Doctors doubting darwinism

[Gman]

I think we all can agree that they are in charge to decide what ID is about and we have to accept what they say. I have nothing to say against ID as a world view.
I honestly do not remember where I claim it to be gargage.
If I did I meant a "scientific garbage" which is a precise concern of mine about the actual evidences supporting their ideas.

I'm confused... You don't remember when you said that ID was garbage? Have you looked at your first thread of this post? Also you wanted to defend your children and not science?

Quote Angel: "I personally would prevent my children to attend a school in which ID (or any other garbage) is tought in science class.
This is not to defend science. It would be to defend my children."

As a Christian I do believe that God created us. I could even believe that
it created us as written in Genesis.
I could accept that it created everything in six literal days about in 6000bC.
I have absolutely no problem with any of this views. As you see I have no
preconceived idea to defend.

Again I don't know what to say.. In other posts you stated the case for a common designer was a lazy and unimaginative one... What gives now?

A completely different story is when one claims there are scientific evidences to support ID. Because simply there are not, at least until differently proven.

And Darwinian evolution has never been proven either... That's why it is still called to this very day a theory..

I asked about how well designed are some human features. We are still discussing about them.

Of course I am still waiting for answers to these basic points of ID.
If someone can show me how to spot designed sequences or similar features from random ones,
I am honestly ready to reconsider my position.

What flavor do you want?

http://www.godandscience.org/evolution/ ... esign.html
http://www.godandscience.org/evolution/index.html
http://www.godandscience.org/evolution/optimal.html
http://www.godandscience.org/apologetics/designss.html
http://www.godandscience.org/evolution/ ... nebad.html

Or search the forum...

http://discussions.godandscience.org/search.php

Even if I would force the universe to agree that there is no scientific evidence supporting
ID or against creation of new species, I honestly cannot see how this should be considered
something against "the Christian world view". Just to mention the whole Vatican Church
is accepting common ancestors and I would have some difficult in considering them
atheists. I might not agree with all their religious views, but they have as much
right to call themselves "Christians" as I have.

I don't understand, before you stated that the case for an intelligent designer was garbage...

Also about the Catholic church and their school teachings (where I attended). They permit belief in either special creation or developmental creation in certain cases, the Catholic Church under no circumstances permits belief in atheistic evolution. Please ask Byblos if you want as well on this subject...

I am not supporsting neo-Darwinism. And I am not atheist.
I simply believe that there is no scientific evidence that God is acting on the world.
I am not even claiming that it did not acted. I simply say that we do not have still evidence that it did.
I think there are a class of creationists (theistic creationists) who could agree on these point

This would be contrary to Biblical teachings then because God says that he DOES and IS acting in the creation and in the affairs of this world...

In particular I NEVER claimed evolution to be unguided, unintelligent, purposeless, material process.
I NEVER discussed about evolution in general terms. On the ocontrary I always consider specific issues
(such as humand and chimps sharing a common ancestor.) I cannot see how one could claim my view on evolution is
preconceived, materialistic or atheistic. I am just discussing scientific evidences.

There are only two possibilities for the existence of life.... There are no grey areas here just black and white... What color are you taking now?

1. Chance assembly of life from chemicals.
2. There is a Creator who designed biological systems.

http://www.godandscience.org/evolution/chemlife.html

Also biologists Scott Todd and Richard Lewontin would disagree with you..

Scott Todd C., a professor in the Department of Biology at Kansas State University says: "Even if all the data point to an intelligent designer, such a hypothesis is excluded from science because it is not naturalistic." "A View from Kansas on the Evolution Debates," Nature (vol. 401, September 30, 1999), p. 423.

"We take the side of science in spite of the patent absurdity of some of its constructs, . . . in spite of the tolerance of the scientific community for unsubstantiated commitment to materialism. . . . we are forced by our a priori adherence to material causes to create an apparatus of investigation and set of concepts that produce material explanations, no matter how counterintuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door." Lewontin, Richard, Review of the Demon-Haunted World, by Carl Sagan. In New York Review of Books, January 9, 1997.

Also please read again what August posted for you if you don't think your theory is materialistic or naturalistic....

I don't have time to debate this. Go read what evolutionists say:
Theodosius Dobzhansky: "Evolution comprises all the stages of the development of the universe: the cosmic, the biological, and human or cultural development. Attempts to restrict the concept of evolution to biology are gratuitous. Life is a product of the evolution of inorganic nature, and man is a product of the evolution of life."

Julian Huxley: "The concept of evolution was soon [after its appearance] extended into other than biological fields. Inorganic subjects such as the life-histories of the stars and the formation of the chemical elements on the one hand, and on the other hand subjects like linguistics, social athropology, and comparative law and religion, began to be studied from an evolutionary angle, until today we are enabled to see evolution as a universal and all pervading process. Furthermore, with the adoption of the evolutionary approach in non-biological fields, from cosmology to human affairs, we are beginning to realize that biological evolution is only one aspect to evolution in general."

Robert Jastrow: "Basic building blocks of life--amino acids and nucleotides--were made in earth's atmosphere by the passage of lightening bolts through primitive gases. Then they drained out of the atmosphere into the oceans and made a kind of "chicken soup" in which collisions occurred. Eventually, the first self-replicating molecule was formed by accident, and as soon as a molecule could divide and reproduce itself, you had a magic law broken for the first time."

Wynn & Wiggins: "Aristotle believed that decaying material could be transformed by the “spontaneous action of Nature” into living animals. His hypothesis was ultimately rejected, but... Aristotle's hypothesis has been replaced by another spontaneous generation hypothesis, one that requires billions of years to go from the molecules of the universe to cells, and then, via random mutation/natural selection, from cells to the variety of organisms living today. This version, which postulates chance happenings eventually leading to the phenomenon of life, is biology's Theory of Evolution".

John Waldon: "The term "evolution" is used to refer to the general theory that all life on earth evolved from non-living matter and progressed to more complex forms in time; hence, it refers to macroevolution and not microevolution."

One of the most vocal supporters of evolution in the USA is the National Academy of Sciences. They publish this:
http://www.nap.edu/catalog/1541.html#description
"The field of planetary biology and chemical evolution draws together experts in astronomy, paleobiology, biochemistry, and space science who work together to understand the evolution of living systems.
This field has made exciting discoveries that shed light on how organic compounds came together to form self-replicating molecules--the origin of life."

[Byblos]

Byblos
The fact is you have no proof, no data, no test results, no scientific steps,
no peer-reviewed analysis, you have nothing other than an a-priori assumption which you insert in the end as a conclusion.

I read through your posts. I beg your pardon byblios. Sometimes I am slow in getting your point. I was wondering...


Are you simply saying that I have no scientific evidences supporting my belief that we actually share (at least 7) viral insertions with chimps?
Or are you saying that EVEN accepting these insertions they would not be considered evidences of a common ancestor?

What I do not understand is how you can find my posts ambiguous in any way. Where did I state there is no evidence that we have common retroviral insertion points with chimps? In fact, we share several with other animals as well, including rodents, guinea pigs, even roaches. I don't know about you but I wouldn't call any of them Grandpa. What I am saying and what is IMO perfectly clear from my posts is that the commonality is by no means an indication of common descent. It could just as well be a case of common design. There simply is no way to tell the difference. What makes your claim for common descent any more scientific than my claim?

It might be that I simply misunderstood your critique to my argument.
Please clarify.

I hope it's clear[er] by now.

The problem is that HGT disagrees with your entire theory of 'a single common human/chimp' ancestor.

Provided you proved HGT occurred not only among bacteria but among mammals as well.

Hey, I'm not the one advancing multiple LUCAs via HGT, it's a bunch of atheist scientists who're doing so. If you have any beef with their theory please take it up with them.

It might be so, but I suppose we could agree that that is a subject that deserves a sepapare discusssion.

Certainly. As long as we both recognize that it is a theory among many.

[Byblos]

Judah
I am left wondering if you are seeking to find a way to be more considerate
towards the Christian world view which is more in favour of creationism/ID - or if you are convinced that such ideas are not for you?

I completely agree with your concerns. As I said in the past I have no idea made on Christianity. As I claimed in the past I consider myself a believer.

I believe your concerns are originate by the improper identification
of ID with Christian world views.
Notice that it is not an opinion of mine that such an identification is improper.
ID people claim all the time that ID is not about religion but it is about *science*.

I think we all can agree that they are in charge to decide what ID is about and
we have to accept what they say. I have nothing to say against ID as a world view.
I honestly do not remember where I claim it to be gargage.
If I did I meant a "scientific garbage" which is a precise concern of mine about
the actual evidences supporting their ideas.

As a Christian I do believe that God created us. I could even believe that
it created us as written in Genesis.
I could accept that it created everything in six literal days about in 6000bC.
I have absolutely no problem with any of this views. As you see I have no
preconceived idea to defend.


