Re: [ECOLOG-L] "real" versus "fake" peer-reviewed journals

[Bill Silvert]

I support Martin in this, although I think that James raises a valid point. 
Peer review is only a poor indicator of the quality of a paper, and often 
editors end up sending papers to graduate students or even people in other 
fields. About a third of the reviewing requests I receive are inappropriate, 
and often I can't even understand what the paper is about.


Of course this depends on the particular discipline. In fields where there 
is a standard methodology peer review can certify that the work was done 
correctly. In other fields though the reviewer may only be certifying that 
the paper follows the current paradigm (note the quote from Hilborn in 
another posting on this topic).


Basically we have no definitive way of separating valid results from junk. I 
am sure that there were plenty of senior scientists who would have rejected 
the papers of Darwin, Einstein, Wegener and many others. There are also 
hundreds of papers published in good journals which turned out to be wrong.


The suggestion that you look at the journal's mission statement may help. 
Reputable journals abound, the problem arises with obscure new journals that 
may have an agenda. (Certainly no respectable scientist would want to 
publish a complicated model in the online Journal of Simple Systems, 
www.simple.cafeperal.eu - I can say this with confidence, since I am the 
editor and publisher). If the journal seems strange or inappropriate, think 
about why the paper ended up there,


Bill Silvert

- Original Message - 
From: "James Crants" 

To: 
Sent: Wednesday, July 08, 2009 3:22 PM
Subject: Re: [ECOLOG-L] "real" versus "fake" peer-reviewed journals



Martin,

This all sounds good in the abstract, but it's beyond me how we could do
better than peer-review to establish which science is done well and which 
is
not.  No matter how reliable a system is, it's always easy to say "we 
should
do better than this."  But what would you propose to improve on our 
current

systme of vetting scientific research?

You don't have to get very far from your own field to run into research 
you

aren't equipped to validate.  Most pollination biologists probably aren't
prepared to properly assess the quality of research on insect cognition, 
for

example, so they have to rely on other scientists to evaluate the research
for them.  To what better authority could they possibly appeal?

I would certainly not want people who don't "have faith" in the scientific
method deciding which papers can and cannot be published.

Jim Crants

On Wed, Jul 8, 2009 at 10:34 AM, Martin Meiss  wrote:


 I find this exchange very interesting, and it points up a major
problem caused by the burgeoning of scientific knowledge and the
limitations
of the individual.  As scientists, we believe (have faith) that the
scientific method is the best means of arriving at truth about the 
natural

world.  Even if the method is error-prone in some ways, and is subject to
various forms of manipulation, it is historically self-correcting.
  The problem is that no individual has enough time, knowledge, and
background to know if the scientific method is being properly by all 
those

who claim to be doing so. We hear someone cite a suspicious-sounding fact
(i.e., a fact that doesn't correspond to our perhaps-erroneous
understanding), and we want to know if it is based on real science or
pseudo-science.  So what to we do?  We ask if the supporting research
appeared in a peer-reviewed journal (i.e., has this been vetted by the
old-boys network?).  This sounds a little like the response of the people
who first heard the teachings of Jesus.  They didn't ask "How do we know
this is true?"  They asked "By whose authority do you speak?"
   These two questions should never be confused, yet the questions 
"Did

it appear in a peer-reviewed journal" and "Is that journal REALLY a
peer-reviewed journal?" skate perilously close to this confusion.  We are
looking for a short-cut, for something we can trust so we don't have to 
be

experts in every branch of science and read every journal ourselves.  I
don't know the answer to this dilemma, and perhaps there is none, but we
should be looking for something better than "Does this have the stamp of
approval of people who think like I do?"  We should be looking for
something
that is not just an encodement of "Does this violate the doctrine of my
faith?"  The pragmatic necessity of letting others decide whether certain
research is valid should be no excuse for relaxing our personal vigilance
and skepticism. Otherwise, we fall into the same trap that ensnares the
religionists who are trying to undermine science because it threatens 
their

faith.

Martin M. Meiss


2009/7/8 Kerry Griffis-Kyle 

> I am teaching a Sophomore/Junior level evolution cou

Re: [ECOLOG-L] "real" versus "fake" peer-reviewed journals

[Bill Silvert]

Unfortunately Martin is looking for a magic bullet that doesn't exist. 
There are too many cases where scientific concensus has been wrong. Although 
quarks and Higgs bosons may exist, phlogiston and W-rays do not even though 
they were once well-accepted physical concepts. As for current climate 
issues, I don't see any easy way to resolve the controversy. Of course we 
discount the testimony of experts who work for the oil industry just as we 
did the medical researchers employed by tobacco firms, but how far does this 
get us? I subscribe to a fisheries list where most  of the subscribers feel 
that any research funded by the Pew Foundation is automatically biased.


R. Bruce Lindsay taught me that we never truly know anything, the best we 
can do is construct the best possible models of what we observe. When you 
read a scientific paper you are not reading facts, you are reading about a 
model that the author has constructed to explain observations. It boils down 
to your ability to evaluate models.


Fortunately the fields where we are least able to judge the quality of 
research are usually not of great concern to us. Martin's world will not 
collapse if the Higgs boson is not found.


Bill Silvert

- Original Message - 
From: "Martin Meiss" 

To: 
Sent: Wednesday, July 08, 2009 7:33 PM
Subject: Re: [ECOLOG-L] "real" versus "fake" peer-reviewed journals



 Yes, Dr. Greenberg, I concede your point. In one's immediate research
one must go far beyond having faith in the publishing process.
   By the way, do journals keep accurate data on their rejection 
rates,

on re-submission rates, etc.  This would be the sort of information that
could be used to distinguish between legitimate journals and journals with
political agendas.
 However, at least in part, my remarks were directed toward our
acceptance of work well outside our field.  I would like to hold 
intelligent

opinions on climate change, for instance, without having to understand all
the climatology, meteorology, oceanography, paleontology, modeling, etc.
that truly enlightened opinions are based on.  I would like to believe 
that
the voodoo-sounding stuff and the particle zoo that physicists talk about 
is

well-founded in theory and experiment, but I don't understand their
mathematics and I never will.  So when physicists say they have found the
top quark, or that there ought to be a Higgs boson, I have to take that on
faith, or perhaps, as Dave Raikow suggested in an earlier post, we should
call it "confidence."  Condidence that those guys know what they're 
talking

about, that their journal editors and reviewers aren't nuts or corrupt,
confidence that their mathematics isn't black magic. 

Re: [ECOLOG-L] Mosquitoes as keystone species?

[Bill Silvert]

It is not clear what Paul means by "extensive direct evidence". Flynn 
indicated that he had a team of colleagues working over several years who 
made this observation. Isn't this extensive direct evidence? Nor is it 
unreasonable to postulate that maybe the reason that there are fewer 
mosquitoes is that they were killed.


Bill Silvert, trying to think critically.

- Original Message - 
From: "Paul Cherubini" 

To: 
Sent: Thursday, July 09, 2009 1:10 PM
Subject: Re: [ECOLOG-L] Mosquitoes as keystone species?



Conor_Flynn wrote:


we've noticed something interesting: there are no
mosquitoes in or near Alamosa. This is because the
city sprays for them regularly. We have also noticed
fewer grasshoppers, bees, and  frogs than we might
otherwise expect.



A critical thinker would say it wildly speculative for anyone to
claim, without , that:

1) There really are no mosquitoes and fewer grasshoppers, bees,
and  frogs in Alamosa, Colorado.

2) Mosquito spraying is the underlying cause of these declines. 

Re: [ECOLOG-L] technical writing: comma at thousand mark?

[Bill Silvert]

One reason for leaving out the comma is that it creates confusion in 
international journals. An American could write one thousand twelve and a 
half as 1,012.5, but in Europe the comma and period are reversed so it is 
1.012,5. It is better to use just one separator for the decimals to minimise 
confusion.


There is a tendency in journals to Americanise (oops, Americanize) 
everything, including spelling. It seems strange that a European writing in 
a European journal is expected to follow American rather than UK spelling. 
Ironically I have had editors in Hong Kong try to change my UK (actually 
Canadian) spelling.


I suppose that if Melissa is in the US and writing reports for US readers 
the commas might be justified, but if writing for an international audience 
she should be able to have it omitted.


Bill Silvert
Portugal

- Original Message - 
From: "Melissa McCanna" 

To: 
Sent: Monday, July 13, 2009 9:10 AM
Subject: [ECOLOG-L] technical writing: comma at thousand mark?


Recently, I have been "edited" to place a comma at the thousand mark in my 
technical reports.? It was my understanding and my preference for nearly 
20 years that the comma in 1000/1,000 was optional, and preferred absent 
in technical writing.? What is the general feeling out there?


Also, I have been noticing more and more a comma added for a month-year 
designation: July, 2009.? I thought the comma was unnecessary.


I turn 40 this year.? Is this just the natural order of things that I 
become a writing curmudgeon? :-)


-Melissa








No virus found in this incoming message.
Checked by AVG - www.avg.com
Version: 8.5.375 / Virus Database: 270.13.10/2230 - Release Date: 07/10/09 
17:57:00

Re: [ECOLOG-L] Shannon-Wiener Div Index Question - dealing with zero species per plot??

[Bill Silvert]

After reading this posting and several replies I am getting more and more 
confused. Of course both n=0 and n=1 correspond to zero diversity. What is 
the issue?


More fundamentally, what is the point of all of this? In the rest of her 
posting (which I have omitted) she describes a project for which she wants 
an index, but I think that the output of an ecological study should be a 
statement about the ecosystem, To say that bees prefer substrate X to 
substrate Y is informative, but to simply report the value of some 
arbitrarily chosen diversity index is not, at least not so far as I can 
tell.


Perhaps if she has some biologically meaningful hypotheses to test it would 
be easier to identify some index that can be used to distinguish between 
them. She writes "I am studying substrate preferences of ground nesting 
bees" but it isn't clear how any diversity index fits into the analysis.


Bill Silvert

- Original Message - 
From: "Maria Van Dyke" 

To: 
Sent: Thursday, July 16, 2009 6:39 PM
Subject: [ECOLOG-L] Shannon-Wiener Div Index Question - dealing with zero 
species per plot??




I have a question about utility of the Shannon-Wiener diversity index in
regards to sampling units that have no species in them at a given sampling
time. Normally this would get a value of zero, however with Shannon-Wiener 
a

sampling unit that has only one individual of one species would also earn
the value of zero when input into the formula -∑(1*ln1) 
= -∑(1*0) = 0;

therefore there becomes an issue of two different species scenarios having
the same values (0 for no species individuals and 0 for 1 ind of one 
species). 

Re: [ECOLOG-L] Shannon-Wiener Div Index Question - dealing with zero species per plot??

[Bill Silvert]

If you are trying to synthesize results from different communities, then 
having some undefined really messes things up. Better to have a poor 
definition than run to "undefined". An alternative is to weight the measure 
by the number of species so that with zero species you have a real zero.


It sounds to me like UA or US (which is it?) may have too many philosophers 
on staff!


Bill Silvert

- Original Message - 
From: "Eric Lamb" 

To: 
Sent: Friday, July 17, 2009 12:14 PM
Subject: Re: [ECOLOG-L] Shannon-Wiener Div Index Question - dealing with 
zero species per plot??




The consensus seems to be that diversity should be zero, but we should
consider the larger question before the mechanics of calculating a
particular index.

I recently had to deal with a similar question: what is the evenness of a
community with zero species?. The consensus among those I discussed this
issue with was that evenness (and hence diversity) should be undefined 
when
there are no species. The reason is that diversity or evenness is a 
property
of a community, not a patch of ground or a pot. If there are no species 
then

there is no community, and thus we cannot define evenness.

Cheers, Eric

--
Eric Lamb
Assistant Professor, Plant Ecology and Biostatistics
Dept. of Plant Sciences, University of Saskatchewan
http://homepage.usask.ca/egl388/index.html

4D68 Agriculture Building
306-966-1799
eric.l...@usask.ca 

Re: [ECOLOG-L] Are ecologists the problem?

[Bill Silvert]

I agree with Malcolm's posting that strict vegetarianism has its own 
problems, but the basic idea of eating lower on the food chain certainly has 
some benefits. This is particularly true where fish are concerned - most of 
the land animals killed for food are herbivores, but the most prized fish 
tend to be carnivores. This has raised a lot of concern.


However I think that we should encourage people to think about the problem 
and make suggestions, even though we may disagree with some of them. 
Arrogant putdowns like the one below don't encourage people with ideas to 
speak out, and some of them may even  have good ideas that should not be 
suppressed.


Bill Silvert


- Original Message - 
From: "Benjamin Lee" 

To: 
Sent: Wednesday, September 09, 2009 5:26 AM
Subject: Re: [ECOLOG-L] Are ecologists the problem?


Maybe ESA could conduct a poll of members that live in highly populated
desert areas that by definition are unsustainable like Tempe, Arizona. Or
maybe vegans and vegetarians should not brag about themselves over the
ECOLOG listserv. 

Re: [ECOLOG-L] Are ecologists the problem?

[Bill Silvert]

I think that a lot of confused thinking is going into this issue. Aside from 
the recurring question of whether ecologists and environmentalists are the 
same, I think we need to distinguish between personal and professional 
footprints. Most ecologists I know live quite modestly and are not wasteful. 
However research is demanding. How do you survey a large savannah without an 
airplane, or at least a 4x4? How do you conduct marine research without 
ships, and ships burn a lot of fuel?


Other fields face even more drastic contrasts. The search for low-impact 
energy through fission or the use of high-temperature superconductors 
requires research that consumes a tremendous amount of energy.


There is also a political issue here. If we follow some lines of reasoning 
then ecologists/environmentalists would not fly to meetings or use energy 
guzzling computers, we would communicate by mailing letters to each other 
and hand-deliver press releases to the media by bicycle. The "bad guys" 
could of course take full advantage of modern technology to shout us down. 
How effective would we green people be in that case?


Bill Silvert

- Original Message - 
From: "Lesley Campbell" 

To: 
Sent: Wednesday, September 09, 2009 5:56 PM
Subject: Re: [ECOLOG-L] Are ecologists the problem?


While I'm more than happy to agree that the amount that ecologists
travel (relative to the average earth resident) is an outrageous
disaster,... 

[ECOLOG-L] Hippos in Columbia

[Bill Silvert]

This story from the New York Times, September 11, 2009, raises issues 
relevant to the list!


Bill Silvert
Colombia Confronts Drug Lord's Legacy: Hippos
By SIMON ROMERO
DORADAL, Colombia - Even in Colombia, a country known for its paramilitary 
death squads, this hunting party stood out: more than a dozen soldiers from 
a Colombian Army battalion, two Porsche salesmen armed with long-range 
rifles, their assistant, and a taxidermist.


