What “junk DNA” does

A major discovery:

It turns out that “junk DNA”, once thought to comprise most of the genetic material packed into our cells, isn’t junk. Instead, it plays a complicated — and still shadowy — role in regulating our genes.

That’s the essential insight of a five-year project to study the 98 percent of the human genome that is not, strictly speaking, genes. It now appears that more than three-quarters of our DNA is active at some point in our lives.

“This concept of ‘junk DNA’ is really not accurate. It is an outdated metaphor to explain our genome,” said Richard Myers, one of the leaders of the 400-scientist Encyclopedia of DNA Elements Project, nicknamed Encode.

“The genome is just alive with stuff. We just really didn’t realize that before,” said Ewan Birney of the European Bioinformatics Institute in England.

The new insights are contained in six papers published Wednesday in the journal Nature. More than 20 related papers from Encode are appearing elsewhere.

The human genome consists of about 3 billion DNA “letters” strung one to another in 46 chains called chromosomes. Specific stretches of those letters (whose formal name is “nucleotides”) carry the instructions for making specific proteins. Those proteins, in turn, build the cells and tissues of living organisms.

The Human Genome Project, which identified the correct linear sequence of those letters, revealed that human cells contain only about 21,000 genes — far fewer than most biologists predicted. Furthermore, those genes took up only 2 percent of the cell’s DNA. The new research helps explain how so few genes can create an organism as complex as a human being.

The answer is that regulating genes — turning them on and off, adjusting their output, manipulating their timing, coordinating their activity with other genes — is where most of the action is.

The importance and subtlety of gene regulation is not a new idea. Nor is the idea that parts of the genome once thought to be “junk” may have some use. What the Encode findings reveal is the magnitude of the regulation.

It now appears that at least 4 million sections of the genome are involved in manipulating the activity of genes. Those sections act like switches in a wiring diagram, creating an almost infinite number of circuits.

“There is a modest number of genes and an immense number of elements that choreograph how those genes are used,” said Eric D. Green, director of the National Human Genome Research Institute, the federal agency that paid for the research.

via ‘Junk DNA’ concept debunked by new analysis of human genome – The Washington Post.

So every cell of every living organism contains not just genetic information but a whole system for activating, directing, timing, and animating that information.

We sure are lucky that millions of years of random mutations and natural selection evolved into something so infinitely complex.

Oh, wait.  All of that had to be in place in order to make reproduction possible; that is, before natural selection could happen.

About Gene Veith

Professor of Literature at Patrick Henry College, the Director of the Cranach Institute at Concordia Theological Seminary, a columnist for World Magazine and TableTalk, and the author of 18 books on different facets of Christianity & Culture.

  • rebecca w

    Wow. So complex. So awesome!

    PS: Mr. Veith, Your blog should have a “checkbox” setting that allows “Notify me of all new blog posts via email”. (Similar to the “Notify me of followup comments via email” option you currently have available for all your postings.)

    Any chance that can be activated? :)

  • rebecca w

    Wow. So complex. So awesome!

    PS: Mr. Veith, Your blog should have a “checkbox” setting that allows “Notify me of all new blog posts via email”. (Similar to the “Notify me of followup comments via email” option you currently have available for all your postings.)

    Any chance that can be activated? :)

  • WebMonk

    Oh boy. Instead of taking my word for it that this is nothing new, and it’s just the typical sensationalized press release further exaggerated by reporters who don’t understand it making a hyped up headline, allow me to link you to a YEC genetic biologist who says it:

    http://toddcwood.blogspot.com/2012/09/everyones-excited-about-encode.html

    If you don’t feel like clicking through, allow me to pull a couple quick excerpts:

    Me? It’s cool science, no doubt about that. Project leader Ewan Birney is to be commended. No doubt about that either. But I’m not sure the ENCODE results are worth all the attention they’re getting in the creation/evolution world.
    ……
    Meanwhile, yes, the press and press releases are exaggerating and distorting things as usual. Yes, it’s annoying.
    ……
    I too frequently rail against exaggerations by the popular press. Perhaps you should write a letter to Nature? Or maybe a whole paper documenting the exaggeration of the “junk DNA” myth? Then you could put out your own press release and put another paper on your CV. I’d even blog about your paper when it was published. That would be groovy.

    For now, that’s all I have to say about ENCODE. Bravo to the team, but a lot of us wish your press releases didn’t prey upon misconceptions.

    Did you get that last line? “… a lot of us wish your press releases didn’t prey upon misconceptions.”

    Or that line up in the middle that mentions the “junk DNA myth”. Yes, it’s a myth propagated by news and many creationists.

