"If ENCODE is right then Evolution is wrong"

[Lily of Valleys]

A recent 11 July 2017 paper of Dan Graur "An upper limit on the functional fraction of the human genome" concludes that the functional fraction within the human genome cannot exceed 25%, and is probably considerably lower:

For 80% of the human genome to be functional, each couple in the world would have to beget on average 15 children and all but two would have to die or fail to reproduce. If we use the upper bound for the deleterious mutation rate (2 × 10−8 mutations per nucleotide per generation), then becomes ~5 × 1042, i.e., the number of children that each couple would have to have to maintain a constant population size would exceed the number of stars in the visible universe by ten orders of magnitude.

even for unrealistically low estimates of deleterious mutation rates, the fraction of the genome that can be functional cannot exceed 25%. If the fraction of deleterious mutations out of all mutations in functional regions is even slightly higher than 4%, then the fraction of the genome that can be functional becomes much lower. Realistically, the functional fraction of the genome cannot exceed 10–15%. These results agree with empirical estimates in the literature on the fraction of the human genome that is evolutionarily constrained​

upper limit on the functional fraction of the human genome | Genome Biology and Evolution | Oxford Academic​

However, in 2012, the ENCODE concluded that more than 80% of the human genome sequence is functional:

During the new study, researchers linked more than 80 percent of the human genome sequence to a specific biological function and mapped more than 4 million regulatory regions where proteins specifically interact with the DNA. These findings represent a significant advance in understanding the precise and complex controls over the expression of genetic information within a cell. The findings bring into much sharper focus the continually active genome in which proteins routinely turn genes on and off using sites that are sometimes at great distances from the genes themselves. They also identify where chemical modifications of DNA influence gene expression and where various functional forms of RNA, a form of nucleic acid related to DNA, help regulate the whole system.

"During the early debates about the Human Genome Project, researchers had predicted that only a few percent of the human genome sequence encoded proteins, the workhorses of the cell, and that the rest was junk. We now know that this conclusion was wrong," said Eric D. Green, M.D., Ph.D., director of the National Human Genome Research Institute (NHGRI), a part of the National Institutes of Health. "ENCODE has revealed that most of the human genome is involved in the complex molecular choreography required for converting genetic information into living cells and organisms."​

2012 Release: ENCODE data describes function of human genome​

Ewan Birney, the ENCODE project's Lead Analysis Coordinator said it is likely that 80% will go to 100%, which is in line with what the creationists claimed:

The remaining 20 percent may not be junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator. He explains that while ENCODE looked at 147 different types of cells, there are a couple of thousand in total. If other cell types are examined, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” Birney said. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.”​

http://www.the-scientist.com/?articles.view/articleNo/32583/title/Getting-to-Know-the-Genome/​

In July 2013, at the presentation "How to Assemble a Human Gemome?" at the Society for Molecular Biology and Evolution, Dan Graur said, if organisms are designed, then as much as possible all DNA is expected to exhibit function.

"If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome. If on the other hand organisms are designed, then all DNA, or as much as possible, is expected to exhibit function. If ENCODE is right, then evolution is wrong."​

Comment on: Ohno, So Much Junk in our Genome, 1972 | Berean Archive

​

EDIT:
An integrated encyclopedia of DNA elements in the human genome : Nature : Nature Research
Defining functional DNA elements in the human genome

A Test to Determine Whether or Not We Have a Creator – Proslogion
The ENCODE Embroilment, Part II by Casey Luskin

 

[SkyWriting]

A recent 11 July 2017 paper of Dan Graur "An upper limit on the functional fraction of the human genome" concludes that the functional fraction within the human genome cannot exceed 25%, and is probably considerably lower:

For 80% of the human genome to be functional, each couple in the world would have to beget on average 15 children and all but two would have to die or fail to reproduce. If we use the upper bound for the deleterious mutation rate (2 × 10−8 mutations per nucleotide per generation), then becomes ~5 × 1042, i.e., the number of children that each couple would have to have to maintain a constant population size would exceed the number of stars in the visible universe by ten orders of magnitude.

even for unrealistically low estimates of deleterious mutation rates, the fraction of the genome that can be functional cannot exceed 25%. If the fraction of deleterious mutations out of all mutations in functional regions is even slightly higher than 4%, then the fraction of the genome that can be functional becomes much lower. Realistically, the functional fraction of the genome cannot exceed 10–15%. These results agree with empirical estimates in the literature on the fraction of the human genome that is evolutionarily constrained​

upper limit on the functional fraction of the human genome | Genome Biology and Evolution | Oxford Academic​

