Gary D. Grossman, PhD
Fellow, American Fisheries Soc.

Professor of Animal Ecology
Warnell School of Forestry & Natural Resources
University of Georgia
Athens, GA, USA 30602

Website - Science, Art (G. Grossman Fine Art) and Music 
www.garygrossman.net<http://www.garygrossman.net>
Blog - https://medium.com/@garydavidgrossman
Board of Editors - Animal Biodiversity and Conservation
Editorial Board - Freshwater Biology
Editorial Board - Ecology Freshwater Fish

Hutson Gallery Provincetown, MA - 
www.hutsongallery.net/artists.html<http://www.hutsongallery.net/artists.html>

Re: [ECOLOG-L] Discussion Panel Topic Suggestions

[Jeff Houlahan]

Hi all, my difficulty with this is that what I see as a difference of opinion 
continues to get characterised as a misunderstanding of evolution.  Mitch, how 
can you state definitively that species 3 billion years ago were just as well 
adapted to their environment as those that exist today? It seems to me that's 
an empirical question.   It's possible they were but why MUST it be so.  And if 
I can provide an empirical example (Lenski's experiments) where later 
generations of an E.coli population were better adapted for their environment 
than an earlier one (by directly testing the competitive ability of the two 
strains) then why is it not possible that organisms today, on average, are 
better adapted for their environment than past organisms.  I want to emphasize 
that I am not saying current organisms ARE better adapted, only that it's a 
legitimate question to ask.  The answer will be in the data. 

' In evolution different species can't be compared as better or worse - they 
just succeed or they are replaced by
others.'

So, we can use the term successful but not better?  OK.  So, is there any 
evidence that current organisms have more success dealing with their 
environment than ones from 3 billion years ago?

'The upshot is that populations and species are never adapted to their
environments.'

It's not clear to me what you mean here, Mitch.  That they aren't perfectly 
adapted to their environments?  I don't think anybody has suggested they are.  
'That environments are always changing so 'adapted' is a moving target?  That 
is almost certainly true but it doesn't mean, necessarily, that one step 
forward and one step back.  It could be that there is a noisy and variable walk 
towards organisms that are more successful at dealing with their environments.  
But, bear in mind, I'm not asking anybody to believe that's true - just to 
acknowledge that it's possible and therefore a reasonable question to ask.

There is no confusion on my part about the role of complexity.  I don't think 
that complex organisms are necessarily better adapted and have never suggested 
they are (I only suggested that on the axis of complexity we have seen 
progress, not that increased complexity necessarily makes an organism better 
adapted for its environment)

Liz, I've never suggested that the process would be linear.  In fact, I've 
never even suggested that I think organisms are better adapted to their current 
environments than ancient organisms were to theirs.  I've only asserted that it 
is not a nonsensical question.  The fact that we keep coming back to the 
argument that 'environments are constantly changing therefore organisms are 
always trying to catch up with the changes' implies that, in fact, organisms 
could end up better adapted to their environments.  Implicit in your statement 
'...environment that 'shapes' them also changes through time.' is that if the 
environment didn't change through time that we would see a trend towards 
organisms that were better adapted for their environment.  If that's true, then 
why would we assume that somehow the changes in the environments occur at a 
rate that is perfectly synchronized with the rate at which a population evolves 
and so how well organisms are adapted to their environment stays constant?  
That just seems extraordinarily coincidental.  What I could believe is that at 
different times in history organisms have been more or less adapted to their 
environments but on average they are no better adapted today than they were in 
the past.  But. I can't see that there is anything that necessarily makes that 
true.  

Best, Jeff H.



From: Mitch Cruzan [cru...@pdx.edu]
Sent: December 7, 2012 3:03 AM
To: Jeff Houlahan
Cc: ECOLOG-L@LISTSERV.UMD.EDU
Subject: Re: [ECOLOG-L] Discussion Panel Topic Suggestions

Hi Jeff, Joey, and all the rest.
   I think several people have expressed a core principle of the
misunderstanding of evolution - I will try to explain.  Some 3 billion
years ago the Earth was occupied by organisms that were certainly
simpler than many extant species, but they were also just as well
adapted to their environments as anything existing today.  The
confusion, I think, comes from equating complexity with improvement, but
that is not the case.  As others have stated, some of the most
successful organisms are also some of the least complex.

   So where does complexity get us?  The answer is - probably just to
novel ways of resource acquisition.  In a Precambrian world (the time
that Jeff referred to), the main difference compared to later was that
the number of trophic levels was limited.  There were photosynthetic
autotrophs and herbivores that fed off of them, but the evolution of
larger predators required an increase in complexity.  The important
thing is that all of the species from that time period were subjected to
strong selection so they were as adapted to their environments as
anything you would

Re: [ECOLOG-L] Discussion Panel Topic Suggestions

[Jeff Houlahan]

Hi all, admittedly evolution by natural selection has no goal - it just 
happens. But, the logical outcome of natural selection is a population 
containing fitter organisms.  Richard Lenski's experiments have shown 
conclusively that the E. coli in his cultures that have evolved for longer are 
fitter (using competitive ability as an index of fitness).  If we can't call 
that 'progress' then we've put some pretty narrow constraints on the word 
progress and presumably progress can only be used in human contexts where there 
are explicit and clearly defined goals.  OK. But that just means we need to 
rephrase the question to avoid the use of the word progress (although it's the 
same question, I think) - as we move from the first living organisms to the 
current group of living organisms, have living organisms, on average, become 
better adapted to their environments?  I don't know if this is a testable 
question but it doesn't seem like an illogical one.  And I have to confess, I 
see it as semantic hairsplitting to be unwilling to talk about 'better adapted 
to their environment' as progress.  Best, Jeff Houlahan.



From: Ecological Society of America: grants, jobs, news 
[ECOLOG-L@LISTSERV.UMD.EDU] on behalf of Rachel Bolus [r...@bio.umass.edu]
Sent: December 6, 2012 2:15 PM
To: ECOLOG-L@LISTSERV.UMD.EDU
Subject: Re: [ECOLOG-L] Discussion Panel Topic Suggestions

Hello
I think that the interesting debate generated by the issue of
evolutionary progress is exactly why it's a good topic for this panel.
It makes people think carefully about definitions and the processes. I
also think that Chris Edge just hit the nail on the head about our
misuse of the word progress. Progress or advancement suggests
teleology, which has been largely rejected by evolutionary biologists.

One of the reasons why we stumble over the question, Do organisms
advance over time? is that we confuse complexity with progress. Yes, on
average, organisms become more complex over time, because the process of
evolution is the accumulation of changes in traits of individuals in
populations over time. Although losses are part of this process, gains
are added on top of previous gains, resulting in more complexity
(especially in the multi-celled organisms that more frequently catch our
eye).