    But, don’t let little details like facts get in the way of anything. This of course turns all of evolutionary genetics on its head and proves something or other that proves a YEC.

  • WebMonk

    Oh boy. Instead of taking my word for it that this is nothing new, and it’s just the typical sensationalized press release further exaggerated by reporters who don’t understand it making a hyped up headline, allow me to link you to a YEC genetic biologist who says it:

    http://toddcwood.blogspot.com/2012/09/everyones-excited-about-encode.html

    If you don’t feel like clicking through, allow me to pull a couple quick excerpts:

    Me? It’s cool science, no doubt about that. Project leader Ewan Birney is to be commended. No doubt about that either. But I’m not sure the ENCODE results are worth all the attention they’re getting in the creation/evolution world.
    ……
    Meanwhile, yes, the press and press releases are exaggerating and distorting things as usual. Yes, it’s annoying.
    ……
    I too frequently rail against exaggerations by the popular press. Perhaps you should write a letter to Nature? Or maybe a whole paper documenting the exaggeration of the “junk DNA” myth? Then you could put out your own press release and put another paper on your CV. I’d even blog about your paper when it was published. That would be groovy.

    For now, that’s all I have to say about ENCODE. Bravo to the team, but a lot of us wish your press releases didn’t prey upon misconceptions.

    Did you get that last line? “… a lot of us wish your press releases didn’t prey upon misconceptions.”

    Or that line up in the middle that mentions the “junk DNA myth”. Yes, it’s a myth propagated by news and many creationists.

    But, don’t let little details like facts get in the way of anything. This of course turns all of evolutionary genetics on its head and proves something or other that proves a YEC.

  • #4 Kitty

    Oh, wait. All of that had to be in place in order to make reproduction possible; that is, before natural selection could happen.

    All of our DNA had to be in place in order to make reproduction possible? Then how do you explain…

  • #4 Kitty

    Oh, wait. All of that had to be in place in order to make reproduction possible; that is, before natural selection could happen.

    All of our DNA had to be in place in order to make reproduction possible? Then how do you explain…

  • Michael B.

    “We sure are lucky that millions of years of random mutations and natural selection evolved into something so infinitely complex.”

    Billions of years. (4.5 billion). And how are we “infinitely complex”? Very complex does not mean infinitely complex. Finally, human reproduction is far from perfect. The process that causes evolution also causes many diseases when imperfect copying of DNA happens. What’s that? God’s curse?

    “Oh, wait. All of that had to be in place in order to make reproduction possible; that is, before natural selection could happen.”

    It’s true, science doesn’t have a theory yet on how life originated. It seems as if you are arguing that because science can’t figure out why, the only explanation must be “God must have done it supernaturally”. Are you saying the origin of life couldn’t have had a natural cause?

  • Michael B.

    “We sure are lucky that millions of years of random mutations and natural selection evolved into something so infinitely complex.”

    Billions of years. (4.5 billion). And how are we “infinitely complex”? Very complex does not mean infinitely complex. Finally, human reproduction is far from perfect. The process that causes evolution also causes many diseases when imperfect copying of DNA happens. What’s that? God’s curse?

    “Oh, wait. All of that had to be in place in order to make reproduction possible; that is, before natural selection could happen.”

    It’s true, science doesn’t have a theory yet on how life originated. It seems as if you are arguing that because science can’t figure out why, the only explanation must be “God must have done it supernaturally”. Are you saying the origin of life couldn’t have had a natural cause?

  • Klasie Kraalogies

    Sigh….

  • Klasie Kraalogies

    Sigh….

  • SKPeterson

    While this is cool I thought the best thing in science news was
    light vomiting shrimp .

  • SKPeterson

    While this is cool I thought the best thing in science news was
    light vomiting shrimp .

  • Jon

    @4 “Are you saying the origin of life couldn’t have had a natural cause?”

    Yes. That is, until you can show it to be testable, repeatable, observable.

    Otherwise I’m not convinced a historical science theory of what happened supposed billions or millions of years ago.

    So, there. I guess I’ve just blown any chance of being a useful scientist or engineer, according to Bill Nye the “science” guy.

  • Jon

    @4 “Are you saying the origin of life couldn’t have had a natural cause?”

    Yes. That is, until you can show it to be testable, repeatable, observable.

    Otherwise I’m not convinced a historical science theory of what happened supposed billions or millions of years ago.

    So, there. I guess I’ve just blown any chance of being a useful scientist or engineer, according to Bill Nye the “science” guy.

