EVOLUTION: was Re: Salt

September 6, 2006

I was merely cutting and pasting from the dictionary. If it is

irrelevant..lol.....I'm not the one to confront with that. And as far as

" massive scientific evidence " why is it still called a " theory? "

Re: EVOLUTION: was Re: Salt

,

> 1.. Change in the genetic composition of a population during

>successive generations, as a result of natural selection acting on the

>genetic variation among individuals, and resulting in the development of

>new species.

I'm not sure why you posted that very long list of largely irrelevant

definitions, but as you can see from the above definition, it is

populations, not species, that evolve. That is why it explicitly

notes the development of a new species, but says nothing about the

cessation of the original species.

> Gene, in answer to your question as to whether or not I think that

>discounts evolution, absolutely not. However, I too search for the truth in

>everything. One thing that I find interesting is that Darwin was a " self

>taught " geologist. And I am probably far less an expert in evolution as

>you are, but isn't geology the study of rocks and of the earth's crust and

>such?

The theory of evoultion in its current state does not rest on Darwin's

findings (though they are still illustrative and supportive), and no

theory in any science whatsoever depends on the background of its

advocates and certainly not of a mere one of its advocates.

> Darwin was a confessed Agnostic, he wasn't sure either way

>whether God existed or not.

What does his faith have to do with yours, mine, or anyone else's?

> One of the arguments for Darwin was that

>he " had to be sure of his theory, otherwise why would he have suffered

>the persecution of the religious world? "

I have never heard anyone argue for Darwin; I'm not even sure what it

would mean to " argue for Darwin. " Likewise I would immediately

dismiss anyone who argued for *evolution* on the basis of Darwin's

willingness to endure any type of persecution, and if that was the

only argument for evolution I would certainly dismiss the theory off

the bat. Likewise, even if a good many of its proponents suggested

that such an argument was evidence for evolution, I would be highly

skeptical of the theory on the basis that most of its advocates were

obvious kooks.

Since that is not the case, I believe evolution takes place based on

the massive scientific evidence and the absolute self-evidence of

evolution that stares back at you when you look at how the inside of a

cell is ordered.

> And in using that question, I

>have to say why would men for over the last 2000 years give their lives for

>something they believed in, if they too weren't sure?

This likewise does not prove that the faith they died for was true.

Nevertheless, there is nothing mutually exclusive about evolution and

Christianity, which is why millions of Christians believe in

evolution.

Chris

--

The Truth About Cholesterol

Find Out What Your Doctor Isn't Telling You:

http://www.cholesterol-and-health.com

September 6, 2006

On 9/6/06, <bible770@...> wrote:

>

> honestly, I've never met a Christian who believed in evolution. When someone

comes

> and says that the bibles says such and such, I always ask for chapter and

verse. I'm

> asking you where you get your information from on the Christians viewpoint on

evolution,

> as far as believing in it.

> Sorry

>

As an example, I had two professors in college who taught aspects of

evolution (one anthropologist and one geologist) and both were

Christians. Neither saw any difficulty in reconciling the two. And

these were people who had actually studied both the science and the

religion, not just people having knee-jerk reactions.

There doesn't have to be any conflict. What conflict exists is

artificial and the result of ignorance or obduracy on one side or the

other.

September 6, 2006

On 9/6/06, <bible770@...> wrote:

>

> I was merely cutting and pasting from the dictionary. If it is

irrelevant..lol.....I'm not the

> one to confront with that. And as far as " massive scientific evidence " why is

it still called

> a " theory? "

>

Is that really going to be the extent of the argument? That it's

called a theory? If anyone actually has something to say then maybe

this discussion is worthwhile, but otherwise why not just end it?

has tried repeatedly to have an actual conversation and has been

met with a brick wall of repetition, rants about communists and

meaningless quipped retorts. How utterly boring.

September 6, 2006

On 9/6/06, Masterjohn <chrismasterjohn@...> wrote:

> On 9/6/06, Brown <brobab@...> wrote:

> > The

> > foundation of the evolutionary model is the geologic column,

>

> This statement is absolutely absurd. Given the limitations of each

> area of science, we would expect the absolute worst evidence for

Name the specific gene sequences additionally created. And prove that

any such changes are beneficial and necessary for the survival of the

species.

> evolution to come from paleontology. Unsurprisingly, paleontology is

> not the leading line of evidence used by evolutionists to argue for

> evolution. Again, unsurprisingly, your argument rests well over 90

> percent on paleontology.

This is not the case. My biological arguments and paleontological

arguments stand separately, neither one depends on the other for

support, evolutionists routinely refer to the geologic column to find

support that the minute variations are part of the grand principle of

evolution.

>

> >but it an

> > elaborate and massive construct.

>

> I remain agnostic towards your interpretation of the paleontological

> evidence because I don't know enough about it. You clearly know much

> more about paleontology than you know about molecular biology, so I

> don't take your thorough misrepresentation of the latter to

> necessarily reflect on your representation of the former, but it gives

> me pause before attributing any credibility to your paleontological

> assessment.

