[_ Old Earth _] Theory of Evolution crash course/Q&A

[felix]

You've already learned that the ENCODE researchers said nothing of the sort. In fact, their finding is that mutations and natural selection are required for evolution to proceed:

Evolution is the process by which organisms change over time. Mutations produce genetic variation in populations, and the environment interacts with this variation to select those individuals best adapted to their surroundings. The best-adapted individuals leave behind more offspring than less well-adapted individuals. Given enough time, one species may evolve into many others.

http://www.genome.gov/Glossary/index.cfm?id=60

That is the statement of the ENCODE team, concerning evolution. As you see, they have found exactly the opposite of what you've attributed to them.

The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation.

(The ENCODE Project Consortium, "An integrated encyclopedia of DNA elements in the human genome," Nature, Vol. 489:57-74 (September 6, 2012)

ENCODE didn't say "mutations are no longer a viable source to evolution" - but their results do. If there is no or little junk DNA then there is no possibility of speciation.

 

[Barbarian]

The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation.

I already showed you that. And none if it remotely says what you claimed it does.

ENCODE didn't say "mutations are no longer a viable source to evolution"

You bet they didn't.

but their results do.

In fact, they said the opposite. Francis Collins, their director, is an evangelical Christian, and he points out that their work supports evolution. It's a little bit of concern that you didn't make it clear this odd idea was yours, not theirs.

If there is no or little junk DNA then there is no possibility of speciation.

Before anyone knew of non-coding DNA, no one thought DNA was a problem for evolutionary theory. But feel free to show us why you think so. The fact that the people who know most about the issue don't agree with you is a pretty good clue that you're wrong.

 

[felix]

I already showed you that. And none if it remotely says what you claimed it does.



You bet they didn't.



In fact, they said the opposite. Francis Collins, their director, is an evangelical Christian, and he points out that their work supports evolution. It's a little bit of concern that you didn't make it clear this odd idea was yours, not theirs.

If there is no or little junk DNA then there is no possibility of speciation.

Before anyone knew of non-coding DNA, no one thought DNA was a problem for evolutionary theory. But feel free to show us why you think so. The fact that the people who know most about the issue don't agree with you is a pretty good clue that you're wrong.

What does Francis Collins being an evangelical Christian have anything to do with results of ENCODE ?

Twelve years after the completion of the Human Genome Project, its successor made a big splash with one big number: Around 80 percent of the human genome is "functional," the researchers leading the Encyclopedia of DNA Elements (ENCODE) project said. Their claim drew immediate criticism from biologists, many of whom said it is evolutionarily impossible for so much of the genome to truly function for human health.

Ref: http://www.scientificamerican.com/article.cfm?id=friction-over-function-encode

I think every evolutionary biologist except you think there is a problem ;)

I suggest you read the critiques of ENCODE: http://gbe.oxfordjournals.org/content/early/2013/02/20/gbe.evt028.full.pdf

It states:
We have already seen that ENCODE uses an evolution-free definition of “functionality.”

and the response for it:
http://www.guardian.co.uk/science/2013/feb/24/scientists-attacked-over-junk-dna-claim

ENCODE is right in every way, only the evolutionists are jumping up and down.

The Encode project involved 442 researchers, based at 32 institutes, who used 300 years of computer time and five years in the lab to get their results.

I like this response from ENCODE:
But Birney said: "I think this attack is really a complaint about big science, about big projects that absorb lots of money. These people don't like that."

 

[Barbarian]

What does Francis Collins being an evangelical Christian have anything to do with results of ENCODE ?

He's the director of the project.

Twelve years after the completion of the Human Genome Project, its successor made a big splash with one big number: Around 80 percent of the human genome is "functional," the researchers leading the Encyclopedia of DNA Elements (ENCODE) project said. Their claim drew immediate criticism from biologists, many of whom said it is evolutionarily impossible for so much of the genome to truly function for human health.

And support from other biologists. The findings are still controversial; they may yet be shown to be correct. This is why there are so many biologists on both sides of the issue.

I think every evolutionary biologist except you think there is a problem

Francis Collins clearly doesn't see it as a difficulty for evolution. Since the 70s, people have been working at seeing how much of non-coding DNA is actually functional. But I'd be interested in seeing your poll of scientists on this issue, and your evidence for it. I'm guessing you just made it up. Show us what you have.