  • #4 Kitty

    @Jon

    Yes. That is, until you can show it to be testable, repeatable, observable.

    But, can you show how magic or …what is the word… “creationism” is testable, repeatable, and observable? And if not, why are you giving theories based in the supernatural a free pass?

  • #4 Kitty

    @Jon

    Yes. That is, until you can show it to be testable, repeatable, observable.

    But, can you show how magic or …what is the word… “creationism” is testable, repeatable, and observable? And if not, why are you giving theories based in the supernatural a free pass?

  • http://www.geneveith.com Gene Veith

    Could we focus on this particular finding, before launching into the overall creationist/evolution issues?

    Webmonk, I couldn’t tell from the link exactly what is incorrect or exaggerated in this press report. It doesn’t matter whether this is “new”; it was new to me. That 80% of the DNA that some had assumed had no function actually performs a very complex function is surely significant, reminding us that genetics is not just about genes but about whatever controls and activates those genes. Of course that might be just a logical deduction, but this study seems to give evidence for that. Or is all of this inaccurate?

    Here is what I found intriguing as it relates to evolution: Organisms are said to evolve through natural selection; that is, qualities that aid in survival are transmitted to future generations.
    But that assumes the ability to reproduce. And reproduction requires a genetic ability that has to be prior to natural selection. Maybe I’m misunderstanding, or maybe Darwinists have an answer to that. I’d be glad to hear it.

  • http://www.geneveith.com Gene Veith

    Could we focus on this particular finding, before launching into the overall creationist/evolution issues?

    Webmonk, I couldn’t tell from the link exactly what is incorrect or exaggerated in this press report. It doesn’t matter whether this is “new”; it was new to me. That 80% of the DNA that some had assumed had no function actually performs a very complex function is surely significant, reminding us that genetics is not just about genes but about whatever controls and activates those genes. Of course that might be just a logical deduction, but this study seems to give evidence for that. Or is all of this inaccurate?

    Here is what I found intriguing as it relates to evolution: Organisms are said to evolve through natural selection; that is, qualities that aid in survival are transmitted to future generations.
    But that assumes the ability to reproduce. And reproduction requires a genetic ability that has to be prior to natural selection. Maybe I’m misunderstanding, or maybe Darwinists have an answer to that. I’d be glad to hear it.

  • Jon

    Dr. Veith your question is a great one, but I don’t see how the article necessarily raises it, without a few more steps. I think you are really begging the question of life origins.

    I reckon this article is news to most of the general public also who don’t closely follow these developments. But then again, why should it be surprising that parts of DNA whose functions were preveiously unknown are slowly becoming known?

    And Kitty, why can’t I point to a supernatural cause? You can’t point to a natural cause for the origin of life. Neither of us was there when it began. It is a matter of faith for bth of us. For the naturalist, that one day they will find the holy grail of naturalism–spontaneous generation of life from non-life caught in the act. For my ilk, faith in the Creator and His revealed Word of Truth.

    Kitty, your article on mice still being mice with a 1% removal of unknown-action genes isn’t really shocking or disproving of anything either. Did you read the experimeters’ conclusions? They say they can’t observe any difference yet, but they don’t know what changes they caused or didn’t cause.

  • Jon

    Dr. Veith your question is a great one, but I don’t see how the article necessarily raises it, without a few more steps. I think you are really begging the question of life origins.

    I reckon this article is news to most of the general public also who don’t closely follow these developments. But then again, why should it be surprising that parts of DNA whose functions were preveiously unknown are slowly becoming known?

    And Kitty, why can’t I point to a supernatural cause? You can’t point to a natural cause for the origin of life. Neither of us was there when it began. It is a matter of faith for bth of us. For the naturalist, that one day they will find the holy grail of naturalism–spontaneous generation of life from non-life caught in the act. For my ilk, faith in the Creator and His revealed Word of Truth.

    Kitty, your article on mice still being mice with a 1% removal of unknown-action genes isn’t really shocking or disproving of anything either. Did you read the experimeters’ conclusions? They say they can’t observe any difference yet, but they don’t know what changes they caused or didn’t cause.

  • WebMonk

    It’s new, definitely, but it’s the press release and resultant media hype that have blown it WAY out of proportion and WAY outside what the study actually says.

    There are a couple key phrases in the abstract that people are using beyond what they mean. The phrase “biochemical functions for 80% of the genome” is one that is getting misused and misunderstood. The phrase “biochemical function” means very little, and it isn’t a significant change over what was already understood. For example, “biochemical function” includes a section being copied into a directly coding portion of our DNA even when it shouldn’t be copied.