They stalked Pepe through the backlands of Colombia for three days in June 
before executing him in a clearing about 60 miles from here with shots to 
his head and heart. But after a snapshot emerged of soldiers posing over his 
carcass, the group suddenly found itself on the defensive.


As it turned out, Pepe - a hippopotamus who escaped from his birthplace near 
the pleasure palace built here by the slain drug lord Pablo Escobar - had a 
following of his own.


The meticulously organized operation to hunt Pepe down, carried out with the 
help of environmentalists, has become the focus of an unusually fierce 
debate over animal rights and the containment of invasive species in a 
country still struggling to address a broad range of rights violations 
during four decades of protracted war with guerrillas.


"In Colombia, there is no documented case of an attack against people or 
that they damaged any crops," said Aníbal Vallejo, president of the Society 
for the Protection of Animals in Medellín, referring to the hippos. "No 
sufficient motive to sacrifice one of these animals has emerged in the 28 
years since Pablo Escobar brought them to his hacienda."


Sixteen years after the infamous Mr. Escobar was gunned down on a Medellín 
rooftop in a manhunt, Colombia is still wrestling with the mess he made.


Wildlife experts from Africa brought here to study Colombia's growing 
numbers of hippos, a legacy of Mr. Escobar's excesses, have in recent days 
bolstered the government's plan to prevent them - by force, if necessary - 
from spreading into areas along the nation's principal river. But some 
animal-rights activists are so opposed to the idea of killing them that they 
have called for the firing of President Álvaro Uribe's environment minister.


Peter Morkel, a consultant for the Frankfurt Zoological Society in Tanzania, 
compared the potential for the hippos to disrupt Colombian ecosystems to the 
agitation caused by alien species elsewhere, like goats on the Galápagos 
Islands, cats on Marion Island between Antarctica and South Africa, or 
pythons in Florida.


"Colombia is absolute paradise for hippos, with its climate, vegetation and 
no natural predators," Mr. Morkel said.


"But as much as I love hippos, they are an alien species and extremely 
dangerous to people who disrupt them," he continued. "Since castration of 
the males is very difficult, the only realistic option is to shoot those 
found off the hacienda."


The uproar has its roots in 1981, when Mr. Escobar was busy assembling a 
luxurious retreat here called Hacienda Nápoles that included a 
Mediterranean-style mansion, swimming pools, a 1,000-seat bull ring and an 
airstrip.


"He needed a tranquil place to unwind with his family," said Fernando 
Montoya, 57, a sculptor from Medellín who built giant statues here of 
Tyrannosaurus rex and other dinosaurs for Mr. Escobar.


Hired by private administrators of the seized estate, part of which is now a 
theme park (imagine mixing "Jurassic Park" and "Scarface" into a theme), Mr. 
Montoya rebuilt the same statues after looters tore them apart searching for 
hidden booty.


But Mr. Escobar was not content with just fake dinosaurs and bullfights. In 
what ecologists describe as possibly the continent's most ambitious effort 
to assemble a collection of species foreign to South America, he imported 
animals like zebras, giraffes, kangaroos, rhinoceroses and, of course, 
hippopotamuses.


Some of the animals died or were transferred to zoos around the time Mr. 
Escobar was killed. But the hippos largely stayed put, flourishing in the 
artificial lakes dug at Mr. Escobar's behest.


Carlos Palacio, 54, head of animal husbandry at Nápoles, said Mr. Escobar 
started in 1981 with four hippos. Now, he said, at least 28 live on the 
estate. "With our current level of six births a year set to climb, we could 
easily have more than 100 hippos on this hacienda in a decade," Mr. Palacio 
said.


"Some experts see this herd as a treasure of the natural world in case 
Africa's hippo population suffers a sharp decline," Mr. Palacio continued. 
"Others view our growth as a kind of time bomb."


The number of hippos on the hacienda could have reached 31 had Pepe, the 
slain hippo, not clashed about three years ago with the herd's dominant 
hippo, then left with a mate for other pastures. Once established near 
Pu

[ECOLOG-L] Population control

[Bill Silvert]

Recently there was a long discussion of whether ecologists are the problem, 
and a few posters pointed out that the biggest problem is overpopulation. 
There was not much discussion of this, as it is a hrad problem to solve, it 
is easier to get rid of ecologists. However the following Economist article 
is quite intriguing.


Bill Silvert

Green.view
Fewer feet, smaller footprint
Sep 21st 2009

From Economist.com


A world with fewer people would emit less greenhouse gases

FAMILY planning is five times cheaper than conventional green technologies
in combating climate change. That is the claim made by Thomas Wire, a
postgraduate student at the London School of Economics, and highlighted by
British medics writing in the Lancet on September 19th.

Ever since Thomas Malthus, an English economist, published his essay on the
principle of population in 1798, people have been concerned about population
growth. Sir Julian Huxley, the first director general of the United Nations
Education, Science and Cultural Organisation when it was established in
1945, remarked that death control made birth control a moral imperative. Sir
Julian went on to play a role in establishing what was then the World
Wildlife Fund, a nature conservation agency, linking population growth to
environmental degradation.

According to Roger Short of the University of Melbourne, the world's
population is 6.8 billion and is expected to reach 9.1 billion by 2050. Some
95% of this growth is occurring in developing countries. In a paper
published on September 21st in the Philosophical Transactions of the Royal
Society B, he points out that fewer people would produce less
climate-changing greenhouse gas.

A companion study published in the same issue by Malcolm Potts of the
University of California, Berkeley, reckons that there are 80m unintended
pregnancies every year. The vast majority of these result in babies. If
women who wanted contraception were provided with it, 72% of these
unintended pregancies would have been prevented, according to a report by
the United Nations Population Fund called "Adding it Up: the Benefits of
Investing in Sexual and Reproductive Healthcare".

The study by Mr Wire was commissioned by the Optimum Population Trust, a
British environmental charity. It examined the cost-effectiveness of
providing global access to family planning between 2010 and 2050. Mr Wire
totted up the cost of supplying contraception to women who wished either to
delay their childbearing years or to end them artificially but who were not
using contraception. He examined projections of population growth and of
carbon-dioxide emissions made by the United Nations and concluded that
reducing carbon emissions by one tonne would cost just $7 spent on family
planning, as opposed to at least $32 spent on green technologies.

Mr Wire points out that if all women who wanted contraception were provided
with it, it would prevent the release of 34 billion tonnes of carbon dioxide
between 2010 and 2050. Given the myriad of other reasons to limit human
fertility (Dr Potts notes, for example, that slowing population growth is
essential if poverty is to be eradicated), your correspondent cannot help
but commend the report to mandarins meeting in Bangkok on September 28th to
discuss the forthcoming United Nations Climate Change Conference in
Copenhagen.

Copyright © 2009 The Economist Newspaper and The Economist Group. All rights
reserved.

Re: [ECOLOG-L] Population control

[Bill Silvert]

Empowering women is just one of many steps in the right direction. Education 
helps, even though one list member in an off-list message complained that 
since educated people make more and thus have larger footprints, education 
is bad. Health care is another good step. Poor people often have large 
families so that the children can work, so anything that alleviates 
desperate poverty can be beneficial.


Bill Silvert

- Original Message - 
From: "Abraham de Alba A." 

To: 
Sent: Tuesday, September 22, 2009 6:56 PM
Subject: Re: [ECOLOG-L] Population control


I thought this argument was done fore a long time ago, I mean, the 
sociologists found that "enpowering" women was more profitable, that is, 
women that find that can contribute to their well-being WILL use 
concraception, otherwise it doesn`t matter if all the drug stores are full 
of contraceptives.


It's anybodies guess HOW to empower women, it has been done and it's 
probably being done right now, but it`s not an overnight thing. Here Mexico, 
it has finally been accepted by government officials that given money to 
men, is just another way of subsidicing the beer industry or tequila, but 
when they give to women's groups it usually flourishes into a small 
buisness, so much for our macho economy.


Abraham de Alba Avila 

Re: [ECOLOG-L] Spontaneous fermentation

[Bill Silvert]

While it is certainly true that this quote is wrong, the underlying 
ecological principle is correct. During Franklin's time water was considered 
an unsafe drink, and in general it was. Sanitation was poor and beverages 
like beer and cider were safer and thus considered preferable. According to 
some sources Franklin actually was more of a water drinker than most people 
of his time, but the erroneous quote accurately reflects the ecological 
views of the time.


These attitudes persist to the present time and account for the popularity 
of bottled water.


Bill Silvert

--
From: "Matt Chew" 
Sent: Sunday, September 12, 2010 9:40 PM
To: 
Subject: Re: [ECOLOG-L] Spontaneous fermentation


It has been politely suggested that the Franklin "bacteria" quotation is
dubious.  It is worse than that, in two ways.

First, the salient facts are readily available but were apparently never
checked or even questioned before they were posted.  Such naive and
incurious assertions should not be emanating from ESA email addresses – no
matter how useful they seem for promotional purposes.

Second, as the instructor for an upper-division undergraduate (BIO-) 
course
in the History of Biology, I regret to report that ecology students (and 
the

professionals they become) share today's generally profound historical
illiteracy–and apathy.  This is a pity in a field whose motivations,
hypotheses and conclusions are so deeply affected and occasionally even
determined by cultural and intellectual fashions.

If you don't know the history of ecology, you don't know ecology.

Matthew K Chew 

Re: [ECOLOG-L] Transformations for Normalized Data

[Bill Silvert]

I'm not clear on whether this is a thread about ecology or statistics. Jane
writes "My goal is simply to do a regression" which seems a strange kind of
goal. If she wants to predict abundances or identify causative factors, that
I understand, but what kind of goal is doing a regression?

How do we even know that the regression she is looking for exists? Even
obvious regressions can be misleading. I was once approached by a colleague
who asked for my help finding the relationship between parental biomass and
surviving offspring, but a quick look at the data showed that no
relationship existed. So instead we set about looking for factors that
determined the number of offspring and found a good correlation with
environmental factors (Koslow, J. Anthony, Keith R. Thompson, and William
Silvert. 1987. Recruitment to Northwest Atlantic Cod (Gadus morhua) and
Haddock (Melanogrammus aeglefinus) Stocks: Influence of Stock Size and
Environment. Can. J. Fish. Aquat. Sci. 44:26-39). We not only identified a
predictive pattern, but we could conclude that even though the fish were
extremely fecund, the number of survivors depended on an environmental
bottleneck so that the number of eggs was not very important.

William Silvert

-Original Message- 
From: Jane Shevtsov

Sent: Friday, October 29, 2010 12:31 AM
To: ECOLOG-L@LISTSERV.UMD.EDU
Subject: Re: [ECOLOG-L] Transformations for Normalized Data

Hi Mike,

Dividing by the mean helps. Still, there are definitely too many zeros
in my data, so what should I do with the distributions you mentioned?
My goal is simply to do a regression.

Thanks,
Jane

On Thu, Oct 28, 2010 at 8:11 PM,   wrote:


1) divide by the mean instead of the maximum

2) abundance data is rarely normal even before normalization because A)
abundance can never be negative and B) it usually has too many zeros
because one is convolving two processes (probability of presence times
abundance given presence).  If your data shows (B) I recommend using a
zero-inflated distribution while if it shows (A) I would recommend a
distribution that is positive (e.g. lognormal or gamma).  Because I
usually work with count data I prefer the zero-inflated Poisson or
zero-inflated Negative Binomial, but once you've normalized that's no
longer an option.  I'd probably try a zero-inflated lognormal or
zero-inflated gamma, with the former being conceptually simpler because it
doesn't require a link function.  If neither (B) nor (A) is present in
your data you're very luck and can stick to the normal (possibly with
transformation).

 -- Mike


I have abundance data for a number of different species that I need to
use in a regression. Since the data encompasses a variety of taxa
(from trees to soil mites)  whose abundances are measured differently,
I normalized it, dividing abundances of each species by the maximum
abundance of that species. This, of course, produces numbers ranging
from 0 to 1, with a 1 for every species.

Now I'm trying to transform the data into something approaching
normality. I've tried various combinations of arcsin, square root,
fourth root, and log (after adding 1, as there are plenty of zeros in
the data), but nothing seems to help much. The problem appears to be
the presence of a 1 in every column. Any ideas for what might work?

Thanks,
Jane Shevtsov

--
-
Jane Shevtsov
Ecology Ph.D. candidate, University of Georgia
co-founder, 
Check out my blog, Perceiving
Wholes

"The whole person must have both the humility to nurture the
Earth and the pride to go to Mars." --Wyn Wachhorst, The Dream
of Spaceflight









--
-
Jane Shevtsov
Ecology Ph.D. candidate, University of Georgia
co-founder, 
Check out my blog, Perceiving Wholes

"The whole person must have both the humility to nurture the
Earth and the pride to go to Mars." --Wyn Wachhorst, The Dream
of Spaceflight 

Re: [ECOLOG-L] ECOLOGY Fundamentals Principles Laws Other

[Bill Silvert]

"discipline" ? Ecology suffers from too much concern with philosophy and not 
enough science.


Consider Gauss' Competitive Exclusion Principle. It is very useful, provides 
a guide to identifying the niche of an organism, but it has been identified 
as tautological by the late Rob Peters so we aren't supposed to use it.


Lawrence Slobodkin used to complain about theorists invoking principles like 
conservation of energy as if that were optional for living creatures. 
Basically the answer to Wayne's question is that if ecologists come up with 
something useful that might serve as a law or principle, then it would be 
drowned out by claims that it was not rigorous enough. We worry too much 
about being "scientific" and not enough about learning how things work.


Bill Silvert


-Original Message- 
From: Wayne Tyson

Sent: Sunday, October 31, 2010 2:39 AM
To: ECOLOG-L@LISTSERV.UMD.EDU
Subject: [ECOLOG-L] ECOLOGY Fundamentals Principles Laws Other

Ecolog:

In recent years the debate about Laws of Ecology has been re-heated.* If the 
study of the interactions of living organisms with environments is to have 
discipline, it seems to me that it should have produced some observations 
about how things work or function that, when applied, never fail to prove 
valid. Can such observations, rendered as statements or equations, be termed 
"laws" or "principles," or?


WT

*For example, see 
http://philosophy.unc.edu/people/faculty/marc-lange/Oikosfile.pdf 

Re: [ECOLOG-L] ECOLOGY Fundamentals Principles Laws Other

[Bill Silvert]

Wow, to be a law or principle it has to be perfect? I have a PhD in Physics 
and thought that we had lots of laws, but they seldom pass that test. For 
hundreds of years we talked about and taught Newton's Laws of Motion, but 
then Einstein came along with examples of cases where they FAIL. As for 
propping up, where do hypothetical particles like neutrinos and quarks come 
from?


Do we really want ecology to be a much more rigid and philosophically pure 
science than physics, astronomy and the rest? Or can we just focus on trying 
to figure out how nature works?


