Re: [asa] historical versus experimental sciences

David:

In your examples below, you are granting more knowledge about the species
(some knowledge of the biochemistry, some knowledge of mitochondrial DNA,
etc.) than we originally supposed in our scenario. (Or at least, than I
supposed.) All of my argument was based on the assumption that we had *no*
genetic or physiological knowledge of the new fruit fly, but knew only what
it looked like, and its eating habits and such behavioural characteristics
as were obvious to the despairing farmers whose crops were being destroyed.
My complaint, based on that assumption, was that you would not have enough
information to determine evolutionary relatives, and your line of diagnosis
and prescription would thus be stopped in its tracks. Of course, if you
have more information, then I understand how you could arrive at
evolutionary relationships.

However, then the *second* part of my argument would kick in, i.e.: even if
you could determine the evolutionary relationships, it would be superfluous
to do so. The similarities in DNA and/or and/or general biochemistry would
point the scientists and policy-makers in the direction of the solution. I
see no benefit in arguing

"Often close evolutionary relatives have similar pheromones",

if you cannot determine close evolutionary relationship without *first*
determining genetic, biochemical or morphological similarity, and if it is
just as true that

"Often species with very similar DNA have similar pheromones"

or

"Often species with very similar morphology have similar pheromones"

or

"Often species with very similar biochemistry have similar pheromones".

If I need to do my laundry, I could take all my quarters, go to the bank,
turn them into bills, then go to the laundromat, and put the bill in a
change machine to get quarters back, to insert into the laundry machines.
Or I could just take the quarters to the laundromat and put them into the
machines. The second method is the most efficient. Your proposed
"evolutionary agriculture" technique, even if it works perfectly well, is
intellectually inefficient because it goes through an unnecessary step. But
that's exactly what we'd expect if, as Professor Skell has said, as far as
most experimental science is concerned, neo-Darwinism is an interpretive
gloss which is not necessary to conduct the research or validate the
results.

This glossing occurs all the time. The other day, some scientists
discovered the gene that gives the water strider its characteristic mode of
skimming across the surface of the water, and the news story (perhaps
following the lead of the reporting scientists, I don't know) gave the
matter an evolutionary twist: scientists have discovered the evolutionary
mechanism by which the water strider acquired its ability. In fact, the
*empirical* science had uncovered nothing about evolutionary mechanisms at
all. All it had uncovered was the gene which controls the insect's
water-walking ways. An evolutionary gloss was then put upon the discovery,
thus making it look like another gap in the evolutionary story had been
filled. In fact, the results were quite compatible with six-day
creationism. The gloss could have been: "Science has now discovered the
genetic means by which God endowed the water-strider with its abilities". I
am not of course championing six-day creationism over evolution; my point is
merely that the evolutionary twist given to the news story was gratuitous,
and propagandistic, if not in intent (which was likely), at least in effect.
Evolutionary biologists seem incapable of simply honestly reporting the
facts as discovered, without giving them a neo-Darwinian slant.

I find it interesting that you automatically associate "mitochondrial DNA"
with evolutionary theory. From a non-doctrinaire, non-historical point of
view, the mitochondria are simply organelles in the cell which contain DNA,
and the sequences in that DNA can be studied, just as the sequences in
nuclear DNA can be studied. One can ask the question "How much different is
the mitochondrial DNA of *this* species from the mitochondrial DNA of *that*
species?" without speaking of evolution at all. It's a question for
biochemists to settle. By the way, are you familiar with the work of the
evolutionary biologist Paul Hebert at the University of Guelph, who is one
of the world's leading experts on genetic bar-coding? Hebert, a
neo-Darwinian, employs mitochondrial DNA to assess similarities and
differences between species. He and his team have "bar-coded" many, many
species. He stated in an interview a few years ago that, to his chagrin,
the results of genetic bar-coding using mitochondrial DNA seem to support
the view of the "creationists". (He doesn't say whether by that he means
creationists proper, ID proponents, or both.) He surely had no interest in
promoting "creationism", as his remarks in the interview demonstrated. So I
have to smile when you say the use of mitochondrial DNA is a technique which
employs "evolutionary" theory. How can an analysis whose results appear to
imply creationism be said to be an "evolutionary" analysis? In this case,
evolutionary theory appears to be more dangerous than a merely useless gloss
upon the empirical facts uncovered in the lab; it appears to be a willful
distortion of what the lab results tell us.