    The term “junk DNA” is one that was spread by media and latched onto by YEC groups, but is not something that scientists agree with.

    Put both of those concepts together, and the headlines make it sound like all of a sudden scientists discovered that instead of 20% of our DNA doing stuff that suddenly 80% of our DNA does stuff.

    That’s a wildly, crazily false impression to give. It certainly doesn’t stop the media from spreading that idea, and it doesn’t stop people from using that idea.

    Look at your statement for a perfect example of drawing a reasonable conclusion from what is reported, but the conclusion being completely wrong: “That 80% of the DNA that some had assumed had no function actually performs a very complex function is surely significant”.

    Both parts of that statement are false. 1) Scientists did NOT assume 80% of our DNA had no function. 2) This study does NOT say it performs a very complex function.

    But, if you get your science from media and YEC groups, then that’s the sort of conclusion you can draw.

    Like Dr. Wood (YEC geneticist) said: “Bravo to the [ENCODE] team, but a lot of us wish your press releases didn’t prey upon misconceptions.”

  • WebMonk

    It’s new, definitely, but it’s the press release and resultant media hype that have blown it WAY out of proportion and WAY outside what the study actually says.

    There are a couple key phrases in the abstract that people are using beyond what they mean. The phrase “biochemical functions for 80% of the genome” is one that is getting misused and misunderstood. The phrase “biochemical function” means very little, and it isn’t a significant change over what was already understood. For example, “biochemical function” includes a section being copied into a directly coding portion of our DNA even when it shouldn’t be copied.

    The term “junk DNA” is one that was spread by media and latched onto by YEC groups, but is not something that scientists agree with.

    Put both of those concepts together, and the headlines make it sound like all of a sudden scientists discovered that instead of 20% of our DNA doing stuff that suddenly 80% of our DNA does stuff.

    That’s a wildly, crazily false impression to give. It certainly doesn’t stop the media from spreading that idea, and it doesn’t stop people from using that idea.

    Look at your statement for a perfect example of drawing a reasonable conclusion from what is reported, but the conclusion being completely wrong: “That 80% of the DNA that some had assumed had no function actually performs a very complex function is surely significant”.

    Both parts of that statement are false. 1) Scientists did NOT assume 80% of our DNA had no function. 2) This study does NOT say it performs a very complex function.

    But, if you get your science from media and YEC groups, then that’s the sort of conclusion you can draw.

    Like Dr. Wood (YEC geneticist) said: “Bravo to the [ENCODE] team, but a lot of us wish your press releases didn’t prey upon misconceptions.”

  • WebMonk

    Also, Dr. Veith @9,
    You started your comment with a plea to focus on the actual finding before launching into the creation/evolution aspect.

    And then launched into the creation/evolution aspect.

    In respect to your initial request, I didn’t address your paragraph that launched into the creation/evolution aspect.

  • WebMonk

    Also, Dr. Veith @9,
    You started your comment with a plea to focus on the actual finding before launching into the creation/evolution aspect.

    And then launched into the creation/evolution aspect.

    In respect to your initial request, I didn’t address your paragraph that launched into the creation/evolution aspect.

  • fjsteve

    Monk, #2,

    Before you start bagging on creationists, realize that the term junk DNA was coined by an evolutionary biologist and the idea “propagated” by researchers at a little place called the Salk Institute.

    I’ve had numerous encounters with evolutionists who claim God must not be a very good creator considering most DNA has no purpose.

    I think there’s enough bagging to go around here, don’t you?

  • fjsteve

    Monk, #2,

    Before you start bagging on creationists, realize that the term junk DNA was coined by an evolutionary biologist and the idea “propagated” by researchers at a little place called the Salk Institute.

    I’ve had numerous encounters with evolutionists who claim God must not be a very good creator considering most DNA has no purpose.

    I think there’s enough bagging to go around here, don’t you?

  • #4 Kitty

    @Jon #10

    Kitty, your article on mice still being mice with a 1% removal of unknown-action genes isn’t really shocking or disproving of anything either.

    Yes, I believe the article is quite shocking when you compare it to Dr Veith’s “Oh Wait” statement above.
    He argues for some sort of irreducible compleixity when he states that “all” of the DNA needs to be in place in order for reproduction to occur. The article I referenced proves this is not true.

  • #4 Kitty

    @Jon #10

    Kitty, your article on mice still being mice with a 1% removal of unknown-action genes isn’t really shocking or disproving of anything either.