Bill Silvert


-Original Message- 
From: Wayne Tyson

Sent: Sunday, November 07, 2010 1:55 AM
To: ECOLOG-L@LISTSERV.UMD.EDU
Subject: Re: [ECOLOG-L] ECOLOGY Fundamentals Principles Laws Other

My original question was about whether or not the discipline of ecology (I 
meant in the broadest sense) recognizes or should try to recognize, some 
observations about how "things" function or work  that amount to laws or 
statements (hypotheses), when applied NEVER FAIL to prove valid--pass the 
test for a law or a principle. (And, I might add, one [or more?] that needs 
no propping up with qualifiers. (This, I will confess, is one issue I have 
with the referenced paper, but the author might be right and I might be 
wrong.) 

Re: [ECOLOG-L] Taxonomy and Ecology Integrating or Disintegrating?

[Bill Silvert]

Wayne's story reminds me that the eminent ecologist Larry Slobodkin once 
observed that "ecology without species is the ultimate abomination." I was 
giving some lectures on size-structured ecosystems, so I introduced myself 
as an "abominable ecologist". It seemed a fitting title. Still does.


Bill Silvert

-Original Message- 
From: Wayne Tyson

Sent: Friday, November 12, 2010 7:18 PM
To: ECOLOG-L@LISTSERV.UMD.EDU
Subject: [ECOLOG-L] Taxonomy and Ecology Integrating or Disintegrating?

Honourable Forum:

Recently there was a discussion about the importance of getting nomenclature 
right in ecological studies. The general conclusion was that this is 
important. To me, the implication was that ecologists need taxonomists on 
the team (this may or may not always or even rarely be possible), or at 
least a procedure by which taxonomic accuracy can be assured.


I recently attended a lecture by a botanist of regional and international 
repute who described a large project to compile a checklist of the vascular 
flora of an inadequately-explored, but quite large region. It is undeniable 
that this is important work, and through this person's leadership, 
significant additions to knowledge of the area have been made. The lecture 
included maps of "bioregions" or "ecoregions." This botanist dismissed the 
value and importance of them, adding that they were the province of the 
ecologists and were highly flawed (I can't quote the lecturer precisely, but 
this is the best of my recollection and my distinct impression). The 
lecturer essentially dismissed ecology, remarking that the lecturer was 
interested only in individual plants and seemed contemptuous of ecologists 
in general, and particularly those involved in establishing the ecoregions 
that were a part of the lecture. I may have misunderstood, as I have long 
held this person in high regard, and those remarks seemed inconsistent with 
past behavior.


Do you find this state of mind to be common among taxonomists in general or 
botanists in particular? Is this apparent schism real or imaginary? Other 
comments?


WT

PS: During the lecture, the speaker remarked about ecological phenomena 
which were not understood (no clue), but at least one reason for one 
phenomenon was apparent to me. I said nothing, as the lecture had been very 
long and the question period short. 

Re: [ECOLOG-L] moving from a PC to a Mac???

[Bill Silvert]

Scott is right, Vista is a good reason to move to a Mac. However I might 
point out that PC makers are beginning to offer XP again. The high end Sony 
Vaios actually come with both, including an optional "downgrade" from Vista 
to XP, and I suspect that by the end of the year most suppliers will be 
offering XP.


So all is not lost. A PC with XP is a useful machine, a PC with Vista is 
nothing but a headache.


Of course if you have a desktop machine, you can simply install XP. However 
the operating systems for laptops are usually tweaked for the hardware, so 
if you have a laptop with Vista, you are screwed - installing XP is a risky 
option.


Bill Silvert

- Original Message - 
From: "Scott D Lapoint" <[EMAIL PROTECTED]>

To: 
Sent: Monday, August 11, 2008 6:47 PM
Subject: [ECOLOG-L] moving from a PC to a Mac???



Hello Ecologers,

  It's time for me to invest in a new computer. I've long been a fan  of 
Dell computers and PCs in general, but because of the issues I've  seen 
with Vista, I've been considering a switch to Mac.

Re: [ECOLOG-L] moving from a PC to a Mac???

[Bill Silvert]

Maybe my criticisms of Vista were excessive, assuming that you want to spend 
a lot of time tweaking it. One of my problems is that Windows Explorer 
doesn't work (I have installed all the Windows upgrades, but it still keeps 
crashing about 80% of the time I try to do a file copy). So I'll take Joe's 
advice and get the file handlers he recommends. As for UAC (user access 
control) I still have not figured out how to access some of my directories 
despite having an administrator's account, but perhaps that will come with 
time.


Still, it is awfully slow, especially doing things in Windows Mail. Maybe 3 
GB is not enough.


I should add that our Vista machine is a Sony Vaio laptop, and when I went 
to the web for advice I found lots of similar complaints from Sony owners. 
It may be that my hardware is the problem, not Vista. Still, I know that 
many people who bought new desktops with Vista soon decided to go back to 
XP. It's an operating system that some people love and others hate. I am one 
who hates it.


By the way, my comment about problems upgrading laptops from XP to Vista are 
based on discussions with PC technicians, not on my own experience.


Bill Silvert

- Original Message - 
From: "Joe Ledvina" <[EMAIL PROTECTED]>

To: 
Sent: Tuesday, August 12, 2008 4:09 AM
Subject: Re: [ECOLOG-L] moving from a PC to a Mac???



More and more people are coming around to Vista, and for some good
reasons...

I've been using Vista since January, and I love it. I used to use a
3rd-party file manager (FreeCommander) and copy handler (TeraCopy),
but Explorer improvements have made them unnecessary. UAC can be
adjusted to be hardly obtrusive, and it works. 

Re: [ECOLOG-L] Mac or PC? Software issue

[Bill Silvert]

I appreciate all the information that has been provided on this topic, but 
noting that some responses are based on the idea that Mac software is often 
better than PC software, a note of warning may be necessary - some 
conferences require that submissions be in MS Word, and while I strongly 
object to this policy, it can be a real pain. MS Office for the Mac is 
expensive (I don't get the student rate) and there are still compatibility 
problems with Open Office. Even worse is the situation with uisng 
PowerPoint, which doesn't always come out right if you have a complicated 
presentation developed on a Mac and then you have to use the conference PC. 
If you opt for a Mac, it is a good idea to check your files on a PC before 
you get to the conference!


Although I really like Unix and am planning to run Linux on an old PC of 
mine, compatibility problems can be even worse there. I'm struggling with a 
co-author who uses TeX, and while it is really a nice package (I used to use 
it in my Unix days) it is really hard to collaborate.


Of course even with different PCs running the same software you can have 
problems. I wrote a paper on a Canadian computer with colleagues in Germany 
and Israel and even though we had nominally identical versions of MS Word, 
the files did not appear the same, especially where math symbols were used. 
I find that when sending manuscripts around I pretty much have to rely on 
PDFs.


Bill Silvert

- Original Message - 
From: "Scott D Lapoint" <[EMAIL PROTECTED]>

To: 
Sent: Sunday, August 17, 2008 3:20 AM
Subject: [ECOLOG-L] Mac or PC? A Summary of reponses


  About a week ago I posted a message asking for input on whether I 
should move from a PC to a Mac. I was particularly concerned with the 
higher costs of a Mac and if one can run Windows programs such as  ArcGIS 
and some statistics packages. I received ~200 e-mailed  responses from 
Ecolog alone, not to mention the dozens that I received  from my 
additional efforts... 

Re: [ECOLOG-L] ecologcal modeling

[Bill Silvert]

I find this kind of request similar to asking about courses in microscopy. I 
really don't think that anyone could construct a course that covered all 
different kinds of ecological modelling. You start with a problem and try to 
solve it, you don't start with a hammer and look for the right kind of nail.


Bill Silvert

- Original Message - 
From: "John Claydon" 

To: 
Sent: Tuesday, January 20, 2009 3:59 AM
Subject: [ECOLOG-L] ecologcal modeling



I was interested if there were any intensive courses on ecological modeling
available during this summer. Country is not an issue.

I would be grateful for any advice.

Thanks

John Claydon 

Re: [ECOLOG-L] ecologcal modeling

[Bill Silvert]

I guess I should elaborate on my brief posting. I agree with Jane, but most 
courses on ecological modelling (EM) start with cabinet making. I've given a 
numberf of short courses on EM at various universities, and almost always 
the organisers start by asking what software I plan to use. And in fact many 
(perhaps most) courses deal with the use of a specific package, such as 
Stella, MatLab or ECOPATH. These packages are restrictive, none can 
implement all the different modelling approaches that might be appropriate. 
For example, almost none can handle something as simple as a Leslie matrix.


There no "principles of ecological modeling" that I would describe as such, 
but there are many concepts that I think should be discussed in a course but 
are often omitted when the students dive straight into programming. These 
include the concepts of stability and resilience, the various forms of time 
series analysis and system identification. As for chaos and catastrophe 
theory 


There is no clearly defined set of principles and approaches in EM, and 
basically every course is different and depends on the views of the teacher. 
A student who passes one course would likely fail the exam in a different 
course. By comparison, a student who passes a course in microbiology could 
probably pass the exams in other courses. This chaotic situation can have 
disastrous results.


I am sure that most modellers would consider me crazy for some of the things 
I do and teach (a view I often reciprocate!). Some of the materials I have 
used in modelling courses are on my website, 
http://ciencia.silvert.org/models/.


Bill Silvert

- Original Message - 
From: "Jane Shevtsov" 

To: 
Sent: Wednesday, January 21, 2009 1:17 AM
Subject: Re: [ECOLOG-L] ecologcal modeling


Ideally, you learn some carpentry before you need to build kitchen 
cabinets.


Jane Shevtsov


And Wayne Tyson wrote:
Bill, what about the principles of ecological modeling; are they uniform 
across applications?


in response to my posting


On Tue, Jan 20, 2009 at 4:04 PM, Bill Silvert  wrote:
I find this kind of request similar to asking about courses in 
microscopy. I

really don't think that anyone could construct a course that covered all
different kinds of ecological modelling. You start with a problem and try 
to
solve it, you don't start with a hammer and look for the right kind of 
nail.


Bill Silvert

- Original Message - From: "John Claydon"

To: 
Sent: Tuesday, January 20, 2009 3:59 AM
Subject: [ECOLOG-L] ecologcal modeling



I was interested if there were any intensive courses on ecological
modeling
available during this summer. Country is not an issue.

I would be grateful for any advice.

Thanks

John Claydon






--
-
Jane Shevtsov
Ecology Ph.D. student, University of Georgia
co-founder, http://www.worldbeyondborders.org";>World Beyond 
Borders

Check out my blog, http://perceivingwholes.blogspot.com";>Perceiving Wholes

"Political power comes out of the look in people's eyes." --Kim
Stanley Robinson, _Blue Mars_

[ECOLOG-L] Apologies for misspelled posting - Wiegert

[Bill Silvert]

After I mentioned a paper by "Weigert" in a posting I have received numerous 
requests for the reference. The correct spelling is Wiegert. My apologies to 
all of you, especially Prof. Wiegert.

I am currently travelling and do not have the reference with me, but I found 
his website and the paper may be

Wiegert, R.G. 1975. Simulation models of ecosystems. Ann. Rev. Ecol. Syst. 
6:311-338.

although I thought it was earlier. The paper describes about half a dozen 
models of a simple salt spring ecosystem, and as I wrote earlier, he found that 
the best performance came with an intermediate level of complexity.

I've been asked in another posting why complex models do not work too well. 
There are many reasons for this, including the need for too many parameters and 
resultant magnification of errors, but in ecological modelling when you get too 
specific and try to model individual species you need to describe the factors 
behind zonation and succession, which is hard to do. In general I find that 
fairly aggregated models work well, especially when aggregated on the basis of 
function rather than taxonomy.

Another problem is that very precise models are more susceptible to problems 
arising from discontinuous processes, such as insect outbreaks and blooms 
(algal, jellyfish, etc.). Unless we know precisely what triggers these events 
and know how to predict the events, the models will not perform well.

I recall a modelling exercise where the components of an estuarine ecosystem 
were modelled by separate groups of scientists. All went well, except that the 
head of the zooplankton group insisted that all four of the Acartia species he 
was studying be modelled individually. They never managed to do this (again, 
problems of zonation and succession) and the project would have been aborted if 
the rest of us hadn't thrown together a simpler but working submodel.

Not everything can be successfully predicted. This is a property of natural 
systems, not just ecological models. I have already mentioned the cod-haddock 
issue on this list. Modelling fish recruitment is tricky because it depends on 
the overlap between larval emergence and plankton blooms, which we generally 
cannot predict. We cannot do very well at predicting earthquakes either. And in 
mathematics, remember Gödel's famous proof that not all true theorems can be 
proven. Failure to do the impossible is not really failure (unless you are a 
Marine!).

Ciência Silvert
www.ciencia.silvert.org

[ECOLOG-L] Forest fluxes

[Bill Silvert]

I was intrigued to see this in the New York Times. I have no   background
in this area and would be interested in seeing what more knowledgable
list members might have to say.

Also I recently heard a statement that there is a significant   amount of
anaerobic decomposition under old growth forests that should be   factored
into calculations of biogeochemical fluxes, and it would be interesting
to hear about that too.

Bill Silvert


January 30, 2009

New Jungles Prompt a Debate on Rain   Forests
By [LINK:
http://query.nytimes.com/search/query?ppds=bylL&v1=ELISABETH%20ROSENTHAL&fdq=19960101&td=sysdate&sort=newest&ac=ELISABETH%20ROSENTHAL&inline=nyt-per]
ELISABETH   ROSENTHAL


CHILIBRE, [LINK:
http://topics.nytimes.com/top/news/international/countriesandterritories/panama/index.html?inline=nyt-geo]
Panama   — The land where Marta Ortega de Wing raised hundreds of pigs
until 10 years ago   is being overtaken by galloping jungle — palms,
lizards and ants.

Instead of farming, she now shops at the supermarket and her grown
children   and grandchildren live in places like Panama City and New York.


Here, and in other tropical countries around the world, small holdings
like   Ms. Ortega de Wing’s — and much larger swaths of farmland — are
reverting to   nature, as people abandon their land and move to the cities
in search of better   livings.

These new “secondary” forests are emerging in Latin America, Asia and
other   tropical regions at such a fast pace that the trend has set off a
serious debate   about whether saving primeval [LINK:
http://topics.nytimes.com/top/news/science/topics/forests_and_forestry/rain_forests/index.html?inline=nyt-classifier]
rain   forest — an iconic environmental cause — may be less urgent than
once   thought. By one estimate, for every acre of rain forest cut down
each year, more   than 50 acres of new forest are growing in the tropics on
land that was once   farmed, logged or ravaged by natural disaster.

“There is far more forest here than there was 30 years ago,” said Ms.
Ortega   de Wing, 64, who remembers fields of mango trees and banana
plants.