>

> > Neither the fossil record nor real

> > time obsevation and experimentation supports the elaborate construct.

> > It is easy to see how evolutionary scientists have faith that the

> > variations obseved in nature are manifistations of evolution displayed

> > in classic text books, but the geologic column is a construct rife

> > with massive omissions, massive reversals, circular and unvarifiable

> > dating, the " universal principle of evolution " evaporates like a puff

> > of mist.

>

> If the dating is as unreliable as you claim, then there is no evidence

> *against* evolution from these datings either. Since paleontology is

> not the primary argument for evolution and never has been, this does

> not give any reasonable person rational license to ignore the piles

> and piles of evidence accumulated from other fields.

Numerous evolutionists take one side or the other and use one side to

prove the other.

Evolutionist biologists repeatedly use paleontology as GIGANTIC

framework for interpreting the MINUTE variations observed in real time

organisms.

> I have repeatedly refuted numerous assertions of yours about what we

> observe in real time, and you repeatedly have ignored them.

This is merely microevolution, not the grand scale macroevolution.

>

> As an example, you stated unequivocally that when different species

> interbreed, their offspring are sterile or reduced in either viability

> or fitness. I gave you two examples directly refuting that -- the

> hybrids between Townsend warblers and hermit warblers, and the hybrids

> between tiger salamanders and axolotl salamanders. The first you

> ignored with no mention. The second you engaged after I repeated it

> three times, repeatedly noting your failure to engage it, but in doing

> so, you argued that it was not an example of a mechanism of

> macroevolution, but never admitted to the obvious fact that it was a

> direct refutation about the viability of hybrid species.

Hybrid species simply demonstrate that they are of the same kind, not

that one kind was derived from another. This is irrelevant to the

grand macrobiotic hypothesis. These are minute variations and

recombination's, not great leaps of genetic changes. Crabs are crabs.

Salamanders are salamanders. Proves nothing else.

>

> As a second example, you have repeatedly stated that " no new genetic

> material " arises except adverse changes due to radiation or other

> types of cellular damage, and that these " random, " as you erroneously

> call them, changes are incapable of generating " new genetic material. "

> I have listed numerous other mechanisms by which new genetic material

> is incorporated into the genome, and you have flat-out ignored all of

> them.

Give the gene sequences that have been generated and the specific code

affected. You must prove that the gene sequences were not

pre-existing that were newly generated. Then you must prove that over

successive generations, that code is not only beneficial for the

survival of the new species but also viable enough to be spread into

the gene pool. If you can catalog these new changes specifically,

then we have somewhere to go. Otherwise there is no evidence of

macroevolution on a grand scale.

>

> Your idea that macroevolution requires " new genetic material must be

> introduced into offspring that was not in the ancestor, not merely

> recombination of genes, but entirely new genetic material, " reaches

> the height of absurdity. The very basis of the entire theme of

> evolution is that forms of life do not appear suddenly ex nihilo, but

> evolve from pre-existing forms of life. This applies to organisms

> right down to genes.

This is not so because, new organs must be fully functional to be

beneficial to an organism. And the new code must not disrupt the rest

of the functions of the organism. If a new heart chamber develops,

for example, it must be connected to the properly to venal AND

arterial connections AND the nerves must be connected right AND the

valves must be in the right place AND it must not leak AND it must not

be too large AND it must not constrict the flow of blood AND the new

changes must not interfere with the functioning of other organs and

organ systems, etc. By the time the organism makes complex new gene

sequences, it will die do to waiting for the right combinations. This

goes for one organ and organ system after another. Organ systems are

very very complex and cannot stand a myriad of nonbenefical changes

while waiting for the right combination of simultaneous developments.

Observable beneficial variation that we do observe is minuscule to the

massive simultaneous random additions that would have to be required

to form wholly different organisms.

>

> If you look at proteins, what you see is the same types of homology

> and analogy that you see in macroscopic anatomical structures, and it

> is *abundantly* evident that genes and proteins are largely made by

> reconstructing the same parts of other genes and proteins. There are

> large superfamilies of proteins that involve the same basic protein

> unit, and thus the same basic genetic unit, simply repeated over and

> over again, arranged in different numbers per molecule or hinged

> together at different orientations, certain small parts of which may

> have degrees of variability where only several amino acids vary

> between the proteins yet these amino acids dramatically change their

> binding affinity.

But getting these proteins to work together requires a vast array of

complex code that would have to be disassembled and reassembled, to

produce wholly new organs and organ systems, there is no observed

mechanism for this. This would have to require entirely different

mechanism than what we observe.

>

> Now, you would expect, then, that the *primary* mechanism of

> evolutionary change would not be the " random " point mutations induced

> by radiation that the body tries to prevent and fix as much as

> possible -- although these are clearly a source of genetic variation

> -- but you would instead expect it to occur through a mechanism of

> domain shuffling. That is, taking large sections that code for

> self-stable functional units of proteins, and mixing them together in

> different ways.