    Yes, I believe the article is quite shocking when you compare it to Dr Veith’s “Oh Wait” statement above.
    He argues for some sort of irreducible compleixity when he states that “all” of the DNA needs to be in place in order for reproduction to occur. The article I referenced proves this is not true.

  • http://www.biblegateway.com/versions/Contemporary-English-Version-CEV-Bible/ sg

    Web Monk @2

    ” it’s just the typical sensationalized press release further exaggerated by reporters who don’t understand it making a hyped up headline”

    The reporter is David Brown, a physician. Now if he can’t understand evolution, and writes this kind of stuff, how is it we figure the average high school students are going to understand it? I don’t really care about getting people to “believe” evolution, but it would be nice if those who do could at least grasp it. You know?

    David Brown, a journalist and physician, has been a staff writer for The Washington Post since 1991. He has covered medical research, the AIDS epidemic, clinical practice, medical ethics, epidemiology, global health, and numerous non-medical scientific subjects. He majored in American Studies at Amherst College, graduating in 1973. He worked as a reporter at The Greenwood (Miss.) Commonwealth and The Baltimore Sun before entering the Medical College of Pennsylvania, from which he graduated in 1987. He works four days a week at the Post and two-thirds of a day at a general internal medicine clinic in Baltimore supervising third-year medical students.

  • http://www.biblegateway.com/versions/Contemporary-English-Version-CEV-Bible/ sg

    Web Monk @2

    ” it’s just the typical sensationalized press release further exaggerated by reporters who don’t understand it making a hyped up headline”

    The reporter is David Brown, a physician. Now if he can’t understand evolution, and writes this kind of stuff, how is it we figure the average high school students are going to understand it? I don’t really care about getting people to “believe” evolution, but it would be nice if those who do could at least grasp it. You know?

    David Brown, a journalist and physician, has been a staff writer for The Washington Post since 1991. He has covered medical research, the AIDS epidemic, clinical practice, medical ethics, epidemiology, global health, and numerous non-medical scientific subjects. He majored in American Studies at Amherst College, graduating in 1973. He worked as a reporter at The Greenwood (Miss.) Commonwealth and The Baltimore Sun before entering the Medical College of Pennsylvania, from which he graduated in 1987. He works four days a week at the Post and two-thirds of a day at a general internal medicine clinic in Baltimore supervising third-year medical students.

  • WebMonk

    fjsteve #13
    Yes, the phrase was coined way back by an evolutionary biologist, Dr. Ohno. He used the phrase in a different way than what it has come to mean over the last 40 years. Even when it is used by scientific papers, it is virtually always in a colloquial manner and in the abstract portion of the paper.

    It has been propagated because it is so popular a term, and it is propagated in the abstracts of papers – the parts which are designed to give a quick overview and to attract attention.

    There are lots of “evolutionists” (random people who believe evolution to be a fact) who use the term, but not geneticists. Lot’s of “creationists” maintain that the dust on the moon proves a young moon, but that doesn’t mean it’s an idea held by YEC scientists.

  • WebMonk

    fjsteve #13
    Yes, the phrase was coined way back by an evolutionary biologist, Dr. Ohno. He used the phrase in a different way than what it has come to mean over the last 40 years. Even when it is used by scientific papers, it is virtually always in a colloquial manner and in the abstract portion of the paper.

    It has been propagated because it is so popular a term, and it is propagated in the abstracts of papers – the parts which are designed to give a quick overview and to attract attention.

    There are lots of “evolutionists” (random people who believe evolution to be a fact) who use the term, but not geneticists. Lot’s of “creationists” maintain that the dust on the moon proves a young moon, but that doesn’t mean it’s an idea held by YEC scientists.

  • WebMonk

    sg 15, I’m an engineer right now, but you don’t want to drive across any bridges I might design and build.

    Did you pay attention to the medical part of his resume? Majored in American Studies. Worked as a reporter. Graduated from a medical school. Did a three years of of residency, interrupted by a year of journalism. Now he’s a reporter 80% of the time and works 5 hours per week supervising med students.

    That’s like a mechanical engineer who worked as an intern in an engineering firm, but is primarily a reporter writing a story on computer network security. His reliability is only marginal compared to a random reporter.

    That’s a problem with just about EVERY bit of reporting on any sort of science. The reporters almost NEVER have the expertise to know if what they’re writing is actually correct, and they are strongly incentivised to emphasize a catchy story over an accurate one.

    You’ve witnessed enough of my rants on the subject (whether it’s biology, astronomy, computer, geology, statistics, whatever) to know my views.

    This story is no better than all the other crappy science reporting out there.

  • WebMonk

    sg 15, I’m an engineer right now, but you don’t want to drive across any bridges I might design and build.

