I'm excited by the first results of the ENCODE project

[ChetSinger]

I'm referring to the "ENCODE Project Consortium", the largest attempt ever to map the human genome.

For years I've been beaten about by atheists who pointed to our genome and claimed that because 90% of it was leftover evolutionary junk, we clearly weren't designed. After all, what's junk isn't designed, right?

But now it looks like at least 80% of it is active. Here's the abstract from one of the papers released last fall:

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. 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 newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

Here's a link to the article itself: An integrated encyclopedia of DNA elements in the human genome

This was completely unexpected by atheists I converse with, and I think is great testimony of God's design.

 

[SkyWriting]

I'm referring to the "ENCODE Project Consortium", the largest attempt ever to map the human genome.
For years I've been beaten about by atheists who pointed to our genome and claimed that because 90% of it was leftover evolutionary junk, we clearly weren't designed. After all, what's junk isn't designed, right?
But now it looks like at least 80% of it is active. Here's the abstract from one of the papers released last fall:
Here's a link to the article itself: An integrated encyclopedia of DNA elements in the human genome

This was completely unexpected by atheists I converse with, and I think is great testimony of God's design.

The implication is that 100% is in use. Consider that my dad was born before DNA was confirmed. So the field is young. With 80% confirmed as "non-junk" the remaining percentage will most likely be crossed off the junk list as well.





"a ‘Function’ for Junk DNA? Facts and Hypotheses"

" Our conclusion is that, in animals but not in plants, most of the “junk” is intron DNA."

 

[ChetSinger]

The implication is that 100% is in use. Consider that my dad was born before DNA was confirmed. So the field is young. With 80% confirmed as "non-junk" the remaining percentage will most likely be crossed off the junk list as well.

"a ‘Function’ for Junk DNA? Facts and Hypotheses"

" Our conclusion is that, in animals but not in plants, most of the “junk” is intron DNA."

I agree that's likely. The ENCODE project hasn't yet mapped all of the kinds of cells we have. Also, what other functions might remain undetected because they're turned on only during our embryonic stage, as we're being assembled?

 

[mark kennedy]

I'm referring to the "ENCODE Project Consortium", the largest attempt ever to map the human genome.

For years I've been beaten about by atheists who pointed to our genome and claimed that because 90% of it was leftover evolutionary junk, we clearly weren't designed. After all, what's junk isn't designed, right?

But now it looks like at least 80% of it is active...

This was completely unexpected by atheists I converse with, and I think is great testimony of God's design.

I remember about 5 years ago I stumbled onto research into how the genome uses parts thought to be nonfunctional. Apparently the genome can create an RNA single stranded molecular mechanism virtually anywhere in the code. It's a fascinating area of research and I'm glad you have taken an interest.

Would you like to explore the paper further?

Grace and peace,
Mark

 

[ChetSinger]

I remember about 5 years ago I stumbled onto research into how the genome uses parts thought to be nonfunctional. Apparently the genome can create an RNA single stranded molecular mechanism virtually anywhere in the code. It's a fascinating area of research and I'm glad you have taken an interest.

Would you like to explore the paper further?

Grace and peace,
Mark

Sure! But I should warn you that I'm no expert so I can't promise how well I'll follow it.

 

[Carmella Prochaska]

After analyzing all of the different kinds of genomic elements, the project found:

Accounting for all these elements, a surprisingly large amount of the human genome, 80.4%, is covered by at least one ENCODE-identified element. The broadest element class represents the different RNA types, covering 62% of the genome (although the majority is inside of introns or near genes). Regions highly enriched for histone modifications form the next largest class (56.1%). Excluding RNA elements and broad histone elements, 44.2% of the genome is covered. Smaller proportions of the genome are occupied by regions of open chromatin (15.2%) or sites of transcription factor binding (8.1%), with 19.4% covered by at least one DHS or transcription factor ChIP-seq peak across all cell lines.

The paper concludes that researchers have uncovered an "unprecedented number of functional elements":

The unprecedented number of functional elements identified in this study provides a valuable resource to the scientific community as well as significantly enhances our understanding of the human genome.

And of course, the implications of this study for fighting disease are profound:

The broad coverage of ENCODE annotations enhances our understanding of common diseases with a genetic component, rare genetic diseases, and cancer, as shown by our ability to link otherwise anonymous associations to a functional element.

The NY Times further commented on the complexity of what we're finding:
There also is a sort of DNA wiring system that is almost inconceivably intricate.