The new forests, the scientists argue, could blunt the effects of rain
forest   destruction by absorbing carbon dioxide, the leading heat-trapping
gas linked to   [LINK:
http://topics.nytimes.com/top/news/science/topics/globalwarming/index.html?inline=nyt-classifier]
global   warming, one crucial role that rain forests play. They could also,
to a   lesser extent, provide habitat for endangered species.

The idea has stirred outrage among environmentalists who believe that
vigorous efforts to protect native rain forest should remain a top
priority. But   the notion has gained currency in mainstream organizations
like the [LINK:
http://topics.nytimes.com/top/reference/timestopics/organizations/s/smithsonian_institution/index.html?inline=nyt-org]
Smithsonian   Institution and the [LINK:
http://topics.nytimes.com/top/reference/timestopics/organizations/u/united_nations/index.html?inline=nyt-org]
United   Nations, which in 2005 concluded that new forests were “increasing
  dramatically” and “undervalued” for their environmental benefits. The
United   Nations is undertaking the first global catalog of the new
forests, which vary   greatly in their stage of growth.

“Biologists were ignoring these huge population trends and acting as if
only   original forest has conservation value, and that’s just wrong,” said
Joe Wright,   a senior scientist at the Smithsonian Tropical Research
Institute here, who set   off a firestorm two years ago by suggesting that
the new forests could   substantially compensate for rain forest
destruction.

“Is this a real rain forest?” Dr. Wright asked, walking the land of a
former   American cacao plantation that was abandoned about 50 years ago,
and pointing to   fig trees and vast webs of community spiders and howler
monkeys.

“A botanist can look at the trees here and know this is regrowth,” he
said.   “But the temperature and humidity are right. Look at the number of
birds! It   works. This is a suitable habitat.”

Dr. Wright and others say the overzealous protection of rain forests not
only   prevents poor local people from profiting from the rain forests on
their land   but also robs financing and attention from other approaches to
fighting global   warming, like eliminating coal plants.

But other scientists, including some of Dr. Wright’s closest colleagues,
disagree, saying that forceful protection of rain forests is especially
important in the face of threats from industrialized farming and logging.


The issue has also set off a debate over the true definition of a rain
forest. How do old forests compare with new ones in their environmental
value?   Is every rain forest sacred?

“Yes, there are forests growing back, but not all forests are equal,” said
  Bill Laurance, another senior scientist at the Smithsonian, who has
worked   extensively in the Amazon.

He scoffed as he vie

[ECOLOG-L] Google Earth goes to Sea

[Bill Silvert]

I think that this update to Google Earth will interest anyone doing ocean 
science. From the NY Times.

Ciência Silvert
www.ciencia.silvert.org


The New York Times

February 3, 2009
Google Earth Fills Its Watery Gaps
By ANDREW C. REVKIN

Two and a half years ago, the software engineers behind Google Earth, the 
searchable online replica of the planet, were poised to fill an enormous data 
gap, adding the two-thirds of the globe that is covered by water in reality and 
was blue, and blank, online.

But until then all of the existing features on Google Earth — mountains, 
valleys, cities, plains, ice sheets — were built through programming from an 
elevation of zero up.

“We had this arbitrary distinction that if it was below sea level it didn’t 
count,” recalled John Hanke, the Internet entrepreneur who co-created the 
progenitor of Google Earth, called Keyhole, and moved to Google when the 
company bought his company in 2004.

That oversight had to be fixed before the months and months of new programming 
and data collection could culminate in the creation of simulated oceans. On 
Monday, the ocean images will undergo the most significant of several upgrades 
to Google Earth, with the new version downloadable free at earth.google.com, 
according to the company.

Another feature, Historical Imagery, provides the ability to scroll back 
through decades of satellite images and watch the spread of suburbia or erosion 
of coasts.

Click a function called Touring and you can create narrated, illustrated tours, 
on land or above and below the sea surface, describing and showing things like 
a hike or scuba excursion, or even a research cruise on a deep-diving submarine.

The two-year push to fill in the giant blue blanks came through a chance 
encounter in March 2006. Mr. Hanke was poised to receive an award from the 
Geographical Society of Spain for his pioneering work building Web-based models 
of the planet.

But he was preceded at the dais by Sylvia Earle, a former chief scientist at 
the National Oceanic and Atmospheric Administration who was there to receive 
her own award for deep-sea exploration and popularizing ocean science.

She turned to him and said she loved the way Google Earth allowed users to see 
how one thing relates to another on the planet. But Dr. Earle bluntly added: 
“You’ve done a great job with the dirt. But what about the water?”

Since that time, Dr. Earle and Mr. Hanke have been partners in the long effort, 
as she explained, “to make sure the mountains don’t end at the beach.”

She assembled an advisory panel including Jane Lubchenco, the Oregon State 
University marine biologist since chosen by President Obama to head the oceanic 
and atmospheric agency.

“I’ve been struggling my whole life to figure out how to reach people and get 
them to understand they’re connected to the ocean,” Dr. Earle said.

“But I go to the supermarket and still see the United Nations of fish for 
sale,” she said. “Marine sanctuaries are still not really protected. Google 
Earth gets all this information now and puts it in one place for the littlest 
kid and the stuffiest grownup to see in a way that hasn’t been possible in all 
preceding history.”

By choosing among 20 buttons holding archives of information, called “layers” 
by Google, a visitor can read logs of oceanographic expeditions, see old film 
clips from the heyday of Jacques-Yves Cousteau and check daily Navy maps of sea 
temperatures.

The replicated seas have detailed topography reflecting what is known about the 
abyss and continental shelves — and rougher areas where little is known.

With only 5 percent of the ocean floor mapped in detail, and 1 percent of the 
oceans protected, Google executives and the marine scientists who helped build 
the digital oceans said they hoped the result would inspire the public to 
support more marine exploration and conservation.

During a recent test drive of the new features at Google’s San Francisco 
office, I swooped in over Hawaii and dived beneath the undulating wave-dappled 
surface of the Pacific to explore canyons, reefs and other features that are 
now charted precisely everywhere that government data exist.

I also revisited Greenland, the North Pole and Alaska’s North Slope. And, in 
less than a minute using the Touring feature, I created a rough narrated 
travelogue retracing reporting assignments in the Arctic, dropping in YouTube 
videos for any visitor to view on location.

By hovering over Galveston, Tex., clicking on a pointer and sliding it forward 
along a bar reflecting years of data, I was able to watch seaside communities 
expand and then abruptly wash away after Hurricane Ike.

The feature powerfully conveys the increasing interplay of humans and the 
environment, for better and worse, as populations grow and spread.

The addition of the oceans posed many technical hurdles, not the least being 
the aligning of disparate data sets so water meets land in precisely the right 
places, 

Summary comments on gender discrimination

[Bill Silvert]

The discussion of gender on the list has died down, and a couple of comments 
come to mind. One is that many women wrote to say that they succeeded 
because of supportive husbands. This is great, but the fact that a woman is 
not very happily married is not a good reason for her to fail. Men in some 
fields also rely heavily on supportive spouses, such as lawyers and 
physicians who have to go through a long period of low-paid indentured 
servitude, but I do not think that all married men in our field would say 
that they needed the support of a super-wife to succeed.

A related point is that several posters commented on the importance of state 
support, and this is basically what I was talking about in my earlier 
posting. Gender equality is a social goal and should be supported by society 
as a whole -- the costs should not be dumped on individual departments so 
that the better they behave, the harder their situation. Even poor countries 
can provide decent infrastructure -- my wife's lab (a government facility) 
provides full day care facilities, even though Portugal is far poorer than 
Norway.

We should also keep in mind that sex ratios alone may not provide conclusive 
evidence of gender discrimination. I'm a biological oceanographer, and there 
are relatively few women in the field in North America (but in Portugal, 
women are the majority!). However, if you go to an ASLO meeting there are 
plenty of women. My impression is that women tend to go into Limnology while 
men are more likely to choose Oceanography. Is this because of 
discriminatory practices? Possibly, but I suspect that it is related to the 
fact that oceanographers tend to be at sea for long times, and oceanographic 
equipment is often heavy and cumbersome. It would be nice to know for sure.

Bill Silvert
Portugal 

Corn editorial in NY Times

[Bill Silvert]

In light of the recent discussion of biofuels and the consequences of 
growing corn to produce ethanol, the following editorial from today's NY 
Times may be of interest -- it points out yet another aspect of the problem.

I might also draw attention to Michael Pollan's recent book, "The Omnivore's 
Dilemma", which goes into great detail about the environmental and social 
cost of growing corn.

Bill Silvert

The Consequences of Corn

By now most farmers know what they'll be planting this spring. And all 
across the country the answer is the same: corn, corn, corn. The numbers are 
surprising. Farmers will plant some 90.5 million acres of corn this year - 
12 million more than last year and the most since 1944. Soybean acres are 
down by more than 10 percent, and there are similar decreases in wheat and 
cotton. The reason for this enormous shift is, of course, the ethanol boom 
and the corn rush it has created.

If it were just a matter of shifting the balance in already planted 
acreage - more corn, less wheat - a point of economic equilibrium might be 
found soon enough. The real trouble comes at the edges. This corn boom puts 
pressure on land that has been set aside as part of the United States 
Department of Agriculture's Conservation Reserve Program. Since the 
mid-1980s, farmers have enrolled some 37 million acres of farmland in the 
program. This is land that has been returned to nature, and it is part of 
what Americans pay for through the farm bill. Much of it is unsuitable for 
crops - too hilly, too wet, too valuable as wildlife habitat - but when corn 
prices are this high, the idea of suitable changes swiftly.

Agricultural interest groups have begun to call on the Department of 
Agriculture to release some of this land from the reserve so that farmers 
can put it into corn production. The U.S.D.A. has temporarily halted new 
enrollments in the program, and though it will probably not release land 
this year, the pressure to do so will only increase.

Much as we like the idea of ethanol production - and especially the 
potential of cellulosic ethanol, from sources other than corn - it would be 
a tragic mistake to jettison two decades of farm-based conservation for 
short-term profit. Corn ethanol will replace only a small fraction of the 
petroleum we use, and if it does so at the cost of a new agricultural land 
rush, then we will have lost much more in conservation than we gained in 
energy independence. 

Re: calculating standard error of turnover times

[Bill Silvert]

Why would you expect the confidence limits on the parameters of a non-linear 
model to be symmetrical? In general they are not. For example, if you fit 
the von Bertalanffy curve to data for young fish the confidence range for 
L-infinity can run from some finite value to infinity.

I have not been following this discussion so perhaps the following reference 
is off-topic, but my pragmatic approach to nonlinear parameter estimation 
can be seen in:

Silvert, W. 1979. Practical curve fitting. Limnol. Oceanogr. 24:767-773.

and the PDF can be downloaded from 
http://bill.silvert.org/pdf/Practical%20Curve%20Fitting.pdf.

Bill Silvert


- Original Message - 
From: "Ben Bond-Lamberty" <[EMAIL PROTECTED]>
To: 
Sent: Monday, April 16, 2007 2:26 PM
Subject: Re: calculating standard error of turnover times


> Erika,
>
> If you use a nonlinear regression package to fit your curve to existing
> data, it should compute standard errors for each parameter estimate.
> Ideally, I would just report these; certainly don't take 1/k as the
> "standard error of turnover time," because this is a nonlinear
> transformation.  Perhaps calculate
>
> 1/k (turnover time estimate)
> 1/(k+se(k)) (turnover estimate plus error)
> 1/(k-se(k)) (turnover estimate minus error)
>
> and report those.
>
> Regards,
> Ben
>
>
> On 4/13/07 5:50 PM, "Erika Marín-Spiotta" <[EMAIL PROTECTED]> wrote:
>
>>  Hello, I have a quick question on how to convert the standard error of a
>> slope (k) of an equation of the type:
>> ln (y) = b + kx
>> where y = fraction of mass remaining
>> x = time in years, and
>> where 1/k gives you a turnover time in years.
>> In other words, how do you report standard error of turnover time?
>
> 

Re: Heads up: The new Global Warming Denial Front

[Bill Silvert]

Since any serious problem will generate concern and undoubtedly proposals to 
deal with it, we should therefore be suspicious -- and if we are of a 
sceptical nature, as Paul is, we will infer that serious problems are 
fraudulent. Whech makes the world a much better place to live in!

Bill Silvert

- Original Message - 
From: "Paul Cherubini" <[EMAIL PROTECTED]>
To: 
Sent: Saturday, October 20, 2007 2:29 PM
Subject: Re: Heads up: The new Global Warming Denial Front


> In other words, scientists are not simply interested in seeing federal
> money spent on direct and immediate solutions to greenhouse gas
> pollution. They are seeking federal funding to study, monitor and
> manage species that might be substantially affected by
> climate change - funding that could create or enhance the
> professional careers of many hundreds, perhaps thousands of them.
>
> So naturally a situation like this raises suspicions.
>
> Paul Cherubini
> El Dorado, Calif.

Re: [SSWG] Denial * 2: Climate Change and Economic Growth

[Bill Silvert]

I hope that David posted this as a joke. This is the most inaccurate 
stereotype of scientists that I have seen. If there are scientists that 
think this way I have yet to meet them.