    Did you pay attention to the medical part of his resume? Majored in American Studies. Worked as a reporter. Graduated from a medical school. Did a three years of of residency, interrupted by a year of journalism. Now he’s a reporter 80% of the time and works 5 hours per week supervising med students.

    That’s like a mechanical engineer who worked as an intern in an engineering firm, but is primarily a reporter writing a story on computer network security. His reliability is only marginal compared to a random reporter.

    That’s a problem with just about EVERY bit of reporting on any sort of science. The reporters almost NEVER have the expertise to know if what they’re writing is actually correct, and they are strongly incentivised to emphasize a catchy story over an accurate one.

    You’ve witnessed enough of my rants on the subject (whether it’s biology, astronomy, computer, geology, statistics, whatever) to know my views.

    This story is no better than all the other crappy science reporting out there.

  • http://www.biblegateway.com/versions/Contemporary-English-Version-CEV-Bible/ sg

    “That’s like a mechanical engineer who worked as an intern in an engineering firm, but is primarily a reporter writing a story on computer network security. His reliability is only marginal compared to a random reporter.”

    Okay, but how does he compare to a high school student? By definition half are below average. I think it is fair to assume that David Brown is well above average because he got into medical school in the first place. So what is the problem? Why would a smart person want to look so dumb? It is just so danged weird. I mean is he just incurious? or what?

  • http://www.biblegateway.com/versions/Contemporary-English-Version-CEV-Bible/ sg

    “That’s like a mechanical engineer who worked as an intern in an engineering firm, but is primarily a reporter writing a story on computer network security. His reliability is only marginal compared to a random reporter.”

    Okay, but how does he compare to a high school student? By definition half are below average. I think it is fair to assume that David Brown is well above average because he got into medical school in the first place. So what is the problem? Why would a smart person want to look so dumb? It is just so danged weird. I mean is he just incurious? or what?

  • WebMonk

    He’s writing articles to catch readers’ attention – to get readers over to the WaPo. Reporters are heavily judged and measured according to how much their stories bring readers to the newspapers.

    He’s not dumb, I’m sure. That has nothing to do with it.

    Genetics is outside his expertise, he isn’t a practicing physician, he probably hasn’t read the paper and is just working off the abstract, he has probably created this story with less than 8 hours of work on it, he’s trying to make it as catchy as possible, and he’s trying to dumb the entire subject down to the reading level (and general science knowledge) of a 10th grade high school student.

    It has nothing to do with the intelligence of the reporter and has everything to do with the nature of general news reporting.

  • WebMonk

    He’s writing articles to catch readers’ attention – to get readers over to the WaPo. Reporters are heavily judged and measured according to how much their stories bring readers to the newspapers.

    He’s not dumb, I’m sure. That has nothing to do with it.

    Genetics is outside his expertise, he isn’t a practicing physician, he probably hasn’t read the paper and is just working off the abstract, he has probably created this story with less than 8 hours of work on it, he’s trying to make it as catchy as possible, and he’s trying to dumb the entire subject down to the reading level (and general science knowledge) of a 10th grade high school student.

    It has nothing to do with the intelligence of the reporter and has everything to do with the nature of general news reporting.

  • http://www.toddstadler.com/ tODD

    WebMonk (@2), take a deep breath. Please. Keep holding it. Okay, now let me reply (I didn’t say let it out yet).

    Or that line up in the middle that mentions the “junk DNA myth”. Yes, it’s a myth propagated by news and many creationists.

    Please. For someone complaining about people who “don’t let little details like facts get in the way of anything”, you’re kind of, um, doing that. (Still holding it?)

    To Wikipedia! (You can research the citations yourself.)

    Junk DNA is a term that was introduced in 1972 by Susumu Ohno …

    Susumu Ohno … was an Asian American geneticist and evolutionary biologist, and seminal researcher in the field of molecular evolution.

    And no less than Leslie Orgel and Francis Crick (both creationists and mythmongers, of course) said (back in 1980, admittedly):

    The conviction has been growing that much of this extra DNA is ‘junk’, in other words, that it has little specificity and conveys little or no selective advantage to the organism…

    So, um, yeah. I guess you can let your breath out now.

  • http://www.toddstadler.com/ tODD

    WebMonk (@2), take a deep breath. Please. Keep holding it. Okay, now let me reply (I didn’t say let it out yet).

    Or that line up in the middle that mentions the “junk DNA myth”. Yes, it’s a myth propagated by news and many creationists.

    Please. For someone complaining about people who “don’t let little details like facts get in the way of anything”, you’re kind of, um, doing that. (Still holding it?)