However, in 2012, the ENCODE concluded that more than 80% of the human genome sequence is functional:

During the new study, researchers linked more than 80 percent of the human genome sequence to a specific biological function and mapped more than 4 million regulatory regions where proteins specifically interact with the DNA. These findings represent a significant advance in understanding the precise and complex controls over the expression of genetic information within a cell. The findings bring into much sharper focus the continually active genome in which proteins routinely turn genes on and off using sites that are sometimes at great distances from the genes themselves. They also identify where chemical modifications of DNA influence gene expression and where various functional forms of RNA, a form of nucleic acid related to DNA, help regulate the whole system.

"During the early debates about the Human Genome Project, researchers had predicted that only a few percent of the human genome sequence encoded proteins, the workhorses of the cell, and that the rest was junk. We now know that this conclusion was wrong," said Eric D. Green, M.D., Ph.D., director of the National Human Genome Research Institute (NHGRI), a part of the National Institutes of Health. "ENCODE has revealed that most of the human genome is involved in the complex molecular choreography required for converting genetic information into living cells and organisms."​

2012 Release: ENCODE data describes function of human genome​

Ewan Birney, the ENCODE project's Lead Analysis Coordinator said it is likely that 80% will go to 100%, which is in line with what the creationists claimed:

The remaining 20 percent may not be junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator. He explains that while ENCODE looked at 147 different types of cells, there are a couple of thousand in total. If other cell types are examined, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” Birney said. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.”​

http://www.the-scientist.com/?articles.view/articleNo/32583/title/Getting-to-Know-the-Genome/​

In July 2013, at the presentation "How to Assemble a Human Gemome?" at the Society for Molecular Biology and Evolution, Dan Graur said, if organisms are designed, then as much as possible of DNA is expected to exhibit function.

If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome. If on the other hand organisms are designed, then all DNA, or as much as possible, is expected to exhibit function. If ENCODE is right, then evolution is wrong.​

Comment on: Ohno, So Much Junk in our Genome, 1972 | Berean Archive​

God is pretty smart. Just because
a man can determine how DNA
changes over time, does not mean
it's an accident, just as you are claiming.

 

[Bugeyedcreepy]

Well, evolution is a fact - what is it about this combination of blogs, media releases and opinion pieces leads you to believe that the actual scientific research papers don't entirely support evolution? Perhaps you could pull up this peer reviewed research paper & point out the section to support this position?

 

[sfs]

However, in 2012, the ENCODE concluded that more than 80% of the human genome sequence is functional:

Except Graur and ENCODE are using completely different meanings of "functional". In fact, Graur's point is that ENCODE's definition is ridiculous. ENCODE defines "functional" as "biochemically active", which actually says very little about whether the DNA does the organism any good or not. For example, introns are chunks of DNA in genes that are transcribed into RNA, and then chopped out and discarded to form the mature messenger RNA that will end up producing proteins. But ENCODE counts all introns as functional because they are transcribed. Graur is right: it's a dumb definition of "functional".

The best estimate we have of the fraction of the human genome that has a function in the ordinary sense -- that affects how well people can survive and reproduce -- also comes from the ENCODE project, from the paper by Kellis and colleagues. They put the fraction around 11%, as I recall.

 

[SkyWriting]

Well, evolution is a fact - what is it about this combination of blogs, media releases and opinion pieces leads you to believe that the actual scientific research papers don't entirely support evolution? Perhaps you could pull up a peer reviewed research paper to support this position?

God is pretty smart. Just because
a man can determine how DNA
changes over time, does not mean
it's a random accident.

(There is no such thing as random in engineering.
In engineering "Random" is a catch phrase for
unpredictable conditions)

Hidden Treasures in Junk DNA - Scientific American
Junk DNA — Not So Useless After All | TIME.com

Is junk DNA bunk? A critique of ENCODE

Is “Junk” DNA Mostly Intron DNA?

 

[Bugeyedcreepy]

God is pretty smart. Just because
a man can determine how DNA
changes over time, does not mean
it's a random accident.

(There is no such thing as random in engineering.)

I agree it's not random. It might have a random component but then natural selection cleans out and ship-shapes that random component into something hopefully ever so slightly more useful.

 

[SkyWriting]

I agree it's not random. It might have a random component but then natural selection cleans out and ship-shapes that random component into something hopefully ever so slightly more useful.