See this link:

http://www.bolinfonet.org/pdf/20060411_135940_TheBarcodeOfLifeTakesFlight_04_2006.pdf

Cameron.

----- Original Message -----
From: "David Campbell" <pleuronaia@gmail.com>
To: "asa" <asa@calvin.edu>
Sent: Monday, August 17, 2009 3:30 PM
Subject: Re: [asa] historical versus experimental sciences

>> I have no objection to the basic logic of such an approach. The
>> difficulties I was posing were further along the line. If you don't know
>> very much about a species to start with (and we were talking about just
>> such
>> a case), how are you going to determine its close evolutionary relatives?
>> You can't determine that X and Y are close evolutionary relatives unless
>> you
>> know at least something about both X and Y. Now in the case of the fruit
>> fly invader, you've already suggested that we would have no direct
>> knowledge
>> of its biochemistry and won't have sequenced its genome yet. So the
>> evolutionary classification you are talking about can't be based on
>> either
>> of those things. On what is it based, then?
>
> Not necessarily "no direct knowledge of its biochemistry", just not
> knowing the specific issue of interest (e.g., a pheromone). The
> evolutionary classification could be based on morphological
> features-not merely "these two flies look similar" from you or me, but
> in the judgement of an actual entolomogist who has studied the group
> and has determined what features give a consistent pattern within the
> group of interest. It could also be based on genes unrelated to the
> character of interest, such as mitochondrial genes.
>
> Perhaps a real-life example that I am familiar with would be less
> confusing, involving fewer hypotheticals. Freshwater mollusks have
> the highest rate of imperilment (extinction, endangerment, etc.) of
> any major group of organisms, with land snails close behind. In order
> to effectively protect them, we need to know about their life history.
> This is especially an issue for freshwater mussels, which have a
> juvenile stage parasitic on certain fish and so need the host fish
> protected and available, too. Many species are too rare to make
> experimenting on them a practical option. How do we know what more
> common species would be the best model to use? Molecular and
> morphological studies help us identify the closest relatives, which
> then can be checked for relevant patterns such as sensitivity to
> pollutants, ecological requirements, host needs, etc. For example,
> the purple pigtoe was placed in Fusconaia, the sculptured pigtoe in
> Quincuncina, and the purple wartyback in Cyclonaias, all often
> assigned to the tribe Pleurobemini. In fact, all three belong in
> Rotundaria (based on genetic data, as well as some previously
> neglected morphological and anatomical features), tribe Quadrulini, a
> group with very different characteristic strategies for getting larvae
> and host together. Conversely, enough genetic variation exists
> within the sculptured pigtoe, corresponding to geographic separation,
> to suggest that not all populations will be identical in their
> biology. These data can help us narrow down what to anticipate
> regarding the rarer species for currently unknown features (such as
> host fish for the two pigtoes).
>
> Evolutionary theory gives us the reason to extrapolate from one
> similarity to another when we know about some similarities but not
> about some other feature of interest.
>
> Likewise, based on observed patterns of relationships, I can predict
> patterns in other organisms. For example, many ordinary pond snails
> belong to the family Lymnaeidae. A few oddballs belong there, too.
> Lantzia and Erinna are unusual ones, somewhat similar in shell form,
> from Mauritius and Hawaii, respectively. Every lymnaeid from close to
> the Indian Ocean that's been sequenced groups as relatives of Radix
> (chromosome number and anatomical features also support the grouping,
> whereas shell shape is quite variable). The minimal available data on
> the Hawaiian ones relates them to primarily North American forms. I
> predict (and once a colleague finishes the anatomical work, will be
> submitting a paper for publication mentioning this) that detailed
> anatomy, chromosome number, sequencing, etc. will associate Lanztia
> with Radix and its relatives, whereas the Hawaiian ones will show
> additional similarities to the primarily North American group.
>
>> More arguments with detailed examples aren't necessary here. Just give me
>> *a list of the criteria* by which a biologist could deduce that two fruit
>> flies are close evolutionary relatives if the biologist had *zero*
>> knowledge