Is complexity progress? As humans, our intuition tell us, yes because
we like shiny complex things (perception bias, perhaps?). If we are
handed two tablets, one that is a chalkboard and one that is an iPad, we
know which one we think is better. But when the flood comes, which one
is still functional afterwards? Adaptation results in organisms fitting
their environment better, but the more adapted we are to a particular
environment, the less flexible we are to change. In a large time scale,
flexibility should trump complexity. Sometimes more complex things are
better able to adjust to changes in the environment, sometimes they
aren't. In a stable environment (if it exists) what organism is best
able to survive and reproduce may be complex or may be simple.

What is better is largely subjective- is it complexity, adaptation
(resistant microbes!), size (currently, blue whales!), intelligence
(humans!), ability to produce the most offspring and biomass possible
(fungi!), ability to persist relatively unchanged across epochs
(sponges!)... ?

As an interrelated topic (the previous one is mostly evolutionary, with
ecology included as part of the process of adaptation), it might be fun
to include the changing ideas of forest succession (getting back to the
issue of Do communities evolve?). Previously, it was thought that
forest communities progressed towards climax stages, but now we realize
how patchwork, stochastic, and cyclical this process is.

Rachel Bolus
Ph.D. Candidate
Organismic  Evolutionary Biology
University of Massachusetts Amherst

On 12/6/2012 10:03 AM, Chris B. Edge wrote:
 Hello all,
 I have spent some time thinking about this topic over the last several
 years. As a relatively 'green' evolutionary ecologist I rarely enter these
 debates in public forums.
 My opinion's are heavily influenced by Jared Diamond's writing on the
 topic. In not as eloquent words 'progress' implies that there is a goal or
 target that evolution is moving towards. Of course we can define the goal
 or target post hoc, complexity, invasion of terrestrial habitats, etc. and
 conclude that evolution has made progress. However non of these
 goals/targets apply to all organisms or habitats, and non of them can be
 defined a priori.
 'Progress' may capture the essence of the message we want to get across it
 is not a good word to use to describe major evolutionary trajectories
 unless the statement it is used in also includes the axis or scale progress
 is to be measured on. Instead major trajectories should be described as
 they are, observed trajectories/trends. For example, consider these two
 statements; 1) 'evolution has resulted

Re: [ECOLOG-L] Discussion Panel Topic Suggestions

[Jeff Houlahan]

Hi Joey, I am not arguing that evolution has led to progress on some axis - 
that's an empirical question. I am only arguing that it is not a 
misunderstanding of evolution by natural selection to suggest that it is 
possible.  You've stated conclusively that evolution by natural selection 
cannot lead to progress.  So, if I could provide empirical evidence that, on 
average, current organisms are better adapted to their environments than 
organisms were 3,000,000, years ago would you still deny that was progress? 
 I'm OK with that but it's just a semantic issue then - something that I would 
be willing to call progress you wouldn't be willing.  On the other hand, if 
you're saying that it's not possible that over time time organisms have become 
better adapted to their environments then our difference of opinion is more 
fundamental. But, keep in mind - this is not a debate about whether evolution 
by natural selection HAS resulted in progress, it is about whether it's 
reasonable to ask the question, has evolution resulted in progress?  Just 
because the answer might be no doesn't mean the question doesn't make sense.
And what about the example from Lenski's work - he has absolutely demonstrated 
in his population of E. coli that later generations were more fit than earlier 
generations.   The population that had been around longer was better adapted. 
Why would it be possible over 75,000 generations of E.coli but not possible as 
a general rule?
The problem I have is not that you believe that evolution by natural selection 
has not resulted in better adapted organisms - it's that you believe that 
anybody who suggests it's possible, misunderstands evolution by natural 
selection.  Best, Jeff Houlahan



From: Ecological Society of America: grants, jobs, news 
[ECOLOG-L@LISTSERV.UMD.EDU] on behalf of Joey Smokey 
[northwestbird...@gmail.com]
Sent: December 6, 2012 7:24 PM
To: ECOLOG-L@LISTSERV.UMD.EDU
Subject: Re: [ECOLOG-L] Discussion Panel Topic Suggestions

Ecolog:

I would like to commend Wayne for his devil's advocate approach to
suggesting the third question and starting this discussion. It seems my
original interpretation was correct: the whole purpose of the question was
to dispel the misconceptions around the semantics of evolution.

I find it interesting how several of you use the word progress in
different contexts, and I especially like the idea of defining progress
along some sort of axis, such as increasing complexity. This all being
said, I do have some retorts. Firstly, if the argument is to be made that
evolution leads to increasingly complex life forms, it should be noted that
this has happened many times in evolutionary history. Adaptive radiations
and mass extinctions produce a cycle of simple-to-diverse organisms over
millenia. However, at the end of every mass extinction, the diversification
of organisms and their niches is eliminated, and complexity of life is
severely reduced. So, given our idea of progress, however you want to
define it, you still cannot use it. If organisms did in fact progress over
whatever axis you'd like to use, then despite mass extinctions they would
continue to become more and more advanced. We are currently in the middle
of an anthropogenic mass extinction, whether or not some folks want to
accept that, and at the end of it, the complexity of life as we know it
will vanish. Fact: prokaryotes have remained simple unicellular organisms
for billions of years for a reason. :)

To the point of evolution of individuals, populations, and communities:
Individuals and communities do not evolve. I think the idea of community
evolution has been sufficiently put the rest already. To use semantics
correctly: natural selection acts on individuals and has consequences on
allelic frequencies in populations. One individual organism cannot evolve,
because its allelic frequency never changes throughout its life. But,
natural selection can cause it to influence the allelic frequency of future
generations in the population, and that -is- evolution. Also, when folks
use the terms of fittest and survival of the fittest, etc., that should
be avoided. The four postulates of natural selection lead to relative
fitness. In other words, one individual can only have a slightly higher
fitness than another. Liz already alluded to this; and I also quite like
her noting that even our own species is by no means perfect.

Recapping: Evolution is not directional. Evolution is not perfect. And
evolution does not lead to the good of the species (example: infanticide).
Evolution leads to organisms being well-adapted to their environment at a
specific time. Temporal environmental changes (i.e. climate change) lead to
organisms no longer being well-adapted to their environment, and they must
either adapt or face extinction.