There is also no such thing as a random component in engineering.

 

[Bugeyedcreepy]

There is also no such thing as a random component in engineering.

Given no engineer is apparent, not surprised...

EDIT: That said, engineers build in random components all the time - often there's a requirement for it.

 

[dannheim]

Well, evolution is a fact - what is it about this combination of blogs, media releases and opinion pieces leads you to believe that the actual scientific research papers don't entirely support evolution? Perhaps you could pull up this peer reviewed research paper & point out the section to support this position?

Most evolutionists are also atheist.

 

[pitabread]

Most evolutionists are also atheist.

Not in America. Most people in America who accept evolution appear to be theists based on poll data. I have another thread looking at poll numbers: Are creationists dwindling in number?

 

[dannheim]

I csn see then how many according to you believe these lies. Probably our schools are to blame for the heresy of evolution.

 

[pitabread]

I csn see then how many according to you believe these lies. Probably our schools are to blame for the heresy of evolution.

Evolution is a useful science with real-world application and therefore real impacts on human welfare and economy. Why else do you think it's taught?

 

[mark kennedy]

A recent 11 July 2017 paper of Dan Graur "An upper limit on the functional fraction of the human genome" concludes that the functional fraction within the human genome cannot exceed 25%, and is probably considerably lower:

For 80% of the human genome to be functional, each couple in the world would have to beget on average 15 children and all but two would have to die or fail to reproduce. If we use the upper bound for the deleterious mutation rate (2 × 10−8 mutations per nucleotide per generation), then becomes ~5 × 1042, i.e., the number of children that each couple would have to have to maintain a constant population size would exceed the number of stars in the visible universe by ten orders of magnitude.

even for unrealistically low estimates of deleterious mutation rates, the fraction of the genome that can be functional cannot exceed 25%. If the fraction of deleterious mutations out of all mutations in functional regions is even slightly higher than 4%, then the fraction of the genome that can be functional becomes much lower. Realistically, the functional fraction of the genome cannot exceed 10–15%. These results agree with empirical estimates in the literature on the fraction of the human genome that is evolutionarily constrained​

upper limit on the functional fraction of the human genome | Genome Biology and Evolution | Oxford Academic​

However, in 2012, the ENCODE concluded that more than 80% of the human genome sequence is functional:

During the new study, researchers linked more than 80 percent of the human genome sequence to a specific biological function and mapped more than 4 million regulatory regions where proteins specifically interact with the DNA. These findings represent a significant advance in understanding the precise and complex controls over the expression of genetic information within a cell. The findings bring into much sharper focus the continually active genome in which proteins routinely turn genes on and off using sites that are sometimes at great distances from the genes themselves. They also identify where chemical modifications of DNA influence gene expression and where various functional forms of RNA, a form of nucleic acid related to DNA, help regulate the whole system.

"During the early debates about the Human Genome Project, researchers had predicted that only a few percent of the human genome sequence encoded proteins, the workhorses of the cell, and that the rest was junk. We now know that this conclusion was wrong," said Eric D. Green, M.D., Ph.D., director of the National Human Genome Research Institute (NHGRI), a part of the National Institutes of Health. "ENCODE has revealed that most of the human genome is involved in the complex molecular choreography required for converting genetic information into living cells and organisms."​

2012 Release: ENCODE data describes function of human genome​

Ewan Birney, the ENCODE project's Lead Analysis Coordinator said it is likely that 80% will go to 100%, which is in line with what the creationists claimed:

The remaining 20 percent may not be junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator. He explains that while ENCODE looked at 147 different types of cells, there are a couple of thousand in total. If other cell types are examined, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” Birney said. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.”​

http://www.the-scientist.com/?articles.view/articleNo/32583/title/Getting-to-Know-the-Genome/​

In July 2013, at the presentation "How to Assemble a Human Gemome?" at the Society for Molecular Biology and Evolution, Dan Graur said, if organisms are designed, then as much as possible all DNA is expected to exhibit function.

"If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome. If on the other hand organisms are designed, then all DNA, or as much as possible, is expected to exhibit function. If ENCODE is right, then evolution is wrong."​

Comment on: Ohno, So Much Junk in our Genome, 1972 | Berean Archive​

It's certainly very interesting, I've heard from time to time RNA regulatory genes can be encoded all over the genome. I don't think it's especially relevant to evolution as natural history, I'm not sure I see the connection. Thanks for the links though, I've always been skeptical of most of our DNA being 'junk DNA'. I remember they used to tell us that humans didn't actually use 80% of our brain. I always took that to mean they only understood how 80% worked.