A completely different story is when one claims there are scientific evidences
to support ID. Because simply there are not, at least until differently proven.

Believe it or not, I would tend to agree with you that, to a large extent, ID is not scientific. The problem is that you are not extending DE (Darwinian Evolution) the same courtesy. If scientists are honest enough to stick to the observable and the testable and not make sweeping generalizations particularly inter-specially, I and so many other Christians and God-believing people would not have any problem with evolution whatsoever. But alas, that is not the case.

I asked if someone is able to explain how a designed sequence can be recognized
fromm a random one. ID people claim it to be possible. Nobody was able to show me how to do.
It is hence my opinion that the possibility of single out designed characteristics
is just in their dreams. Again I am ready to reconsider my position if someone will show
how to do it. I hope we all agree that it is not necessary to be Christian to accept
such possibility on FAITH!

But that is PRECISELY the point, Angel. We're not able to tell the difference between a designed sequence and a random one. So what makes your choice of a random act better than my design theory? Answer me that and I'll reconsider my position.

I asked about the possibility of make precise the arguments about how "unlikely"
some events connected with evolution are. I got no definite answer. I might be dummy, but that is
what I got from the discussion.

I asked about how well designed are some human features. We are still discussing about them.

Of course I am still waiting for answers to these basic points of ID.
If someone can show me how to spot designed sequences or similar features from random ones,
I am honestly ready to reconsider my position.

Considered this, I honestly believe to be well within the guidelines.

I think Gman answered this quite well.

In any event HERE we are discussing a different point which has nothing to do with
ID. We are discussing viral insertions as evidences for common ancestors between human and chimps.
This started because I was said that there are (scientific) evidences that no such
common ancestor existed.
Byblios ((s)he could confirm it) started to discuss about it.
We are currently discussing about this issue. The discussion might be affected by some incomprehensions
(which is my intention to check and discuss with byblios directly).
It is currently on the way.

First, it's Byblos, not Byblios. Second, my name is John. Third, I'm not sure this started with the claim that there is scientific evidence against common descent. It started with the unfounded claim that common descent is scientific when it is nothing more than an unproven theory among many.

Once again I think the topics is only marginally regarding religion. I know many Christians and
believers who accept common ancestors. I would not say that they have made up their mind against
religion, would you?

If it's not about religion, it is certainly about God. Discussions of this nature will invariably lead into the source of life discussion. By not acknowledging the scientific uncertainty of the origin of life, DErs have painted themselves into a corner. There is no escaping it.

Even if I would force the universe to agree that there is no scientific evidence supporting
ID or against creation of new species, I honestly cannot see how this should be considered
something against "the Christian world view". Just to mention the whole Vatican Church
is accepting common ancestors and I would have some difficult in considering them
atheists. I might not agree with all their religious views, but they have as much
right to call themselves "Christians" as I have.

The difference is that even Theistic Evolutionists most definitely believe God has always interfered with his creation. 14 billion years is but a millisecond to an eternal being. Otherwise what do you call the Bible? What would you call Moses, Elijah, Iseiah, and the rest of the prophets? What would you call Jesus, if not a mass intervention? To believe in a passive God that wound a clock and let it run is to believe in a weak God that has no control over his creation. Your position is untenable, Angel. All scientific discussions aside, either you believe in an omnipotent God or you simply are not a believer, no matter how much you wish to believe it.

Concerning the guidelline you mentioned

To be clear, we will heavily moderate those who attempt to support a neo-Darwinian
form of evolution, which is strictly Materialistic and Atheistic, and which rules out
any possible influence or intervention from a divine being such as the Christian God within creation.

I am not supporsting neo-Darwinism. And I am not atheist.
I simply believe that there is no scientific evidence that God is acting on the world.

Like I said, this is what it boils down to.

I am not even claiming that it did not acted. I simply say that we do not have still evidence that it did.
I think there are a class of creationists (theistic creationists) who could agree on these point.

If they do, they do not believe in the same God I believe in. And Angel, God is not an 'it'.

In particular I NEVER claimed evolution to be unguided, unintelligent, purposeless, material process.

Huh? what do you call this:

I simply believe that there is no scientific evidence that God is acting on the world.

I NEVER discussed about evolution in general terms. On the ocontrary I always consider specific issues
(such as humand and chimps sharing a common ancestor.) I cannot see how one could claim my view on evolution is
preconceived, materialistic or atheistic. I am just discussing scientific evidences.

Where are these scientific evidences you keep referring to, Angel? I haven't seen any just yet. What you've shown is that two distinct species have something in common. Out of some 98,000 insertion points, there happens to be 7 common ones between humans and chimps. Out of this observed commonality you conclude a common ancestor. I know analogies most often fail miserably but I will offer one anyway. Uncle Bob has 6 toes on his right foot and uncle Tom has six toes on his right foot. Therefore, uncle Bob and uncle Tom must be twins. Except they're 10 years apart and not even brothers (from 2 different parents, one on my mother's side and the other on my father's). That is the argument you are forwarding re common retroviral insertion points and common descent. I believe it is called the fallacy of the undistributed middle.

[angel]

Let me clarify few things:

First of all, I don't want to discuss my faith this GMan nor with Byblos
(unless he acts as a moderator).
What I said above is just because I accept moderator right to enforce the guidelines.
I was asked few questions by a moderator, I tried to answer (honestly) to that.
Said that this discussion is not about my faith but about scientific evidences
for a common ancestor of humans and chimps.
GMan claimed there is no such a common ancestor.
Byblos asked me and I posted some which are IMO strong evidences.
Currently I am discussing with Byblos about viral insertions.

Second: English is not my first language (as you certainly guessed) so it may happen
that I misspel words, or that I find hard to follow your arguments, expecially if, as some of you
is used to, they are presented in an ellyptic way, with no clear distinction about what are opinions
and claims. In that case I usually ask to see if I got it plain.
Hence Byblos there is really no reason for you to get upset about my question.

What I do not understand is how you can find my posts ambiguous in any way.
Where did I state there is no evidence that we have common retroviral insertion points with chimps?

Even because I did not claim that your post was ambiguos. I just said that I might have
misunderstood your posts.
For the future: don't doubt I will state clearly that your posts are ambiguous when they are.

Third: If I can advise you, do not try to think what I mean to say. I usually mean exactly what I write.
Except for the typos. I never try to imply things indirectly.
For example when I say "I do not remember where I say "garbage"" I do not mean "I never said that".
Usually if I want to say "I never said that" I write "I never said that".
BTW As GMan was so kind to quote, I was there referring to ID as a scientific theory as I think anyone can
see by going back to the post. Exactly as said to the moderator I have nothing against ID
as I have nothing against Santa Claus or Jedy knights. They are IMO perfectly honest wordviews.
Just they are not supported by science.
I am sure we all agree that not anything need to be scientific. As I stated clearly in the past
I believe religion does not need to be scientific. That does not mean that I consider that badly.
But this is going away from the main subject under discussion here.

Fourth: Byblos, God is not a human male, nor a human female. For that reason, if you don't mind and unless
you find it unbarebly offensive, I will get stuck to neutral form.
With it I mean no offence.
As far as your gender is concerned, now that I know I will use the correct one when referring to you.


I do not want to start a discussion with GMan. I had enough of that on another thread.
However, it might be that he is really asking me to explain. Being in doubt about his true intentions I will
provide comments about some of his questions. Others have been exausted elsewhere.

In other posts you stated the case for a common designer was a lazy and unimaginative one...

As I said, the designer of ID is IMO lazy and immaginative.
That does not extend to any kind of possible designer.
For example, I do believe that God concerned the universal laws so that there is no need of
its action. I do believe that even the creation of the universe, if there was a beginning,
can be understood on a rational and scientific basis because it was not produced by divine action.
I believe the divine is encoded into the definition of what is rational and scientific and that the universe
will be understood to necessarily follow by that premises.
That is an "intelligent" designer.
IMO an engineer-like assembler of genomes and proteins is more a biologist than a god.
Of course, I cannot prove any of that. As ID people cannot support their claims.
Here I am talking about FAITH, not science.

And Darwinian evolution has never been proven either...
That's why it is still called to this very day a theory..

That is a naive position to hold.
On one hand there is not a single piece of science that should not be called a theory
according to your standard.
On the other hand I think that you simply do not understand science.
If I had to support this opinion, it would be enough to list the sources you are used to quote.
I think, you are just repeating arguments you heard around. None of them has proven to be substantial.
I could defend such opinion but this is not the place to do it, I guess.

I don't understand, before you stated that the case for an intelligent designer was garbage...