Regards,

Joey Smokey
WSU Vancouver


On Thu, Dec 6, 2012 at 12:31 PM, Jeff Houlahan jeffh...@unb.ca wrote:

 Hi all, admittedly

Re: [ECOLOG-L] Discussion Panel Topic Suggestions

[Jeff Houlahan]

Hi all, I think the fact that I feel compelled to respond to Joey's comments 
illustrate how questions 3 and 4 might be worth including  in the discussion.  
One common view of evolution is that it is not progressive but , of course, 
it's impossible to make that claim unless you define what axis evolution 
doesn't 'progress' along.  I think we could make the claim that organisms, on 
average, have evolved to be more complex than they were shortly after life 
began.  So, on the complexity axis, I would claim that life has progressed.  
Joey's example of the move to terrestrial ecosystems, I think, is evidence 
against his argument that there was no progression.  Early terrestrial 
organisms would not have been able to exploit the wide variety of terrestrial 
niches that were available.  Now almost every terrestrial habitat is being 
exploited.  I would say that implies that living organisms have progressed on 
the 'exploiting terrestrial environments' axis.  In fact, I would assert that 
the theory of natural selection implies that species are not only well-adapted 
to their environments but continuously better-adapted to their environments 
over time.  One logical conclusion, if environments were perfectly stable over 
time, is that species would be much better adapted to their environment  as 
time progressed.  Lenski's experiments with E. coli show exactly that kind of 
progression.  The question is, Are environments stable enough over 
evolutionary time to make the claim that there has been progression along some 
axes or is evolution more like a random walk because environments are 
constantly changing?  I don't know the answer to that question.  
I think one reason we discourage the idea of progression is a concern that it 
implies some kind of 'creator' behind the scenes prodding us ever forward but 
that is not at all what I'm suggesting.  I'm saying that a process that works 
in a way that selects the fittest individuals over time surely has the 
potential to result in 'progress' along some axes, no?  Whether that potential 
is realised is an empirical question but to state conclusively that evolution 
does not cause progress seems, to me, to be an extreme position.
As for the fourth question, I agree with Joey right up to ...do have 
meaningful impact on evolutionary trajectories of species.  This is an 
empirical question.  There are many processes that can drive evolutionary 
trajectories (genetic drift, abiotic conditions, biological interactions etc.) 
and the question of where interactions stand in relative importance is, I 
think, an important one.
These all seem like worthy questions to me.  Best, Jeff H.




From: Ecological Society of America: grants, jobs, news 
[ECOLOG-L@LISTSERV.UMD.EDU] on behalf of Joey Smokey 
[northwestbird...@gmail.com]
Sent: December 4, 2012 5:51 PM
To: ECOLOG-L@LISTSERV.UMD.EDU
Subject: Re: [ECOLOG-L] Discussion Panel Topic Suggestions

Jason,

I strongly advise against the third question. Evolution is not directional,
and the question is worded to suggest that it is. If the point of the
question is to dispel the idea of evolution being directional, then it
would be fine.

There are many common misconceptions of organisms progressing through
evolution. The most common is the typical classroom image of human
evolution moving from ape-like toward human-like over time. Transition
species in the fossil record do not suggest a progressive change from one
type of body form into another. The transition to terrestrial life is the
same way; transition species such as Tiktaalik, Eusthenopteron, and
Ichthyostega did not march along until they were well-adapted for life on
land. Evolution does not craft improved species or advanced species. It
simply results in organisms being well-adapted for their environment at a
given time.

In regards to the fourth question, ecological time refers to immediate
interactions between organisms and their environment. It does lead into
evolutionary time and the change in allelic frequencies through
generations. So, ecological interactions can and do have meaningful impact
on evolutionary trajectories of species.

I think the first two questions will lead into some good discussion.

Best of luck on your discussion panel,

Joey Smokey
WSU Vancouver


On Tue, Dec 4, 2012 at 8:37 AM, jason.strickland 
jason.strickl...@knights.ucf.edu wrote:

 Dear group,

 I have compiled some of the ideas that were given to me about my
 discussion panel. The response was much lower than I expected so if you
 have any ideas, feel free to share those as well. Thank you to all those
 that contributed.


 1.   Will most organisms be capable of adapting quickly enough to
 respond to climate change/sea level rise to be evolutionarily relevant?

 2.   What impact will Genetically Modified Organisms have on the
 ecology and evolution of the modified species and other species?

 3.   Do organisms 

[ECOLOG-L] Ph.D. opportunity in amphibian ecology

[Jeff Houlahan]

Ph. D. in Amphibian Ecology

We are looking for a highly motivated, independent and naturally  
inquisitive Ph. D. student with excellent verbal and written  
communication skills as well as creative problem solving capability  
and strong work ethic to work on questions related to amphibian  
population and community ecology in New Brunswick, Canada.  The  
standard Ph.D. stipend offered through UNB-St. John will be offered  
from available project financial resources that are guaranteed for 3  
years.  In relation to provision of this funding,  constraints on the  
successful candidates project must  include:


(1) detailed work on bioacoustic monitoring including development and  
application of automated recognizers to detect amphibian community  
change in relation to multiple long-term monitoring sites under  
various disturbance regimes and


 (2) experimental manipulations of some or all of 42 experimental  
ponds extant at the Long-term Experimental Wetlands Area in New  
Brunswick, Canada.


Working within those constraints the student will be expected and  
encouraged to develop their own specific hypotheses for testing as a  
basis of their dissertation research.  The only absolute requirements  
are that you be curious, creative, independent and self-motivated,  
that you have reasonably good quantitative skills, and that you have a  
driver?s license.


Preference will be given to students who already have

(1) an M. Sc. (but we would consider exceptional B. Sc. students who  
believe they are ready to step into a Ph. D. program),

(2) some experience with amphibian ecology,
(3) training in acoustic monitoring, and
(4) field experience.

The successful candidate will be enrolled at UNB Saint John in Saint  
John, New Brunswick under the co-supervision of Dr. Jeff  
Houlahan(UNB-SJ) and Dr. Dean Thompson (Canadian Forest Service, Sault  
Ste. Marie and UNB-SJ adjunct).


 Ideally, we would prefer that you start by May 1, 2012 but delayed  
startup in the fall of 2012 will be considered for exceptional  
candidates.


Applications for this position must include a Curriculum vitae,   
graduate and undergraduate academic transcripts, a cover letter and  
full contact information for a minimum of three academic/research  
references.  Application materials should be sent to Jeff Houlahan at  
jeffh...@unb.ca.

Re: [ECOLOG-L] EcoTone: Speaking of species and their origins

[Jeff Houlahan]

Hi all, not that Esat needs me to defend him but the list of species  
that can be 'googled' and identified as invasive scourges is, I  
suspect, longer than the list that actually are scourges.  One of the  
species that was identified in Amyarta's list, purple loosestrife, is  
a classic example.  You can go to hundreds of websites that will  
identify it as a species that competitively excludes native plant  
species and causes local extirpations.  The empirical evidence to  
support this claim is almost non-existent (or was a couple of years  
ago when I checked last).  There have been several reviews done on the  
topic and most conclude that there is little evidence that loosestrife  
causes extinctions at almost any scale.  This isn't to suggest that  
invasives are never a problem but my understanding of the literature  
is that there is lots of evidence of extinctions caused by invasive  
predators and relatively little evidence of extinctions caused by  
competitive exclusion (zebra mussels are probably an exception to that  
general statement).  I don't think it's a bad idea to actually step  
back and see if the investment in controlling invasive species is  
warranted.