>> of the first fruit fly's genome, biochemistry, and physiology. A list of
>> words or phrases will do, e.g.: "We could ascertain beyond a reasonable
>> doubt that the two fruit flies were close evolutionary relatives if they
>> had
>> similar flight patterns, similar mating habits, a similar response to
>> high-pitched noises, or a similar diet."
>
> Things like that would be possible, but I expect that the features are
> more likely to be along the lines of pattern of hairs on a particular
> body part, shape of the eyes, particular color patterns, exact wing
> vein configuration, etc.
>
> Searching reveals that Bactrocera albistrigata is the newly found
> invasive fruit fly. It's not that closely related to the lab favorite
> Drosophilia.
>
> http://delta-intkey.com/ffl/www/bac_albi.htm has some specific
> features of relevance for the larvae.
> http://www.padil.gov.au/viewPestDiagnosticImages.aspx?id=1291 has some
> morphological features.
>
>
> www.aphis.usda.gov/plant_health/plant_pest_info/fruit_flies/downloads/bactrocera-susceptibility-analysis.pdf
> "The genus Bactrocera is comprised of over 500 fruit fly species, of
> which many are considered serious
> pests that threaten the agricultural crops of countries in which they
> are found. The majority of these species
> are native to the South Pacific, Australia, India, and Southeast Asia
> (zipcodezoo.com), although many have
> moved into Africa, Europe, and South America. It appears that some
> have been so recently discovered or
> separated from like species (B. dorsalis group, Clarke et al., 2005)
> that very little information is available
> on their life cycles and host preferences. "
>
> In other words, there are several fruit flies in this group that are
> currently rather poorly known, providing uncertainty about whether
> they are a threat and how to control them.
>
> Phylogenetic relationships among Bactrocera species (Diptera:
> Tephritidae) inferred from mitochondrial DNA sequences
> Paul T. Smith, Srini Kambhampati and Karen A. Armstrong
> Molecular Phylogenetics and Evolution
> Volume 26, Issue 1, January 2003, Pages 8-17
> Abstract
> Several members of the dipteran family Tephritdae are serious pests
> because females lay eggs in ripening fruit. The genus Bactrocera is
> one of the largest within the family with over 500 described species
> arranged in 28 subgenera. The phylogenetic relationships among the
> various species and subgenera, and the monophyly of specific groups
> have not been examined using a rigorous phylogenetic analysis.
> Therefore, phylogenetic relationships among 24 Bactrocera species
> belonging to 9 subgenera were inferred from DNA sequence of portions
> of the mitochondrial 16S rRNA, cytochrome oxidase II, tRNALys, and
> tRNAAsp genes. Two morphological characters that traditionally have
> been used to define the four groups within the subgenus Bactrocera
> were evaluated in a phylogenetic context by mapping the character
> states onto the parsimony tree. In addition, the evolutionary trend in
> male-lure response was evaluated in a phylogenetic context. Maximum
> parsimony analyses suggested the following relationships: (1) the
> genus Bactrocera is monophyletic, (2) the subgenus B. (Zeugodacus) is
> paraphyletic, (3) the subgenus B. (Daculus) is a sister group to
> subgenus B. (Bactrocera), and (4) the subgenus B. (Bactrocera) is
> monophyletic. The mapping analyses suggested that the morphological
> characters exhibit a simple evolutionary transition from one character
> state to another. Male-lure response was identified as being a labile
> behavior that has been lost on multiple occasions. Cue-lure response
> was plesiomorphic to methyl-eugenol response, and the latter has
> evolved independently within the Bactrocera and Zeugodacus groups of
> subgenera. The implications of our results for devising a coherent,
> consolidated classification for Bactrocera is discussed.
>
>
> In other words, they ran an evolutionary analysis of one feature
> (mitochondrial DNA) and examined the correlation with a feature of
> interest (response to particular trap types), so that analysis of
> mtDNA for another species will help us to predict what traps are
> likely to be most effective, even though evolution provides the only
> link between the trap vulnerability and the mtDNA pattern.
>
> Genome is not known for the species, but a handful of genes have been
> sequenced.
>
> --
> Dr. David Campbell
> 425 Scientific Collections
> University of Alabama
> "I think of my happy condition, surrounded by acres of clams"
>
>
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Received on Thu Aug 20 07:24:35 2009