I suggest you read the critiques of ENCODE

I'm guessing you haven't read a lot of the comments. The most strident was by Graur et al, who, I think, went over the line in their attack. There are some concerns about the methodology, which Graur did include in his paper, but there are certainly some unfair and even misleading claims therein.

On the other hand, as you learned earlier, the fact that some non-coding DNA is functional has been known since the 60s. Over the years, more of it has been identified, but 80% is probably an overestimate, given the way that the ENCODE scientists estimated it.

I suspect you haven't read the report or the literature about it.

It states:
We have already seen that ENCODE uses an evolution-free definition of “functionality.â€

Graur's paper. Most biologists, even those who doubt the 80% claim, have criticized Graur et al for the unrestrained (and unfair) characterization of the report as being "evolution-free."

ENCODE is right in every way, only the evolutionists are jumping up and down.

The ENCODE scientists are evolutionists. Collins, for example, has written a book explaining how evolution is consistent with Christian belief. You've been lied to about who's on each side of the controversy. As you learned here, ENCODE scientists explain how their discovery fits evolutionary theory.

I like this response from ENCODE:
But Birney said: "I think this attack is really a complaint about big science, about big projects that absorb lots of money. These people don't like that."

Might be some of that. Unlike a lot of scientific disciplines, a lot of the best science comes out of relatively small, underfunded projects. It's the nature of biology.

But no one can say that the Human Genome Project wasn't a huge step forward in evolutionary science. It allowed us to understand a great deal more about those things that evolved to make us human.

This analysis perhaps explains the issue in a more understandable way:

Recent analysis by the ENCODE project indicates that 80% of the entire human genome is either transcribed, binds to regulatory proteins, or is associated with some other biochemical activity.[2]

It however remains controversial whether all of this biochemical activity contributes to cell physiology, or whether a substantial portion of this is the result transcriptional and biochemical noise, which must be actively filtered out by the organism.[11] Excluding protein-coding sequences, introns, and regulatory regions, much of the non-coding DNA is composed of: Many DNA sequences that do not play a role in gene expression have important biological functions. Comparative genomics studies indicate that about 5% of the genome contains sequences of noncoding DNA that are highly conserved, sometimes on time-scales representing hundreds of millions of years, implying that these noncoding regions are under strong evolutionary pressure and positive selection.[12]
http://en.wikipedia.org/wiki/Human_genome_sequence_map

 

[felix]

He's the director of the project.



And support from other biologists. The findings are still controversial; they may yet be shown to be correct. This is why there are so many biologists on both sides of the issue.



Francis Collins clearly doesn't see it as a difficulty for evolution. Since the 70s, people have been working at seeing how much of non-coding DNA is actually functional. But I'd be interested in seeing your poll of scientists on this issue, and your evidence for it. I'm guessing you just made it up. Show us what you have.

I suggest you read the critiques of ENCODE

I'm guessing you haven't read a lot of the comments. The most strident was by Graur et al, who, I think, went over the line in their attack. There are some concerns about the methodology, which Graur did include in his paper, but there are certainly some unfair and even misleading claims therein.

On the other hand, as you learned earlier, the fact that some non-coding DNA is functional has been known since the 60s. Over the years, more of it has been identified, but 80% is probably an overestimate, given the way that the ENCODE scientists estimated it.

I suspect you haven't read the report or the literature about it.

It states:
We have already seen that ENCODE uses an evolution-free definition of “functionality.”

Graur's paper. Most biologists, even those who doubt the 80% claim, have criticized Graur et al for the unrestrained (and unfair) characterization of the report as being "evolution-free."

ENCODE is right in every way, only the evolutionists are jumping up and down.

The ENCODE scientists are evolutionists. Collins, for example, has written a book explaining how evolution is consistent with Christian belief. You've been lied to about who's on each side of the controversy. As you learned here, ENCODE scientists explain how their discovery fits evolutionary theory.

I like this response from ENCODE:
But Birney said: "I think this attack is really a complaint about big science, about big projects that absorb lots of money. These people don't like that."

Might be some of that. Unlike a lot of scientific disciplines, a lot of the best science comes out of relatively small, underfunded projects. It's the nature of biology.

But no one can say that the Human Genome Project wasn't a huge step forward in evolutionary science. It allowed us to understand a great deal more about those things that evolved to make us human.