"It is like opening a wiring closet and seeing a hairball of wires," said Mark Gerstein, an Encode researcher from Yale. "We tried to unravel this hairball and make it interpretable."
There is another sort of hairball as well: the complex three-dimensional structure of DNA. Human DNA is such a long strand -- about 10 feet of DNA stuffed into a microscopic nucleus of a cell -- that it fits only because it is tightly wound and coiled around itself. When they looked at the three-dimensional structure -- the hairball -- Encode researchers discovered that small segments of dark-matter DNA are often quite close to genes they control. In the past, when they analyzed only the uncoiled length of DNA, those controlling regions appeared to be far from the genes they affect.

Tom Gingeras, a senior scientist affiliated with ENCODE, states that "Almost every nucleotide is associated with a function":

According to ENCODE's analysis, 80 percent of the genome has a "biochemical function". More on exactly what this means later, but the key point is: It's not "junk". Scientists have long recognised that some non-coding DNA probably has a function, and many solid examples have recently come to light. But, many maintained that much of these sequences were, indeed, junk. ENCODE says otherwise. "Almost every nucleotide is associated with a function of some sort or another, and we now know where they are, what binds to them, what their associations are, and more," says Tom Gingeras, one of the study's many senior scientists.

 

[SkyWriting]

I agree that's likely. The ENCODE project hasn't yet mapped all of the kinds of cells we have. Also, what other functions might remain undetected because they're turned on only during our embryonic stage, as we're being assembled?

Plus much of the "Junk" has been found to be of "mechanical" use and brilliant design. Much has been found to be structures that aid in the process of other mechanical changes. And more has been found to be "options" for different environments but they only get used as needed. In this way a population can evolve very quickly to changing factors.

 

[Papias]

Chetsinger wrote:

I'm excited by the first results from the ENCODE project

So am I! What a glorious creation God has made!

But now it looks like at least 80% of it is active. Here's the abstract from one of the papers released last fall:

Be careful not to misunderstand that. It says that 80% has a biochemical function - that only means that it is transcribed and changes something biochemically. That doesn't mean the resulting chemical is useful or good, and certainly doesn't say it is necessary or evidence of "design". This is because the chemical reaction it causes can be a "dead end" - that chemical could be not used and just cleaned up as debris afterwards. For instance, think of a tin can in your garbage - metal in the can can be said to have a "function" - it makes up the wall of the tin can - but it is still useless garbage.

It may well be that 80% is "useful". We don't know yet. However, regardless of whether or not 80% is found to be useful and needed, the fact that the genome refutes any design argument is clear for a number of reasons.

• Sections of genome are made up of ERVs - we can see how they got there, and it wasn't design
• Sections of the genome are made up of psuedogenes - broken, redundant copies of other functional genes
• The genomes of many, many animals refute the design hypothesis, for instance, two identical paramecia one of which has a genome over 20 times the total size of the other paramecia's genome. If the information for a paramecium could be encoded in the smaller genome, then what is the majority of the other paramecia's genome for?
• The C-value paradox itself refutes design, by showing that organism complexity is unrelated to genome size.
• The entire human genome has many cases where descent is as clear as a paternity test
• The scientists who are a part of this study don't dispute evolution - and they know their ENCODE data better than us.
• Broken genes like our broken vitamin C gene (look up the gulop gene) - would a designer design in a broken gene?
• and so on........

Plus, the whole design hypothesis has been repeatedly refuted by overall animal designs, as show by the examples in post #4 of this thread:

http://www.christianforums.com/t7712553/

These, along with the genetic evidence, mean that anyone who says God designed the details of our bodies or those of other animals is in effect calling God incompetent or cruel.

For years I've been beaten about by atheists who pointed to our genome and claimed that because 90% of it was leftover evolutionary junk, we clearly weren't designed.

I think this is the import point. We cannot allow atheists to use any of this to make atheism look like an acceptable conclusion. For all the evidence against detailed design, both the sloppyness of our genome or the other ones mentioned earlier, pointing out that God is not a micromanager restores God as creator.

Common descent by evolution not only fits the data, but shows why we have all of these things, and are still created by God, who used evolution to create. Arguing against evolution only makes us into reality deniers, and discredits Christianity as a realistic option. That's why a recent Barna poll showed that evolution denial is one of the main reasons why people are leaving Christianity.

Papias

 

[sfs]

The ENCODE papers were one of the more annoying pieces of scientific flim-flam in my memory. The project itself and its results are great. ENCODE is basically a boring but really useful cataloging project, whose goal was to list everything that could currently be determined about the entire genome. This list is enormously useful for all kinds of other research.

The results were dressed up, however, to make them sound sexier, both in the main paper and in the press releases and interviews associated with the project. Announcing that 80% of the genome had a function got them on the front page of the NY Times, but badly obscured what their results actually meant. By any normal definition of "function", ENCODE did not show that 80% of the genome had function. They showed that 80% was somehow biochemically active. I've heard one of our ENCODE researchers (my research institute was one of the institutions involved in the project) say in a talk that what they really showed was that no more than 20% of the genome had a real function, meaning that the sequence present in at least 80% of the genome makes no difference to the well-being of the organism. At this point, 90% of the genome is still probably junk, and there are quite strong reasons for thinking that this is simply the way the genome is.