Intelligent design is not the only possibility of a designer, as I discussed above.
I honestly don't know what you are talking about when you called Catholics "atheistic evolutionist".
I never said that (probably I used the expression "theistic evolutionist"; I hope you see the slight difference).

This would be contrary to Biblical teachings then because God says that he DOES and IS acting
in the creation and in the affairs of this world...

I don't thgink any rational being can consider the bible as a scientific evidences.
You would be better to read what I wrote.

There are only two possibilities for the existence of life...

You forgot to mention:
- life could be proven to spontaneusly emerge from non-life,
not by chance but because of the natural laws we still don't know
- life being produced by a chaotic designer
- or by extraterrestial civilization
- or has always existed
- or by flying spaghetti monster

There are more things in the skies that in your philosophy.

Not to mention that no neo-evolutionists would claim that evolution is lead by chance.
Natural selection is not chance. Have you read what they have just posted in a parallel thread.
The biologist there exactly claims that!

But now let me come to more serious stuff:

In fact, we share several with other animals as well, including rodents, guinea pigs,
even roaches. I don't know about you but I wouldn't call any of them Grandpa.

I hope you are joking here. I never said that we descend from chimps!
Is it clear to you what I mean by "sharing a common ancestor"?
For that reason I should call chimps (as well as rodents, guinea pigs,
even roaches) cousins, not grandpa!

It could just as well be a case of common design.

I perfectly agree with that. I also pointed that out in the past posts.
I have been discussing at ARN forum for a while and it was "clearly" stated by
ID people that ID is not incompatible with common descendent.
BTW they also claimed that common descended is neither implied by ID.

Adding the two I must say that ID is indifferent with the hypothesis of common ancestor.
That repeated for basically any practical question I answer there.
That experience is the basis for my belief that ID actually does not claim anything about biology.
That is the main motivation for me to claim that ID is not science.
I am not saying that it is wrong. I am saying that they are not saying ANYTHING.
All irreducible complexity and complex specified information arguments, in the end boil down to nothing.

A scientific theory must live dangerously, claiming hard fact that can kill it.
Evolution for example claimes that viral insertions cannot be distributed as one like.
You asked

The answer is simple. Either one prove that insertion points have been selected among maly less
possibilities then previously believed, or evolution as a theory based on random mutations
and natural selections would be FALSIFIED.
Can you mention a hard fact that would falsify ID?

What makes your claim for common descent any more scientific than my claim?

Sorry Byblos, I should have missed it. What is your positive claim about the origin of species?

I hope it's clear[er] by now.

Yes it is. Thank you.
I have to say that my doubts were not originated by your posting directly.
I was only trying to save some of your claims.
Now that you clarified that you really meant whaat you wrote, I am left with one only option
you have strange ideas about what is science and/or what are viral insertion.

I do not want to be offensive, but I honestly cannot see how you could oversee the evidence
based on viral insertion.
Maybe you could try to explain to me what is a viral insertion.
Just to check if you understood it the same way.
I did explained the argument in details above. You replied it was nonsense but provided
no argument. Could you, Byblos?
BTW have you rad that post of mine?

Hey, I'm not the one advancing multiple LUCAs via HGT, it's a bunch of atheist scientists
who're doing so.

I understood that. However, we could check if any of those atheist scientist consider HGT
a possible alternative explanation for the emergence of humans and chimps from older apes.
As I said. I would drop this argument here.

Certainly. As long as we both recognize that it is a theory among many.

Of course evolution is a "scientific theory".
There is however a continous quite upsetting confusion about what a scientific theory is.
I understand "theory" in common English means something which is not very well established.
This has nothing to do with what a scientific theory actually is.
Anything in science, including Big Bang, gravitational theory, quantum mechanics, is "just a theory".
With that we mean that one day any piece of science can be replaced by a BETTER theory.

However, not all theories are the same. We should be much more confident with quantum mechanics
than with string theory. That is because we have plenty of evidences about quantum mechanics
and none (yet) supporting string theory.
And both are better theories than astrology.
BTW you know that according to Behe standards, astrology is a scientific theory?
He claimed that at Dover's trial. I fear that would lead us too far away from the subject, though.
I do not see how discussing "theories" would help in agree on whether we share a common ancestor with chimps.

The problem is that you are not extending DE (Darwinian Evolution) the same courtesy.
If scientists are honest enough to stick to the observable and the testable and not
make sweeping generalizations particularly inter-specially, I and so many other
Christians and God-believing people would not have any problem with evolution whatsoever.

What do you mean by observable and testable?
I can do predictions with DE.
For example that we do not share viral insertions with Gorillas which are not shared by Chimps as well.
Or that the number of synonimous genetic differences between Gorillas and Humans and not less than the one
between Chimps and Humans.
That my son will not share viral insertions with you which are not shared by me as well.
and so on.

If you want to fight DE in a scientific way, feel free to search and prove any of this.
If you don't feel free to fight in court, but that way you are not doing science.

But that is PRECISELY the point, Angel. We're not able to tell the difference
between a designed sequence and a random one.

Who tells I cannot tell the difference.
By random, I and all "atheist scientists" means the probability of each kind of mutation is
independent of the "functionality".
I can spot pretty well the mutations occurred in human histories and I can check if the frequency
of such mutations depends on the functionality it exploits.

Until today, no such dependence emerged.
I am sure tomorrow such an evidence will not emerge?
No I am not. As for any other experiment in science.
You must accept this. Rejecting evolution on philosophical position is as rejecting any other piece of science.
There is nothing philosophically wrong with DE. Only experiments can defeat a scientific theory.
Period.

Of course, once I confirmed random mutations, I cannot rule out a designer.
That is way I disagree with Dawkin when he says that we have scientific evidences that God
does not exist.
I consider a perfectly honest faith position to assume that the designer decided to hide itself
behind random appearence. And no sientific evidence can confute this believe.
That is why I do not think DE rule out a designer. Just it constrains it to act according to what we learned
from evolution.

There is no philosophical defence of DE on my side. I do believe there is no philosophy behind DE.
I hope you see the difference between not being able to rule the designer out and claiming that
genome has obviously be designed.

I honestly don'y believe I did any claim I cannot support by experiments. ID people did.
Of course I may be wrong about the first part.

So what makes your choice of a random act better than my design theory?

In other words, tell me exactly what is your design theory.
If you accept that your designer acted in disguise as if it were random,
there is absolutely no scientific difference between the two models.
But that is not what ID people claim. They claim the are (or will be) able to produce
positive evienced that the designer acted differently.
Well, we shall see. When they will do that, I would convert to ID.

I think Gman answered this quite well.

I was not aware GMan waas in charge for enforcing the guidelines.
His post was improper as I said above.

It started with the unfounded claim that common descent is scientific
when it is nothing more than an unproven theory among many.

Excuse me if I ask it again Byblos. Are you sure you understand viral insertion argument?
Again, if you were so kind to summarize the argument we could avoid misunderstandings.

By not acknowledging the scientific uncertainty of the origin of life, DErs
have painted themselves into a corner.

I did acknowledge that. Can you mention one peer reviewed paper in which a DEr
claims that we know everything about the origin of life?

Your position is untenable, Angel.

Maybe it is untenable on a rational basis. That is why I called FAITH for it.
I suppose we agree that there is no reason for God/faith to be rational.

My point, really the unique point of all my post, is that we shoudl not filter facts.
If evidences points to random mutations, one does no good service to God by refuting the fact.
What if your faith would tell that algebra is wrong. There is no possible conflict between faith and
reason if you accept what reason tells you.
That is the only way my faith can go. Sorry if you don't like it.
Nor I wish to enforce my views on you.

If they do, they do not believe in the same God I believe in.

What a news. It is not the first time in history that people disagree on the nature of God.
Nor it is the first time that this leads to war.

I hope you are not meaning that your vision is BETTER than their one ON A RATIONAL BASIS!

Huh? what do you call this:

angel wrote:
I simply believe that there is no scientific evidence that God is acting on the world.

I call it a misquote.
There I claimed there is NO SCIENTIFIC EVIDENCE of God action.
I don't think producing physical action is the only way God could "guide" the universe.
do you?

What you've shown is that two distinct species have something in common.
Out of some 98,000 insertion points, there happens to be 7 common ones between humans and chimps.
Out of this observed commonality you conclude a common ancestor.

That is what you understood of viral insertions argument?
That would explain your attitude!
Read back to my post. That is not a fair rendering of the argument.

Let us talk about probabilities. Can you anwer the following question for me?
Which is the probability that the seven insertion happened independently though they
end up at the same positions?

I know analogies most often fail miserably but I will offer one anyway.
Uncle Bob has 6 toes on his right foot and uncle Tom has six toes on his right foot.
Therefore, uncle Bob and uncle Tom must be twins.
Except they're 10 years apart and not even brothers
(from 2 different parents, one on my mother's side and the other on my father's).
That is the argument you are forwarding re common retroviral insertion points and common descent.