Bill Silvert

- Original Message - 
From: "David Johns" <[EMAIL PROTECTED]>
To: 
Sent: Tuesday, October 30, 2007 2:16 AM
Subject: Re: [SSWG] Denial * 2: Climate Change and Economic Growth


> Many years back David Ehrenfeld wrote a great book (The Arrogance of
> Humanism) that amounted to a critique of some Enlightenment assumptions 
> that
> he thought many scientists subscribed to with religious-like faith. Among
> them were:
>
>
>
> All problems humans confront are solvable by them.
>
> Most can be solved with technology.
>
> If they cannot be solved by technology they can be solved by changes in
> social organization.
>
> If we get it wrong (e.g. Biosphere) we just didn't know enough & we'll get
> it right next time.
>
> In tough times we will hunker down & do what we need to do to make it
> through.
>
> Some resources are infinite; finite resources have substitutes.
>
> Our civilization will survive.
>
>
>
> He suggested that the observation of history lent itself to a different 
> set
> of principles, i.e. ones that better fit the "data":
>
>
>
> The world is too complex for humans to fully model or even understand,
> especially living systems.
>
> Techno-social solutions never completely solve problems; we only generate
> quasi solutions or patches.
>
> The quasi-solutions implemented generate new problems at a faster rate 
> than
> can be solved; these new problems are usually more complex, costly to
> address, require that more systemic inertia be overcome, etc.
>
> Resources do run out.
>
> Social systems and entire civilizations do tank when the patches fail and
> problems become overwhelming.
>
>
>
> Ehrenfeld did not regard himself as a pessimist-just someone who noted 
> that
> societies have always risen and fallen and that it's foolish to think we 
> are
> different. He also noted that given the size of our foorprint and how much
> natural capital we have drawn down, some options are no longer available.
>
>
>
>
>
>  _
>
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Prato, Anthony A.
> Sent: Thursday, October 25, 2007 8:14 AM
> To: [EMAIL PROTECTED]; ECOLOG-L@LISTSERV.UMD.EDU
> Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED]; [EMAIL PROTECTED];
> [EMAIL PROTECTED]; [EMAIL PROTECTED]; [EMAIL PROTECTED]; [EMAIL PROTECTED];
> [EMAIL PROTECTED]; [EMAIL PROTECTED]; [EMAIL PROTECTED]; 
> [EMAIL PROTECTED];
> [EMAIL PROTECTED]; [EMAIL PROTECTED]; [EMAIL PROTECTED];
> [EMAIL PROTECTED]; [EMAIL PROTECTED]; [EMAIL PROTECTED];
> [EMAIL PROTECTED]
> Subject: Re: [SSWG] Denial * 2: Climate Change and Economic Growth
>
>
>
> Brian makes a good point. However, there has been a lot of discussion 
> about
> using technologies (e.g., injection of CO2 into the wells) that can reduce
> carbon emissions from coal-fired power plants. This suggests to me there 
> is
> not a one-to-one lockstep relationship between economic growth and global
> warming. It's not that simple.
>
>
>
> Tony Prato
>
> University of Missouri-Columbia
>
>  _
>
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] 
> On
> Behalf Of [EMAIL PROTECTED]
> Sent: Tuesday, October 23, 2007 4:55 PM
> To: ECOLOG-L@LISTSERV.UMD.EDU
> Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED]; [EMAIL PROTECTED];
> [EMAIL PROTECTED]; [EMAIL PROTECTED]; [EMAIL PROTECTED];
> [EMAIL PROTECTED]; [EMAIL PROTECTED]; [EMAIL PROTECTED];
> [EMAIL PROTECTED]; [EMAIL PROTECTED]; [EMAIL PROTECTED];
> [EMAIL PROTECTED]; [EMAIL PROTECTED]; [EMAIL PROTECTED];
> [EMAIL PROTECTED]; [EMAIL PROTECTED]; [EMAIL PROTECTED]
> Subject: [SSWG] Denial * 2: Climate Change and Economic Growth
>
>
>
> I've been following the ECOLOG discussion on climate change "denial 
> science"
> with great interest.  Many of the climate change deniers have much in 
> common
> with those who deny that there is a conflict between economic growth and
> environmental protection.  For example, both camps of deniers tend to be
> comprised of hirelings of, or were selected in a process strongly 
> influenced
> by, "big money" (i.e., pro-growth, typically corporate and anti-regulatory
> entities).
>
>
>
> This point would be too obvious to be worth mentioning, except that now we
> are seeing a fascinating denial dialog developing regarding the 
> relationship
> of economic growth and climate change.  I noticed this at a climate change
> conference yesterd

Re: [SSWG] Denial * 2: Climate Change and Economic Growth

[Bill Silvert]

What it boils down to is that the people who do the science usually know the 
limitations of their field. I did not mean to imply that scientists in one 
field would fully appreciate what is the case in other fields.

In other words, I don't know many scientists who overrate the capabilities 
of the work that they are doing, although there are some unfortunate 
exceptions.

Bill Silvert

- Original Message - 
From: "Robert Fireovid" <[EMAIL PROTECTED]>
To: 
Sent: Wednesday, October 31, 2007 1:57 AM
Subject: [SSWG] Denial * 2: Climate Change and Economic Growth


> Unfortunately, I know too many economists (social scientists) - some
> in high-level policy-recommending positions within the government -
> who think in this way.
>
> - Bob Fireovid
>
>>Date: Tue, 30 Oct 2007 06:10:54 +
>>From: Bill Silvert <[EMAIL PROTECTED]>
>>
>>I hope that David posted this as a joke. This is the most inaccurate
>>stereotype of scientists that I have seen. If there are scientists that
>>think this way I have yet to meet them.
>>
>>Bill Silvert
>>
>>- Original Message -
>>From: "David Johns" <[EMAIL PROTECTED]>
>>To: 
>>Sent: Tuesday, October 30, 2007 2:16 AM
>>Subject: Re: [SSWG] Denial * 2: Climate Change and Economic Growth
>>
>>
>> > Many years back David Ehrenfeld wrote a great book (The Arrogance of
>> > Humanism) that amounted to a critique of some Enlightenment assumptions
>> > that
>> > he thought many scientists subscribed to with religious-like faith. 
>> > Among
>> > them were:
>> >
>> >
>> > All problems humans confront are solvable by them.
>> >
>> > Most can be solved with technology.
>> >
>> > If they cannot be solved by technology they can be solved by changes in
>> > social organization.
>> >
>> > If we get it wrong (e.g. Biosphere) we just didn't know enough & we'll 
>> > get
>> > it right next time.
>> >
>> > In tough times we will hunker down & do what we need to do to make it
>> > through.
>> >
>> > Some resources are infinite; finite resources have substitutes.
>> >
>> > Our civilization will survive.
>> >
>> >
>> > He suggested that the observation of history lent itself to a different
>> > set
>> > of principles, i.e. ones that better fit the "data":
>> >
>> > The world is too complex for humans to fully model or even understand,
>> > especially living systems.
>> >
>> > Techno-social solutions never completely solve problems; we only 
>> > generate
>> > quasi solutions or patches.
>> >
>> > The quasi-solutions implemented generate new problems at a faster rate
>> > than
>> > can be solved; these new problems are usually more complex, costly to
>> > address, require that more systemic inertia be overcome, etc.
>> >
>> > Resources do run out.
>> >
>> > Social systems and entire civilizations do tank when the patches fail 
>> > and
>> > problems become overwhelming.
>> >
>> >
>> > Ehrenfeld did not regard himself as a pessimist-just someone who noted
>> > that
>> > societies have always risen and fallen and that it's foolish to think 
>> > we
>> > are
>> > different. He also noted that given the size of our foorprint and how 
>> > much
>> > natural capital we have drawn down, some options are no longer 
>> > available.
> 

Re: population control

[Bill Silvert]

I am not certain that this is true, at least not in every case. Although 
developed countries are certainly depleting fossil resources at a disastrous 
rate, in the long term that will have to end. If we look at less advanced 
cultures we see less resource use but sometimes more serious damage.

The largest ecological footprint is the widespread desertification that is 
largely due to overgrazing by early agriculturalists. The Sahara is widely 
believed to be a man-made desert, and others may be the same. Widespread 
extinctions in the Americas were not caused by roadkills but by early man 
with spears. Slash and burn farming was and still is a widespread practice. 
Many mangrove swamps have been cut down for firewood.

Even in advanced countries the footprint is not always associated with very 
modern practices. The loss of many cubic kilometers of irreplaceable topsoil 
in the central USA is the result of carelessness, although modern 
monoculture is part of the problem.

My point is that the problem is people in general -- to point at the more 
developed countries and say that they are the culprits is not a constructive 
approach. Bad environmental practices are pretty much universal.

Bill Silvert


- Original Message - 
From: "Amartya Saha" <[EMAIL PROTECTED]>
To: 
Sent: Monday, December 03, 2007 5:59 PM
Subject: Re: population control


> After people moved out of caves and trees, EVERY single house that man has
> built
> anywhere in the world HAS displaced something-- forest, natural grassland,
> desert sand habitat, whatever. The point is that a third world shanty has 
> a
> much lower PER CAPITA space usage than say houses in American (or 
> Brazilian)
> suburbs.
> And they are not heated or centrally airconditioned, to the point where 
> folks
> wear shorts while its -30 degrees outside, or folks cuddle up in bed with
> blankets with the AC full blast while its actually nice and cool outside. 
> Not
> that I am advocating favelas, but Cara is right that the per capita 
> footprint
> in the third world is a lot less.
>
> I'd like to add that this is especially true of the old world.
> which has had a high population for the last several millenia, unlike 
> latin
> america which has been *colonized* and "settled" only in the last 400 
> years (
> from a land transformation point of view). 

Re: Are organisms really 4 dimensional objects?

[Bill Silvert]

The 3/4 allometry holds for terrestria organisms, but for marine species it 
is more close to 2/3. An explanation and detailed discussion can be found in 
Platt, Trevor, and William Silvert. 1981. Ecology, physiology, allometry and 
dimensionality. J. Theor. Biol. 93:855-860.

Bill Silvert

- Original Message - 
From: "Oskar Burger" <[EMAIL PROTECTED]>
To: 
Sent: Tuesday, December 04, 2007 11:20 PM
Subject: Are organisms really 4 dimensional objects?


>A paper just made available on the American Naturalist website takes a 
>novel
> and curious perspective on fundamental scaling relationships in ecology. 
> The
> paper, by Ginzburg and Damuth, is titled "The space-lifetime hypothesis:
> viewing organisms in 4 dimensions, literally." The authors argue that
> organisms can literally be viewed as four dimensional objects, three 
> spatial
> and one temporal. While many traits scale with body size, they 
> specifically
> focus on the well-known finding that metabolic rate scales as the +3/4 
> power
> of body mass whereas lifespan goes as the +1/4 power. This makes the 
> product
> of the two an isometric relationship (m3/4 x m1/4 = m1), such that a
> doubling in an organism's size predicts a doubling in the energy it
> metabolizes in a lifetime. While many researchers take this as a 
> consequence
> of other scaling relationships it is a fundamental role in the 4D view... 

Re: curriculum question

[Bill Silvert]

At the risk of repeating myself I feel compelled to respond to Ryan Walker's 
post. Unless the teaching of statistics can be totally changed, I would 
argue for less statistics, not more. As I have pointed out before, most 
ecologists can spout ANOVA and t-tests in their sleep, but almost none can 
do something as basic as adding two numbers (remember my earlier post about 
adding 100+-3 to 200+-4?). Most statistics courses deal exclusively with 
linear models to the extent that the majority of books I have surveyed hew 
to the old line that transformations are for the purpose of linearising data 
(they should be used to normalise variances).

Over all I have seen little of value come out of statistical analyses, which 
usually just confirm the obvious, but I have some incredibly stupid 
conclusions drawn from incorrect use of statistics. In balance I think that 
the value of statistics is not significantly greater than zero, if indeed it 
is positive at all.

Of course this can vary with the subfield. In terrestrial work where 
sampling tends to be easier and one can lay out quadrats on foot, etc., 
statistical methods can be very useful. The use of statistical models in the 
design of agricultural experiments is clearly essential for example. But in 
areas where data are collected in a more opportunistic way the use of 
statistics is often a diversion rather than a help. In aquatic ecology, and 
especially biological oceanography, statistics can be a real nuisance - if 
anyone ever captured the Loch Ness monster they couldn't publish the news 
because one is not statistically significant!

For a particular example of what I mean, look at fisheries oceanography. The 
literature of the field is full of schemes for stratified random sampling 
and negative binomial distributions, but virtually no real ecology. 
Basically the statistics has edged out the ecology, and it is too hard to do 
both.

Bill Silvert


- Original Message - 
From: "Walker, Ryan" <[EMAIL PROTECTED]>
To: 
Sent: Tuesday, November 01, 2005 6:18 PM
Subject: Re: curriculum question


> Having come from a good undergraduate program (University of Wisconsin - 
> Stevens Point) and working on a graduate degree at a university with a 
> somewhat lacking undergraduate program (Texas Tech University), I have 
> seen both sides of the coin.  Regardless of the focus of the program 
> (Ecology, Wildlife Management, etc.), there is a general need for more 
> statistics and experimental design.  My undergraduate program was more 
> focused on management and techniques of wildlife ecology and its limited 
> statistical requirements are still more than other programs.  Focusing on 
> statistics that may be useful for students to know, such as 
> non-parametrics and multi-variate analyses.  I realize that students may 
> have difficulty grasping some of these more complicated topics, but I feel 
> it is necessary to expose students to this material.  A simple knowledge 
> of the tools that are available for research would be extremely helpful. 

Re: Questionable Research Practices

[Bill Silvert]

I don't know how common this practice is, but I have received multiple 
submissions to referee and once even received the same paper three times 
simultaneously. Aside from being immoral and against publication 
guidelines - most journals require you to confirm that the paper has not 
been submitted elsewhere - I suspect that if you get found out you will have 
a lot of trouble publishing in the same journals again.

On the other hand, if a paper gets rejected you are then free to submit 
elsewhere - it just requires a bit of patience.

Bill Silvert


- Original Message - 
From: "Andrew Park" <[EMAIL PROTECTED]>
To: 
Sent: Monday, October 31, 2005 11:56 PM
Subject: Questionable Research Practices


> A really heinous practice is to farm out your manuscript to a number of
> different publications, dropping those that either rejected the MS or did 
> not
> return a review too quickly. 

Re: curriculum question

[Bill Silvert]

I didn't expect much agreement with my posting, and I'll just comment on two 
points that Roper raises, interspersed with his posting below:

- Original Message - 
From: "James J. Roper, Consultor - Tradutor" <[EMAIL PROTECTED]>
To: 
Sent: Wednesday, November 02, 2005 9:28 PM
Subject: Re: curriculum question


> Every really good paper published in Ecology and
> many other ecological journals required the statistics that was included
> to make their point.

True, but that doesn't justify the statistics. I've taken a cynical approach 
to this, on occasion when my colleagues have asked if I can suggest 
statistical methods to analyse the data I usually find that the conclusions 
are obvious just from looking at the data - so I discuss the conclusions 
with them, and then once we know the result they find it easy to come up 
with enough statistical filler to get the paper past the referees.

> Bill goes on to contradict himself when he says:
>
> "In terrestrial work where
> sampling tends to be easier and one can lay out quadrats on foot, etc.,
> statistical methods can be very useful."

It's not really a contradiction. I pointed out that there are exceptions, 
and my criticism of the use of statistics was not categorical. Moderation in 
debate is not always a vice, no matter what Barry Goldwater said.

Bill Silvert 

Re: curriculum question

[Bill Silvert]

While I agree with the issues that Max Taub raises, I don't think that 
relying on statistics is the answer. First of all, it is certainly true that 
variation is important. In fact, a colleague of mine used to argue that 
understand the variability of natural phenomena is more important than 
knowing the mean values. If students look at scatter plots or histograms 
they can see and discuss variability and try to interpret it. But if they 
know their statistics they find it difficult to do this - they automatically 
assume that all error distributions are normal and consider only the 
standard deviation, no matter what the distribution looks like. In the 
published literature you often see serious discussions of the variance of 
highly skewed or bimodal distributions.

A particularly pernicious example of this is the use of normal distributions 
to describe data where the numbers have to be positive, like lengths or 
concentrations - what does it mean to use a normal distribution to describe 
such a variable when the distribution gives a 20% probability that the value 
is negative?

As for correlation, do you really need a statistics course to see a 
relationship in a scatter plot? Max, your students will see a strong 
negative correlation if you show it to them. But if they know their 
statistics they will only be able to see a linear correlation - in fact, I 
earlier posted an example of a scientist who presented a clearly nonlinear 
correlation to a meeting and not only claimed it was linear, but used an 
incorrect statistical test to prove that it was linear!