 

[SkyWriting]

The ENCODE papers were one of the more annoying pieces of scientific flim-flam in my memory. The project itself and its results are great. ENCODE is basically a boring but really useful cataloging project, whose goal was to list everything that could currently be determined about the entire genome. This list is enormously useful for all kinds of other research. The results were dressed up, however, to make them sound sexier, both in the main paper and in the press releases and interviews associated with the project. Announcing that 80% of the genome had a function got them on the front page of the NY Times, but badly obscured what their results actually meant. By any normal definition of "function", ENCODE did not show that 80% of the genome had function. They showed that 80% was somehow biochemically active. I've heard one of our ENCODE researchers (my research institute was one of the institutions involved in the project) say in a talk that what they really showed was that no more than 20% of the genome had a real function, meaning that the sequence present in at least 80% of the genome makes no difference to the well-being of the organism. At this point, 90% of the genome is still probably junk, and there are quite strong reasons for thinking that this is simply the way the genome is.

That's some sweet Jibber-Jabber there. If only you had any science for backing.



Whole Genome Duplications and a ‘Function’ for Junk DNA? Facts and Hypotheses

Is “Junk” DNA Mostly Intron DNA?

Anecdotal, Historical and Critical Commentaries on Genetics:
A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution

 

[SkyWriting]

Be careful not to misunderstand that. It says that 80% has a biochemical function - that only means that it is transcribed and changes something biochemically. That doesn't mean the resulting chemical is useful or good...

The odds of any DNA having no positive value are zero. And that would be from a natural perspective. It's a biological energy thing.
Not much gets wasted but except what is relieved behind bushes.

 

[sfs]

The odds of any DNA having no positive value are zero. And that would be from a natural perspective. It's a biological energy thing.
Not much gets wasted but except what is relieved behind bushes.

No, that's really not true. Everything is a trade-off in biology. Eliminating junk DNA (e.g. new transposable elements) also requires energy, so it's not clear that doing so would actually be beneficial to the organism. It also requires a strong enough selective pressure to make for it to matter; if the selective advantage of any variant is less than ~1/4N, the variant is effectively neutral, and selection will matter little. The effect of varying amounts of nonfunctional DNA is likely very, very small for eukaryotes; this explains why some simple eukaryotes (like some amoebas) have far more DNA than humans do. It really makes very little difference.

 

[ChetSinger]

I've been watching the subject of junk DNA from a distance for about ten years now, and I see a clear trend: what we've been calling junky is slowly being understood to be functional. So now I think those initial pronouncements of junk included some ignorance and arrogance.

Paul wrote that the creation points to the creator. Is it a coincidence that just as we think we have it all figured out, we learn of a new level of complexity?

1. Naturalists in Europe once believed in spontaneous generation, contrary to church teaching that all living things came from parents. Then spontaneous generation was debunked by Louis Pasteur.
2. Charles Darwin's generation thought that cells were little blobs that could be assembled without difficulty. Then we began learning about cellular chemistry.
3. In the 1950s, the Miller-Urey experiment was thought to demonstrate that abiogenesis wouldn't be so difficult to duplicate. Then we discovered DNA.
4. Recently, our genome was thought to be almost completely made of leftover evolutionary junk. Now, every year brings new papers demonstrating how more of that "junk" seems to be doing something.

I think that as believers this evidence of God's workmanship is something to celebrate, and to evangelize with.

 

[sfs]

That's some sweet Jibber-Jabber there. If only you had any science for backing.



Whole Genome Duplications and a ‘Function’ for Junk DNA? Facts and Hypotheses

Is “Junk” DNA Mostly Intron DNA?

Anecdotal, Historical and Critical Commentaries on Genetics:
A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution

I have quite a lot of science for backing; here is a nice summary of some of it.

As I recall, the last time you made scientific claims to me and posted links to scientific papers, you later said that the papers weren't supposed to support the claim. (Apparently they were for decoration or something.) Which is it this time: are these papers relevant to the claim that 80% of the genome has a real function or not?

 

[Papias]

We are pretty fortunate to have an actual Christian geneticist posting here, who has the expertise to help us sort through a very complex topic. Thanks sfs!

Papias

 

[SkyWriting]

I have quite a lot of science for backing; here is a nice summary of some of it.

That link is to a BLOG. The BLOG states that "Noncoding DNA is part junk, part regulatory, part unknown."