    To Wikipedia! (You can research the citations yourself.)

    Junk DNA is a term that was introduced in 1972 by Susumu Ohno …

    Susumu Ohno … was an Asian American geneticist and evolutionary biologist, and seminal researcher in the field of molecular evolution.

    And no less than Leslie Orgel and Francis Crick (both creationists and mythmongers, of course) said (back in 1980, admittedly):

    The conviction has been growing that much of this extra DNA is ‘junk’, in other words, that it has little specificity and conveys little or no selective advantage to the organism…

    So, um, yeah. I guess you can let your breath out now.

  • http://www.toddstadler.com/ tODD

    Okay, well, now that I’ve read through all the comments, I see that my previous comment to WebMonk had already been addressed to some degree.

    Still, as you often do when you get all excited about such things, WebMonk, you have vastly overstated your case (even as you really haven’t spent much time telling us what the actual issues are that have you so kerfuffled).

    There are lots of “evolutionists” (random people who believe evolution to be a fact) who use the term, but not geneticists.

    So um, is Francis Crick a geneticist?

    Lot’s of “creationists” maintain that the dust on the moon proves a young moon, but that doesn’t mean it’s an idea held by YEC scientists.

    You and your “YEC scientists”. I’ll never know why you care about what they think, given that you always then proceed to shoot them down, anyhow. Are they just convenient straw men for you?

    Did you pay attention to the medical part of his resume? Majored in American Studies. Worked as a reporter. Graduated from a medical school.

    So you’re just attempting to smear the man now? Who cares what his undergraduate major was? Quite a few universities allow pre-meds to major in whatever, so long as they take the required courses. My roommate was pre-med but majored in PoliSci. So?

    Also, um, he graduated from medical school. So I kind of feel his grasp on biology is probably sufficient to write an article like this. Which he’s doing because he’s a reporter.

    His reliability is only marginal compared to a random reporter.

    Seriously? That’s a ridiculous claim. He has a medical degree. Slam him for actual mistakes he’s made (you really haven’t spent as much on that as you have the man’s resume — that’s called an ad hominem where I’m from), but I think he likely knows more about any science, much less biology, than the average reporter. You’re not really making a case for logic here, WebMonk!

    Genetics is outside his expertise, he isn’t a practicing physician…

    Well, then. Based on your reasoning, I should be listening to him, not you. Because you’re not a practicing physician, either. And hey, guess what? Nor do you have a medical degree. Or — and here I’m guessing — you don’t even have a degree in any sort of genetics field at all! Which means that genetics is more his area of expertise than it is yours, according to this logic derived from resumes.

    …he probably hasn’t read the paper and is just working off the abstract, he has probably created this story with less than 8 hours of work on it…

    Oh thank goodness! We finally get to the part where you just pull things out of your butt in order to slander the man! Fine, then nor have you read the paper, and every one of your comments here was generated by a monkey farting onto an iPad.

    Hey, you know what would be great? If you informed us about the topic, rather than spending all your time on ad hominem attacks! Maybe tell us specifically what is wrong in the article. That would be swell. Thx.

  • http://www.toddstadler.com/ tODD

    Okay, well, now that I’ve read through all the comments, I see that my previous comment to WebMonk had already been addressed to some degree.

    Still, as you often do when you get all excited about such things, WebMonk, you have vastly overstated your case (even as you really haven’t spent much time telling us what the actual issues are that have you so kerfuffled).

    There are lots of “evolutionists” (random people who believe evolution to be a fact) who use the term, but not geneticists.

    So um, is Francis Crick a geneticist?

    Lot’s of “creationists” maintain that the dust on the moon proves a young moon, but that doesn’t mean it’s an idea held by YEC scientists.

    You and your “YEC scientists”. I’ll never know why you care about what they think, given that you always then proceed to shoot them down, anyhow. Are they just convenient straw men for you?

    Did you pay attention to the medical part of his resume? Majored in American Studies. Worked as a reporter. Graduated from a medical school.

    So you’re just attempting to smear the man now? Who cares what his undergraduate major was? Quite a few universities allow pre-meds to major in whatever, so long as they take the required courses. My roommate was pre-med but majored in PoliSci. So?

    Also, um, he graduated from medical school. So I kind of feel his grasp on biology is probably sufficient to write an article like this. Which he’s doing because he’s a reporter.

    His reliability is only marginal compared to a random reporter.