>

> Sure enough, site-specific recombination does exactly that, and is

> directly observed. As a DNA-repair mechanism, double strand breaks

> are often repaired by taking the allele from the homologous but

> *other* chromosome with the *other* allele, and using this allele to

> copy the part that is missing from the first. Rarely are whole genes

> copied this way. Often, only parts of genes are copied this way.

> Thus, a *new* *different* gene is born. Not from randomly mutating

> things in ways that might not have any functional utility, but by

> taking one *part* of something that already has established functional

> utiltiy, and combining it with something else that has established

> functional utility.

>

> Although this process is most well-described and well-characterized in

> fungi, if you do a search for " HLA gene conversion " on PubMed you will

> see numerous reports of previously unidentified HLA genes in certain

Previously unidentified does not prove to be new, additional material

and the function of the new genes would have to be observed over

generations. Are these just redundant genes that are there as filler?

Do they have a distinct function? For macroevolution to occur, we

must not only have new distinct material, but also functional and

beneficial material that is dependent for the species survival and

continues for successive generations so that it continues and

increases the survivability of the new species, and the new species

must not be able to breed again with its ancestor.

> populations like island populations that appear to have been created

> through this process, and at the very least plausibly attributed to

> this process based on the fact that these *new* and *different* and

> *completely functional* genes are clearly a rearrangement of

> functional units taken from different genes and combined.

Much more than this is required for macroevolution to occur. And the

more complex the organism, the more complex will be the process of any

point addition to the genetic code, there are more things to go wrong.

>

> Nevertheless, you argue that 1) there is no mechanism for genetic

> transfer except random damage induced by radiation and

2) the simple

> lack of clarity and inconclusiveness of the fossil record refutes all

> other evidence for evolution, even though you yourself explicitly

> state that it is inconclusive and therefore can *not* be evidence

> against evolution.

As I stated each branch has its separate problems, but evolutionists

use one branch of evolutionary science to prove the other.

>

> Isn't it interesting that I say something new each time and you repeat

> yourself, regardless of what I say?

I really do not see anything significantly new in your successive

discussions. Whatever the mechanisms we observe in variation, they

must be interpreted through the observation of how those mechanisms

play out in the gene pools. Your continued explanations of various

genetic processes are not able to interpolate to change our

observations of what is happening amongst populations of organisms

throughout nature. What we see microscopically in the genes is

totally dependent on how they play out in the gene pools of real life

organism in nature. Apes are still apes and there is no evidence in

the genes that they have been anything else, but that they exhibit

limits to variation. Hybridization also exhibits limits to variation.

Bacteria are still bacteria. For all the gene swapping and variation

exhibited in bacteria, bacteria are still bacteria. I repeat this

because that is what nature repeats over and over and over as long as

we humans have been observing bacteria.

September 6, 2006

On 9/6/06, <bible770@...> wrote:

> honestly, I've never met a Christian who believed in evolution. When

>someone comes and says that the bibles says such and such, I always

>ask for chapter and verse. I'm asking you where you get your information

>from on the Christians viewpoint on evolution, as far as believing in it.

I don't see how I can cite a chapter or verse from the bible to show

that Christians believe in evolution. The Roman Catholic church's

official position, for example, is that evolution is supported by

science and not in conflict with the church's doctrine. I do not cite

this as evidence that evolution is consistent with the Bible, nor do I

deny that is consistent with the Bible; I'm merely pointing out that

the Roman Catholic church, which is by far the most numerous Christian

organization in the world, takes this stance, and thus most Roman

Catholics who are taught this stance by the instructors in their faith

also believe in the scientifically established concept of evolution.

I'm sure this information is readily available in numerous polls but

the Roman Catholic church's stance is in any case well known.

That you have never met such a Christian reflects your limited

exposure to the diversity of modes of thought that exist among

Christians and suggests that you are familiar only with a relatively

narrow type of Christianity that is, overall, not the norm, but exists

very strongly in specific pockets of the U.S.

I would suggest that you withold judgment on the issue of evolution

until you are familiar with what it actually is. As demonstrated in

the last few posts, you are unfamiliar with the concept, so how can

you decide so easily whether it is consistent or inconsistent with

your faith, or whether it is sensible or insensible, until you

understand its basic concepts?

Chris

--

The Truth About Cholesterol

Find Out What Your Doctor Isn't Telling You:

http://www.cholesterol-and-health.com

September 6, 2006

On 9/6/06, <bible770@...> wrote:

> Is dirt or clay inorganic?

Clay is as far as I know primarily composed of silica and alumina,

which are inorganic. This is interesting as Becker proposed

that life evolved from semi-conducting rocks and actually proposed a

very intriguing mechanism.

