Re: Sexes

NashtOn wrote:
Marc wrote:
NashtOn wrote:

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

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/

Yes, it is.
How you interpret it is another story.


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

Sure it is.


So what is you spin on the PLoS-Biology paper then?

Now _is_ the time to explain what is wrong in their use of the
HapMap data in that study.



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.)

The direct observation I'm talking about is a full sequence of fossils
that tell of an organism's ever increasing complexity.I've been through
this before, so have many others.


This comes down to hairsplitting of the "cup half full or empty" level.
How many fossils must be found? Are you really so arrogant that
you will insist on all of them being found? How will you know?

When any fossils were found at all it should have been a wake up
call that things were not as they had seemed to our ancestors.


Is there some rule you know of which states that organisms must
become ever more complex? Why then do we have just slightly
more genes than a dog, and far fewer than many plants? There
is an answer to this I've mentioned in other threads, and I hope
to write a proper manuscript on this for peer review, but here and
now I'll let you be the theorist.


Of course, what would be even more useful is the kind of data derived
from observing C react with O2 in order to obtain CO2. IOW,were is the
data derived from a species incremental increase in complexity (I mean
to the complexity of Humans-please, don't play epistemology with me, you
know what I mean).

Actually, from what I can tell you are saying here that your knowledge
is somewhat limited - is that what the epistemology comment is about?
What is it that is complex in the human but not in other species?
Surely
not the genome. Just because we have speech and tool use, do you
consider that we are no longer animal in nature, is that it? The gene
regulation of our genome may differ us from chimps, but is that some
form of increase in complexity? No rule exists which says it has to
be.


Have we observed Species A morph into species B.Does species B have a
more complex CNS? *That's* the kind of data I want.

Why is there a blood-brain barrier in some species and not in others?

Over the course of vertebrate immune and CNS co-evolution, the need
for a dilute medium in the synaptic juntions to assist with effective
neurotransmission and the need for high levels of protein in the
plasma and interstitial fluid (complement, immunoglobulins etc.)
for effective immune defense, defined the selective forces which
have given rise to the physiological separation of the CNS


I'll cite this study by Joan Abbott (NJ Abbott) of King's College
University, London, as a reference on blood-brain barrier evolution.
"Dynamics of CNS barriers: evolution, differentiation, and modulation."
Cell Mol Neurobiol. 2005 Feb;25(1):5-23. Review. PMID: 15962506

And this study on early vertebrate genome duplication and the
evolution of key CNS neurotransmitter receptors, by M.G. Darlison,
I. Pahal and C. Thode of Nottingham Trent University
"Consequences of the evolution of the GABA(A) receptor gene family."
Cell Mol Neurobiol. 2005 Jun;25(3-4):607-24. Review. PMID: 16075381

This study by Yin et al. from the Lerner Research Institute, Cleveland
"Evolution of a neuroprotective function of central nervous system
myelin."
J Cell Biol. 2006 Jan 30;172(3):469-78. PMID: 16449196

and this, by A.J. Poustka and others of the Max Planck Institute for
Molecular Genetics in Berlin, "On the origin of the chordate central
nervous system: expression of onecut in the sea urchin embryo."
Evol Dev. 2004 Jul-Aug;6(4):227-36. PMID: 15230963

along with this review by Ian A. Meinertzhagen, Patrick Lemaire and
Yasushi Okamura of the Marine Biological Lab, Woods Hole, Mass.
"The neurobiology of the ascidian tadpole larva: recent developments
in an ancient chordate. Annu Rev Neurosci. 2004;27:453-85.
PMID: 15217340 set a firm background for the evolution of the
Central Nervous System in higher vertebrates. This review seems
very interesting and I will be downloading the full paper from my
work ISP (Sydney Uni) tomorrow. (Do you want a copy by e-mail?)

Note that while these articles are all "pay per view" or restricted,
the abstracts are all available via PubMed (www.pubmed.gov)
and I have included the PubMed ID numbers (PMID) for each so
you can go directly to the article by pasting that number in your
search. (You can even paste pmid: xxxxx into google to get them.)



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?

Why is this relevant? Science is as closed to the layman as it is to
scientists themselves because each of them is a layman outside his/her
narrow specialty. An individual who educates himself needs not the
academic credentials you were hoping for in order to somehow validate my
opinion.

To answer the second part of your coment here first, may I ask...
Have you read the PLoS-Biology paper by Voight et al. yet?
(You can show here how you are able to educate yourself.) Since
you don't seem to have the academic background (or degree) and
you won't look at a recommended citation, you would seem to
be invalidating your own basis for commenting. Enough said.