Jeff Houlahan

Re: [ECOLOG-L] Hypothesis Testing in Ecology

[Jeff Houlahan]

I think Martin identifies one of the problems with a very restrictive  
definition of what science is - it excludes a bunch of stuff that most  
of us would think of as research.  In fact, I would say that  
sequencing the human genome did not involve hypothesis testing - it  
was natural history at the molecular level - and most people would  
consider it one of the greatest scientific achievements of the last  
decade.
However, I also have some sympathy with Pat's take that simply telling  
us what is there often has limited value.  And if we think back to how  
this is 'supposed' to work (based on textbook science), descriptions  
are often the source of hypotheses that we should tyhen test.  I would  
say at this point we have many, many untested or poorly tested  
hypotheses, which may explain why many scientists are not very  
supportive of work that will just provide more hypotheses to test.
Best.


Jeff Houlahan


I am amazed by Pat Swain's statements implying that unless a program of work
includes formal hypothesis testing, it's not even research. (...I think
that pure survey of a property for species (making a list of all the species
of some taxonomic group) encountered isn't research...,  ...some of the
projects that I rejected as not being research might well have been fundable
...)This appears to be defining the word research in a way I have never
seen or heard before.  Does this mean that none of the scientific work that
was done before the rise of modern statistics was not research?  Where the
people doing that work also not really scientists?  And whatever happened to
library research?
 Martin

2011/3/7 Wayne Tyson landr...@cox.net


Honorable Forum:

Re: I think these general surveys are valuable, but they don't overtly
involve hypotheses and testing. However, it can and does include
assumptions/hypotheses; as one of the posters on the topic pointed out there
are always assumptions made. One doesn't walk every square inch of a site,
rather picks areas (from aerials, maps, knowledge, observations when out
there) places that are most likely to be different/interesting (have rare
things). --Pat Swain (Monday, March 07, 2011 6:03 AM)

I don't want to appear to jump to conclusions, so I would be interested in
Swain's expansions upon this issue. I wonder if Pat would have funded a
survey which was based upon random sampling/mapping that would provide a
baseline dataset and provide another level of scrutiny of the
different/interesting as well as an opportunity to discover that which one's
present state of knowledge might otherwise overlook.

Please describe the theoretical foundation for walking the site rather
than randomly sampling it, and how one approaches gaining knowledge of a
site without a (statistically) valid inventory.

WT

- Original Message - From: Swain, Pat (FWE) 
pat.sw...@state.ma.us

To: ECOLOG-L@LISTSERV.UMD.EDU
Sent: Monday, March 07, 2011 6:03 AM

Subject: Re: [ECOLOG-L] Hypothesis Testing in Ecology


 Ecolog-L,


Way back when the question about hypothesis testing in ecology was first
posed to the group, one of the questions was whether anyone had rejected
projects or grant proposals for lack of hypotheses. The discussion has gone
on while I thought about posting a response to that, but with Jane
Shevtsov's prodding, I offer the following thoughts on hypothesis testing
and research.

For some years I was on a committee to review and select graduate student
research proposals for grant support for a regional botanical organization
at the same time that I was involved in evaluating proposals for small
contracts from my office which is focused on rare species and uncommon
natural communities in the state. (I stress the research grants vs.
contracts; and I am no longer on the committee which no doubt has different
biases from mine, and my office doesn't have money for small contracts like
we used to).

On the grad research committee, I was far more likely to approve proposals
for consideration if a hypothesis was stated, and I  tended to  
veto projects
that didn't do that. For example, I think that pure survey of a  
property for

species (making a list of all the species of some taxonomic group)
encountered isn't research, but such a project can be developed  
and proposed

in ways that has research in it (effects of land use history, recreation,
management...). If a student wanted to inventory a property as a research
project, as someone funding grants I wanted the reasons given for why that
property is worth the effort and what will be done with the results. I
recall one otherwise quite good proposal I didn't consider because it just
said that the property was interesting and the nonprofit owning it should
know what was on it. I wanted to be shown what assumptions are being made
(those should be stated as hypotheses to be tested in a proposal for a
research grant), predictions!
 of where differences might be and why and expectations that post

Re: [ECOLOG-L] Hypothesis Testing in Ecology

[Jeff Houlahan]

Hi Jane, great question about how to get students to demonstrate  
understanding.  One I hadn't thought about.  Off the top of my head I  
would say that they would demonstrate understanding if they knew what  
predictions a certain concept would make, which of those predictions  
had been tested, and how much evidence there was for the concept (that  
evidence would be in the form of accurate/precise predictions).
As for causal knowledge that is a tricky one and one I have wrestled  
with because in some ways causes are like those Russian babushka dolls  
- causes ended up nested in causes.  For example, if we're talking  
about causes for amphibian decline and I say low pH is one cause of  
declines, have I identified a cause?  Somebody could say low pH is not  
the cause - it is the form of aluminum that is present at low pH.  
Somebody else could say it's not the amount of aluminum of that form  
that's in the water that is the cause, it is the aluminum binding to  
some receptor inside the frog that is the cause.
So, in theory, pH could perfectly predict amphibian trends and I would  
then conclude we have perfect understanding but in fact there could be  
an explanation beneath pH where we know almost nothing.  So, in my  
opinion, prediction is they only way to demonstrate understanding but  
understanding is often layered and perfect prediction at one level  
wouldn't necessarily imply understanding at another level.
These are really difficult issues and I think it's easy to see them as  
esoteric and of not much practical concern but I think ecology has  
actually done a pretty poor job of quantifying our understanding and  
without that how do we know where to focus our resources?  How well do  
we understand the effects of invasive species on the distribution and  
abundance of native organisms?  I actually have no idea.  Have we  
barely scratched the surface and we should direct more resources at  
that question?  Do we almost have that question completely sorted out  
and so should move on to the next important question?  Should we throw  
up our arms and say that this is an unanswerable question?  Best.


Jeff

PS Sorry for straying so far from the original question


Jeff's comments are good ones. I don't know why all the apostrophes
came through as question marks, but maybe that's appropriate -- these
are difficult issues and I, for one, have more questions than answers.
On one hand, there are certainly examples that demonstrate that
understanding is neither necessary nor sufficient for prediction. On
the other hand, the two are certainly connected. It's been pointed out
that causal knowledge, unlike statistical knowledge, enables us to
predict how a system will behave under interventions. Maybe that helps
-- I don't think you can understand a phenomenon without causal
knowledge. Also, let's look at pedagogical questions. How do we ask
students to demonstrate understanding of concepts?

BTW, I want to clarify a remark I made earlier about chaos. While the
long-term behavior of a system exhibiting chaotic behavior cannot be
predicted in the sense that the time series can't be predicted, we CAN
predict other aspects of its dynamics, such as the parameter values
resulting in different modes of behavior. So maybe before we can
productively discuss the relationship between prediction and
understanding, we ought to clarify what we mean by prediction. How
broadly or narrowly do we want to construe the term?