In any case, whether it is inorganic or organic with respect to carbon

is not very important compared to the fact that the Bible explicitly

states that man was drawn up from non-living matter rather than

created out of nothing. There is nothing about evolution in the

creation story per se, nor is there anything about the creation of

bacteria, archaea, protists or fungi. Thus, anyone who insists that

the absence of details from the creation story indicates that those

details did not actually happen as part of creation is taking the

completely and ridiculously unsupportable position that God did not

create bacteria, archaea, protists or fungi, which means either that

someone else created them, that they spontaneously generated of their

own volition, or that they do not exist.

Chris

--

The Truth About Cholesterol

Find Out What Your Doctor Isn't Telling You:

http://www.cholesterol-and-health.com

September 6, 2006

Hi ,

> I was merely cutting and pasting from the dictionary. If it is

>irrelevant..lol.....I'm not the one to confront with that.

Actually, you are the only person to confront about it, because

whoever put it in the dictionary did not do so with the specific

future event in mind that you would copy and paste all definitions

into a thread on biological evolution regardless of their pertinence.

And actually, the person or people who wrote those definitions made it

very easy for you by listing the two relevant definitions with a

header that read " Biology. "

Usually when people reference information, they reference only the

relevant part, and if they use a direct quote, they quote only the

*most* relevant point and point most useful to quote, and then they

add their own text to state their view of the relevance of that

reference to the discussion. This is not only standard practice but

also the most useful practice.

> And as far as " massive scientific evidence " why is it still called

>a " theory? "

The word " theory " does not connote the degree to which the theory is

substantiated. Thus, substantiation for a theory could be infinitely

massive, such that one would colloquially say it was " proven, " and it

would not be any less of a " theory " than when it originally had only

modest support.

Chris

--

The Truth About Cholesterol

Find Out What Your Doctor Isn't Telling You:

http://www.cholesterol-and-health.com

September 6, 2006

On 9/6/06, Brown <brobab@...> wrote:

> > This statement is absolutely absurd. Given the limitations of each

> > area of science, we would expect the absolute worst evidence for

> Name the specific gene sequences additionally created. And prove that

> any such changes are beneficial and necessary for the survival of the

> species.

Since you are quoting my statement on the limitations in the fossil

record here, I am not sure which gene or genes you are asking me to

catalogue.

> >Again, unsurprisingly, your argument rests well over 90

> >percent on paleontology.

> This is not the case. My biological arguments and paleontological

> arguments stand separately, neither one depends on the other for

> support,

I didn't say they depended upon each other. I said that your argument

rests mostly on paleontology, specifically your insistence that the

dating is inconclusive.

Your genetic arguments rest on the repeated erroneous statement that

no new genetic material is introduced into the genome; thus, it is

meritless because its premise is false.

> evolutionists routinely refer to the geologic column to find

> support that the minute variations are part of the grand principle of

> evolution.

From what I have seen, evolutionists do not trod out such arguments as

" fossil x is 500 million years old; thus, evolution occurs. " Rather,

the *relative* placement of fossils in the geological strata is used.

In support of this, reference 1 trailing this post describes how

numerous studies have shown that the placement of fossils within the

geological strata are statistically significantly correlated with the

expected placement of these species on the phylogenetic tree, that

such analyses yield an increased strength of correlation when a

greater number of fossils have accumulated, and that it is increased

over broader spans of strata compared to narrow spans. Because of the

inherent tendency toward error in the fossil record due to its

incompleteness, the correlations would be expected to strengthen over

larger spans.

When an evolutionist provides introductory evidence for the general

theory of biological evolution, that evidence does not, in my

experience, emphasize something like hominid paleontology, which is

difficult to interpret and takes place in a relatively narrow band of

strata. In the second quoted paragraph of reference 1 below, primates

were analyzed as a group. Their placement comapared to 24 similar

taxa of vertebrates was tested, yielding a high correlation between

the placement in geological strata and the placement of each of these

groups on a phylogenetic tree. I suspect that if they conducted a

similar study at the species level they would not get very good

results.

So, I perhaps misspoke in my last email by diminishing the use of

paleontology. I think I said more clearly and correctly in my first

email today that the relationships rather than the dating forms the

primary evidence from paleontology. In any case, another point I have

been trying to emphasize is that we have many other forms of evidence

in addition to paleontology.

> > If the dating is as unreliable as you claim, then there is no evidence

> > *against* evolution from these datings either. Since paleontology is

> > not the primary argument for evolution and never has been, this does

> > not give any reasonable person rational license to ignore the piles

> > and piles of evidence accumulated from other fields.

> Numerous evolutionists take one side or the other and use one side to

> prove the other.

Perhaps you could provide an example?

> Evolutionist biologists repeatedly use paleontology as GIGANTIC

> framework for interpreting the MINUTE variations observed in real time

> organisms.

I'm not really sure enough of what you mean to respond.

> > I have repeatedly refuted numerous assertions of yours about what we

> > observe in real time, and you repeatedly have ignored them.