I believe it is called the fallacy of the undistributed middle.

That does not even fail miserably.
That analogy would be appropriate if I said that we share a common ancestor with chimps because we
share with them 98% or so of the genome.
Which is not the argument as clearly explained above.

A more appropriate analogy would be if we lived on a planet where humans have 100000 toes in their feet
and a virus is known so that when one is infected one of his toes become green.
The selected toe is known to be chosen at random and to be passed to offstrings.

Now imagine uncle Bob and uncle Tom has the corresponding 7 toes green.
[an even better analogy would consider the tone of green to be different in independent infections.
But I don't want to push it too much....]
Would it be reasonable to expect that they do not share a common ancestor?

Of course, it may not be the case. As it may be that a viral insertion is found to be shared by
gorillas and humans but not by chimps.
In that case, evolution would be wrong.
Until evidences are provided that such uncorrelated match might happen by chance,
I prefer to believe that the mother of your mother could have had an affair with
the father of your father.
You of course are free to believe what you please.

[angel]

Sorry Byblos for the huge post.
If you wish we can drop everything and discuss your analogy only.
I think that should be enough to clarify our positions about the issue under consideration.

[Byblos]

Sorry Byblos for the huge post.
If you wish we can drop everything and discuss your analogy only.
I think that should be enough to clarify our positions about the issue under consideration.

No apologies necessary Angel. I also may have made a few assumptions about your posts/questions that turned out to be skewed. It's very hard to judge intent sometimes just by reading words. And your English is fine by the way; it's not my native language either. In any case, my analogy is the furthest thing from my mind. As you and Bgood aptly demonstrated (and as I predicted from the get-go), analogies most often fail. What I do want to concentrate on, however, is ERVs and their inter-special role, if any . I will respond to your lengthy post (at least the parts relevant to ERVs) and we'll take it from there. One thing I want to make clear (and which you probably have guessed already) is that I am not a biologist. What I am is an analyst and tend to break things down to their minute details only so I can understand them. TBC...

Byblos

[angel]

No apologies necessary Angel.

Thanks for being sympathetic.
Maybe there is no need. Though I hope it could clean the field from
misunderstanding and mutal misconceptions. Both ways of course.

I also may have made a few assumptions about your posts/questions that turned out to be skewed.
It's very hard to judge intent sometimes just by reading words. And your English is fine by the way;
it's not my native language either.

I agree.

Thank you. I meant that I not even live in an English speaking country. I see you live in NY.
English for me is a language for holidays, for conferences or to write papers.
Since we are both non-native speakers, I think that extra care (as well a sympathetic attitude)
is needed and some good will to clean the field from misunderstandings.
I beg your pardon since now for some possibly stupid question I may ask about your position.
I am just trying to understand how you can say that I did not provide any evidence [...]

Of course I am aware that I did not really provide the references for each point of my argument.
Before doing that (and I will in due time) I would like to understand if you simply don't believe
to some of my point (that is why I asked you clarification about your position) or if, even accepting
each single point, they are not enough for you to buy common ancestor.
In this last case, which seems to be the case, there is no reason to document each point before you
follow the whole argument and each point. If this is, as it seems to be, the case then I would like
to understand exactly which points cause you trouble.

First of all, let me clean my field. My intention is not to force you to accept atheistic or material views.
I think I already repeated it enough times.

You asked elsewhere (I am following too many threads by now) how you can distinguish common
ancestor/evolutionary scenario from a designer scenario by means of endogenous viral insertions.

My opinion, let me claim that again, is that you cannot.

By that I mean that one can always assume the designer to act in disguise mimiking any
evolutionary-like (as well as any other) evidence.
I think He (now I am referring the case IDer=Christian God) is (or may be) smart enough to do that and
too smart for us understanding His reasons.

BTW: notice that *usually* (I am far from perfect) I claim "there are plenty of scientific evidences for common ancestor" and not "we share a common ancestor with chimps". In any event that is what I mean.
I hope the difference is clear and it helps clarifying my position.

However, that is NOT what intelligent design is claiming. They are not talking about a designer in disguise!
They claim that they have (or will be able to find) positive evidences supporting the designer action.
Despite this might become true in the future (in which case I will convert to ID) TODAY IMO we have no
positive evidence whatsoever.
In any event, it is a fact that a designer mimiking ERV is not what THEY are talking about.

Said that I have nothing against one believing in "intelligent disguise". One can honestly hold the faith that
God created the universe two days ago mimiking a universe 15 Billions Years old.
There cannot be any scientific evidence contradicting this view, so it is fine to me.
That is why I keep saying that what I am saying is not against religion. I hope it is clear by now.
It is obvious that intelligent disguise view is in a sense not scientific.
Science is based on the assumption that scientific evidences are teaching us something reliable about our universe.
Of course science may be wrong and faith may be correct. That is not what is being discussed.
That is what I meant by "faith does not need to be reasonable".

Second, I think it would be good for everybody to have a faith which does not require contradicting evidences.
Evidences are not something we can choose to ignore or use. As we cannot choose the rules of algebra.
Evidences are something we MUST accept, whatever they say about our beliefs. That was my opinion all my life.
I accept people acting differently (ignoring all evidences). I do not accept people basing their faith on
false evidences (such as "we can easily see that biological systems are clearly designed").
I am NOT saying that you are one in this last group. I am just trying to show there is nothing ideologically
against Christians in my views.

What I do want to concentrate on, however, is ERVs and their inter-special role, if any .
I will respond to your lengthy post (at least the parts relevant to ERVs) and we'll take it from there.

Agreed.
I can offer all the time and efforts needed to agree on the issue. Either way of course!
If you want we can try to go through the argument step by step and solve the matter.

Honestly (with all due respect and no intention to offend) from what you posted to me and BGood
I think you misunderstood the argument.
Nothing that cannot be solved spending some time and effort, however.
Of course I can turn out to be wrong.

BTW: the issue was brought (indirectly. I was just reading the discussion) to my attention in the past
by a creationist who accepted the evidences of ERVs but he kept nonetheless *believing* in a separate
creation for humans. Needless to say that I respect him for that.

One thing I want to make clear (and which you probably have guessed already) is that I am not a biologist.

Neither am I.
I just tried to understand the issue for fun.
I am a student in mathematics with too many interests for my limited time.

What I am is an analyst and tend to break things down to their minute details only so I can understand them.

I like that strategy.

I'll be waiting your reply to the lengthy post, for now.
Please if you need do not keep from asking clarifications.

With respect
Angel

[Byblos]

Let me clarify few things:

First of all, I don't want to discuss my faith this GMan nor with Byblos
(unless he acts as a moderator).

Angel,

When I am engaged in discussion I assume the role of a poster. Moderating is left to others. But I hope you don't feel you have to hold back because you're discussing a topic with a moderator. Having said all of that, we do still have to follow guidelines set forth by the owner of the site.



I considered responding to the rest but thought better of it. They are irrelevant to the topic.

What you've shown is that two distinct species have something in common.
Out of some 98,000 insertion points, there happens to be 7 common ones between humans and chimps.
Out of this observed commonality you conclude a common ancestor.

That is what you understood of viral insertions argument?
That would explain your attitude!
Read back to my post. That is not a fair rendering of the argument.

Angel, I may not understand ERVs the way you do and I did read your posts. I still do fail to see the incontrovertible proof of common ancestry even with the striking similarities of not only insertion points but also with the same sequences. Yes, they are the same. Yes, common ancestry is a possible explanation. Is it the ONLY explanation? I don't think so.

Let us talk about probabilities. Can you anwer the following question for me?
Which is the probability that the seven insertion happened independently though they
end up at the same positions?

Please Angel, let's not talk about probabilities. It's a rabbit trail we'll never get out of.

I know analogies most often fail miserably but I will offer one anyway.
Uncle Bob has 6 toes on his right foot and uncle Tom has six toes on his right foot.
Therefore, uncle Bob and uncle Tom must be twins.
Except they're 10 years apart and not even brothers
(from 2 different parents, one on my mother's side and the other on my father's).
That is the argument you are forwarding re common retroviral insertion points and common descent.

I believe it is called the fallacy of the undistributed middle.

That does not even fail miserably.
That analogy would be appropriate if I said that we share a common ancestor with chimps because we
share with them 98% or so of the genome.
Which is not the argument as clearly explained above.

A more appropriate analogy would be if we lived on a planet where humans have 100000 toes in their feet
and a virus is known so that when one is infected one of his toes become green.
The selected toe is known to be chosen at random and to be passed to offstrings.