This analysis perhaps explains the issue in a more understandable way:

Recent analysis by the ENCODE project indicates that 80% of the entire human genome is either transcribed, binds to regulatory proteins, or is associated with some other biochemical activity.[2]

It however remains controversial whether all of this biochemical activity contributes to cell physiology, or whether a substantial portion of this is the result transcriptional and biochemical noise, which must be actively filtered out by the organism.[11] Excluding protein-coding sequences, introns, and regulatory regions, much of the non-coding DNA is composed of: Many DNA sequences that do not play a role in gene expression have important biological functions. Comparative genomics studies indicate that about 5% of the genome contains sequences of noncoding DNA that are highly conserved, sometimes on time-scales representing hundreds of millions of years, implying that these noncoding regions are under strong evolutionary pressure and positive selection.[12]
http://en.wikipedia.org/wiki/Human_genome_sequence_map

Junk DNA plays a crucial role in evolution:
http://www.sciencedaily.com/releases/2009/05/090528203730.htm

Without Junk DNA no evolution. It does not depend on evolutionist's opinion.

 

[Barbarian]

Junk DNA plays a crucial role in evolution:
http://www.sciencedaily.com/releases...0528203730.htm

Nope. It says pretty much the opposite:
Researchers at K.U. Leuven and Harvard University show that stretches of DNA previously believed to be useless 'junk' DNA play a vital role in the evolution of our genome.

It says, rather that some parts of non-coding DNA, formerly thought to have no function, is important in evolution. Pretty much exactly the opposite of what you claimed it said.

Without Junk DNA no evolution.

Surprise. Read it carefully, and learn.

 

[felix]

Junk DNA plays a crucial role in evolution:
http://www.sciencedaily.com/releases...0528203730.htm

Nope. It says pretty much the opposite:
Researchers at K.U. Leuven and Harvard University show that stretches of DNA previously believed to be useless 'junk' DNA play a vital role in the evolution of our genome.

It says, rather that some parts of non-coding DNA, formerly thought to have no function, is important in evolution. Pretty much exactly the opposite of what you claimed it said.

Without Junk DNA no evolution.

Surprise. Read it carefully, and learn.

I believe I understood correctly. The statement clearly says: previously believed to be useless 'junk' DNA play a vital role in the evolution of our genome.

If there is no Junk DNA, then there is nothing to play a vital role in evolution

 

[felix]

The ENCODE scientists are evolutionists. Collins, for example, has written a book explaining how evolution is consistent with Christian belief.

Can you please explain how evolution is consistent with Christian belief?
From your profile, I can see you are also a Christian. So, make me understand how Evolution fits Christian belief.

 

[VirginShallConceive]

The ENCODE scientists are evolutionists. Collins, for example, has written a book explaining how evolution is consistent with Christian belief.

Can you please explain how evolution is consistent with Christian belief?

Short answer:

It isn't.

From your profile, I can see you are also a Christian. So, make me understand how Evolution fits Christian belief.

Can you admit that there is more evidence for Evolution than there is for what Christians believe?

 

[Barbarian]

From your link:
Researchers at K.U. Leuven and Harvard University show that stretches of DNA previously believed to be useless 'junk' DNA play a vital role in the evolution of our genome.

It saysr that some parts of non-coding DNA, formerly thought to have no function, are important in evolution. Pretty much exactly the opposite of what you claimed it said.

Without Junk DNA no evolution.

Surprise. Read it carefully, and learn.

I believe I understood correctly.

Doesn't matter. It clearly states that non-coding DNA play an important part in evolution.

The statement clearly says: previously believed to be useless 'junk' DNA play a vital role in the evolution of our genome.

If there is no Junk DNA

It doesn't say there is no non-coding DNA. It just says that parts of it, rather than doing nothing, has an important role in evolution.

No way to get out of that.

 

[Barbarian]

Can you please explain how evolution is consistent with Christian belief?

Because it's consistent with Genesis and with Apostolic tradition. St. Augustine, for example, showed that creation occurred instantly, and from that initial creation, all other things developed. (as God says in Genesis, having living thing brought forth from the earth, rather than ex nihilo)

From your profile, I can see you are also a Christian. So, make me understand how Evolution fits Christian belief.

It's just a matter of accepting his creation with no reservations.

 

[felix]

The ENCODE scientists are evolutionists. Collins, for example, has written a book explaining how evolution is consistent with Christian belief.

Can you please explain how evolution is consistent with Christian belief?

Short answer:

It isn't.

Yes, exactly! But I will wait for Barbarian's reply to understand why he referred Collins's view and his own view on how Evolution is consistent with Christianity because he is a Christian.

 

[felix]

Can you please explain how evolution is consistent with Christian belief?