> This is merely microevolution, not the grand scale macroevolution.

My refutation of your assertions is microevolution?

We cannot have a discussion if you bring each specific point back to

the same broad criteria of proving macroevolution. In order to carry

out an actual discussion, we must proceed point by point.

Let's recapitulate some of these points:

You have tautologically stated that we have not observed in real time

a process that takes place over geologic time. This is, of course, a

truism, albeit a meaningless one.

I, in turn, have pointed out that direct observation is not a

reasonable standard of evidence. If, for example, 12 people using

your standard of evidence were placed on a jury, murderers would walk

free everywhere. Yet this is not because our justice system uses a

loose standard of evidence. We DO in fact care if we put innocent

people in jail. Thus, we have due process that puts the burden of

proof on the prosecution rather than the defense. Nevertheless, we do

not hold the standard that the jury must directly observe the murder.

The reason is because the combination of independent lines of evidence

from different forms of forensic evidence that corroborate each other,

witness testimony -- not necessarily witnesses who directly witnessed

the murder -- and other forms of evidence are sufficient to themselves

constitute the demonstration of guilt beyond a *reasonable* doubt.

This is true despite the fact that the jury *never* witnesses the

murder first hand. And this is not a matter of scientific curiosity;

it is much more consequential, because we risk ruining an innocent man

or woman's life. Yet you raise the burden of evidence for an academic

matter to a standard vastly beyond the standard we use to put people

in prison for life or to put them to death! You use a burden of

evidence that, if we were to apply it to our justice system, would let

virtually every single murderer back on the streets.

So, I have offered that instead what we see is the mechanisms of

macroevolution operating. I have pointed out, for example, that

large-scale morphological changes and life mode changes can happen due

to a single allele, giving the axolotl salamander as an example. My

purpose was not to prove that the axolotl came from the tiger

salamander or that humans came from amoebas, but was much more

specific: to show that these major changes, which form the basis for

changes across large taxa, are not necessarily due to changes in a

large multiplicity of genes, but can be triggered by changes in even

one gene.

I have also pointed out that there are numerous mechanisms of

introducing new genetic material, such as mobile genetic elements of

various kinds, duplications, point-mutations, inversions,

site-specific recombination, and so on. I have further pointed out

that site-specific recombination provides a mechanism by which

functional groups are exchanged instead of mutations made at random

points that are likely to lead to non-functionality. This forms a

basis for a rather methodical change. For example, a domain that

might be a binding site for a specific protein or gene regulatory

element could be conferred upon a preexisting protein that would

confer upon it a new or expanded function.

You have repeatedly dismissed all of this on the basis that it is " not

macroevolution. " This is not the point: each of these points stand

alone with specific purposes. Since you bring everything back to the

single criteria that it must either prove macroevolution in one single

shot or be useless, you fail to engage the discussion on any of these

specific points and thus the discussion fails to progress.

> > As a second example, you have repeatedly stated that " no new genetic

> > material " arises except adverse changes due to radiation or other

> > types of cellular damage, and that these " random, " as you erroneously

> > call them, changes are incapable of generating " new genetic material. "

> > I have listed numerous other mechanisms by which new genetic material

> > is incorporated into the genome, and you have flat-out ignored all of

> > them.

> Give the gene sequences that have been generated and the specific code

> affected. You must prove that the gene sequences were not

> pre-existing that were newly generated. Then you must prove that over

> successive generations, that code is not only beneficial for the

> survival of the new species but also viable enough to be spread into

> the gene pool. If you can catalog these new changes specifically,

> then we have somewhere to go. Otherwise there is no evidence of

> macroevolution on a grand scale.

Again, you have *repeatedly* stated that " no new genetic material " is

observed to be incorporated into genomes. I am not obliged to show a

piece of evidence that stands itself as " evidence of macroevolution on

a grand scale " to show that this single point of yours, on which you

base your position on macroevolution, is blatantly false. All I need

do is point out the various mechanisms by which new genetic material

is introduced.

As to gene sequences being pre-existing rather than " newly generated, "

you are correct that unless we actually watch the mutation occur, this

uncertainty exists. But there is only a certain degree of absurdity

which we should tolerate to be applied to the interpretation of

uncertainty.

The introduction of variance into alleles by mutation is an

established concept. Since we know of no other source for this

variation, we *should* be able to conclude that the variance arises by

mutation. It is as if I found a banana peel on the street and claimed

it came from a banana tree, and you insisted that I had not

sufficiently met that burden of proof, having not observed it hanging

from a banana tree before it landed on my street.

Exactly how do you propose genetic variance in the human population

could possibly occur? Mitochondrial DNA evidence indicates that

currently living humans all share a single common mother. The only

known competing explanations for the origins of life are religious

doctrines, most of which also posit a single mother, at least that I

am familiar with. How, then, do you supposed that hundreds of alleles

and polymorphisms of a single gene could arise except by mutations of

that gene?