Now imagine uncle Bob and uncle Tom has the corresponding 7 toes green.
[an even better analogy would consider the tone of green to be different in independent infections.
But I don't want to push it too much....]
Would it be reasonable to expect that they do not share a common ancestor?

Of course, it may not be the case. As it may be that a viral insertion is found to be shared by
gorillas and humans but not by chimps.
In that case, evolution would be wrong.
Until evidences are provided that such uncorrelated match might happen by chance,
I prefer to believe that the mother of your mother could have had an affair with
the father of your father.
You of course are free to believe what you please.

Like I said before, let's also stay clear of analogies (knowing that I'm the one who brought it up).

Yes, I will believe what I want. Each one of us does. If it makes no sense to me or I see no clear evidence of it, I will call you on it.

Byblos.

[Gman]

Third: If I can advise you, do not try to think what I mean to say. I usually mean exactly what I write.
Except for the typos. I never try to imply things indirectly.For example when I say "I do not remember where I say "garbage"" I do not mean "I never said that".
Usually if I want to say "I never said that" I write "I never said that".
BTW As GMan was so kind to quote, I was there referring to ID as a scientific theory as I think anyone can
see by going back to the post. Exactly as said to the moderator I have nothing against ID
as I have nothing against Santa Claus or Jedy knights.

Angel, this is complete rubbish!! You say that you usually mean exactly what you write and then you equate ID with Santa Claus? You don't think you are being antagonistic here? Do you think this is the third grade here or something to fall for this? At this website we do NOT support the case for chaos (as Judah and Byblos have already explained to you)... We support the case for ID and God.

How do your theories support the case for ID? Please explain in detail..

They are IMO perfectly honest wordviews.
Just they are not supported by science.

You still think that your little theory is supported by science? You are trying to make us believe in your plastic blow up common ancestor tree that doesn't even exist... Where is your proof? You have already stated before that there wasn't much in the fossil evidence and that is why certain scientists were looking into genetics now..

I am sure we all agree that not anything need to be scientific. As I stated clearly in the past
I believe religion does not need to be scientific. That does not mean that I consider that badly.
But this is going away from the main subject under discussion here.

But you are advocating that life can evolve out of chaos.. Where is God in your picture here? How do your claims support the case for God and ID? What science are you talking about?

Fourth: Byblos, God is not a human male, nor a human female. For that reason, if you don't mind and unless
you find it unbarebly offensive, I will get stuck to neutral form.
With it I mean no offence.
As far as your gender is concerned, now that I know I will use the correct one when referring to you.

Correct.. Out of all the other stuff you posted you finally got one right. God is not a human male, nor a human female. But possess both qualities.

As I said, the designer of ID is IMO lazy and immaginative.
That does not extend to any kind of possible designer.
For example, I do believe that God concerned the universal laws so that there is no need of
its action. I do believe that even the creation of the universe, if there was a beginning,
can be understood on a rational and scientific basis because it was not produced by divine action.
I believe the divine is encoded into the definition of what is rational and scientific and that the universe
will be understood to necessarily follow by that premises.
That is an "intelligent" designer.
IMO an engineer-like assembler of genomes and proteins is more a biologist than a god.
Of course, I cannot prove any of that. As ID people cannot support their claims.
Here I am talking about FAITH, not science.

Again you are confused... You believe that our universe was not produced by any divine action?? Good grief Angel... This is not a hard concept to understand... Either God created everything or he didn't. What you stated here implies the complete opposite then. Atheism...

That is a naive position to hold.
On one hand there is not a single piece of science that should not be called a theory
according to your standard.
On the other hand I think that you simply do not understand science.
If I had to support this opinion, it would be enough to list the sources you are used to quote.
I think, you are just repeating arguments you heard around. None of them has proven to be substantial.
I could defend such opinion but this is not the place to do it, I guess.

No... Your position naive and cold... You have no standards, no solid evidence, no solid science, and no God. You only have chaos and darkness... Remember?

Intelligent design is not the only possibility of a designer, as I discussed above.
I honestly don't know what you are talking about when you called Catholics "atheistic evolutionist".
I never said that (probably I used the expression "theistic evolutionist"; I hope you see the slight difference).

Again you are confused... Catholics to NOT support atheistic evolutionist... They never have... You cannot equate yourself to the Catholic faith, because you claim that ID is false.. Get it now?

I don't thgink any rational being can consider the bible as a scientific evidences.
You would be better to read what I wrote.

How can I read what you wrote.? You even posted before that you don't know what you are writing.. Do you know what you are saying?

You forgot to mention:
- life could be proven to spontaneusly emerge from non-life,
not by chance but because of the natural laws we still don't know
- life being produced by a chaotic designer
- or by extraterrestial civilization
- or has always existed
- or by flying spaghetti monster

There are more things in the skies that in your philosophy.

Not to mention that no neo-evolutionists would claim that evolution is lead by chance.
Natural selection is not chance. Have you read what they have just posted in a parallel thread.
The biologist there exactly claims that!

LOL.. This is complete BUNK... Again there are only TWO choices for the existence of life..

1. Chance assembly of life from chemicals.
2. There is a Creator who designed biological systems.

The only other choice you have is to say is that you don't know and not choose any direction.. But you have to be an adult first to say this.. It is called telling the "truth."

[angel]

As I said, GMan, I am not interested in discussing with you.

I hope you understand...

[angel]

I think an example can help. Byblos please go through it and tell me which step sound ok to you
and which needs more attention. Of course it is an example and numbers are just representative of
what actually happens.


1. Let us say you sequence the DNA from a cell taken from the skin of my hand.
The sequence is a long series of four bases named T,G,A,C
within the sequence we isolate a subsequence which is divided in three consecutive
parts. Let us call the pasts:

alpha beta gamma

where each alpha="TTCGGTCAA...", beta="CGGCACCT..." and gamma="AACCGTGGGTC..." are genetic sequences.
Let us say for the sake of simplicity that each part is long 10,000 bases.


2. Then we test that that subsequence is found identical in each cell of my body.
Since we know that all the cells of my body should have the same DNA this could sound trivial.
However, it is know that, during our life, viruses may infect particular cells in our body
and they insert their genetic sequence in those cells. Some particular cell
may hence present a different DNA because of these viral insertions.
I think viruses are specialized in infecting particular systems and usually flue virus does
not infect liver cells, for example.
The fact that the sequence is found in any cell of my body indicates that it was already there
in the embryon from which I develop.

3. The sequence can be also compared with the typical human DNA (which is known because it
has been sequences few years ago).
Let's say we found that the corrisponding point of the typical human DNA reads as

alpha gamma

i.e. the part beta is missing.
This inidcates that the sequence beta has been added to the genome of some of my ancestor.
It cannot have been added to me (we already excluded that) so it must come from my parents.
Also my parents and grandpa showed the same insertion I show.
However, most humans "not closely related to me" do not show the insertion.


4. By scanning sequence beta we find the remain of genes which encode for viral proteins.
Such proteins are typical of virus. They are used by virus only.


5. We know viruses may add their genetic material to the host cell for reproducing.


6. We observed that sometimes (quite rarely) the virus can infect the cells for producing gamets.
In that case the viral insertion is passed to offsprings and becomes part of the family genome.
In that case they are called "Endogenous viral insertion".

There is no other known "natural" mechanism to insert such a long sequence as beta in
human DNA.
Hence either the material was inserted artificially (by UFOs, or God) or it was a virus infecting some of mine
ancestor of mine.
Can you imagine any other scenario?

7. IF it was a virus infecting an ancestor of mine (let's call it the "naturalistic explanation")
then I can predict that all descendents of him should share the same insertion at the same position.

[Here the first difficulty. We get our genome half from the father and half from the mother.
It is difficult to say if a relative of mine need to get the insertion since half of his DNA
is from people who are not my relatives. One could works with probabilities but the discussion becomes quite
difficult in that case.
However, there is an exception. The males get their Y chromosome from the father.]

Let us suppose that the found the sequence "alpha beta gamma" in my Y chromosome; then
all the male relatives of mine (I mean the one which are connected to me by going through the
male family tree; for example my cousin Mark is a male relative if he is the son of the brother
of my father.
He is not if he is the son of the brother of my mother.)
should share the same sequence at the same position.


8. I test all my brothers and male cousins and I found the same sequence of mine:

alpha beta gamma

9. Then I tests all second degree cousins of mine. I found that only the descendant of
my grandpa and one of his brother shared the same insertion at the same position.
My grandpa had other two brothers who did not shared the same insertions.
I still have some samples of their genetic material (they were kept as souvenirs! ))
and in fact they did not have the insertions.

Notice that the two brothers with the insertion are the two youngest brothers.
I might guess that my grandgrandpa got infected when he already had two sons and
passed the insertion to the youngest sons only.