 

[dannheim]

Evolution is a useful science with real-world application and therefore real impacts on human welfare and economy. Why else do you think it's taught?

,
Pray tell, give me one example of how the THEORY of. evolution impacts human welfare and the economy

 

[Seejer]

Evolutionary economics - Wikipedia

 

[Seejer]

To be fair creationism has their own economic - literally - flagship.

http://www.rawstory.com/2017/06/cre...ke-news-for-failing-ark-encounter-theme-park/

 

[pitabread]

,
Pray tell, give me one example of how the THEORY of. evolution impacts human welfare and the economy

Here are some examples:

Applications of evolutionary relationships (phylogenetics):

Phylogenies can have practical value in almost every branch of biology, a fact that has become widely recognized only in the last decade. This expansion, however, makes it impossible to review all the applications of phylogenies; instead, some examples are presented that include both classic and novel applications.

(This list includes taxonomy/classification, biogeographies, health science, agriculture, conservation and even linguistics.)

http://awarnach.mathstat.dal.ca/~joeb/biol3046/PDFs/Phylo1b_Introduction.pdf


Various applications:

Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential.

Evolutionary principles and their practical application


More on phylogenetic applications:

These examples demonstrate the practical side of phylogenetics. Knowing how different species are related, which species are likely to have inherited which traits, and the patterns of evolution behind the biodiversity we see around us today can help us understand and solve real world problems.

Trees as tools


Further direct application of phylogenetics for gene discovery:

We used sequence comparisons of an extensive set of Old World and New World monkeys and hominoids to identify functional regions in the human genome. Analysis of these data enabled the discovery of primate-specific gene regulatory elements and the demarcation of the exons of multiple genes. Much of the information content of the comprehensive primate sequence comparisons could be captured with a small subset of phylogenetically close primates.

Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome | Science


Specific agricultural application (bovine genomics and milk):

Because bovine milk is a major human food and agro-economical product, comparison of bovine milk with the milk of other species in the context of the bovine genome sequence is important not only to improve our understanding of mammary evolution but also of bovine milk production and human nutrition. The importance of bovine milk consumption to humans is underscored by the domestication of cattle and the convergent evolution of lactase persistency in diverse human populations.

The bovine lactation genome: insights into the evolution of mammalian milk | Genome Biology | Full Text

 

[xianghua]

first, evolution isnt a fact but a theory. secondly: there is a good evidence that this suppose junk isnt junk at all:

A meta-analysis of the genomic and transcriptomic composition of complex life. - PubMed - NCBI

take a look at figure 1.


there is a great correlation between complexity (in terms of cell types number) and the amount of suppose junk. so this is a good evidence that most of the genome is functional.

 

[xianghua]

Here are some examples:

Applications of evolutionary relationships (phylogenetics):



(This list includes taxonomy/classification, biogeographies, health science, agriculture, conservation and even linguistics.)

http://awarnach.mathstat.dal.ca/~joeb/biol3046/PDFs/Phylo1b_Introduction.pdf


Various applications:



Evolutionary principles and their practical application


More on phylogenetic applications:



Trees as tools


Further direct application of phylogenetics for gene discovery:



Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome | Science


Specific agricultural application (bovine genomics and milk):



The bovine lactation genome: insights into the evolution of mammalian milk | Genome Biology | Full Text

evolution doesnt have any connection to making medicine, we can still made a medicine even if evolution is wrong.

 

[mark kennedy]

first, evolution isnt a fact but a theory. secondly: there is a good evidence that this suppose junk isnt junl at all:

A meta-analysis of the genomic and transcriptomic composition of complex life. - PubMed - NCBI

take a look at figure 1.


there is a great correlation between complexity (in terms of cell types number) and the amount of suppose junk. so this is a good evidence that most of the genome is functional.

Evolution is a phenomenon in nature, no one who seriously explores adaptive evolution doubts it happens on a grand scale. I try to learn a little something about Genomic research because I'm curious what secrets are being uncovered in this kind of genomic research. The Darwinism vs. Creationism controversy is really more of a side line issue, not really effecting or being effected systematic theology or natural science.

So even if it's 100% functional, that doesn't negate adaptive evolution, it may well help to explain it and identify it's limitations.