There is no way to avoid the conclusion that they occurred through the

observed process of mutation without applying an unreasonable degree

of absurdity to your interpretation of the uncertainty.

And no, it is not important to prove benefit in order to prove that

new genetic material is introduced. All that is required to prove

this is that new genetic material is introduced. Again, one point at

a time.

> > Your idea that macroevolution requires " new genetic material must be

> > introduced into offspring that was not in the ancestor, not merely

> > recombination of genes, but entirely new genetic material, " reaches

> > the height of absurdity. The very basis of the entire theme of

> > evolution is that forms of life do not appear suddenly ex nihilo, but

> > evolve from pre-existing forms of life. This applies to organisms

> > right down to genes.

> This is not so because, new organs must be fully functional to be

> beneficial to an organism.

" New organs " do not need new sets of genes. They need a different mix

of signals during their differentiation to modifiy which genes are

silenced.

Further, " fully functional " is relative. A sponge has some degree of

celluar differentiation, but does not have true tissues. A jelly fish

has a nerve net, but not a brain. Brains are essentially complexes of

many nerve nets. The jelly fish did not have to have a whole brain in

order to have nervous tissue; it simply needed rudimentary nervous

tissue.

In any case, your comment does not relate to my point. My point was

that " domain shuffling " is a common theme in the evolution of genes.

We do not observe that each protein is fullly unique. Instead, we

observe a patchwork of distinct protein domains -- that is, functional

units of a protein -- that are shuffled together in many ways. The Ig

superfamily, for example, uses the repeating Ig unit over and over and

over and over again. Even just the antibodies make TRILLIONS of

proteins by combining this one, single Ig unit many times in an

antibody with only a few amino acids in the variable portion that

vary. And the antibodies are only one subclass of the Ig superfamily.

Many other proteins use this same domain as a repeat, put together in

different ways. As another example, vitamin D-binding protein, serum

albumin, and alpha-fetoprotein are all essentially the same three

domains, but they are hinged together at a different angle, making the

domains organized in a different orientation, and thus altering the

affinity of the binding site for certain molecules. It was not

necessary to make each protein anew. All that was necessary was to

swap large functional units around, and then make minor adjustments in

the strings of amino acids that connect them.

> And the new code must not disrupt the rest

> of the functions of the organism.

This is true, but all this means is that not all mutations will be

successful. It does not mean that *no mutations will occur* and that

*no new genetic material will be introduced.* In any case, the point

being discussed here is whether, in your words, it is a requirement of

macroevolution that " new genetic material must be introduced into

offspring that was not in the ancestor, not merely recombination of

genes, but entirely new genetic material. " The fact that a new code

must not disrupt preexisting functions does not in any way indicate a

requirement for totally new genetic material. If anything, it makes

working with the pre-existing genetic code a requirement, because

building on that existing code is less likely to introduce disruption.

> If a new heart chamber develops,

> for example, it must be connected to the properly to venal AND

> arterial connections AND the nerves must be connected right AND the

> valves must be in the right place AND it must not leak AND it must not

> be too large AND it must not constrict the flow of blood AND the new

> changes must not interfere with the functioning of other organs and

> organ systems, etc. By the time the organism makes complex new gene

> sequences, it will die do to waiting for the right combinations.

This is ridiculous. If a new chamber of the heart is to develop, it

does not need a new gene for each lipid in the membrane and for each

three-dimensional coordinate a blood vessel or nerve travels. Each

cell already has the same genome. There is no requirement for a gene

for each chamber or for each part of the chamber. Instead, what is

needed is a change in the mix of signals that influence

differentiation and embryonic development. The direction of the

nerves and blood vessels is not directed by genes! How many genes do

you think we even have? We have about 20,000 and we'd need millions

if we had the incomprehensibly inefficient system of development you

are proposing. Nerves and blood vessels reach their target through

chemical signaling systems that communicate directly with the target.

No new gene required.

> This

> goes for one organ and organ system after another. Organ systems are

> very very complex and cannot stand a myriad of nonbenefical changes

> while waiting for the right combination of simultaneous developments.

And if every minute portion of their placement was mapped out by an

individual gene, this would be meaningful. Since it is not, it isn't.

Moreover, what is being discussed here is whether " entirely new

genetic material that was not present in the ancestor " is needed. On

the contrary, your emphasis on the complexity of organs only proves

the point that it is more possible to work within the pre-existing

genome.

> Observable beneficial variation that we do observe is minuscule to the

> massive simultaneous random additions that would have to be required

> to form wholly different organisms.

Back to the axolotl: ONE ALLELE is responsible for the development of

external gills and the transition from a terrestrial to an aquatic

lifestyle. This is not a brand new gene, but a modification to a

pre-existing gene. You are immensely overestimating the amount of

simultaneous mutation that is required for major changes.

> But getting these proteins to work together requires a vast array of

> complex code that would have to be disassembled and reassembled, to

> produce wholly new organs and organ systems, there is no observed

> mechanism for this. This would have to require entirely different

> mechanism than what we observe.