Statistics has the strange effect of making people blind to the obvious.

Bill Silvert


- Original Message - 
From: "Max Taub" <[EMAIL PROTECTED]>
To: 
Sent: Wednesday, November 02, 2005 11:32 PM
Subject: Re: curriculum question


> While statistical (hypothesis) testing may be overused or misused among
> professional ecologists, I think that a strong introduction to
> statistics is essential for undergraduates. Few undergraduates, prior to
> taking a statistics course have thought about how important variation
> is, or are aware that there are ways to quantitatively describe
> variability in measurements. Students are also naively inclined to take
> ANY difference among the means of experimental groups as meaningful.
> Hypothesis testing can help break them of this habit, and this, I would
> say, is a mighty important lesson to learn about interpreting
> experimental (or observational) results.
> I also value being able to use the vocabulary of statistics in my
> classes; I want it to mean something to students if I say there is a
> strong negative correlation between two variables. So I am one who is
> strongly in favor of  statistics in the undergradute curriculum- early
> and often.
>
> Max Taub 

Re: scientific misconduct survey

[Bill Silvert]

I finally got around to reading the guide and looking at the questionnaire, 
and while I think that Montgomerie raises some interesting issues which it 
would be worthwhile to discuss on this list (but we can't because the 
questionnaire is copyrighted!), I think that these are issues to discuss and 
not simply rank without considering different situations. I found it 
impossible to fill out the questionnaire because for many of the questions I 
could easily envision situations where they action described would be 
serious misconduct and others in which it would be OK, or even praiseworthy.

Perhaps Dr. Montgomerie could be persuaded to modify his copyright so that 
we can discuss these issues on the list. Even though most of the material in 
his list is stuff we talk about all the time, given that the colour BROWN 
has been patented (by UPS) and there is a current lawsuit over whether the 
word VIRGIN is in the public domain (wow, think of the implications for 
ecological research!), I m reluctant to comment on the specifics of his 
questionnaire.

Bill Silvert

-Original Message-
> From: Ecological Society of America: grants, jobs, news
> [mailto:[EMAIL PROTECTED] On Behalf Of Wendee Holtcamp
> Sent: October 31, 2005 8:04 AM
> To: ECOLOG-L@LISTSERV.UMD.EDU
> Subject: scientific misconduct survey
>
> For those who didn't read the May 2005 essay posted by Morty, "A =
> beginners guide to scientific misconduct"=20
> (http://web.unbc.ca/isbe/newsletter/commentaries&editorials/Montgomerie&Birkhead_vol17(1).pdf)
>
> I thought I'd post the URL to a survey mentioned within and currently =
> being conducted by is author Dr Robert Montgomerie:=20
>
> http://biology.queensu.ca/~montgome/sm
>
> Take the survey because I'm interested in his results! :o)
>
> Wendee 

Re: questionable research practices

[Bill Silvert]

It occurred to me that this proposal is similar to what is commonly done in 
physics laboratories. Many experiments have built-in biases and if the 
student reports correct results (i.e., the values in the reference books) 
then it can be assumed that they have fudged the data. I recall experiments 
on gravitational acceleration, the charge to mass ratio of the electron, and 
the Hall effect, as well as a virtually impossible experiment, measuring the 
resistance of a light bulb. Verifying some of Galileo's results is another 
good example (heavier objects really do fall faster than light ones, the 
period of a pendulum depends on the weight as well as the length). I cannot 
immediately think of a good parallel in ecology, but certainly it is a good 
concept worth thinking about.

Bill Silvert


- Original Message - 
From: <[EMAIL PROTECTED]>
To: 
Sent: Sunday, October 30, 2005 2:34 AM
Subject: Re: questionable research practices


> But I have wondered if there would be value  in the following scenario:
>
> 1.  Professor teaches a 'bogus' concept to the students, perhaps in a  way
> that they assume it is a lecture as usual.
>
> 2.  Professor then has the students perform an experiment to 
> "demonstrate"
> the phenomenon.Prefessor expects a full report  write up on intro, 
> methods,
> data results, discussion (of what went right or  wrong, comments, etc).
>
> 3.  Professor evaluates how many students:
>A.  Report that the  data does not support the phenomenon and that
> the phenomenon might be  questionable.
>B.  Rationalize what  went wrong with their experimenting such that
> their particular experiment  'failed'.
>C.  Fudge the  data.
>
> 4.  Ask  the class to do a peer review of each others reported  research
> findings.
>
> Debbie Antlitz 

Copyright Law and Science

[Bill Silvert]

The recent discussion of copyright law seems to have managed to bypass the 
key issues in a very disappointing way. One set of postings comes from 
people who are confused because they don't see what is wrong with copying a 
book that is out of print and totally unavailable, while the other set comes 
from legal scholars who write things like "I love to see discussios over 
copyright lead by people who don't know what they are talking about."

Debate about copyright tend to focus on the right of creators of 
intellectual property to receive fair compensation for their labours, and I 
have never heard copyright defended on the grounds that it is a mechanism 
for the suppression of ideas - but this often happens. Sometimes copyright 
is used to deliberate material intentionally. Hollywood will sometime buy 
the rights to a film, withdraw it from circulation, and replace it with a 
remake. Some very important films, such as the Marcel Pagnol "Fanny" 
trilogy, were suppressed in this way, although many continued to circulate 
in bootleg versions and are again available. Rich companies and individuals 
have often tried to buy the rights to unfavourable books so that they can 
suppress them. More often works are suppressed through a combination of 
negligence and greed, such as when a company drops a CD, book or video game 
from its catalogue but will not release it into the public domain.

While the loss of an art work in this way is sad, in science it is totally 
unacceptable. Scientific progress requires the open exchange of ideas, and 
withdrawing books and journals from the scientific community is tantamount 
to burning them. Suppose that the Vatican, instead of issuing bodily threats 
against Galileo and Copernicus and actually burning Bruno at the stake had 
simply been able to buy up their copyrights? Or that Hitler had been able to 
withdraw from circulation all the German journals where Einstein and others 
published their results?

Although these examples are exaggerated, copyright law is a serious problem 
for modern scientists. If you want to publish you have to transfer the 
copyright to the publisher, giving up even your own rights to what you 
wrote. Your work may simply vanish into limbo - the publisher declares 
bankruptcy, the book never gets printed, the journal becomes defunct - but 
the copyright never reverts to you. Maybe the publisher decides to drop the 
book because it serves a market where books favourable to evoloution are not 
selling well!

Let me end with an example: Suppose that you write a paper in your field 
which you want to distribute in its entirety to your graduate students. 
According to at least some of the expert postings on this list you have no 
right to do this unless you buy the reprints from the publisher. Would you 
really be prepared to tell your graduate students that they can't have 
copies of the paper on which their theses are to be based because you can't 
afford the reprints?

I think that the basic point comes down to this - a scientist should have 
access to all revious work in his field. If he can get access through legal 
means, buying a book or such, that is the proper route to take. But if there 
is no legal access, then copyright law should not be an obstacle to the free 
flow of information.

Bill Silvert 

Re: Copyright Law and Science

[Bill Silvert]

While it would be nice to have scientists organise against the present 
practice with regard to signing away copyright, unless a real movement gets 
started most of us have no choice. We have to publish to function and the 
publishers hold the cards, namely the power to accept or reject our papers. 
It would be good to organise a boycott of publishers who insist on transfer 
of copyright, but that is a big job and would take a long time. Most 
scientists simply do what they consider the right thing and focus on their 
research. Keep in mind that I posted in response to a message about whether 
one could copy a book that was totally unavailable, the author dead, etc. I 
think that the responses that focussed on the technicalities of following 
copyright law, which basically require that the researcher has to do without 
this resource, are wrong.

As for suppression of material, this is common in the movie business. I gave 
one of several examples of cases where Hollywood has decided to remake a 
film, often a classic film, and pulls the original version off the market. 
In fields where creativity requires funding, often creative work can be 
suppressed because the rights belong to the funding party. This can ocur in 
the movies (Hearst vs. Citizen Kane for example, which almost succeeded) and 
in science there is growing concern that drug companies are able to suppress 
the publication of unfavourable results even by supposedly independent 
researchers. I also referred to the practice of letting creative works 
expire by failure to publish them, as often happens with old recordings and 
books. I mentioned video games in particular because there is an interesting 
issue there - fans of the old games for obsolete computers (like the 8-bit 
Ataris) cannot buy these games, but the software companies won't give up the 
copyrights. Since there will never be a profiable market for these games, 
why won't the companies let them go?

Often the copyright ends up in the hands of people who are much tighter 
about it than the creator. I read about a Cambodian musician in the US who 
is delighted that pirated copies of his music are popular all over Cambodia 
even though the publisher is furious - but he points out that almost no one 
in Cambodia could afford the price of an American CD. Scientific journals 
charge for reprints (PDFs) of our papers which we are happy to distribute 
for free.

And by the way I'd like to thank all of you who sent me copies of my own 
paper which Springer refused to send me!

Bill Silvert

PS - A later posting reminded me of the frequent proposal that scientific 
journals enforce copyright for just a short time, maybe a year or so, but 
then release papers into the public domain. Sure sounds like a good 
compromise. But I think the opposite is happening. I recently spent some 
time at a university where they had Science Direct access to many journals 
published within the last ten years, but it turned out that if I wanted 
access to older papers they would have to pay. This makes me pessimistic 
about winning the firms that control scientific publishing over to some 
reasonable solution. And given that there is a lot of consolidation in the 
publishing field, the chances of pressuring individual journals to back off 
on  copyright issues seem dim.


- Original Message - 
From: "David M. Lawrence" <[EMAIL PROTECTED]>
To: 
Sent: Sunday, November 20, 2005 2:40 AM
Subject: Re: Copyright Law and Science


> The problem is not with copyright law, but with scientists who sign
> their rights away in the publication agreements with the journals.  I
> don't know how that system got started, but if scientists organized -- 
> beginning with journals published by scientific societies it would
> change, and copyright law would not be an obstacle to free flow of
> information.
>
> Contracts can be signed granting publishers the rights they need, while
> you retain copyright -- and limited rights to reproduce the work on your
> own.
>
> I haven't heard much about copyright being used to supress ideas.  Given
> the fact that I also work in the creative community, I think I would
> have heard more about that if it was as widespread as hinted in the post
> below.  It is not, and for the most part, it cannot happen WITHOUT the
> WRITTEN consent of the creator of the work.  (Works made for hire, such
> as articles written for a newspaper by its staff, are a common exception.)
>
> Copyright law is good, and should be your friend.  But you have to pay
> attention to what you're signing away when you submit an article for
> publication. 

ESA Copyright

[Bill Silvert]

While I appreciate Robert Peet's explanation of ESA policy, the following 
paragraph seems disingenuous. There are many better ways to deal with this. 
One obvious solution would be to share the copyright so that either the 
author or ESA could authorise further use. There are many other options, 
such as "Creative Copyright" (http://creativecommons.org/), which offer 
refinements on this theme.

Bill Silvert

- Original Message - 
From: "Robert K. Peet" <[EMAIL PROTECTED]>
To: 
Sent: Monday, November 21, 2005 7:42 AM
Subject: Re: ECOLOG-L Digest - 19 Nov 2005 to 20 Nov 2005 (#2005-299)


> Note that ESA does require transfer of copyright.  There is a good reason=
> =20
> for this.  We expect ESA to last a long time, longer than most authors=20
> will live or be locatable.  We want to make sure that in the future it=20
> will be easy to find the owner of an article so that its contents can 
> be=20
> used in another work. 

Online journals and publications

[Bill Silvert]

Werner raises a good point, for some scientists it simply is not reasonable 
to pay to read articles in their field. The result is that science becomes 
concentrated in wealthy countries and labs with institutional subscriptions. 
If you are not in such a place, you just don't have access.

I don't think that science should be just for the wealthy. Those of us with 
institutional subscriptions should be willing to download and transfer 
papers to our less fortunate colleagues. I find it a bit embarassing that I 
have to rely on a former student to help me keep abreast of developments in 
my field, but that is the way that scientific publishing works. It is a 
lousy system, and we should do our best to subvert it.

Bill Silvert


- Original Message - 
From: "DeerLab" <[EMAIL PROTECTED]>
To: 
Sent: Tuesday, December 20, 2005 7:39 PM
Subject: Re: [Tws-l] online journals


> When I am asked to pay 1-2 days-worth of salary to download a paper,
> I just move on. From what I gather, many colleagues are in the same
> boat. There are some good journals which supposedly on purpose do not
> even provide an email contact for the author, that is unacceptable
> because it is counterproductive.
>
> Werner Flueck
> National Research Council
> Argentina 

Re: Online journals and publications

[Bill Silvert]

That works fine for what I assume is a regional society in a rich country, 
but the critical issue raised by Werner is what happens with international 
journals where some of the authors and some of the readers may not be able 
to pay the kinds of fees that we are used to in Canada?

I might point out that even in a country like Canada not every author can 
pay for publication. I retired in 1998 and thus lost support for page 
charges, but I am trying to remain active. Without funding I find I have to 
be very selective in where I submit. We shouldn't assume that everyone has 
access to generous research grants.

Bill Silvert


- Original Message - 
From: "John Simaika" <[EMAIL PROTECTED]>
To: 
Sent: Wednesday, December 21, 2005 9:55 AM
Subject: Re: Online journals and publications


> The Entomological Society of British Columbia asks authors to pay for 
> their
> submissions. However, each submission published in the society's journal 
> is
> available online, free of charge. I think that this is a brilliant way of
> sharing a wealth of knowledge and new developments, if only on a 
> relatively
> regional scale. Certainly, bigger journals should follow this approach.
>
> Best wishes,
>
> JP Simaika.

> -Original Message-
> From: Ecological Society of America: grants, jobs, news
> [mailto:[EMAIL PROTECTED] On Behalf Of Bill Silvert
> Sent: December 20, 2005 2:34 PM
> To: ECOLOG-L@LISTSERV.UMD.EDU
> Subject: Online journals and publications
>
> Werner raises a good point, for some scientists it simply is not 
> reasonable
> to pay to read articles in their field. The result is that science becomes
> concentrated in wealthy countries and labs with institutional 
> subscriptions.
>
> If you are not in such a place, you just don't have access.
>
> I don't think that science should be just for the wealthy. Those of us 
> with
> institutional subscriptions should be willing to download and transfer
> papers to our less fortunate colleagues. I find it a bit embarassing that 
> I
> have to rely on a former student to help me keep abreast of developments 
> in
> my field, but that is the way that scientific publishing works. It is a
> lousy system, and we should do our best to subvert it.
>
> Bill Silvert
>
>
> - Original Message - 
> From: "DeerLab" <[EMAIL PROTECTED]>
> To: 
> Sent: Tuesday, December 20, 2005 7:39 PM
> Subject: Re: [Tws-l] online journals
>
>
>> When I am asked to pay 1-2 days-worth of salary to download a paper,
>> I just move on. From what I gather, many colleagues are in the same
>> boat. There are some good journals which supposedly on purpose do not
>> even provide an email contact for the author, that is unacceptable
>> because it is counterproductive.
>>
>> Werner Flueck
>> National Research Council
>> Argentina
> 

Re: Online journals and publications

[Bill Silvert]

Just a short comment on this. Authors do not always have reprints. Some of 
you may recall my posting a message I received from Springer saying that a 
paper of mine had been published and if my institute subscribed to Springer 
Online I could download the PDF. Several of you were kind enough to send me 
copies of my own paper, but I have not received any reprints, paper or PDF, 
from Springer. I have had the same experience with other journals. And my 
point is that if even an author cannot get copies of his own paper, it won't 
be easier for anyone else who cannot pay. This is a problem that needs 
fixing.