Most scientists have at least the core areas of chemistry, organic
chemistry, biochemistry and molecular biology covered (at least
most scientists in biological fields - the fact the engineers speak
out on evolution without those background classes is just a joke).

On the issue of "narrow speciality", again you are speaking through
you hat. Many scientists are specialists in two areas! <grin> In fact,
many scientists work on a number of different fronts in their labs
and through their careers. Ones who are teaching at university (and
also high school teachers) have to have a broad outlook. When you
take a field like mine, it covers all bases. Autoimmune diseases are
able to target many different organs, and the immune system has a
role to play in every region of the body (even in areas where it has
no general role to play). I have followed the literature on many fronts
and while I read about both T-cells and B-cells in terms of both the
autoimmune diseases and evolution of the immune respones, I also
have been interested in the MHC, chemokine receptors, virus and
host interaction (and evolution) and other general questions about
molecular biology, genomics, evolution and genetics. While there
are areas such as cancer biology I am less well read in, these areas
also come under the heading of Immunology in that tumours must
evade the immune system so my knowledge in the cancer areas
tend to be from the aspect of the "altered self" aspect of immune
surveillance. So, your "narrow field" comment does not widely
apply, in my view, OK?



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.)

Where is the observational data for evolution? Can you show me a time
lapsed motion picture of an organism morphing from on species into another?

Now everyone in this newsgroup knows that you are just being real
stupid with this question, but - FOR THE LURKERS - I will give you
a moment or two of thought here.

Now having though about this for a couple of hours.. , er, moments,
I wonder if you will ever start to understand the difference between
individuals and populations. An increase in genetic complexity can
come about easily in population terms whereas it is impossible
to see in terms of individuals. Three or four sets of genes can each
be undergoing a set of changes, each in it's own family tree as the
generations progress. Other sets of genes come into the family tree
with each generation, but only the offspring with the family tree can
have the specific combination of traits that a gene has collected in
the one family. Quite a number (many dozens) of generations later,
these three or four sets of genes can become interactive within just
one particular family tree and the offspring there might then have
some selective advantage that shifts their decendents away from
the previous gene pool's limits. The effect of the earlier generations
is lost as it was only in the downstream generation that the
combination became greater than the sum of the parts. But now
that a gene pool has had it's haplotype frequency altered, the
question of a species shift can be addressed. But you cannot see
that this took place in the individuals, can you? (Not until the end
result - and that may actuall be spread out over a number of
generations where the individual gene effects enter the one line.)


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?

Irrelevant. Where is the analogous direct observation for "evolution?"

First, it isn't irrelevant. Second, you have agreed about that data
from gels _is_ observational data - and agreed more than once.

A species of yeast was found to be different from another due
to the order of the genes in their genome. When the gene order
was engineered into the same pattern, the barrier to reproduction
was removed. We are learning about these things and while
the age of genomics has just begun, the questions of how the
different areas of the chromosome have shifted to and from are
being answered. In these studies will lie many of the answers to
how species have shifted from one ancestor into the different
downstream species.

Can you tell me what the endogenous retroviral elements in the
primate genomes are and where they came from? You do know,
of course, that for these to become a part of the primate genome
they had to have infected an individual and then the cells that
produced the sperm or egg in that individual to become a part
of the germline in the offspring, don't you? Apart from this sort
of direct observation, the thing you need to look at is the gene
pool of the population, not the gene flow from one individual to
another. While such viral patterns do mark the gene flow, it is
the pool of genes - and the shift between to such subpools - that
makes evolution happen on a species level. (You seem to have
been told this quite a lot, but are you ever really thinking about
it at all? One line retorts are sometimes funny, but it that is
all you are able to show for your self-educated broad science
background it is quite a shame.)


If you could somehow become aware that the gene pool is
the arena of evolution, you might understand how the game
is played.



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.)

Yes and I fail to see how this is relevant to the ToE.
You are merely describing a technique to visualize structures/molecules.


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?

No, because we have the direct result of repeatable experimentation
before our eyes.


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.

It is, but it's just that. Are you saying that this proves
macroevolution and increased complexity?




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!)

Junk probably because it doesn't fit into our narrow view of biology.

Your narrow view. "Junk" tells it's own story to those who can listen.

Have you taken the time to read the Voight paper yet?


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?

Anything you can observe over and over again is valuable and can be used
in science.

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

So when we observe genomes over and over again and see where the
changes are between species, it will tell us how evolution came about,
don't you think?

(signed) marc

..

.