The domain shuffling point offers the capacity to utilize pre-existing

regulatory machinery. This is the entire point. If we needed to make

" entirely new genetic material, " then we would need to build all these

regulatory mechanisms at once. We do not. We can integrate a protein

into a regulatory system simply by shuffling a domain that is related

to that regulator system into that protein.

" Wholly new organs " do not pop up out of nowhere. An organ is just

cells that have differentiated to fulfill a certain function.

Bacterial cells exhibit these types of characteristics when in a

colony, even when considered unicellular. You are assuming that this

organization is all extensively mapped out inside some type of central

genetic directory, when in fact it relies to a very large extent on

the communicatory nature of closely associated cells and their

response to chemical and possibly electrical signals.

> > Although this process is most well-described and well-characterized in

> > fungi, if you do a search for " HLA gene conversion " on PubMed you will

> > see numerous reports of previously unidentified HLA genes in certain

> Previously unidentified does not prove to be new, additional material

> and the function of the new genes would have to be observed over

> generations.

Not for the purpose for which this was brought up here, which was to

demonstrate that new genetic material is introduced into the genome,

which you have so far denied.

> Are these just redundant genes that are there as filler?

The HLA genes regulate what peptides are recognized as antigens.

> Do they have a distinct function? For macroevolution to occur, we

> must not only have new distinct material, but also functional and

> beneficial material that is dependent for the species survival and

> continues for successive generations so that it continues and

> increases the survivability of the new species, and the new species

> must not be able to breed again with its ancestor.

Again, for discussion to occur, we must proceed one step at a time.

We can discuss possible mechanisms for introducing the genetic changes

that macroevolution would require separately from whether in each case

they lead to an event that proves the direct observation of geological

time processes in real time.

> > populations like island populations that appear to have been created

> > through this process, and at the very least plausibly attributed to

> > this process based on the fact that these *new* and *different* and

> > *completely functional* genes are clearly a rearrangement of

> > functional units taken from different genes and combined.

> Much more than this is required for macroevolution to occur. And the

> more complex the organism, the more complex will be the process of any

> point addition to the genetic code, there are more things to go wrong.

Again, the point is the demonstration that new genetic material is

introduced into the organism in an *organized* fashion. Not each

specific point must in itself demonstrate the direct observation of a

macroevolutionary event.

> I really do not see anything significantly new in your successive

> discussions. Whatever the mechanisms we observe in variation, they

> must be interpreted through the observation of how those mechanisms

> play out in the gene pools. Your continued explanations of various

> genetic processes are not able to interpolate to change our

> observations of what is happening amongst populations of organisms

> throughout nature. What we see microscopically in the genes is

> totally dependent on how they play out in the gene pools of real life

> organism in nature. Apes are still apes and there is no evidence in

> the genes that they have been anything else, but that they exhibit

> limits to variation.

Really. Not an ape mitochondria. Had you bothered to be responsive

to the discussion of endosymbiotic theory, perhaps we would have

gotten to discuss the mysterious presence of bacteria-like genes in

mitochondria and chloroplasts.

>Hybridization also exhibits limits to variation.

> Bacteria are still bacteria. For all the gene swapping and variation

> exhibited in bacteria, bacteria are still bacteria. I repeat this

> because that is what nature repeats over and over and over as long as

> we humans have been observing bacteria.

As I pointed out in the last email, the evidence strongly suggests we

are watching certain protists acquire new organelles like

chloroplasts. This is more convincing evidence for the endosymbiotic

theory of chloroplast origins than the fact that you do not see

bacteria randomly morphing into other beings is evidence that these

changes do not take place. You are aware, of course, that

evolutionary theory does NOT predict that we would see apes producing

anything other than apes. Your claim in an yesterday's email was that

the situation is different for bacteria because of their rapid

regeneration; I pointed out that this was not so, and we should see

the most rapid development in protists, who have the basic rudimentary

requirements such as larger amounts of DNA, mitochondria and so on,

who do not produce on a rapid scale. And I pointed out endosymbiosis

as one such mechanism. I do not recall seeing a response from you on

this point.

Chris

=======

REFERENCE 1

http://www.talkorigins.org/faqs/comdesc/section1.html#chronology

The most scientifically rigorous method of confirming this prediction

is to demonstrate a positive corellation between phylogeny and

stratigraphy, i.e. a positive corellation between the order of taxa in

a phylogenetic tree and the geological order in which those taxa first

appear and last appear (whether for living or extinct intermediates).

For instance, within the error inherent in the fossil record,

prokaryotes should appear first, followed by simple multicellular

animals like sponges and starfish, then lampreys, fish, amphibians,

reptiles, mammals, etc., as shown in Figure 1. Contrary to the

erroneous (and unreferenced) opinions of some anti-evolutionists (e.g.