Bill Silvert

- Original Message - 
From: "Ted R. Feldpausch" <[EMAIL PROTECTED]>
To: 
Sent: Wednesday, December 21, 2005 6:36 PM
Subject: Re: Online journals and publications


One could argue that reprints can easily be requested from authors. 

Re: Online journals and publications: time to revolt? Copyright law

[Bill Silvert]

The problem lies not only with the scientific community but also with lab 
directors, university administors and the like. With the internet it is easy 
to publish, and with tools like Google Scholar we can reach a much wider 
audience than we can with normal publications, but we are in this bind of 
peer review and prestigious journals. Other fields, like physics, place less 
emphasis on looking good and more on getting results out. For example, hot 
new results in high energy physics can be published in some of the leading 
journals without peer review if requested. Astronomers have ways of getting 
the word out in a matter of hours if they see a comet or supernova. But if 
we publish on the internet we don't get the necessary brownie points.

I once got a phone call from the editor in chief of a journal who said that 
he had seen a draft of a paper that I had sent to a colleague, that he had 
discussed it with his editorial board, and if I hadn't submitted it 
elsewhere they would like to publish it. I was of course delighted, but when 
I told my lab director the good news he frowned and said, "That would not be 
a peer-reviewed primary publication then." That's the attitude we have to 
fight against.

Some worthy papers are left out of conference proceedings because there is a 
fixed publication budget and too many good papers (too many good papers!). 
When I have suggested putting the overflow on the web the response is 
generally negative. As one editor said, "Papers that appear on the web are 
crap."

Well, I've put most of my papers on the web at www.bill.silvert.org if 
anyone wants to see the kind of crap I write! But I have to be careful about 
copyright, so what I post is always a draft unless I have the right to post 
the final version. Because in answer to Jasja's question, I think that once 
we have transferred copyright we really have no rights at all to our own 
work. Some journals give us the right to post or distribute digital 
reprints, but that is their decision.

Once you have sold or given away copyright to your work, it is someone 
else's intellectual property. They may pay you $20 for the rights and then 
make millions (as has happened with some songs) but you have no recourse. 
They may destroy or otherwise suppress the work and you have no right to 
distribute it against the will of the copyright holder. It really is an 
awful system - although it gets touted as a way to protect the creators of 
intellectual property, it offers far more protection to publishers and other 
business interests.

Can we revolt? It would be pretty hard to fight something so well 
entrenched, and science is a bit player compared to books, songs and movies. 
That is why in an early posting I suggested subversion instead. For example, 
I cannot post copies of all my copyrighted PDFs to my website, but I 
distribute them to anyone who asks. Many people with access to ScienceDirect 
and other download services are happy to help less privileged colleagues 
access the literature. That's a start.

Bill Silvert

- Original Message - 
From: "Dekker, Jasja" <[EMAIL PROTECTED]>
To: 
Sent: Thursday, December 22, 2005 9:15 AM
Subject: Online journals and publications: time to revolt? Copyright law


> Dear all,
>
> So why do we keep submitting papers to this group of journals? Are page
> charges so far spread that fitting, but free-of-charge journals are so
> rare? I think the scientific community, being both primary producer and
> consumer of the journals, has more power than it thinks!
>
> I hope you all will forgive me for starting again on copyright law, BUT:
> does transfering copyright to the journal mean we can not offer our own
> papers on personal websites?
>
> Kind regards,
>
> Jasja Dekker 

Re: DarwinDay.org

[Bill Silvert]

I am suprised that no one responded to this posting with reference to the 
Darwin Awards (http://www.darwinawards.com/) which "... salute[s] the 
improvement of the human genome by honoring those who remove themselves from 
it. Of necessity, this honor is generally bestowed posthumously." Of 
particular relevance is a paper to which they link on the home page which 
provides convincing evidence for intelligent design - the abstract is as 
follows: "Penne Rigate will spontaneously insert itself into Rigatoni (order 
pasta) under liquid to gas transition conditions of H2O to create the 
previously unobserved species Noodleous doubleous. The estimated probability 
of this spontaneous generation event is too low to be explained by 
thermodynamics and therefore apparently represents intelligent design." Also 
relevant is Project Steve (http://en.wikipedia.org/wiki/Project_Steve) - 
'Named in honor of the paleontologist Stephen Jay Gould, Project Steve is a 
parody by the National Center for Science Education (NCSE) of creationist 
lists of scientists who "doubt evolution".'. Unfortunately despite the 
publicity that these efforts have received (the Darwin Awards are well 
publicised and appear in many newspapers), they have little impact on those 
who consider humour a sin and shy away from communist propaganda sheets like 
the New York Times.

However, speaking as an expatriate who has not lived in the US for over 30 
years, perhaps the decline of science education in the US is neither 
surprising nor disastrous. The religious fanatics who are responsible for 
the scientific illiteracy that is spreading across the country also have a 
voice in government, and there is a widespread feeling in the world that the 
US wields too much power and wields it unwisely. That is why the EU has 
started the Galileo project, for example. The drift of scientific expertise 
from the US to other countries, driven both by religious hostility to 
science (as in the case of stem cell research) and by the imposition of 
difficult visa restrictions on foreign scientists, may seem undesirable from 
the viewpoint of those of you living in the US (and costly too, as even 
American scientific organisations are holding more of their meetings in 
other countries), but from a global point of view it may be a good thing.

Countries that are driven by ideology are naturally hostile to science, 
which is the opposite of ideology. I suspect that as long as the US remains 
on the verge of theocracy, patchwork solutions such as the Darwin Day 
concept will have little impact.

Bill Silvert
Portugal


- Original Message - 
From: "David Inouye" <[EMAIL PROTECTED]>
To: 
Sent: Tuesday, January 03, 2006 3:42 PM
Subject: DarwinDay.org


> At a recent meeting of the Geological Society of America, Donald U.
> Wise, an emeritus professor of geology at the University of
> Massachusetts ...
> suggested that one way to do this "is with humor."  Dr. Wise's first
> foray is a parody song about intelligent design called "Marching Song
> of the Incompetents," which had its premiere in October when hundreds
> of geologists sang it enthusiastically at the otherwise conventional
> meeting of the Geological Society of America. 

Re: Questions about using teaching materials from others

[Bill Silvert]

People who put out material on websites may want to look at 
http://creativecommons.org/, "Creative Commons is a nonprofit organization 
that offers flexible copyright licenses for creative works." Under their 
education section they state "" Creative Commons helps you publish your work 
online while letting others know exactly what they can and can't do with 
your work." and they offer a range of standard options stating how your work 
can be used.

Bill Silvert

- Original Message - 
From: "Jonathan Greenberg" <[EMAIL PROTECTED]>
To: 
Sent: Thursday, January 19, 2006 3:34 PM
Subject: Questions about using teaching materials from others


>A colleague of mine recently asked me what my thoughts were on using other
> people's teaching materials posted on course websites for a class he is
> teaching.  This was a very good question, so I thought I'd send it to you
> all for responses.  For a class, how liberal/conservative are you all 
> about
> properly citing other class websites/materials.  If you use a lab exercise
> more or less verbatim, do you need to get permission from the writer to 
> use
> it, or is that more of a courtesy (e.g. if it's online it's fair game)?
>
> Thoughts?
>
> --j 

Re: Role of modeling courses in the undergraduate curriculum

[Bill Silvert]

I was one of those who responded negatively, but I did so because the 
emphasis was on computer simulation modelling. I think that modelling in the 
broad sense is an essential part of science, but I object to the idea that 
anything comprehensible without a powerful computer is not a model.

To give a practical example, the principle of conservation of energy is a 
useful model, even though some ecologists (notably Larry Slobodkin) object 
to it. If I see a system where secondary production is higher than primary 
production it motivates me to ask where the extra energy came from, a point 
which often confuses my experimental colleagues.

Currently I am modelling the environmental impacts of fish farms, and while 
my calleagues understand the importance of quantitative data on nutrient and 
carbon fluxes which can be plugged into computer models, they are confused 
about how to include the stench of hydrogen sulfide bubbling up from the 
bottom, or the presence of slugworms and dead fish - but surely any model of 
environmental impact should include these factors!

One frustrating aspect of the emphasis on teaching computer simulation 
models is that even though they implement systems of equations, which is 
just one kind of model, they often ignore fundamental mathematical issues 
such as stability and resilience.

As for non-mathematical models, although they are subject to the same 
protocols as with mathematical models, because they are not considered 
models they are not evaluated critically enough. I recall once at a 
fisheries workshop advancing some ideas about the spawning behaviour of cod, 
only to be told that the matter had already been settled by experimental 
work which I should have known. Afterwards I asked for the reference, and it 
turned out to be a paper on spawning behaviour of Tilapia in Lake Victoria. 
As a modeller I would be inclined to ask whether a freshwater pelagic fish 
in Africa is a good model for a demersal gadoid in the Atlantic Ocean, but 
the idea that assumptions must be clearly stated and critically reviewed did 
not occur to anyone else.

I have published a number of papers on modelling, including the following, 
and while I have read other papers reflecting similar views, I am currently 
on holidays in Florida and do not have references handy.

Bill Silvert

Silvert, William. 2001. Modelling as a Discipline. Int. J. General Systems 
30: 261-282. A Polish translation was published  in the "Projektowanie i 
Systemy" volume XVII in 2004.





- Original Message - 
From: "John Petersen" <[EMAIL PROTECTED]>
To: 
Sent: Friday, January 20, 2006 11:23 AM
Subject: Re: Role of modeling courses in the undergraduate curriculum


> Back in September of '05 I sent out an announcement about a conference
> at Oberlin College that would focus on the role of computation and
> modeling in the undergraduate curriculum. I was very interested when
> several colleagues responded on this list-serve expressing a rather
> negative view regarding the value of teaching modeling to
> undergraduates. To summarize, the arguments seemed to focus on the
> notion that the development of specialized and technical computer skills
> involved in modeling represents a counterproductive distraction. Has
> anyone seen this argument made anywhere in any literature? I would
> greatly appreciate references to papers or book chapters that adopt this
> view or otherwise criticize the value of modeling education for
> undergraduates. Beyond that I would appreciate suggestions for
> literature that takes any position on the pedagogical role of modeling
> in the undergraduate curriculum.
>
> Thanks!
> John Petersen
> Associate Professor of Environmental Studies and Biology
> Oberlin College
> 

Re: teaching materials moral vs legal

[Bill Silvert]

My understanding is that all original material is under copyright whether or 
not the author states so explicitly, as Malcolm asserts. If your girl firend 
publishes your letters without your permission it is a violation of 
copyright, whether you remembered to write "as always, your devoted 
snookums, copyright 2006" or not.

However as was discussed in another recent exchange about copyright, it is 
unlikely that anyone will drag you into court about copying educational 
material from a website, unless of course you publish it in a best selling 
textbook. Scientists and teachers are more likely to be concerned with 
behaving ethically, and being seen to behave ethically, rather than being 
sued over an issue of no financial consequence. That is why I posted the 
information about creative copyright, which is a way of making clear what 
you consider fair use. Although Wayne Tyson complained that creative 
copyright may have no legal validity, I think that is beside the point. 
There is a lot of trust involved in doing science, such as trust that a 
reviewer will not steal your ideas, and the important point is to make clear 
how people can use your material. If it comes down to a lawsuit, you have 
both lost.

Bill Silvert


- Original Message - 
From: "Malcolm McCallum" <[EMAIL PROTECTED]>
To: 
Sent: Friday, January 20, 2006 10:52 AM
Subject: Re: teaching materials moral vs legal


> We have to remember that there is a difference between morality and =
> legality. Legality is a minimal level of morality that society sets as a =
> standard.  Levels of morality above and beyond this are within an =
> individual's rights.  IF someone posts something on the web, and they do =
> not copyright it (simply put the symbol with the year and their name) =
> then it is legally free for use without permission.  On the flip side, I =
> personally would think that you would at least give credit in the =
> materials to the source.   We all need to be cognizant of what we post =
> on the web.  If we really don't want' someone else using it, it should =
> be in webct or blackboard or similar protected venues.  On my website I =
> have a link for students entitled "Advice for Students." On it I have =
> several of the many common questions that students ask that are frankly =
> redundant and truthfully in many ways self evident.  When the student =
> clicks on the question, audio clip from a movie appears in a uniquely =
> appropriate response.  It gets a lot of laughs from the students.  The =
> audio clips used were once free on the web during the mid-1990's.  Now =
> you can't download the same clips without paying a fee.  If someone =
> wanted to copy my website, they could, and frankly I wouldn't care!  =
> They can link to it or whatever.  On the flip side I have a number of =
> lectures that were frankly difficult to put together. IF someone needed =
> a lecture as a starting point I suppose they could ask, but I put them =
> in Web CT.  That way my knowledge isn't being thrown around for free.  =
> Frankly, what I know is my paycheck!  If used a lecture freely available =
> on the web, I think I would let the person know.  Chances are, it would =
> be changed enough by the time I gave it, that there would be little =
> resemeblance anyway.  Credit should always be given!
> =20
> Malcolm L. McCallum
> Assistant Professor
> Department of Biological Sciences
> Texas A&M University Texarkana
> 2600 Robison Rd.
> Texarkana, TX 75501
> O: 1-903-233-3134
> H: 1-903-791-3843
> Homepage: https://www.eagle.tamut.edu/faculty/mmccallum/index.html
> =20
>
> 
>
> From: Ecological Society of America: grants, jobs, news on behalf of =
> Jonathan Greenberg
> Sent: Thu 1/19/2006 11:54 PM
> To: ECOLOG-L@LISTSERV.UMD.EDU
> Subject: Re: Questions about using teaching materials from others
>
>
>
> Jim:
>
>I think you misunderstood my post -- I was asking if permission =
> is
> required from the author to use online class material in your own =
> course, or
> is it more like a citation -- hence, if the content is online we can =
> assume
> it can be used in our own course (e.g. "is fair game").  I suppose this =
> begs
> the question of what you would consider "stolen"?  I can use other =
> published
> material in research papers without the permission of the authors =
> (=3D=3D
> citations!) but do we treat lectures as "data" or "finished citable
> material"?
>Personally, I've created an entire class more or less from =
> scratch
> (as have many of us), and I would be thrilled to know if someone is =
> using my
> lectures -- I think the only time I would 

Re: archiving data files - question about Excel

[Bill Silvert]

Although I am not familiar with the policy of ESA on data papers, I wonder 
if the situation you describe is correct. Research involves both collecting 
data and analysing it, and it sounds as though your spreadsheets include 
both the raw data and at least part of the analysis. Do the analysis 
portions - namely the formulae - really have to be published in ASCII form? 
Many ecologists use proprietary software for data analysis, and if they have 
to translate all their analyses into a standard form, that seems to pose a 
formidible obstacle to publication.

