Re: Today's logical argument is: Straw Man: Re: the inductive

On Thu, 26 Nov 2009 17:57:28 -0800 (PST), All-Seeing-I
<allseeingi@xxxxxxx> enriched this group when s/he wrote:

On Nov 26, 12:04 pm, John Harshman <jharsh...@xxxxxxxxxxx> wrote:
All-Seeing-I wrote:

Show your work. Where is this common ancestor? What evidence is there
for the ancestorial connection that does NOT have more then one
explanition.

Here.

Evidence for human relationships to the other apes.

Here is a set of DNA sequences. They come from two mitochondrial genes,
ND4 and ND5. If you put them together, they total 694 nucleotides. But
most of those nucleotides either are identical among all the species
here, or they differ in only one species. Those are uninformative about
relationships, so I have removed them, leaving 76 nucleotides that make
some claim. I'll let you look at them for a while.

[                        10         20         30         40         50]
[                        .          .          .          .          .]
                  + 1 2++   3  11 +4 3   ++  52+1     2615+4 14+ 3 3+6+
gibbon          ACCGCCCCCA TCCCCTCCCT CAAGTCCTAT CCAATCTACT GTACTTTGCC
orangutan       ACCACTCCCA CCCTTCCTCC TAAGACTCAC ACAACTCGCC ACACCTCGTC
human           GTCATCATCC TTCTTTTTTT AGGAATTTCC TCTCTCCGTC ACGCTCTACT
chimpanzee      ATTACCATTC CTTTTTTCCC CGGATTCTCC CTTCTTCATT ATGTCTCATT
gorilla         GTTGTTATTA CCTCCCTTTC AAGAACCCCT TTCACCTATC GCGTCCCACT
[                        60         70     ]
[                        .          .      ]
                   +++ +++1 + ++   2 + +++
gibbon          CCTACAGCCC AGCCAAACGA CACTAA
orangutan       CCTACCGCCT AGCCATTTCA CACTAA
human           CCCCTTATTT TCTTGTCCGG TGACCG
chimpanzee      TTCCTCATTT TCTTACTCAG TGACCG
gorilla         TTCCTTATTC TTTCGCCTAG TGATTA

I've marked with a plus sign all those sites at which gibbon and
orangutan match each other, and the three African apes (including
humans) have a different base but match each other. These sites all
support a relationship among the African apes, exclusive of gibbon and
orangutan. You will note there are quite a lot of them, 24 to be exact.
The sites I have marked with numbers from 1-6 contradict this
relationship. (Sites without numbers don't have anything to say about
this particular question.) We expect a certain amount of this because
sometimes the same mutation will happen twice in different lineages; we
call that homoplasy. However you will note that there are fewer of these
sites, only 22 of them, and more importantly they contradict each other.
Each number stands for a different hypothesis of relationships; for
example, number one is for sites that support a relationship betwen
gibbons and gorillas, and number two is for sites that support a
relationship between orangutans and gorillas (all exclusive of the
rest). One and two can't be true at the same time. So we have to
consider each competing hypothesis separately. If you do that it comes
out this way:

hypothesis            sites supporting
African apes (+)      24
gibbon+gorilla (1)     6
orangutan+gorilla (2)  4
gibbon+human (3)       4
gibbon+chimp (4)       3
orangutan+human (5)    2
orangutan+chimp (6)    2

I think we can see that the African ape hypothesis is way out front, and
the others can be attributed to random homoplasy. This result would be
very difficult to explain by chance.

Let's try a statistical test just to be sure. Let's suppose, as our null
hypothesis, that the sequences are randomized with respect to phylogeny
(perhaps because there is no phylogeny) and that apparent support for
African apes is merely a chance fluctuation. And let's try a chi-square
test. Here it is:

These are all the possible hypotheses of relationship, and the observed
number of sites supporting them. Expected values would be equal, or the
sum/7. There are 6 degrees of freedom, and the sum of squares is 57.8.
P, or the probability of this amount of asymmetry in the distribution
arising by chance, is very low. When I tried it in Excel, I got
P=1.25*10^-10, or 0.000000000125. Might as well call that zero, I think.

hypothesis            obs.   exp.
African apes (+)      24     6.43
gibbon+gorilla (1)     6     6.43
orangutan+gorilla (2)  4     6.43
gibbon+human (3)       4     6.43
gibbon+chimp (4)       3     6.43
orangutan+human (5)    2     6.43
orangutan+chimp (6)    2     6.43
sum                   45    45

The difference is significant. Now the question is how you account for
it. I account for it by supposing that the null hypothesis is just plain
wrong, and that there is a phylogeny, and that the phylogeny involves
the African apes, including Homo, being related by a common ancestor
more recent than their common ancestor with orangutans or gibbons. How
about you?