Wise 1994, p. 225-226), studies from the past ten years addressing

this very issue have confirmed that there is indeed a positive

corellation between phylogeny and stratigraphy, with statistical

significance (Benton 1998; Benton and Hitchin 1996; Benton and Hitchin

1997; Benton et al. 1999; Benton et al. 2000; Benton and Storrs 1994;

Clyde and Fisher 1997; Hitchin and Benton 1997; Huelsenbeck 1994;

Norell and Novacek 1992a; Norell and Novacek 1992b; Wills 1999). Using

three different measures of phylogeny-stratigraphy correlation [the

RCI, GER, and SCI (Ghosts 2.4 software, Wills 1999)], a high positive

correlation was found between the standard phylogenetic tree portrayed

in Figure 1 and the stratigraphic range of the same taxa, with very

high statistical significance (P < 0.0001) (this work, Ghosts input

file available upon request).

As another specific example, an early analysis published in Science by

Mark Norell and Novacek (Norell and Novacek 1992b) examined 24

different taxa of vertebrates (teleosts, amniotes, reptiles,

synapsids, diapsids, lepidosaurs, squamates, two orders of dinosaurs,

two orders of hadrosaurs, pachycephalosaurs, higher mammals, primates,

rodents, ungulates, artiodactyls, ruminants, elephantiformes,

brontotheres, tapiroids, chalicotheres, Chalicotheriinae, and equids).

For each taxa, the phylogenetic position of known fossils was compared

with the stratigraphic position of the same fossils. A positive

correlation was found for all of the 24 taxa, 18 of which were

statistically significant. Note that the correlation theoretically

could have been negative. A statistically significant negative

correlation would indicate that, in general, organisms rooted deeply

in the phylogeny are found in more recent strata—a strong

macroevolutionary inconsistency. However, no negative correlations

were observed.

[snip]

Additionally, if the correlation between phylogeny and stratigraphy is

due to common descent, we would expect the correlation to improve over

longer geological time frames (since the relative error associated

with the fossil record decreases). This is in fact observed (Benton et

al. 1999). We also would expect the correlation to improve, not to get

worse, as more fossils are discovered, and this has also been observed

(Benton and Storrs 1994).

==============

--

The Truth About Cholesterol

Find Out What Your Doctor Isn't Telling You:

http://www.cholesterol-and-health.com

September 6, 2006

About Dr. Lynn Margulis and her work Acquiring Genomes

" Probably her most important scientific contribution is the

endosymbiotic theory of the origin of mitochondria as separate

organisms that long ago entered a symbiotic relationship with

eukaryotic cells through endosymbiosis (see also symbiogenesis). "

Cute and creative. The evolutionary model keeps evolving. A little

observation mixed with massive amounts of conjecture about supposed

millions of years worth of assumptions. There continue to be

conflicting speculive renditions.

A flattering review says,

" The result of thirty years of delving into a vast, mostly arcane

literature, this is the first attempt to go beyond – and reveal the

severe limitations of – the dogmatic thinking that has dominated

evolutionary biology for almost three generations. Lynn Margulis, whom

E.O. called 'one of the most successful synthetic thinkers in

modern biology,' presents a comprehensive and scientifically supported

theory that directly challenges the assumptions we hold about the

diversity of the living world. "

I admit it is a cool idea and creative synthesis.

Notice how it " directly challenges directly challenges the assumptions

we hold about the diversity of the living world. "

This is an example how evolutionists have greatly diverge and disagree

as to the causes and effects regarding presumed eons of unseen living

development, yet for all the disagreement as to what is or were the

mechanisms of presumed evolution, it happened. The mechanisms are in

debate. What theoretical organisms transformed into which is in

debate. Whether evolution of totally new kinds was gradual or sudden

is in debate. Disagreement abound, and radical new explanations that

supplant the previous explanations rise up in triumph. Yet let an

evolutionary scientist conclude through years of his own evolutionary

research that evolution is not possible, and see how quickly he is

dethroned!

September 6, 2006

As a result of this recent conclusion that merely 20000 genes contain

viable information for the blueprint of life, conclusions are being

made that we really still know very little about genetics and that

there are other factors which control traits such as RNA coexisting

with DNA. Since we know so little about the actual functions of the

genetic code, it seems premature to even use arguments referring to

genes, therefore it may be more reasonable to discuss traits. One

recent article states that as a result of the discovery that only

25000 genes affect heredity, there is especially little we know about

how genetics relate to the genes. Genetics was a field that existed

long before the discovery of genes, and now it seems that genes are

not all that we thought they were. There seem to be other controlling

factors that we do not yet understand. In that case, to claim that

genes contain the mechanisms to induce whole new organs and organism

is sorely premature, and a leap of unobserved conjecture. Seeing is

believing, and we are not seeing evolution on a grand scale. In spite

of all this new information, organisms are not observed to perform the

great feats of transformation attributed to them, only small everyday

kinds of things which are still amazing none the less.