Re: Sexes


NashtOn wrote:
Marc wrote:
NashtOn wrote:

........... SNiP

The HGP is wonderful, but it has nothing to do with evolution. It's all
speculation and this is how it should be taught in schools.


Tell me, have you ever _looked_ at the genome?

Try using the UCSC Genome browser and comparing
the human, chimp, mouse and pufferfish genomes with
each other (it does this quite easily for you).

http://genome.ucsc.edu/

Or you can use any of several other resources that provide
similar resolution of the data - NCBI or Ensembl for example.

Pick a region of the human genome - somewhere in one of
the arms of a chromosome, such that several dozen genes are
available in your Genome Browser view - click on a few of them
to see the features and resources for that random gene. Learn
a bit about those resources, too. OMIM, PubMed, GeneCard links,
expression array data, protein domain data and - best of all for
our discussion here - hits for homologous genes in other species.

Right there - on your screen - for you to study - with links to
the resources as Ensembl or whatever, the results of evolution
are there to examine. I mean, hey - if I can get these on my
PC then you can too. Now, if you don't want to think that
they are a result of evolution, than that's OK - but don't keep
your head in the sand. Look at a few different genes each day
and compare those genes in a few species that are either close
to each other or quite distant.

Bring some examples here for discussion, or just come into
the threads here to ask about how to use the genome browser
features one way or another. Your one-line retorts have gone
on long enough and so it's time for you to do some actual work
on showing where the problems are - I've suggested a paper
which I'm still not sure you have looked at. Now here I am
suggesting a tool you can use to show us parts of the genome
that you may feel are examples of what you want to show us.

(signed) marc


What I want to show you marc, has nothing to do with how evolutionists
interpret genomes under the light of your postulate. Science is about
direct observation, not only inference from genomes from various species.


So, the complete genome sequence of 356 species is not data that
can be subjected to direct observation? http://www.genomesonline.org/

And then, of course, the haplotype variation within the genome of
a species likewise is not observable data? http://www.hapmap.org/

What do I have to do then, pin some poor creature to a dissecting
board and slice away at it? Is _that_ the sort of observation you
insist that science must obtain? (It's kind of funny.... I am not able
to draw a picture to save my life, like of a cat or a horse, but in
doing postgrad marine invertebrate zoology at Stanford's Hopkins
Marine Station I found I could make drawings in my lab book of
sponge spicules or of muscle tissues from some creature that were
quite good representations of what I was seeing in the microscope.)

Could you please tell me what level of course in science you have
taken that you are so sure where the line of observation is drawn?

I would hope that a M.Sc. in the History and Philosophy of Science
would be your starting point - a few undergrad classes are not quite
enough here to let you make such expert comment, wouldn't you
agree? Even if you are a "hard" science major who has completed
your B.Sc. you might still be shy of what it takes to say what science
is and isn't. I'm sure you mean well, but - really - are you qualified
to make that statement? (I do have to wonder.)

What _is_ observation? (In science...)

I can't see a peptide by eye, but I have done (many) thousands of
"gels" - various forms of gel electrophoresis, such as the original
type of two-dimensional gel O'Farrell developed in the 1970's, to
look at peptides such as the mouse and human MHC genes. Those
assays took a week to do and four weeks or so for the [35]-S isotope
to expose the x-ray film, which gave a pattern the post-docs would
then go drool over and try to get published in J. Exp. Med. or they
would just send me back to run another few dozen gels. (Some of
those papers do have my name in the acknowledgements at the back.)
So... is _that stuff_ observational data? Where a mouse has had to
die to raise antibodies, and other mice have had to die to produce the
pure monoclonal antibody, and virus transformed cells have been used
to produce enough radio-labelled peptide to run the gels? (As a control
of course, fresh blood cells would be used in case the cell lines were
causing some shift in the peptide patterns.)

If "gels" of many types are not observational data, what is?

After the "PCR revolution" in modern biomedical research, lots
of assays were done by "genotyping" an individual for some marker
or another. The aspect of PCR that "errors" can be caused does
not matter in genotyping - only when the PCR products are used
to produce something that is then cloned into a vector and used for
futher work (like sequencing). Out and out genotyping is an end in
itself and just produces a simple data point - you have one form of
a genetic marker, you have the other form or you have both. Of
course, the data is visualized through running the products on an
electrophoretic gel - or were, now they are zapped with a laser in
a different type of gel-like setup. But, it's still genotype data.

Is "genotyping" (by PCR or by any other biochemical assay) an
"observational" form of data? (Again, you _must_ say "Yes" or
all hope is lost in discussing any aspect of evolution with you.)

We could try to do cross-breeding assays, like Mendel did, and
of course his observations and progeny counts are the basis of
genetics - but what about doing such in corn? That drove a lot
of good scientists nuts. Observation of cross-breeding must
then be on your "bad science" list, mustn't it?

So - please tell me if detecting polymorphisms by electrophoresis
is an acceptable part of observational science or not. I'll await
your reply and then make the next few comments I would like you
to consider when I know where we are at with this post.


There is still plenty we do not know, such as the role of so-called junk
genes, chirality, sex and the role of genes in morphogenesis.

I assume you mean "junk DNA" because if it was a gene, it wouldn't
be junk now, would it. (Watch out for long distance regulation!)

Did you know that those pesky HERV elements are really quite
good markers for some aspects of primate evolution? (I'll save
this for another time... but what about simple microsatellites?)

Yes... in the "junk", and sometimes in the genes, there are
little repeats of DNA (like a two, three or four base pattern that
repeats from several to several dozen times), and these are found
to differ quite a lot in the number of repeats between individuals.

Are microsatellite repeat polymorphisms "observational" science?

The answers to these questions are not to be found only by direct
comparison between genomes.

Hummm... answer my questions about observation above while
I crash out for the night and I'll see if I can comment clearly on
this last bit after my second or third cup of tea when I wake up.

(signed) marc

Oh... do have a look at the human genome evolution paper, OK?

Whoops... this was just below the bottom of the window.....

What I want to see is "evolution" being taught with all its
shortcomings, warts and its controversies and *then* let students make
up their minds, especially under the light of the fact that this
particular sphere of biology cannot be considered hard science, because
of the lack of direct observation and experimental data that confirms
that macro-evolution and increased complexity actually occur in nature.


The high school text books have quite enough for students to learn
without getting into really big arguments about what are essentially
really small issues... remember for one that "text books" are about
three to five years out of date when they are first in use. Also, until
you have gone through at least two or three years of college level
chemistry and then a good biochemistry class you are in NO WAY
in a position to think about some of the hair-splitting that you seem
to want to introduce into high school classrooms. It's not fair. Not
fair to the teachers, to the students, to their parents or to the next
level of teachers they will get - their university lecturers.

Now, good night. I'll deal with your reply in the morning.

..

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