10. Various comments:
a. Most of these observations are compatible with artificial action as well.
My grandgrandpa might have been kidnapped by UFOs who inserted the material.
This is, however, does not contradict the "common ancestor hypothesis".
As long as we assume that HE got the insertion which was then passed to descendants
we can always use the sharing of the sequence beta as a criteria to identify the
male components of my family. See below.

b. To break the common ancestor argument you should not only call for artificial action
but to assume that the UFO distributed the same insertion at the same position to many people
AND that they followed a specific patter in choosing who must be inserted.
The pattern being the one that appears to be same as a natural infection.
In this way the two scenarios of artificial disguise and the naturalistic scenario
look exactly the same. In other words they are undistinguishable.

c. ID claims they can produce evidences of the action of the designer. They do not need
a designer who acts in disguise.
So the intelligent disguise scenario is not what they are looking for.
Though I agree it is not a scenario we can rule out.


11. Then we can test many people who are not my male relatives.
None of them is found to share the same insertion at the same position.
Some of them are found to share the similar insertions at different positions.
This means that different virus of the same kind infected independently them or their ancestors.
We can see that sometimes it happens that one is found with a similar insertion at the same position.
It happens that 1/10000 insertions are found at the same position.
Though the insertions are found to be similar but not identical (by this I mean they differ by far too many
mutations to be the mutations occurring AFTER the infection).
I think that these guys have been infected independently but the insertion happened to be
at the same position.
One also can compute the probability of two independent infections to occur at the same position
to be 1/10000.

12. It happens also that one other family who is not connected to me share an identical insertion at the same position.
After some investigations we discovered that their grandgrandma lived next door to my grandgrandpa.
Of course we may imagine all sorts of explanations. I believe the most simple one is that
my grandgrandpa had an affair with their gramdgrandma. Something which can also be supported by sequencing
the rest of their DNA to look for other similarities or insertions.

13. In fact we found 7 endogeneous viral insertions which are shared by that family and my family.
Same insertions at the same positions.
Of course this does not rule out any other scenario (who can predict how UFO choose to act?)
though again they seem to act in disguise.

14. More important of what we see is what we do NOT see.
a. we never found the same insertion in the same location in a person whose grandgrandma
never met my grandgrandpa.
b. we never found a male cousin of mine without that insertion at the same position.

Any of these observation would kill the naturalistic scenario. That is the scentific way to ID.
Without it we are left at most with intelligent disguise.


This pattern has been observed many times, for different endogenous insertions.
It is beginning to be possible to follow human migrations checking insertions and mutations.
This genetic data does not contradict (pre)historical migration records.

The method has shown to be a reliable way of tracing the family tree on the bases of genetic studies.
On the other hand the family tree allows to predict genetic insertions which are then confirmed by direct
observations.

Is it a too wide gap to use the technique to infer family tree from genetic data
even when one has no other anagraphic data?

[Byblos]

I think an example can help. Byblos please go through it and tell me which step sound ok to you
and which needs more attention. Of course it is an example and numbers are just representative of
what actually happens.

Ok, sounds good. But just to clarify something, I'm not arguing for an ID case (although one can be made). My sole point of contention at this stage is that, while fully acknowledging that humans and chimps do share ERVs at the same insertion points and with the same sequences, to conclude a common ancestor based on that is to read too much into the data. The theory of common ancestry came long before discovering common ERVs. One side may see ERVs as a strengthening argument for common ancestry while another side may see it as an a-priori assumption particularly because the common ancestry came first. In other words, it was taken for granted that that must be the reason and no other one was explored. Read on.

[quote="angel"1. Let us say you sequence the DNA from a cell taken from the skin of my hand.
The sequence is a long series of four bases named T,G,A,C
within the sequence we isolate a subsequence which is divided in three consecutive
parts. Let us call the pasts:

alpha beta gamma

where each alpha="TTCGGTCAA...", beta="CGGCACCT..." and gamma="AACCGTGGGTC..." are genetic sequences.
Let us say for the sake of simplicity that each part is long 10,000 bases.


2. Then we test that that subsequence is found identical in each cell of my body.
Since we know that all the cells of my body should have the same DNA this could sound trivial.

Or it may sound silly to ask the following question: Are you sure? Is it not possible to have cells with slightly different DNA sequences?

However, it is know that, during our life, viruses may infect particular cells in our body
and they insert their genetic sequence in those cells. Some particular cell
may hence present a different DNA because of these viral insertions.

Hence my silly question above but I ask it for a different reason.

I think viruses are specialized in infecting particular systems and usually flue virus does
not infect liver cells, for example.
The fact that the sequence is found in any cell of my body indicates that it was already there
in the embryon from which I develop.

I'm not sure what you mean here. I thought viruses insert in some cells, not all. ERVs are not found in every cell; they are found in some cells, though the identical ones to chimps.

3. The sequence can be also compared with the typical human DNA (which is known because it
has been sequences few years ago).
Let's say we found that the corrisponding point of the typical human DNA reads as

alpha gamma

i.e. the part beta is missing.
This inidcates that the sequence beta has been added to the genome of some of my ancestor.
It cannot have been added to me (we already excluded that) so it must come from my parents.
Also my parents and grandpa showed the same insertion I show.
However, most humans "not closely related to me" do not show the insertion.

You lost me a bit here. If beta is missing, how does that indicate that it was added to the genome of your ancestors?

4. By scanning sequence beta we find the remain of genes which encode for viral proteins.
Such proteins are typical of virus. They are used by virus only.

So far as we can tell. They might have other unknown functions.

5. We know viruses may add their genetic material to the host cell for reproducing.

Yes, that's how viruses reproduce. It is one reason why they are not classified as living organisms, because they depend on the host DNA to reproduce.

6. We observed that sometimes (quite rarely) the virus can infect the cells for producing gamets.
In that case the viral insertion is passed to offsprings and becomes part of the family genome.
In that case they are called "Endogenous viral insertion".

I'm with you so far (my questions notwithstanding).

There is no other known "natural" mechanism to insert such a long sequence as beta in
human DNA.
Hence either the material was inserted artificially (by UFOs, or God) or it was a virus infecting some of mine
ancestor of mine.
Can you imagine any other scenario?

Let's not talk about UFOs or even God for that matter. Another possibility that comes to mind that is virtually indistinguishable from ERVs as a viral insertion is that ERVs are part and parcel of the DNA sequencing from the beginning. In other words, they weren't viruses that infected a distant relative and were passed down thru DNA but were part of original DNA sequencing. Is that a possibility?

7. IF it was a virus infecting an ancestor of mine (let's call it the "naturalistic explanation")
then I can predict that all descendents of him should share the same insertion at the same position.

[Here the first difficulty. We get our genome half from the father and half from the mother.
It is difficult to say if a relative of mine need to get the insertion since half of his DNA
is from people who are not my relatives. One could works with probabilities but the discussion becomes quite
difficult in that case.
However, there is an exception. The males get their Y chromosome from the father.]

Let us suppose that the found the sequence "alpha beta gamma" in my Y chromosome; then
all the male relatives of mine (I mean the one which are connected to me by going through the
male family tree; for example my cousin Mark is a male relative if he is the son of the brother
of my father.
He is not if he is the son of the brother of my mother.)
should share the same sequence at the same position.


8. I test all my brothers and male cousins and I found the same sequence of mine:

alpha beta gamma

9. Then I tests all second degree cousins of mine. I found that only the descendant of
my grandpa and one of his brother shared the same insertion at the same position.
My grandpa had other two brothers who did not shared the same insertions.
I still have some samples of their genetic material (they were kept as souvenirs! ))
and in fact they did not have the insertions.

Notice that the two brothers with the insertion are the two youngest brothers.
I might guess that my grandgrandpa got infected when he already had two sons and
passed the insertion to the youngest sons only.

10. Various comments:
a. Most of these observations are compatible with artificial action as well.
My grandgrandpa might have been kidnapped by UFOs who inserted the material.
This is, however, does not contradict the "common ancestor hypothesis".
As long as we assume that HE got the insertion which was then passed to descendants
we can always use the sharing of the sequence beta as a criteria to identify the
male components of my family. See below.

b. To break the common ancestor argument you should not only call for artificial action
but to assume that the UFO distributed the same insertion at the same position to many people
AND that they followed a specific patter in choosing who must be inserted.
The pattern being the one that appears to be same as a natural infection.
In this way the two scenarios of artificial disguise and the naturalistic scenario
look exactly the same. In other words they are undistinguishable.

c. ID claims they can produce evidences of the action of the designer. They do not need
a designer who acts in disguise.
So the intelligent disguise scenario is not what they are looking for.
Though I agree it is not a scenario we can rule out.