Because it's consistent with Genesis and with Apostolic tradition. St. Augustine, for example, showed that creation occurred instantly, and from that initial creation, all other things developed. (as God says in Genesis, having living thing brought forth from the earth, rather than ex nihilo)

From your profile, I can see you are also a Christian. So, make me understand how Evolution fits Christian belief.

It's just a matter of accepting his creation with no reservations.

I still don't understand how it is consistent with evolution?

Can you please help me understand better like - what is the "role of God" in creation?

 

[Barbarian]

I still don't understand how it is consistent with evolution?

It's like asking how trees or people are consistent with evolution. How could they not be?

Can you please help me understand better like - what is the "role of God" in creation?

God creates everything. It's just that after the initial creation, He used nature to do most of it. Hence evolution is consistent with His word in Genesis, while some forms of creationism are not.

 

[felix]

Can you please help me understand better like - what is the "role of God" in creation?

God creates everything. It's just that after the initial creation, He used nature to do most of it. Hence evolution is consistent with His word in Genesis, while some forms of creationism are not.

If God USED nature to do most of it, would that constitute artificial selection and NOT natural selection?

I think you still don't understand the definition of Evolution. Evolution has no place for "artificial selection".

 

[Milk-Drops]

Can you please help me understand better like - what is the "role of God" in creation?

God creates everything. It's just that after the initial creation, He used nature to do most of it. Hence evolution is consistent with His word in Genesis, while some forms of creationism are not.

If God USED nature to do most of it, would that constitute artificial selection and NOT natural selection?

I think you still don't understand the definition of Evolution. Evolution has no place for "artificial selection".

Felix what is your educational background? Its getting annoying that you have been telling Barbarian, who holds a Masters in biology, that he doesn't know the criteria. Barbarian seems to be the only one really responding to what you are saying, so what do you think you are accomplishing here by twisting data and words around? I'm just curious about both of these, yet I don't really expect you to answer either.

 

[Barbarian]

If God USED nature to do most of it, would that constitute artificial selection and NOT natural selection?

If you think nature is "artificial", I suppose. It seems perverse to do that.

I think you still don't understand the definition of Evolution. Evolution has no place for "artificial selection".

In fact, evolution would work with artificial selection. Remember, evolution is a change in allele frequency in a population over time.

 

[felix]

If God USED nature to do most of it, would that constitute artificial selection and NOT natural selection?

If you think nature is "artificial", I suppose. It seems perverse to do that.

If God USED nature for evolution then it is "artificial selection" not "natural selection". If you are trying hard to prove that God using nature is "not artificial", what you are actually doing is trying to prove that god is a non-living, non-intelligent, dumb random being (I believe that is NOT the God who created the Heavens and Earth).

I think you still don't understand the definition of Evolution. Evolution has no place for "artificial selection".

In fact, evolution would work with artificial selection. Remember, evolution is a change in allele frequency in a population over time.

Mechanisms of evolution does not include "artificial selection" - you should be knowing that.

 

[Barbarian]

If God USED nature to do most of it, would that constitute artificial selection and NOT natural selection?

Barbarian chuckles:
If you think nature is "artificial", I suppose. It seems perverse to do that.

If God USED nature for evolution then it is "artificial selection" not "natural selection". If you are trying hard to prove that God using nature is "not artificial", what you are actually doing is trying to prove that god is a non-living, non-intelligent, dumb random being

Nope. You're confusing the hammer with the Carpenter.

(I believe that is NOT the God who created the Heavens and Earth).

The Bible says He is. I believe Him.

I think you still don't understand the definition of Evolution. Evolution has no place for "artificial selection".

Barbarian observes:
In fact, evolution would work with artificial selection. Remember, evolution is a change in allele frequency in a population over time.

Mechanisms of evolution does not include "artificial selection"

Demonstrably, it does. It works just like natural selection. There is random mutation that produces new variation. Then those that are most fit get to reproduce. And then the new population, produced by that selection, again reproduces and the cycle continues. Same for both.

you should be knowing that.

I think, if you gave it some thought, you would get it.

 

[felix]

Barbarian chuckles:
If you think nature is "artificial", I suppose. It seems perverse to do that.

That's the problem. Artificial does not mean ONLY humans. It could also mean ANY intelligent beings.
We are created in the image of God. If what we do is "artificial" how can you say if God Himself did something is not artificial?

If you think God using nature, so does the mutations are NOT random but it can be considered a "process of designing" by God rather than "evolving without a goal".