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Thinking fast about Pete's classroom topic, I suggested: 
<Science:~ the view that reality can be apprehended and manipulated 
to reach a 
consciously formulated goal.>
You disagreed:
<Science ideally is not goal oriented.  Science ideally is you 

and I go out in the world and look at stuff and say, "Hey that's 
weird, maybe 
this is why that is."  And then we test our hypothesis the only 
way you can: 
trying to demonstrate that you're wrong.>
Mind if I comment that you enjoy creating antithesis.
When I 'go out in the world and look at stuff', I'm apprehending 
reality.  The points we're both making are that reality exists 
and we can perceive it.  We've gotten past some major philosophical 
When we 'test our hypothesis', we are creating circumstances 
(manipulating reality) in order to (goal!) obtain results which 
tend to confirm or refute our contention.
I enjoy agreement, and I think we're agreeing.
And you added:
<Science and the scientist cannot remain objective observers 
and collectors of data if we're manipulating reality, especially 
if we're manipulating reality to fit it into a preconceived notion 
of how reality SHOULD be.>
The last part of your sentence is straw (would I say that?), 
but the first part...
Assertion for you:  we observe reality, then manipulate it in 
thought and in practice.
When we do thought experiments, we change reality in our minds 
in order to heighten contrasts and identify significant elements 
for further analysis/synthesis.  When we mix 2 chemicals together 
to see what shakes out, we are acting to create new facts for 
our use.  So, yes, science is very much concerned with manipulating 
reality.  How far would science get if its motto were:  'Leave 
it lay'?

In response to my question about whether cladistic analysis should 
be considered scientific, given that it can produce 2 (approximately) 
equally valid but contradictory answers,  you asseverated forcefully:

<In a word yes.  Cladograms are PHYLOGENETIC HYPOTHESES, they 
are not 
statements of absolute truth writ with the knowlege of the creator 
of the 
[Breaking your paragraph up for comments.  Agreed then.  Cladograms 
will remain hypotheses, inferences forever.  They cannot become 
theories, like evolution, which are backed by so much direct 
and indirect evidence that they become equivalent to observations. 
 This has implications.]
How do you resolve two conflicting hypotheses?  You test them. 
How do you test conflicting phylogenetic hypotheses?  For starters, 
combine the data in the two competing hypotheses and see what 
comes up.  
Perhaps it's one of the previous hypotheses, perhaps it's something 
new and 
[Ok.  What are the hallmarks of the test?  It is done with the 
same data (you said, '...combine the data), and it uses the same 
logic as the initial analysis.  I would argue that what you are 
'testing' here is how the results with a larger aggregation (sample 
of all relevant animals who ever lived) of data compare to the 
results from subsets of the data.  You'd certainly find out something 
about the computer program logic's response to expanding data, 
but the validity of the logic is untested.]

The point I have been making, and will continue to make is that 
phylogenetic hypothesis, a cladogram, is the DATA telling you 
what the hypothesis should and could be.  The just-so-story of 
systematicists is again, the anti-scientific way of looking at 

Let's take the Linnaean view as one based purely on observation. 
 The definition of Aves = bird (shhh) is based on contemporary 
animals.  A cladistic definition of Aves includes the contemporary 
animals, a specific species (Archie) included by assertion, and 
a mrca whose characters are subject to consensus change with 
peer-reviewed notice.
Now, a just-so story starts from the result and reasons back 
to the causes using comfortable premises.  In other words, analysis 
forced to produce a pre-ordained result.  Procrustean.  You can 
say that basing a definition on the animals we see is a just-so 
story because it does start and end with the present situation. 
 I can assert that the cladistic definition is a just-so story 
because Archie MUST be included and that it MUST be possible 
to identify the characters of the mrca.  Even though we can't 
observe or rerun evolution to confirm our very rational guesses.
I think the observational definition includes fewer assertions 
and arguable points, so therefore it is less of a just-so story. 
 You'll disagree, I expect, but the best choice between these 
arguments will not be immediately apparent to everyone.
The birds you can see won't change, so a definition anchored 
on them is going to be unvarying.  That's the very opposite of 

You referred to our need for The (Unbiased) Machine for Discerning 
<You're right, they are different questions [cladistic analysis 
vs nomenclature], but they come up with the same answer if we 
look at the question with our Objective Scientist Goggles (tm) 
on.  Are just-so-stories concerning relatedness more objective 
than computers analyzing data?  Do I even need to answer?  Are 
ranks which have no basis in reality whatsoever and no definition 
except in relation to other ranks objective?  Or is the naming 
of super-specific taxa based on objectively obtained hypotheses 
of evolutionary history more objective?  Hmm... the 
Goggles (tm) say objectivity is more objective.>
The problem is, the Objective Scientist Goggles (tm) have one 
type of polarization and the computer screen showing cladistic 
analysis has a glare shield with a different polarization.  When 
our scientist searching for Truth looks at the cladistic screen 
through his Objective Scientist Goggles (tm), he sees complete 
darkness.  Someone, somewhere has made a decision during her/his 
cladistic analysis, and all chance of perfect objectivity has 
When the scientist, disappointed, looks away, and out the window, 
he sees a beautiful red cardinal near the window glass, and then 
sees and hears the bird's oranger mate screeching at him from 
a nearby branch for getting too close to the erratic humans. 
 The male cardinal stays on the window ledge; it's a cold day.
Our scientist watches, enjoying.  He has found, if not THE answer, 
a perfectly good answer.

PS  Rereading the Jefferson quote lauding Linnaeus for having 
found a classification system everyone could agree upon, I found 
his statement regretting his error in momentarily agreeing that 
bones should be used to clarify distinctions.
Reminded me of John F. Kennedy's comment to a flock of Nobel 
laureates that there was more brain power in the White House 
that night than on any prior occasion, save when Jefferson dined 
there alone.
Whatta guy!  (Jefferson)




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