Again, let's stay away from ID, UFOs, and the like. The issue boils down to 2 possibilities: 1) Is it possible/probable that the same virus could infect 2 distinct species, insert themselves in the exact same positions, and produce the same protein sequencing, however remote that possibility/probability is? And 2) Is it possible/probable that these ERVs are not actually viral insertions after the fact but are part of the original DNA sequencing for reasons as yet unknown? If the answer to both questions is no, then you are begging the question of proof. If the answer is yes to at least one of them, then the common ancestry is by no means a settled issue. It is but a mere theory among many.

11. Then we can test many people who are not my male relatives.
None of them is found to share the same insertion at the same position.
Some of them are found to share the similar insertions at different positions.
This means that different virus of the same kind infected independently them or their ancestors.
We can see that sometimes it happens that one is found with a similar insertion at the same position.
It happens that 1/10000 insertions are found at the same position.
Though the insertions are found to be similar but not identical (by this I mean they differ by far too many
mutations to be the mutations occurring AFTER the infection).
I think that these guys have been infected independently but the insertion happened to be
at the same position.
One also can compute the probability of two independent infections to occur at the same position
to be 1/10000.

12. It happens also that one other family who is not connected to me share an identical insertion at the same position.
After some investigations we discovered that their grandgrandma lived next door to my grandgrandpa.
Of course we may imagine all sorts of explanations. I believe the most simple one is that
my grandgrandpa had an affair with their gramdgrandma. Something which can also be supported by sequencing
the rest of their DNA to look for other similarities or insertions.

13. In fact we found 7 endogeneous viral insertions which are shared by that family and my family.
Same insertions at the same positions.
Of course this does not rule out any other scenario (who can predict how UFO choose to act?)
though again they seem to act in disguise.

14. More important of what we see is what we do NOT see.
a. we never found the same insertion in the same location in a person whose grandgrandma
never met my grandgrandpa.
b. we never found a male cousin of mine without that insertion at the same position.

Any of these observation would kill the naturalistic scenario. That is the scentific way to ID.
Without it we are left at most with intelligent disguise.

And with it we are left long on assumptions and short on observable proof.

This pattern has been observed many times, for different endogenous insertions.
It is beginning to be possible to follow human migrations checking insertions and mutations.
This genetic data does not contradict (pre)historical migration records.

The method has shown to be a reliable way of tracing the family tree on the bases of genetic studies.
On the other hand the family tree allows to predict genetic insertions which are then confirmed by direct
observations.

Is it a too wide gap to use the technique to infer family tree from genetic data
even when one has no other anagraphic data?

I don't know the answer to that last question. What I do know is that it leaves me with the nagging question as to whether or not the theory of common ancestry has any meat to it. What I see is a bunch of similarities and a-priori assumptions. I see a theory that seems to work in one species being generalized inter-specially without any solid proof. I am not asserting a case for ID or God or UFOs or anything else. I am simply looking at the data as objectively as I possibly can and do not see how the leap from one species to another occurs without first assuming common ancestry. Why are the similarities highlighted but the differences ignored? Why are there differences between chimps and humans? If it's the result of random mutation and natural selection, these ERVs have not been shown to have possessed any adaptive functions. Why hasn't RD+NS gotten rid of them? Why are they still carried from one generation to the next? Could it be because they are part of the original DNA? ERVs as viral insertions and the conclusion of which as the result of common ancestry is but one possibility, plausible as it may sound. It is by no means the only one.

Byblos.

[bizzt]

This is really an awesome Discussion... Thanks for sharing both of you and for trying to keep it as respectable as possible.

[BGoodForGoodSake]

Or it may sound silly to ask the following question: Are you sure? Is it not possible to have cells with slightly different DNA sequences?

Generally, no. This is because all the cells in one's body originated from the single fertilized egg. Thus all the genetic material of all of these cells are likely to be the same barring random mutations.

I think viruses are specialized in infecting particular systems and usually flue virus does
not infect liver cells, for example.
The fact that the sequence is found in any cell of my body indicates that it was already there
in the embryon from which I develop.

I'm not sure what you mean here. I thought viruses insert in some cells, not all. ERVs are not found in every cell; they are found in some cells, though the identical ones to chimps.

No, ERV's are found in all somatic(body) cells. The ERV's shared between humans and chimps are in every cell of their respective bodies.

3. The sequence can be also compared with the typical human DNA (which is known because it
has been sequences few years ago).
Let's say we found that the corrisponding point of the typical human DNA reads as

alpha gamma

i.e. the part beta is missing.
This inidcates that the sequence beta has been added to the genome of some of my ancestor.
It cannot have been added to me (we already excluded that) so it must come from my parents.
Also my parents and grandpa showed the same insertion I show.
However, most humans "not closely related to me" do not show the insertion.

You lost me a bit here. If beta is missing, how does that indicate that it was added to the genome of your ancestors?

In this example we are comparing a single family to the rest of the human race. In the general population the "beta" sequence is missing. Hence the hypothesis that the "beta" sequence in this family is the result of a single insertion in the family's past.

Facts "beta" can be found in your whole family.
"Beta" is not found in the general population.
"Beta" looks like a retroviral insertion.
"Beta" appears to be hereditory.

Therefore "beta" must be the result of a viral infection which occurred in the families past.

4. By scanning sequence beta we find the remain of genes which encode for viral proteins.
Such proteins are typical of virus. They are used by virus only.

So far as we can tell. They might have other unknown functions.

They might, but so far the most likely explanation is that they are the result of a viral infection.

Another possibility that comes to mind that is virtually indistinguishable from ERVs as a viral insertion is that ERVs are part and parcel of the DNA sequencing from the beginning. In other words, they weren't viruses that infected a distant relative and were passed down thru DNA but were part of original DNA sequencing. Is that a possibility?

Yes but then we must find a function for these ERV's. As far as we can tell most of these ERV's are non-conserved

A conserved section of code suffers just as many mutations as a non conserved section.
However mutations in this section of the genome cause failure. Thus only those which have the code intact survive to produce offspring. thus the section of code is conserved.
Non-conserved means the following.
Mutations in this section of DNA will not cause an organism to fail. Mutations will occur at a predictable rate based on experimentally measured probabilities.

Think of it like swords throughout the middle ages. A swordssmith would pass down his knowledge of swordmaking from master to student.
If for some reason a student made a sword with a bad edge or his formula for making good steel was bad then the resulting sword would be scrapped. This part of the formula then is "conserved". However the section of the hilt has no "purpose" in terms of defence. Therefore modifications of hilt design and other decorative features of the sword changed quite readilly. Now the ERV cannot be compared to decorative features because it seems to lack any utility in many cases. Thus we can liken ERV's to the source of coke for steel production. It can remain the same from generation to generation, but it can also change at any time and have no effect on the resulting product whatsoever.

If it's the result of random mutation and natural selection, these ERVs have not been shown to have possessed any adaptive functions. Why hasn't RD+NS gotten rid of them? Why are they still carried from one generation to the next?

There is no mechanism to remove bad code. Why would you expect that natural selection would remove the code?

Junk DNA was not expected, but when it was discovered it makes perfect sence. Bad code cannot be "removed". There is no known mechanism for this. It will just get passed from generation to generation, collecting mutations thus junk DNA.

However most of the "junk DNA" doesn't appear to be junk at all. Not in the way just described.
A further understanding of the genetic code leads one to the realization that this "code" is a physical reactive molecule. The form of this code will cause it to interact with other functions of protein formation gene expression etc. It is simply because of this that one cannot compare DNA to computer code. Therefore everything will have a function in some way or another because it all interacts physically together.

[angel]

This is really an awesome Discussion... Thanks for sharing both of you and for trying to keep it as respectable as possible.

We are all here to learn from each other. And we are trying for our best.

But just to clarify something, I'm not arguing for an ID case (although one can be made).
My sole point of contention at this stage is that, while fully acknowledging that humans and chimps do share ERVs at the same insertion points and with the same sequences, to conclude a common ancestor based on that is to read too much into the data.
The theory of common ancestry came long before discovering common ERVs.
One side may see ERVs as a strengthening argument for common ancestry while another side may see it as an a-priori assumption particularly because the common ancestry came first. In other words, it was taken for granted that that must be the reason and no other one was explored. Read on.

I am aware you are not defending ID. It is however my intention and priviledge to remark under which points ID arguments are badly posed on a rational and observational point of view.

The fact that, chronologically speaking, "common ancestry" comes before ERV is not relevant, I think.
Democritus invented atoms (more than) 2000 years ago. His arguments are irrelevant if compared with modern evidences.
Similarly, common ancenstry was first guessed on paleontological and biological basis.
Not for that I should not consider new ERV evidences as the strongest evidencee in favor of it.
Please, I am aware you do not agree on the "strongest" part. I am here just rendering the lines of an argument. I would like you to consider (an possibly agree on) the structure of the argument more than on details which have to be judged on the basis of observations. Read on.