If instead of doing the analysis in Excel you imported the data into a 
program like SAS or SPSS, or a special package that you programmed yourself, 
what would the requirements be?

Bill Silvert

- Original Message - 
From: "David Inouye" <[EMAIL PROTECTED]>
To: 
Sent: Friday, January 20, 2006 5:56 PM
Subject: archiving data files - question about Excel


>I have a large number (900+) of Excel spreadsheets from a 30-year
> (and ongoing) study of flowering phenology from the Rocky Mountain
> Biological Laboratory, with each spreadsheet including data from one
> 2x2 plot that was surveyed every other day for the growing season. To
> publish these data as an ESA data paper they have to be converted to
> ASCII, as no proprietary formats are accepted.  I can understand
> this, having already been caught by having a program (SuperCalc) that
> I used for data storage for this project go extinct.  However, some
> cells in the spreadsheets are formulae (frequency distributions of
> the number of flowers open per inflorescence), and when I save the
> spreadsheet as a .txt file just the value, and not the formula, is 
> exported.
>
> My recollection is that SuperCalc had a way to export a list of all
> non-blank cells (A1, A2, , B1, B2, .) and what their contents
> were, including formulae, but I can't find an easy way to do this
> with Excel.  I would also like a list of all the comments I have
> associated with cells, and their cell references. Any ideas about how
> best to generate this ASCII list?  I'm envisioning two results for
> each spreadsheet: first a version showing the spreadsheet as
> displayed on the screen (the .txt export will do this, although there
> are some formatting issues, so I may explore a .prn option), and
> second, a list of all the cells, or at least those with formulae or
> comments, and the formulae or comments from those cells.
>
> I will probably also archive the files in their original Excel
> format, at the digital repository that our campus library has
> created.  That way, as long as Excel or some program that can read
> its files is available, researchers could access the spreadsheets
> without having to reverse the process I'm trying to institute.
>
>
> David Inouye
> 

Re: What's the best energy source?

[Bill Silvert]

I am surprised by the variety of answers this question generated. To me it 
is like asking "what is the best food to give an animal?". The answer is, 
"it depends".

The world will always require a mix of power sources, depending on 
availability and the type of use. There is no question that Iceland has its 
optimal power source, but geothermal energy is not globally available. Hydro 
power is more widespread, but still confined to certain regions and useful 
only for fixed demand (like factories or aluminum smelters). The same goes 
for wind and tidal power.

Power for mobile applications poses a different set of problems. Even 
Iceland doesn't power its cars with geothermal energy.

There is also the problem of balancing different kinds of environmental 
impacts. Hydro power is basically free, but the dams and power lines can 
have a major impact.

So my answer to what I consider a meaningless question is this - the best 
way to power the world is brain power.

Bill Silvert


- Original Message - 
From: "Leslie Mertz" <[EMAIL PROTECTED]>
To: 
Sent: Wednesday, February 08, 2006 1:29 PM
Subject: What's the best energy source?


>I got an interesting question yesterday. From an environmental point
> of view, what is the best, yet still feasible, way to power the
> world? Any thoughts?
>
> Leslie Mertz, Ph.D.
> science writer/author, educator 

group selection

[Bill Silvert]

I've seen lengthy arguments about group selection, most of which border on 
the religious. I really don't understand why it is such an outrageous idea.

Consider chemical defenses which presumably evolve randomly and persist if 
they enhance fitness. If a chemical makes an organism smell bad, then it is 
clearly a case of individual selection. But suppose that the chemical is a 
poison so that the predators can eat the organisms, but then they die. 
Predators that like that kind of prey will be selected against, and although 
the toxic individuals get consumed, after a while the group's survival is 
enhanced. Is this so outlandish? There are after all lots of living 
organsims out there which are edible but toxic.

Bill Silvert

- Original Message - 
From: "isab972" <[EMAIL PROTECTED]>
To: 
Sent: Tuesday, February 14, 2006 8:49 PM
Subject: Re: current natural selection pressures


> Your reasoning on selection is almost correct but there is one important
> flow: natural selection does not act on clans or groups but only on
> individuals. Group selection indeed does not work in nature. In very few
> cases, there might be traits selected under kin-selection, but very very
> few. 

Re: math modelling

[Bill Silvert]

Actually the critical part of modelling is not the math, but learning to 
look at and understand the underlying assumptions. Most of the math needed 
is pretty simple. For example, practially the only differential equations 
you will encounter are first order ordinary DEs, as higher order DEs and 
partial DEs are virtually unknown (except perhaps in modelling plankton).

There are some lovely results arising from linear algebra, such as stability 
analyses based on the eigenvalues of matrices, which seem to have little 
relevance to the real world. The problem is that to set up linear models in 
ecology you have to make some really inappropriate assumptions.

It is easy to get carried away with the math - that is why so many 
ecologists find modellers and modelling irrelevant!

I recommend Tony Starfield as the best introductory author in the field.

Bill Silvert


- Original Message - 
From: "Patrick Foley" <[EMAIL PROTECTED]>
To: 
Sent: Monday, March 06, 2006 3:50 AM
Subject: Re: math modelling


> Malcolm,
>
> Core courses for ecological modelers are:
> Differential Equations
> Linear Algebra
> Probability and statistics
>
> Each of these is taught for applied scientists at an intermediate, not
> highly rigorous way, and also for mathematicians more rigorously. Watch
> out to find your level. In math, it is important to screen ahead for
> good teachers. Half are awful. Half awesome.
>
> Also be sure to read some of the best population modelers to see how the
> techniques get used (MacArthur, Levins, Maynard Smith, Hal Caswell, and
> others)
>
> Patrick Foley
> [EMAIL PROTECTED]
>
> Malcolm McCallum wrote:
>
>>Hi,
>>I have become interested in learning mathematical modelling because of =
>>the strength it can add to your study.  What key math courses beyone =
>>calc I should one take to develop this skill. =20
>>=20
>>Malcolm L. McCallum 

Re: math modelling

[Bill Silvert]

Ned is right in one respect, IBMs are conceptually straightforward and easy 
to understand, but there are lots of pitfalls along the way. One is that 
they are computer-intensive and can be very slow to run. A more important 
problem is that it is easy to make mistakes in setting up the problem. I 
recall one paper I reviewed which illustrated the method with the old 
fox-rabbit system beloved by Lotka-Volterra theorists, but the foxes ended 
up starving to death even though there were rabbits within 100 m - it was 
just to hard to get the search algorithm right.

To be fair, IBMs are most often used to model spatial effects (moving from 
one grid cell to another) and these are very difficult to get right. Spatial 
models are probably the hardest to build due to the problems of 
understanding and predicting how animals will move around. That is why there 
are really no spatial fisheries models to speak of.

If anyone wants to experiment with IBMs without getting into the heavy 
programming that they often involve, I recommend the free modelling package 
NetLogo from Northwestern U. which is easy to use and will get you into the 
field relatively painlessly. I took a complicated C++ model of the North Sea 
that I developed with two other colleagues and came up with a NetLogo 
approximation in an afternoon (the model is on their website - I don't have 
the URL handy since I live in the country far from broadband, but do a 
search on NetLogo to find it.).

Someone asked for the Starfield citation, he has written quite a few books 
and papers, but his classic is: Starfield, A.M. and A.L. Bleloch. 1991. 
Building Models for Conservation and Wildlife Management. Second edition, 
The Burgess Press, Edina, Minnesota. It's hard to find and the title is 
awful, but it's a really good book. I particularly like his concept of 
"frames" which offers a way to deal with discontinuities such as 
metamorphosis.

I guess I'll put in a plug for one of my own papers, Silvert, William. 2001. 
Modelling as a Discipline. Int. J. General Systems 30: 261-282. A Polish 
translation was published  in the "Projektowanie i Systemy" volume XVII in 
2004, and the PDF (of the English version) is on the web at 
http://bill.silvert.org/pdf.

Bill Silvert



- Original Message - 
From: "Ned Dochtermann" <[EMAIL PROTECTED]>
To: 
Sent: Monday, March 06, 2006 7:23 PM
Subject: Re: math modelling


> To follow on the below post, DeAngelis and Mooj (2005) provide a concise
> overview of individually-based models (IBMs). IBMs have several advantages
> over other approaches. First, they emphasize the conceptual model 
> underlying
> the system you're attempting to understand. Second they, obviously, 
> operate
> at the level of the individual which arguably is where many/most 
> ecological
> and evolutionary processes should be approached from. Finally, they are 
> far
> more accessible for those of us that may not have the mathematical skills
> we'd desire or required of other approaches... 

Re: "Hamerstrom science" (deliberate non-use of statistical analysis)

[Bill Silvert]

While I agree with stan that too much emphasis is placed on statistics, 
phrases like the one below alarm me. I recall a talk by a distinguished 
professor in which he had his students review 400 papers and concluded that 
only two were scientifically correct. My conclusion was that 99.5% of 
scientists disagreed with his idea of how to do science.

Bill Silvert

- Original Message - 
From: "stan moore" <[EMAIL PROTECTED]>
To: 
Sent: Wednesday, March 08, 2006 1:47 PM
Subject: "Hamerstrom science" (deliberate non-use of statistical analysis)


> S.H. Hurlbert concluded that of 176
> experimental studies published between 1960 and 1983, 27% were designed
> inappropriately... 

Re: "Hamerstrom science" (deliberate non-use of statistical analysis)

[Bill Silvert]

Although Mike doesn't use the term, this is a nicely put statement of the 
message that modellers have been trying to get across for eons, that one 
should model a system before doing the field work in order to design the 
experiments optimally. Too often I have had people approach me with masses 
of data, but without the critical information that is needed to understand 
the system.

On the other hand, if one only carries out field work to test pre-existing 
ideas, how can you discover anything new? One of the greatest scientific 
events of the past century was the discovery of ecosystems based on 
chemosynthesis rather than photosynthesis, but this was just the result of 
sending down a ROV and had nothing to do with hypothesis testing. And Darwin 
did not set out to test evolution, he joined the Beagle as a field 
naturalist and developed his theory from his observations. I suspect that 
these and other major scientific developments would not pass the rigorous 
tests of "correct science".

Bill Silvert


- Original Message - 
From: "Michael Sears" <[EMAIL PROTECTED]>
To: 
Sent: Thursday, March 09, 2006 1:00 AM
Subject: Re: "Hamerstrom science" (deliberate non-use of statistical 
analysis)


> If you can design an elegant experiment that only requires a t-test for 
> its
> analysis, that is admirable. But the simple truth of the matter, in my
> experience, is that many folks don't take the time to design a good 
> experiment,
> often collect data with disregard to any theory, and simply collect what 
> is easy
> or is the data that everyone else collects, hoping in the end that somehow
> through mathemagic, they can make something out of their efforts. To 
> paraphrase
> Burnham and Anderson, 90% of our time should be spent thinking and only 
> 10%
> doing. I'd suggest folks be aware of theory and design experiments with 
> regard
> to it, such that the design and analysis are set BEFORE the data are 
> collected.
> Often, but not always, if that is done, an overly complex analysis may not 
> be
> necessary...but some complicated hypotheses do require complex analyses. 
> This is
> the nature of good science.
>
>
> Mike Sears 

Re: "Hamerstrom science" (deliberate non-use of statistical analysis)

[Bill Silvert]

Ned misses an important point, that statistical models don't give you any 
idea what to measure. They simply tell you how to do what you are planning 
to do anyway in a way that might give statistically meaningful results. They 
do not have any underlying natural structure.

When I referred to doing the modelling first I was referring to models that 
actually describe the system and have some scientific basis.

As an example of what I mean, I was once invited to develop a model of 
aquaculture impacts after several years of data had been collected. I began 
the workshop by asking about the nitrogen fluxes, since previous studies had 
shown that these were the most critical variables and would be a key element 
of any model. After a long pause I was informed that nitrogen had not been 
measured because no one thought it was important (actually, they didn't have 
the right equipment). If they had built a simple model first we might have 
had some useful data to work with.

And of course I am not ruling out the possibility that the data might 
contradict the model. That is fine. That is how science develops.

So I assure Ned that I am not talking about statistics, but science.

Bill Silvert


- Original Message - 
From: "Ned Dochtermann" <[EMAIL PROTECTED]>
To: "'Bill Silvert'" <[EMAIL PROTECTED]>; 
Sent: Thursday, March 09, 2006 4:23 PM
Subject: RE: "Hamerstrom science" (deliberate non-use of statistical 
analysis)


> Generally however those concerned, after the fact, about the rigor of 
> their
> statistics (or lack thereof) are not reporting naturalistic observations 
> but
> attempting to hammer their round data pegs into the square holes of 
> already
> established theory.
>
> If your concern is naturalistic observation, you don't have to have too 
> much
> concern about whether or not you've properly articulated (or understand) 
> the
> underlying statistical model you're testing.
>
> Ned Dochtermann 

Re: "Hamerstrom science" (deliberate non-use of statistical analysis)

[Bill Silvert]

Nonsense. Science involves understanding what is going on, and some 
arbitrary definition of "scientific method" is more often a hinderance than 
a help. Remember what Einstein said - Nature is subtle but not malicious 
(Raffiniert is der Herrgott, aber Bösehaft ist er nicht). We have to be 
clever to unravel these secrets. If we get at the truth we are doing 
science.

Bill Silvert


- Original Message - 
From: "Malcolm McCallum" <[EMAIL PROTECTED]>
To: 
Sent: Thursday, March 09, 2006 5:13 AM
Subject: Re: "Hamerstrom science" (deliberate non-use of statistical 
analysis)


> Good science is a falicy.  Either its science following the scientific =
> method or its not science. Period.
> I agree with most of the rest of what you said.
> =20
> Malcolm L. McCallum 

Book search, Biology of Calanoid Copepods by John Mauchline

[Bill Silvert]

I am trying to find a copy of The Biology of Calanoid Copepods (Advances in 
Marine Biology, Vol 33) by John Mauchline which is out of print. If anyone 
has a copy that they are willing to sell, please let me know.

William Silvert
[EMAIL PROTECTED]