Best,
Jane

On Thu, Mar 3, 2011 at 7:19 AM, Jeff Houlahan jeffh...@unb.ca wrote:

In response to Jane?s comments ? I admit that understanding and prediction
are not the same thing but they are much more closely related than most
people appreciate, in my opinion.  I would go so far as to say that
prediction is a necessary if not sufficient condition of understanding.  So
while it is possible to predict without understanding (as in Jane?s
Babylonian?s example ? although I knew nothing about the Babylonians and
their ability to predict, I have no doubt that?s true) I think it is
impossible to demonstrate understanding without prediction.  In fact, I
realized that I can?t come up with a definition of understanding that
satisfies me without talking about prediction (none of the on-line
definitions that I found worked very well for me).  My definition of
understanding would be  ?The ability to make specific predictions based on a
general description of how the world works.?  Now, I guess it?s possible
that somebody could understand how the world works but not be able to make
any predictions but that means that they can?t demonstrate their
understanding.  In my opinion, understanding that can?t be demonstrated has
little(no?) value because I can?t distinguish that person from all the
people who claim they have understanding but have none.
My above definition leaves room for ?thinking? you understand when you
don?t, in situations where you make good predictions for the wrong reasons.
 But, even here

Re: [ECOLOG-L] Hypothesis Testing in Ecology

[Jeff Houlahan]

Hi Chris and all, I actually think that it's a mistake to diminish the  
role of p-values.  My opinion on this (stongly influenced by the  
writings of Rob Peters) is that there is only one way to demonstrate  
understanding and that is through prediction.  And predictions only  
demonstrate understanding if you make better predictions than you  
would make strictly by chance.  The only way to tell if you've done  
better than chance is through p-values.  So, while there is a great  
deal more to science than p-values, the ultimate tests of whether  
science has led to increased understanding are p-values.  Best.


Jeff Houlahan
Dept of Biology
100 Tucker Park Road
UNB Saint John

[ECOLOG-L] Ph. D. positions

[Jeff Houlahan]

Could you please post for the positions described below.  Thanks.   
Jeff Houlahan


GRADUATE POSITIONS AVAILABLE

As a collaborating group of academic and government scientists, we are  
seeking 5 Ph. D. students to work as a part of a multidisciplinary  
team conducting manipulative experiments designed to examine the  
effects of multiple stressors in small wetland ecosystems.  The focus  
of this NSERC funded research program will be on the potential effects  
of climate change on amphibians and other aquatic organisms alone and  
in combination with herbicide use.  This would be the 3rd in a series  
of experiments conducted at the ?Long-term Experimental Wetlands Area  
(LEWA),? on Canadian Forces Base Gagetown in New Brunswick Canada.   
All positions are contingent on funding ? we will know funding  
decision by October 2010.


1 Ph. D. position at the University of Ottawa

A Ph. D student will be examining climate change/herbicide effects on  
gene expression, sexual development and metamorphosis in amphibians.  
They will be supervised by Dr. Vance Trudeau (University of Ottawa;  
see www.teamendo.ca) and Dr. Vince Palace (DFO, Winnipeg, Manitoba)  
and work out of The University of Ottawa Centre for Advanced Research  
in Environmental Genomics. Qualifications: Candidates should have a  
background in comparative physiology or vertebrate endocrinology, and  
have demonstrated experience with basic molecular biology methods  
(PCR, gene cloning, etc). A keen interest in climate change effects on  
aquatic ecosystems would be an asset to the team.


3 Ph. D. positions with the Biology Department and The Canadian Rivers  
Institute at the University of New Brunswick Saint John (UNB Saint John)


1.	One Ph. D. student will be examining climate change/herbicide  
effects on DOC and UV radiation attenuation.  The student will be  
supervised by Drs. Nelson O?Driscoll and Jeff Houlahan (UNB Saint  
John).  Qualifications: An M. Sc. in chemistry, biology, environmental  
science or a related discipline is preferred.  Exceptional B. Sc.  
students will be considered.  All candidates should have good  
statistical skills (i.e. are comfortable with traditional analyses  
such as ANOVA and regression) and be comfortable with independent  
laboratory and field work.
2.	One Ph.D. student will examine the effects of climate  
change/herbicide use on planktonic and benthic invertebrate  
communities in these experimental ponds. The student will be  
supervised by Dr. Karen Kidd (UNB Saint John).  Qualifications: An  
M.Sc. in ecotoxicology, aquatic ecology or a related discipline.  The  
student should have experience conducting field work on aquatic  
systems and good statistical skills.  Experience in macroinvertebrate  
identifications is an asset.
3.	One Ph. D student will be examining the effects of climate  
change/herbicide stressors on primary production and plant abundance  
and diversity.  The student will be supervised by Dr. Jeff Houlahan.   
Qualifications: An M. Sc. in ecology, conservation biology, botany or  
a related discipline is preferred.  We would consider a statistics,  
math or computer modelling graduate if there is a strong natural  
history interest and background.  Exceptional B. Sc. students will be  
considered.  All candidates should have good statistical skills (i.e.  
are comfortable with traditional analyses such as ANOVA and  
regression).   Experience in aquatic plant identification is an asset.


1 Ph. D. position with the Department of Physical and Environmental  
Sciences  at the University of Toronto


One Ph. D student will be using the output from 24 Global Climate  
Models and four Regional Climate Models applied to Canada in  
conjunction with a common regression-based stochastic weather  
generator software to develop realistic regional climate projections  
under different future scenarios of climate change.  The student will  
be supervised by Dr. Adam Fenech.  Qualifications:  A Masters degree  
in physical geography or physics with specific courses in climatology  
and/or meteorology. All candidates should have numerical skills, and  
enjoy database development and manipulation. Geographic information  
system experience is an asset.


Additional qualifications: The importance of candidates being  
effective team players cannot be overstated.  Excellent verbal and  
written communication skills as well as interpersonal relation skills  
are considered vital personal attributes.  This project will involve  
many students and senior researchers (as well as, a number of field  
technicians) working on the same set of 24 ponds for at least the next  
3 years and therefore the ability to collaborate effectively will be a  
critical, perhaps the most critical, attribute determining the success  
of this project.  We are looking for that rare combination - the  
ability to think and work independently while also being a collegial,  
collaborative and cooperative team

Re: [ECOLOG-L] Evolution Population Ecology Competition or Adaptation

[Jeff Houlahan]

Hi Wirt and all, I think it's a reasonable question to ask 'How important is 
competition in driving evolutionary change?'.  Fitness is a measure of how well 
an organism is adapted to its environment. An environment is more than just 
competing species.  I can imagine many systems where the way an organisms 
looks, acts, respires, metabolizes etc. has been shaped relatively little by 
competitors but relatively a lot by predators, mutualists, pathogens and 
abiotic environmental conditions.  It may not be an either-or question but it 
certainly is a 'relative importance' question.  Best.

Jeff H

PS My own sense is that competition is not that important
-Original Message-
From: Wirt Atmar [EMAIL PROTECTED]
To: ECOLOG-L@LISTSERV.UMD.EDU
Date: Thu, 28 Feb 2008 22:01:45 -0700
Subject: Re: [ECOLOG-L] Evolution  Population Ecology  Competition or Adaptation

Wayne Tyson asks:

 I would like to know how many (what percentage of?) ecologists think
 competition drives evolution or whether it's adaptation.

