Re: Propping up the theory of Evolution

On Jul 3, 1:23 am, rick_so...@xxxxxxxxxxx wrote:
So we have a common ancestor, and so now billions of generations
later, here we are. In one person, we will say, by some fluke of
nature they develop an improvement to the genome, through natural
selection after a strand of DNA is hit by a cosmic ray.
Now then they develop a very good horn on the top of their head and
doctors don't remove it, and if that person person has offspring it
will develop that horn because it ends up creating a dominant gene for
this marvelous horn and it looks nice. So then how does that person
now become the common ancestor so that 2 million years from now
everyone will have that horn?

Sex. You have probably heard of it.

Yes I see horny people, but no people with horns.
Although, there are probably some deformed horned people out there.

And yes, scientists have modified crops, but haven't they just spliced
DNA and used existing DNA?

Which, of course, is exactly what happens in evolution. No magical
poofing of new DNA already coding something. Mutational duplication
of pre-existing DNA coding something that can then be modifed in a few
steps to perform a slightly different function.

Has anyone created any new code?

Yes, if you mean DNA sequences that do not occur in nature. No if you
mean DNA sequences that cannot even in principle occur in nature.

Or are
they merely using function calls, like a toolset?

Yes. Evolution uses DNA like a tool set which can be modified to
perform somewhat different functions. Some of this occurs by
duplication of a 'tool' and modifying the 'working end' so that it
matches a slightly different object. This is called 'duplication and
divergence' or 'internal duplication' depending on the exact mechanism
that occurs. Sometimes polyploidy is at work -- that is a duplication
of the entire genome followed by loss-of-function for most duplicates
and modification for some. Some of it involves the equivalent of
changing the head on a socket wrench with a piece that fits a new
object while the wrench part stays the same. This is called 'chimeric
duplication' or 'translocation' or 'inversion' or 'insertion'
depending on which exact mechanism produced the new 'tool'.

Is anyone, or is nature, writing any new functions?

Depends what you call "new". Evolution is descent with modification,
not magical poofing of stuff out of some ether.

I don't think we see very much variety in design, although we see lots
of variation within design parameters.

How do you know what the "design parameters" are? What is *actually*
observed is variation within species. Between closely related species
one sees minor differences (as minor as a different mating song or
different timing of mating, which are closely related to the
reproductive isolation that determine 'species'). As you get more
distant relationships, the common features drop off bit by bit and you
observe more differences.

Just because people speak of intelligent design, does not mean they
are talking about instantaneous spontaneous creation.

That is right. Intelligent design is "big tent". It can encompass
multiple contradictory ideas because it has no testable content.

There are people who talk about intelligent design in the same way
people attribute it to nature. That you need to write code to get
something to work.

The difference being nature has no mind, and so how could it see
anything, at all, beyond, what molecular processes see, which is
positive charge, negative charge, covalent bonding, simple opportunism
such as a heavy hydrogen atom can fit into a hydrogen slot, simple
molecules can come together to create complex molecules, how do you
get from that, to an eye that works and has 30 centers in the brain
related to sight?

Because organisms reproduce their genetic code. And environments
preferentially discriminate between those genetic codes that reproduce
better in that specific environment and those that reproduce more
poorly. *When* the environment makes the expense of having vision
preferable to not having it wrt the reproductive success of the
organism, then any changes that favors vision would be selected for
(at base, vision is simply the absorption of light by a molecule that
changes shape when it absorbs that energy, everything else is chemical
reaction transferring the information of that changed shape --
incidentally, the chemical process beyond the first couple of
molecular steps differs in vertebrates and mollusks).

One piece at a time? One accident at a time? One random chance at a
time? If there are a billion ways to do something wrong and one way to
do something right, then it makes sense that the enzymes want to
replicate DNA exactly with as little variation as possible, which
reduces dramatically, you r chances of variety from which to choose
from.

Mutation rates are a balancing act between the cost (in speed and
resources) between replicating DNA with as little variation as
possible and the value (in fewer deleterious variants) in perfect
copying of a gene. Like any mass-production project the cost of the
next x% toward perfection can be higher than the value of gaining it.
Who will pay for the perfect $2,000,000 mass-production car?

So then, you have to wait for a mistake to get through the safeguards,
then you have to hope, that it will lead to some useful function, like
flagellar motility, when all the requisite pieces come together.

The *function* of rotary motility can arise by linking together two
*pre-existing* useful systems already present in cells. The number of
mutational steps to do this can amount to the formation of a single
chimeric protein in one mutational step, since a single chimeric
protein (one end interacts with one subsystem (a rotatable pore with a
whip); the other interacts with the motor subsytem) is present in both
the eubacterial and the simpler (and independently generated) archaean
rotary flagella. There is experimental evidence for the
reasonableness of this claim in a model system of eubacteria in which
flagellar activity is restored by chimera protein formation that is
*different* from the original linkage.

Never
knowing what that useful function might be.

The usefulness of a function (by the only measure that counts --
relative reproductive success) is determined, rather ruthlessly, by
the environment.

And so then you would expect lots of these little proto functions
around that might end up as being useful, which are not presently
killing the person.
Yet, again what we see, is that if you have a genetic defect, chances
are you will not survive without constant care.

Not all genetic changes are "defects". Some are merely genetic
"differences". Do you consider blue eyes a "defect"? Blond hair a
"defect". Do you consider a short person as having no reason to
live? A tall person to be a freak? There is a range of *genetic*
*heritable* variation in size (as well as size being influenced by
environment -- e.g., Japanese in the U.S. are taller than in Japan,
but the tallest U.S. Japanese typically have parents that were tall
for Japanese in old Japan).

So the system is not tolerant of half baked ideas, it needs full on
fully functional ideas, that work together with the entire system, and
don't cause a bug somewhere else in the code.

Actually, the system (living organism) quite often *is* quite tolerant
of half-baked ideas (especially in recessive and quantitative traits).

Or else the person will
die. So to me that doesn't leave room for lots of trial and error when
all the data we have regarding genetic abnormalities, is that they are
detrimental to the organism.

The reason that we call some *differences* "abnormalities" is
*because* those particular differences are detrimental. You are
mistaken if you think that all *differences* are *abnormalities*.
Abnormalities are a *subset* of genetic differences, not the universe
of all genetic differences.

Yet somehow, in one fell swoop, we went from ape to man?

Nope. Ancient H. sapiens are not identical to modern H. sapiens.
And, in cladistic terms, we *are* apes. There is a whole series of
more recent branchings in the hominid lineage. Chimpanzees are our
closest *living* relatives. Whether or not they reach a level of
species, neandertals are our closest relatives, living or extinct.
Before that, it likely was some branch population of H. erectus.
There is a chain of intermediates between the common ancestor of the
three still living species (two chimp species and humans) and humans.
Fossil data is largely missing on the chimp side because they lived
(and still live) in areas that were poor for fossil formation.

The amount of genomic difference between chimps and humans is about
what one would expect *if* the entire difference were due to fixation
of selectively neutral traits (in the 97% of our genomes that is
relatively sequence-irrelevant). Actually, the amount of difference
is a little less than that expectation. That is because of
selection. Most selection is selection *against* change. The number
of sites that differ between chimp and human that can be clearly
identified as having a selective pressure *for* change can be numbered
to be in the range of 50 or so sites (none a protein coding region).


.

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