About the fact that common ancestor is one among many equally possible scenario I am a bit skeptical.
I have been said that thing many times but until now alternative scenarios never proved to be solid enough.
Of course this time could be different and it mostly depends on precisely which *other scenarios* you will suggest.
I suppose we are better to agree on facts first, be sure we understand facts in the same way and just afterwards discuss about interpretations of these facts. Do you agree?

Or it may sound silly to ask the following question

Let me tell you once for all: questions are never silly, only answers might be.

Is it not possible to have cells with slightly different DNA sequences?

I oversimplified for the sake of simplicity. But if you ask it, yes it is possible.
During cell multiplications errors occur. The result is that the new cell might be slightly different (in its DNA) from the original. This mechanism is well known and we know that for example in humans one has a specific
probability of mutation per each position per year.
Now imagine we know from that probability that we have 90% of having no mutations in the sequence alpha beta gamma
in the last 70 years, 9% of having 1 mutation, 0.9999998% of having two mutations and 0.0000002% of having 3 or more mutations.
Now when I said the sequence are identical in all cells I should have said they reflect such distribution.
That means that I do not expect to find a cell in my body (I mean a cell of mine, cos of course a bacteria in my body is not expected to have human dna at all) with a hundred mutations in the sequence alpha beta gamma.

Your remark allows me to stress another feature I had simplified away...
My cousing sequence is expected to be a bit more different from my sequence that my brother one.
That is because my brother sequence just accumulated the mutations of one life, while my cousin's one accumulated for two lives mutations (my uncle life and my cousin life).
The number of mutations in the sequence can be used to date for the last common ancestor.
This estimate can be then compared against historical or anagrafical data.

That is why I can distinguish a ERV from an independent infection. If my cousin got infected independently even at the same position, the beta sequence inserted by the virus would not be identical. It would have in general many more mutation than expected (because the virus itself evolves).

I hope now it is clearer.

ERVs are not found in every cell; they are found in some cells, though the identical ones to chimps.

I agree with bGood explanation. ERV are insertions we inheredited by parents.
We developed from a single cell. The material contained in that single cell (including the insertion beta) is copied in all our cells. And in all the cells of our sons and daughters.

What you say is correct for ordinary viral infections, not for the endogenous ones. If a virus infects me then its DNA is found in some of my cells only. If it infected sexual cells, that that insertion becomes endogenous in my sons.

The ERV we shared with chimps are in all human and chimp cells.

If beta is missing, how does that indicate that it was added to the genome of your ancestors?

beta is not part of the original human dna (being adam created or evolved! )
otherwise it would be shared by all humans (who all descend from adam, don't they?)
It is too long to have been produced by mutations.
It has hence be added at some point (either by a virus or by a designer).
It cannot be added by a virus to me directly (otherwise it would not be shared by all my cells as you remarked).
Of course the designer might have added it to all my cells. That would be intelligent disguise.
Or it must be a virus infecting some ancestor of mine.

If you want to suggest other scenarios please feel free. I think any scenario should be discussed separately analyzing its consequences
and possibly testing its predictions.

So far as we can tell. They might have other unknown functions.

There are two comments about that.
First, biologists can tell if a particular portion of DNA is used for encoding proteins.
The ERV are not. The portions of DNA which are not used for encoding proteins are called JUNK DNA.
In other words, ERV are known to be part of junk dna.
The expression junk dna does not mean that the portion has no function whatsoever, just not THAT function of encoding for proteins.

Second, in evolutionary biology one can test if a portion of dna has a function BEFORE knowing which function it is.
The test is based on natural selection. The possible mutations occurring in that part of dna can be divided in synonimous mutations and non-synonimous ones depending on which aminoacid the triple encodes for (there are more that one triple encoding for the same aminoacid;
if the mutation change one triple in another with the same meaning it is called synonimous).

Now synonimous and non-synonimous mutations both happen and if that area of dna is functionless the mutations simply accumulate. Since there is no function all mutations are neutral and selection does not enter.

If the dna portion has a function whatsoever, mutations can be malicious or beneficial. Selection suppresses malicious mutations and preserves beneficial mutations.
Now even if I do not know the function the natural selection action produce a frequency of different mutations which is not uniform.
Such non-uniform frequency is recognised to indicate some (possibly unknown) function of the dna.

I am sure you heard of the fact that some portions of junk dna have been found to have a SLIGHT non-uniform mutation rate indicating some unknown function.
(If you ever quoted these evidences, I would like to know how one could refer to this piece of evidence rejecting Darwinian evolution. The argument is BASED entirely on Darwinian assumptions on random mutations and natural selection. Do you agree?)

My point however, is that there is a precise observational quantitative definition of function which is not based on our knowledge of the specific function. Now ERVs have very little function in our genome, if any.
That is a fact we can look for scientific peer review support.
For now I am interested to know if you will accept the argument once data will be documented.

Another possibility that comes to mind that is virtually indistinguishable from ERVs as a viral insertion is that ERVs are part and parcel of the DNA sequencing from the beginning.
In other words, they weren't viruses that infected a distant relative and were passed down thru DNA but were part of original DNA sequencing. Is that a possibility?

Yes it is. It is what I called the "intelligent disguise".
I mean there is no way a viral 10000 long genetic sequence may be produced naturally in the expected time framework all within human junk dna.
But of course a designer can do what it pleases.
Still it is acting mimiking natural evolution (which is not what ID is claiming).
However, if it is part of the original human dna it must be shared by all humans (which is not the case we are discussing here) but I suppore you were here refering to the chimps-humans ERVs.
In that case the evolutionary answer to your question is a capital *YES*.
The ERV IS part of the original human genome. It has been inheredited by non-human ancestors in fact.

In any case the material origin is either viral or from intelligent disguise.
I mean it cannot be used as evidence for a designer in either case.
Unless you produce a different scenario to be discussed.

Again, let's stay away from ID, UFOs, and the like.

What a pity I like the ufos example. I was not using it to imply that your scenarios are silly.
I was implying only that EVEN allowing ID one is not necessarily lead to divine actions.
Let me drop it anyway, as you requested.

1) Is it possible/probable that the same virus could infect 2 distinct species, insert themselves
in the exact same positions, and produce the same protein sequencing, however remote that
possibility/probability is?

It seems to me a pretty remote possibility. Still I agree it is a possibility.
Notice that the very low possibility of ONE ERV to occur multiple times independently (ie. the possibility of ERV to be indistinguishable from viral insertions) is elevated to the 7th power in case of sever ERV shared.
Ending in a even lower probability.

Still it is a possibility. As it is a possibility that a child gets mine genome without being my son.
Would this falsify parental genetic tests used in courts?

2) Is it possible/probable that these ERVs are not actually viral insertions after the fact but are part
of the original DNA sequencing for reasons as yet unknown?

Not in my example because the beta insertion is not shared by everybody.
For human-chimps insertions are in fact part of the original human genome since they come from non-human ancestors.

If the answer is yes to at least one of them, then the common ancestry is by no means a settled issue.
It is but a mere theory among many.

I disagree on this. Although I may agree that there is a remote possibility, not all possible scenarios are equally good. I suppose we agree that one can consider as possible the scenario in which humans
are assembled by chance in a livingless world. Not for that that scenario is likely to occur.
If you want to present those scenarios as alternatives to evolutionary evolution we have to be more precise on details and show that they are as good as the scenario you want to fight.
If you are looking for a qualitative claim that many scenarios are possible (though it is not your intention to argue about how likely they are) well I might agree since the beginning.

And with it we are left long on assumptions and short on observable proof.

I am not sure I got your point here. If you are referring to the fact that we don't see the items listed and you consider it as some shortness in observation I have to clarify what I posted.
The fact that we never see the item listed is a positive evidence, not a lack of observation.
It would be a negative argument if we were not able to test what happens, if the listed items or the opposite.
THIS IS NOT THE CASE. We see many instances of the opposite and no instance of the listed items.

Since in many non-naturalistic explanations there is no a priori reason to assume that only the opposite of the item listed must occur, we are back again to intelligent disguise.



Please tell me if you change your mind about any of the points above. And let us summarize the main argument again.


I agree with everything Bgood posted as well. Probably you should be able to review your position crossing the twoposts. If something sounds contradictory please let us know.

PS: Thanks Bgood for "hereditory". Now I know how it is spelled, finally. I'll try to remember it.


BTW It is my opinion that the "function" of junk DNA might be in improve evolvability. It is like for representation problem in evolutionary systems.
The genotype --> fenotype map (which by definition does not affect fitness) has been shown to be under selective control.
In the same way junk DNA might be under selective control even without affecting the fitness.
But that is just an opinion of mine, otherwise I would be a pretty famous biologist!