The question isn't either-or. Competition for resources within a bounded arena
results in adaptation.

Darwinian evolutionary theory is composed of only five components:

   (i) a bounded arena,
  (ii) a replicating population which must eventually expand beyond
   the bounds of the arena,
 (iii) thermodynamically inescapable replicative error,
  (iv) competition for space in that arena among the inevitable
   variants, and
   (v) consequential competitive exclusion of the lesser fit.

Darwinian evolutionary theory is an optimization algorithm. The most overt
attribute of the process is the accumulation of increasingly appropriate
behaviors within the evolving lineage of trials.

Adaptation is simply the overt response to that evolution of increasingly
appropriate behaviors. The agent of evolution is natural selection, which is
mediated by the constant culling of the least appropriate phenotypes from the
inevitable excess population locked within that finitely bounded arena at every
generation.

If you want to read a ponderously technical description of this process, written
for engineers, you might look at:

   http://aics-research.com/research/notes.html

When a process is understood well enough, and we do understand the Darwinian
algorithm very well now, it can be exploited for engineering purposes. Indeed,
that may be the ultimate test for how well we understand a process.

I mentioned the other day that all sciences eventually become predictive, and
that prediction is the only way we have of measuring how well we understand a
subject, but engineering exploitation of a scientific discipline represents yet
a higher level of understanding.

There are now hundreds of engineering organizations employing Darwinian
evolutionary methods to design structures and processes now. One of them is a
group at NASA Ames Research Center, Moffett Field, CA, headed by Jason Lohn. One
of the more interesting things that Jason's group has done recently is design
the first spacecraft-flyable antennas using evolutionary methods:

   http://ic.arc.nasa.gov/projects/esg/research/antenna.htm

The results of their design work appears at the bottom of the page. As Jason has
said, no matter how drunk you got an antenna engineer, he never would have
designed anything that looks like this, but the evolved antennas have a higher
gain and better angular coverage than do the best of all of the previously
human-designed antennas.

Leslie Orgel's Second Law, evolution is cleverer than you are, now appears on
more engineering PowerPoint slides than it does on those of biochemists, the
audience for whom he originally meant the comment.

Wirt Atmar

Re: [ECOLOG-L] Anderson's new book,

[Jeff Houlahan]

Hi Wirt, I completely agree with almost all of what you (and David) wrote.  
Feynman is talking about a real hypothesis that arose from a great deal of 
thought and creativity...not one that has been attached with baling wire, duct 
tape and a little leftover Juicy Fruit to a pile of data that happened to be 
sitting around.  
That said, science is many things - 'a predictive
enterprise, not some form of mindless after-the-fact exercise in number 
crunching.' - fits under the umbrella but I don't think captures the whole 
enterprise.  Sequencing the human genome was, in my opinion, a version of 
mindless number crunching (although perhaps somebody can put that effort in a 
hypothesis testing context that I haven't thought of).  I think most people 
would be hard pressed to say it wasn't science.  In fact, there is an emerging 
field of statistics (data mining) that seems to be useful in developing 
scientific hypotheses and is all about the 'mindless after-the-fact exercise in 
number crunching'.  My feeling is that data can provide hypotheses or test 
them.  When it does the first, it is a very useful part of science but it is 
not predictive and it does not test hypotheses (null, competing or otherwise).  
When it does the latter it falls ito the category that Feynman was describing.  
I think the reason we often get these trivial tests of hypotheses is because 
there is this sense that science is only about testing hypotheses - therefore 
to do science I must test a hypothesis...whether there is a meaningful one or 
not.  In my opinion, science can also just be about looking for patterns that 
we can use to suggest hypotheses.  Hypotheses have to be tested to be useful 
but the patterns we see in nature (and those patterns are often less distinct 
without number crunching)are almost always the birthplace of hypotheses. Best.

Jeff H

-Original Message-
From: Wirt Atmar [EMAIL PROTECTED]
To: ECOLOG-L@LISTSERV.UMD.EDU
Date: Wed, 20 Feb 2008 12:03:54 -0700
Subject: [ECOLOG-L] Anderson's new book, Model Based Inference in the Life 
Sciences

I just purchased David Anderson's new book, Model Based Inference in the Life
Sciences: a primer on evidence, and although I've only had the opportunity to
read just the first two chapters, I wanted to write and express my enthusiasm
for both the book and especially its first chapter.

David and Ken Burnham once bought me lunch, and because my loyalties are easily
purchased, I may be somewhat biased in my approach towards the book, but David
writes something very important in the first chapter that I have been mildly
railing against for sometime now too: the uncritical overuse of null hypotheses
in ecology. Indeed, I believe this to be such an important topic that I wish he
had extended the section for several more pages.

What he does write is this, in part:

It is important to realize that null hypothesis testing was *not* what
Chamberlin wanted or advocated. We so often conclude, essentially, 'We rejected
the null hypothesis that was uninteresting or implausible in the first place, P
 0.05.' Chamberlin wanted an *array* of *plausible* hypotheses derived and
subjected to careful evaluation. We often fail to fault the trivial null
hypotheses so often published in scientific journals. In most cases, the null
hypothesis is hardly plausible and this makes the study vacuous from the
outset...

C.R. Rao (2004), the famous Indian statistician, recently said it well, '...in
current practice of testing a null hypothesis, we are asking the wrong question
and getting a confusing answer' (2008, pp. 11-12).

This is so completely different than the extraordinarily successful approach
that has been adopted by physics.

In ecology, an experiment is most normally designed so its results may be
statistically tested against a null hypothesis. In this procedure, data analysis
is primarily a posteriori process, but this is an intrinsically weak test
philosophically. In the end, you rarely understand more about the processes in
force than you did before you began. But the analyses characteristic of physics
don’t work that way.

In 1964, Richard Feynman, in a lecture to students at Cornell that's available
on YouTube, explained the standard procedure that has been adopted by
experimental physics in this manner:

How would we look for a new law? In general we look for a new law by the
following process. First, we guess it. (laughter) Then we... Don't laugh. That's
the damned truth. Then we compute the consequences of the guess... to see if
this is right, to see if this law we guessed is right, to see what it would
imply. And then we compare those computation results to nature. Or we say to
compare it to experiment, or to experience. Compare it directly with
observations to see if it works.