By itself, this is pretty good evidence for the African ape connection.
But if I did this little exercise with any other gene I would get the
same result too. (If you don't believe me I would be glad to do that.)
Why? I say it's because all the genes evolved on the same tree, the true
tree of evolutionary relationships. That's the multiple nested hierarchy
for you.

So what's your alternative explanation for all this? You say...what?
It's because of a necessary similarity between similar organisms? But
out of these 76 sites with informative differences, only 18 involve
differences that change the amino acid composition of the protein; the
rest can have no effect on phenotype. Further, many of those amino acid
changes are to similar amino acids that have no real effect on protein
function. In fact, ND4 and ND5 do exactly the same thing in all
organisms. These nested similarities have nothing to do with function,
so similar design is not a credible explanation.

God did it that way because he felt like it? Fine, but this explains any
possible result. It's not science. We have to ask why god just happened
to feel like doing it in a way that matches the unique expectations of
common descent.

It is not always a matter of "common design".

Good, because any designer should be shot for the shoddy job.

It can also be a matter
of "common material" and "common parts" doing various jobs depending
on the part's location and dependencies within the common design.

There is no design.

Also. Please note. You had to say " I account for it by supposing"

Which is what? What exactly is "supposing"? Supposing is INFERRING
FROM THE DATA. Which is what i have noted here and in many other
threads.

infer
n verb (infers, inferring, inferred) deduce from evidence and
reasoning rather than from explicit statements.

DERIVATIVES
inferable (also inferrable) adjective

ORIGIN
C15 (in the sense 'bring about, inflict'): from Latin inferre
'bring in, bring about'.

USAGE
Do not confuse the words infer and imply. They can describe
the same situation, but from different points of view. If a speaker or
writer implies something, as in he implied that the General was a
traitor, it means that the person is suggesting something though not
saying it directly. If you infer something from what has been said, as
in we inferred from his words that the General was a traitor, this
means that you come to the conclusion that this is what they really
mean.

So, yes, Mudbrain, We do deduce things from the evidence.

deduce
n verb
1 arrive at (a fact or a conclusion) by reasoning.
2 archaic trace the course or derivation of.

DERIVATIVES
deducible adjective

ORIGIN
Middle English: from Latin deducere, from de- 'down' + ducere
'lead'.

Not the brightest of people are you Mudbrain?

And what happens when we infer from data? The data COULD BE INACCURATE
based on the fact that man himself is notoriously inaccurate.

Rubbish.

Why is man inaccurate? Because man does not even have the same level
of perception of a common house pet. THATS why.

Rubbish.

I applaud your scientific efforts. But as long as there is more then a
single interpretation of the data, you have to "suppose and infer" the
evidence for evolution in order for it to be relevant to mankind's
origins.

Do you have an alternative scientific theory?

No. Of course not.

Through all of this you still have not shown where man's common
ancestor is? What physical evidence is there for the ancestral
connection that does NOT have more then one explanation?

The fossil record, genetics etc.

Because as it stands now, All you have offered is your interpretation
of data. Which could have more then one interpretation.

If you have another one then present it.

it really IS that simple JH

The only simple thing is your mind.



Madman (aka Mudbrain) is on record as claiming:-

Science causes disease.

That 3.5% actually means 25%...

That the actor Paul Newman was a creationist...

That "Dr." Kent Hovind has made lots of *scientific* discoveries...

That wars have been fought because some scientific finding discredited
some facet of some religion...

To have a "higher education" than most posters to this news group...

To understand how geologists determine the age of any given sample of
rock...

That trilobites were Cambrian mammals... [that one still makes me
laugh]

And that he has "created genes" and not evolved ape genes...

That linguists have traced all the world's languages to the Middle
East region and back to around the same time as the bible claims Noah
and his sons rebuilt mankind.

Claimed that talk.origin's moderator was a troll.

Claimed cigarettes do not cause cancer.


Now, I ask you, is this the sort of guy you would give an credence to?
Certainly I don't.

--
Bob.

.

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