So that's either 1 or 2 thirds useful with the last third defined as "unknown".
A perfectly logical conclusion is that the last 2/3 or 1/3 third is simply not yet understood. Given that my parents saw the discovery of DNA in the news, likely we don't currently know 1/1000 of what we will know in 20 years.

As I recall, the last time you made scientific claims to me and posted links to scientific papers, you later said that the papers weren't supposed to support the claim. (Apparently they were for decoration or something.) Which is it this time: are these papers relevant to the claim that 80% of the genome has a real function or not?

(One of my guidelines, as an information marketer, is to ensure that you get at least 10 times as much value as you paid for.)
As usual, it's up to you to decide. I offer them because I find them relevant. Like Rob Serling's Night Gallery, "Offered for your consideration."

 

[SkyWriting]

No, that's really not true. Everything is a trade-off in biology. Eliminating junk DNA (e.g. new transposable elements) also requires energy, so it's not clear that doing so would actually be beneficial to the organism. It also requires a strong enough selective pressure to make for it to matter; if the selective advantage of any variant is less than ~1/4N, the variant is effectively neutral, and selection will matter little. The effect of varying amounts of nonfunctional DNA is likely very, very small for eukaryotes; this explains why some simple eukaryotes (like some amoebas) have far more DNA than humans do. It really makes very little difference.

That's a fine excuse for the existence of junk DNA. But having acceptable excuses is not the same as validating that it has no value. Just eliminate it all and follow the results for a few 100 generations then get back to us with the hard data please.

 

[sfs]

That link is to a BLOG.

A blog by a scientist which provides, as I said, a nice summary of the scientific evidence.

The BLOG states that "Noncoding DNA is part junk, part regulatory, part unknown."

So that's either 1 or 2 thirds useful with the last third defined as "unknown".

One or two kinds, not one or two thirds. The first category is ~50% of noncoding DNA, the second is ~5%, and the third makes up the remainder.

A perfectly logical conclusion is that the last 2/3 or 1/3 third is simply not yet understood.

That's not a perfectly logical conclusion from the evidence that we have. If most DNA is functional, why do simpler organisms have 100 times as much DNA as we do? If it's functional, why doesn't most of it cause disease when it mutates? If it's functional, why does each of us carry around millions of changes to it? If it's functional, why is the bulk of it obviously made up of genetic elements that copy themselves into new places in the genome?

Given that my parents saw the discovery of DNA in the news, likely we don't currently know 1/1000 of what we will know in 20 years.

Forty years ago, the best guess was that 20% of the human genome was functional. Today, the best guess is that somewhere between 8 and 20% is functional. We've learned a great deal in those forty years, and yet none of that has given any reason to think that most of the genome is functional.

More to the point, the issue in this thread is not, "is most of the genome junk?" The issue is, "Do the ENCODE results show that most of the genome is not junk." Regardless of whether we can eventually find evidence for real function for most of the genome, ENCODE does not supply that evidence.

 

[sfs]

That's a fine excuse for the existence of junk DNA. But having acceptable excuses is not the same as validating that it has no value.

It's just as well, then, that I didn't offer it as a validation that most of the genome is junk. I was refuting an incorrect argument that you made.

Just eliminate it all and follow the results for a few 100 generations then get back to us with the hard data please.

Sorry, but that would be grossly unethical (since we're talking about humans here).

 

[SkyWriting]

That's not a perfectly logical conclusion from the evidence that we have. If most DNA is functional, why do simpler organisms have 100 times as much DNA as we do?

Simpler by what percentage using what standard of measure? Where can I find this "simple" comparison data?
I understand that organisms can pick up DNA from their environmental. My life would be more complicated
if I was a worm and had my naked body in constant contact with decomposing organic matter. I absorb oxygen
through my outer slimy skin and stick my face into muck to eat. My world is one big decaying muck pit and
I'm lying in it 24/7. As an organism, does that sound like a simple life to you? It sounds 100 times
as difficult to avoid infection to me. I'd pick up as much spare DNA as I could find.

If it's functional, why doesn't most of it cause disease when it mutates?

If it performs a function correctly why would it be designed to change?

If it's functional, why does each of us carry around millions of changes to it?

Carrying around spare DNA that is "on Call" should conditions change offers an organism
the ability to adapt to changes in one generation.

If it's functional, why is the bulk of it obviously made up of genetic elements that copy themselves into new places in the genome?

I have bricks I can use on the left OR the right side of my house. I can even take some windows at use the same window throughout the house.

Forty years ago, the best guess was that 20% of the human genome was functional. Today, the best guess is that somewhere between 8 and 20% is functional. We've learned a great deal in those forty years, and yet none of that has given any reason to think that most of the genome is functional.

Intron DNA has a function.
Is Junk DNA Mostly Intron DNA?