If it disagrees with experiment, it's wrong. In that simple statement is the
key to science. It doesn't make a difference how beautiful your guess is. It
doesn't make a difference how smart you 

Re: Discussion invited on peer review

[Jeff Houlahan]

To follow up on the points that Val made - do we see the fact that papers with 
flaws get past reviewers as a fundamental flaw in the review process?  I 
believe that sets the bar too high - every paper that gets to publication 
should, in my opinion, be seen as passing the first step in the review process. 
 From that point on it is in the public forum and open to continued criticism 
and rebuttal.  If the paper is of little interest we may never hear much about 
it again.  If it is of great general interest (and controversial) it may get 
'reviewed' several more times before it's conclusions are accepted by the 
larger scientific community.  
If I to approach every paper I review as if it is my responsibility to catch 
every single mistake I'm not sure I could in good conscious agree to review any 
papers.  There are areas where I believe I have strengths and I tend to focus 
on those areas when I review papers.  For example, I am not a great writer and 
so don't often have a whole lot to say about writing style.  You do the best 
you can and hope the paper is not fundamentally flawed and the better for 
having been reviewed - I suspect we are usually (but not always) successful in 
meeting those goals.  That doesn't mean the rest of the scientific community 
should abdicate its responsibility to read these papers carefully and 
critically.  Best.

Jeff Houlahan

Re: Equilibrium/Steady State and Complexity/Evolution

[Jeff Houlahan]

Just a quick addendum to some of the economic barriers to moving away from the 
growth paradigm (I hate to use the 'p' word, but if it has ever been 
appropriate it is appropriate in this context).  I believe that one  large 
barrier to moving towards a steady-state economy is that it means a dramatic 
shift in ethical beliefs.  In a growth economy one can be a rich consumer and 
an ethical, moral person, because the wealth that you are creating (and 
spending) is creating wealth for everybody - you are making a contribution to 
the growing pie.  In short, you can be rich and go to heaven.  A steady-state 
economy implies a pie of constant size - that means thet every additional steak 
you eat is food someone else doesn't get, every additional mile you drive is a 
mile somebody else has to walk.  In a steady-state economy every act of 
consumption is, explicitly, a moral and ethical decision.  In short, put down 
your fork or you're going to hell.  In my opinion, that fundamental philos!
 ophical shift has to be made before we will see a change in policies...and 
that seems like a large barrier.  Best.

Jeff Houlahan

-Original Message-
From: Andrew Park [EMAIL PROTECTED]
To: ECOLOG-L@LISTSERV.UMD.EDU
Date: Thu, 5 Apr 2007 19:05:17 -0400
Subject: Re: Equilibrium/Steady State and Complexity/Evolution

Re: economic growth versus steady state,

There is a big problem with getting from where we are (catastrophic  
EXPONENTIAL economic growth) to where some of us would like to be  
(Steady state, dynamic flux around some mean value, call it what you  
will).

The problem is that there is nobody anywhere in the world who can  
envision a practical, politically feasible, and equitable version of  
where we want to be.  I have read Daly and others on this subject, adn  
their major weakness always revolves around the policies that will  
give us steady state.

Its not their fault though.  The problem is that we all have a vested  
interest in seeing growth continue.  Yes folks, growth is not just a  
sop for politicians and the opiate of uber capitalists.  Surpluses  
generated by growth are what pays for roads, social services, and  
other infrastructure of civilization.  Growht is what pays for your  
pension (if you have one) and it provides dividends on your  
investments so that you can retire.  Growht is what pays for foreign  
aid, even though that is only a pitifully small part of our bloated  
GDPs.

And of course the alternative to growth is stagnation courtesy of the  
multiplier effect.  Loosely speaking (economists, please correct me),  
due to the fact that money circulates in the economy, an additional  
dollar of investment translates into several additional dollars of  
consumer and other spending.  Thus the net effect of spending an  
additional dollar is disproportionately translated through the economy  
(positive feedback?).

Unfortunately, it can work in reverse.  If you choose not to buy that  
one dollar pack of gum (or that shiny new SUV or a cell phone or a  
second helping of dessert for that matter), the effect of money  
withdrawn from the economy can ripple through it, reducing aggregate  
demand disproportionately to the original withdrawal.  A positive  
feedback with very negative consequences :(

So how do we get off this treadmill.  Beats me..

Andy

Re: Equilibrium/Steady State and Complexity/Evolution

[Jeff Houlahan]

Ashwani and all, I think the critical point that Brian and Herman and others 
like them make is that, while it may be difficult to manage an economy to 
achieve steady-state, it is almost certainly impossible to do when the reigning 
paradigm is that growth is good.  When every policy or economic decision is 
aimed at growing the GNP/GDP it is very unlikely that we will achieve a steady 
state. I think to suggest that steady-state economy implies 'staying put' 
creates a straw man - yes, as individuals, communities, a species we are 
inevitably going to change over time.  Steady state implies (I believe, in the 
context we are talking here) zero-growth.  That doesn't mean 'no change'.  Best.

Jeff Houlahan

-Original Message-
From: Ashwani Vasishth [EMAIL PROTECTED]
To: ECOLOG-L@LISTSERV.UMD.EDU
Date: Mon, 2 Apr 2007 21:58:22 -0700
Subject: Re: Equilibrium/Steady State and Complexity/Evolution

At 12:21 AM + 4/3/07, [EMAIL PROTECTED] wrote:
  - no politburo required when the democratic rider is strong enough for the
capitalist horse.


Respectfully , Brian, that's a rather substantial caveat to slip in 
to the conversation.  All evidence that I see from tracking everyday 
politics and policy shows me that democracy is steadily losing out to 
corporate capitalism--every where.  Not only does it no longer matter 
that people should get what they want, people often don't know what 
they should want.  (And even when they know what they want and do get 
it, it turns out to be connected to all sorts of things that they 
definitely don't want.) Then what is to be done?

But more importantly, show me the mechanism that would keep any 
economy at an actual steady state.  It seems to me that we 
currently expend huge amounts of effort in attempting to keep the 
economy on an even keel, but even there, we fail more often than 
not.  The idea that we can stay put, in any fashion, seems to me 
completely an unnatural state of affairs, except if it is taken 
metaphorically.  (And then it does very little for us, near as I can 
tell.)

I like Daly et al., and agree with them about the need to manage for 
a different set of objectives than physical or morphological  growth. 
I buy the quite meaningful distinction between growth and 
development.  But the root reason(s) that an ecosystem approach is 
imperative to the management of life is because the world is a 
dynamical place that, further, can not be singularly defined.  Show 
me what specific steps we could take--both as individuals and as 
groups (ontogeny and phylogeny both have standing in this, yes?)--to 
get away from growth and toward a steady state?

I don't doubt in the least that there are a host of policies that 
would move us toward development and away from growth (adopting Cobb 
et al.s' Genuine Progress Indicators is only one example), but how 
does one stay put, in life, without first needing to deny both 
complexity and evolution?

By the way, a wonderful history of the idea of equilibrium in US 
social science is:

Russett, Cynthia E.  1966. The Concept of Equilibrium in American 
Social Thought. New Haven, London: Yale University Press.

And on the idea of evolutionary progress, see:

Nitecki, Matthew H. (ed.).  1988.  Evolutionary Progress.  Chicago: 
University of Chicago Press.

Cheers,
-
   Ashwani
  Vasishth[EMAIL PROTECTED]  (818) 677-6137
 http://www.csun.edu/~vasishth/
 http://www.myspace.com/ashwanivasishth

Re: invasive plants

[Jeff Houlahan (by way of Steve Brewer)]

Jeff and Teresa,

You make an excellent point about the need for us to back up our 
statements with evidence. Although many have provided very believable 
and plausible arguments for why invasive species have caused native 
plant extinctions, I find it interesting that hardly anyone is 
offering clear cut published examples.

I'd like to see these examples, because in my experience, documenting 
even local losses of plant species is very difficult (as Andy Dyer 
alluded to).  I have personally seen cogongrass (Imperata cylindrica) 
displace about 2/3 of the native longleaf pine savanna species in 
those portions of the site it has invaded. How do I know this? It 
produces discrete patches that expand radially. So, you can literally 
witness the disappearance of natives as each patch expands via 
clonal growth (much the same way as in Phragmites). However, to truly 
document their local loss, you also have to look at the seed bank, 
especially if the species that are disproportionately lost are 
annuals with persistent seed banks. In their case, the invader may 
simply be preventing seedling emergence in these species (for the 
time being). I've looked at the seed bank in infested areas, and it 
turns out that it is depauperate as well. However, one only has to 
walk a few meters out of the patch to find the displaced species. 
So, no extirpation, just reduced numbers.

All this brings back the original question that Teresa raised, are 
there documented instances in which an invasive plant has extirpated 
native species? I'm not aware of ANY (but I haven't read Davis' 
article yet). Although I have certainly seen cogongrass (considered 
one of  the worst weeds in the southeastern US) dramatically reduce 
species richness in longleaf pine savannas, I cannot say that I have 
seen it extirpate any species. I believe this is simply because its 
competitive effects operate at too small a spatial scale to cause 
such losses in the short term. I recognize that reduced numbers mean 
reduced population viability, but even then, given the  potential for 
rescue effects, I would feel more confident saying that invasive 
species caused extinctions if there were actual direct evidence, as 
opposed to inferences from stochastic simulations on a computer or 
negative correlations. Turning the population viability question 
around, I have just witnessed 100% mortality of woody goldenrod 
(Solidago pauciflosculosa) on three barrier islands as a result of 
the storm surge associated with Hurricane Katrina (though there may 
be a few viable seeds left in its short-lived seed bank, assuming 
they weren't washed away). Would anyone suggest that I need not 
bother monitoring this species on these islands anymore? I'm inclined 
to think that this species won't recover on these islands, but I 
wouldn't bet more than $50. Also, I think we should be careful about 
assuming extinction when we document that an invasive species has 
altered the ecosystem (e.g., fire regime, nutrient regime) in a way 
that is incompatible with the persistence of some native species. I 
think it is sufficient to say that the invasive species has altered 
the ecosystem in a way that is harmful to native species. Period.

I agree with Jeff that perhaps we can be confident in saying that 
some invasive species have reduced the numbers and have threatened 
the viability of some native species. I fear that skeptics will brand 
all of us who are genuinely concerned about the impacts of invasive 
species as chicken littles prone to hyperbole if we make claims we 
can't back up with empirical evidence. Furthermore, I believe that if 
make overly pessimistic assumptions about extinctions, this will lead 
some to conclude that, once an invasive species has taken over an 
area, there is nothing we can do.

Anyway, as far as documentation is concerned related to cogongrass, 
Teresa, you might check out:

Lippincott, C. L. 1997. Ecological consequences of Imperata 
cylindrica (cogongrass) invasion in Florida sandhill. Ph.D. 
dissertation, University of Florida, Gainesville, Florida, USA.

Brewer, J. S. and S. P. Cralle. 2003. Phosphorus addition reduces 
invasion of a longleaf pine savanna (southeastern USA) by a 
non-indigenous grass (Imperata cylindrica). Plant Ecology 167:237-245.

The first one deals more directly with negative effects of cogongrass 
on natives. The second study indirectly shows displacement (i.e., 
more native species in adjacent to patch than within a 
cogongrass-dominated patch). The other evidence I alluded to has not 
been published.

Steve Brewer



I think Teresa is raising a very good point and to the best of my 
knowledge the answer to her question is no, there is little in the 
way of empirical evidence that invasive species cause extinctions or 
even local extirpations.  The empirical evidence on loosestrife for 
example, is that although we see it everywhere it has not caused 
extinctions.  Best.

jeff Houlahan

-Original Message

Re: invasive plants

[Jeff Houlahan]

Hi all.  I think the responses to Teresa's question have been pretty 
informative. There have been a dozen responses giving logical and/or anecdotal 
evidence of invasive species causing extirpations...and one citation. The 
published examples are very rare (I'm not saying there is none, there is just 
surprisingly little considering how many people are studying invasive species) 
and the kind of evidence is similar to the evidence that we find in the 
Conservation Biology paper on Phragmites.  We are presented with evidence that 
species richness is higher in marshes without Phragmites than marshes with 
Phragmites, but we also find out that sites with high Phragmites cover also 
have higher nutrient levels, lower salinity, and higher surrounding 
development.  All of these things quite reasonably could be expected to cause 
declines in species richness without help from Phragmites (a removal experiment 
might actually get at this question).  But let's take this a bit further - the 
aut!
 hors are not saying that there has been a local extirpation, only that in a 
particular zone of the marsh, species richness is lower.  Is there any evidence 
that Phragmites invasion is causing extirpations in marshes?  I don't see any.  
What prediction would we make if invasive species cause local extirpations of 
native species?  Well, I think a crude first prediction would be that if I look 
in a bunch of quadrats in a homogeneous system there would be a negative 
relationship between the number of native and the number of invasive species.  
Any literature I have seen on this (and my own analyses) have shown a positive 
relationship between native and exotic species richness.  Now, people will 
argue that invasive species have an effect but it is lost in the 'noise'.  That 
may be so but at a minimum these positive relationships suggest that the 
effects of invasive species are not very important - certainly not important 
enough to provide a measurable signal. 
Further, there is all kinds of theory suggesting that competition is unlikely 
to cause local extirpations.  Tilman suggested that as long as there is a 
tradeoff between dispersal and competitive ability the poorer competitor would 
persist in a community indefinitely.  I don't follow this literature very 
closely but I suspect there is some evidence that simple stochasticity (even 
without the tradeoff between dispersal and competitive ability) can allow 
persistence.
Lastly, I think a great point has been made about using extirpations or 
extinctions as the bar by which we measure the effects of invasive species.  
But we, the conservation minded ecologists, have set that bar by writing blurbs 
on every website about purple loosestrife, describing the terrible effect that 
loosestrife has had on the diversity of wetlands, when there is a pile of 
empirical evidence to the contrary.  If we are going to state that the problem 
with exotic species is that they cause extirpations/extinctions we can't be 
annoyed when people ask to see the evidence.  If we really mean that invasive 
species cause declines in the abundance of native species, let's say so (and 
make sure that that statement is true and at what spatial scale it is true).  
Best.

Jeff Houlahan