    Seriously? That’s a ridiculous claim. He has a medical degree. Slam him for actual mistakes he’s made (you really haven’t spent as much on that as you have the man’s resume — that’s called an ad hominem where I’m from), but I think he likely knows more about any science, much less biology, than the average reporter. You’re not really making a case for logic here, WebMonk!

    Genetics is outside his expertise, he isn’t a practicing physician…

    Well, then. Based on your reasoning, I should be listening to him, not you. Because you’re not a practicing physician, either. And hey, guess what? Nor do you have a medical degree. Or — and here I’m guessing — you don’t even have a degree in any sort of genetics field at all! Which means that genetics is more his area of expertise than it is yours, according to this logic derived from resumes.

    …he probably hasn’t read the paper and is just working off the abstract, he has probably created this story with less than 8 hours of work on it…

    Oh thank goodness! We finally get to the part where you just pull things out of your butt in order to slander the man! Fine, then nor have you read the paper, and every one of your comments here was generated by a monkey farting onto an iPad.

    Hey, you know what would be great? If you informed us about the topic, rather than spending all your time on ad hominem attacks! Maybe tell us specifically what is wrong in the article. That would be swell. Thx.

  • Jon

    @14 Kitty

    The point of your article about the mice is that its too early to tell what effects the removal of unknown-gene segments might have. In fact the experiementers hypothesize that the coding might be most important during prenatal development.

    Highlighted in a side box, one of the experiementers is even quoted saying “Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years.” And this was a 2004 article.

    It might just be too early to tell what changes or damage is incurred by the induced mutation–loss of information.

    Any updated on if the mouse line is still going or how its going?

  • Jon

    @14 Kitty

    The point of your article about the mice is that its too early to tell what effects the removal of unknown-gene segments might have. In fact the experiementers hypothesize that the coding might be most important during prenatal development.

    Highlighted in a side box, one of the experiementers is even quoted saying “Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years.” And this was a 2004 article.

    It might just be too early to tell what changes or damage is incurred by the induced mutation–loss of information.

    Any updated on if the mouse line is still going or how its going?

  • #4 Kitty

    The point of the mouse article is summarized here: Edward Rubin’s team at the Lawrence Berkeley National Laboratory in California has shown that deleting large sections of non-coding DNA from mice appears not to affect their development, longevity or reproduction.
    This contradicts Dr Veith’s assertion that “All of that had to be in place in order to make reproduction possible.

  • #4 Kitty

    The point of the mouse article is summarized here: Edward Rubin’s team at the Lawrence Berkeley National Laboratory in California has shown that deleting large sections of non-coding DNA from mice appears not to affect their development, longevity or reproduction.
    This contradicts Dr Veith’s assertion that “All of that had to be in place in order to make reproduction possible.

  • Joanne

    Has it been already since way back in the 70s that we all first heard the term, “junk DNA.” My reaction then and now was simply that they didn’t yet know what this extra DNA did/does, but one day they well. The complexity of human biology gets only more and more complex and less and less mathematically probable to be random.

    When I first started reading about epigenetic, and that whole world of DNA complexity, again, the epi parts can actually change the phenotype coded in the DNA. Whoa, talk about another magnitude of complexity in human biology.

    When I was in sicence classes by back in the 60s, it was just a mater of time before our scientists discovered the chemicals that bumped together in a tidal pool just as a jolt of electricity created life. No one talks like that anymore. Since the 1960s, cell biologists have found nothing but more and more complexity. The fools today are those who still think or even talk about creating life in a test tube.

    The complexity, of the human, and most animal cells is mind boggling. The arithmetic chance of it happening at random has reached the miniscule point, much lower than the mathematical possibility that aliens put life on our planet.

    With sicence there is always more to know. It is a certainty that more and more complexity will be found. Nothing is here by accident. And for time to progress forward, the continued growth of entropy is a scientific expectation, till time unravels at the end.

    You know, when I was in science classes by in the 60s, scientists didn’t believe in a beginning or an ending for this existance. Now they do. There is always more to learn. God is playing with you, letting you know so much at a time to see what our corrupt mental capabilities congure up next. I actually enjoy it; read about the new stuff all the time. It’s fascinating. As much as I would love to simply kill all my white adipose cells, we will learn that this is reason for them way beyond the simple storage of energy. Ever growing complexity.

  • Joanne

    Has it been already since way back in the 70s that we all first heard the term, “junk DNA.” My reaction then and now was simply that they didn’t yet know what this extra DNA did/does, but one day they well. The complexity of human biology gets only more and more complex and less and less mathematically probable to be random.

    When I first started reading about epigenetic, and that whole world of DNA complexity, again, the epi parts can actually change the phenotype coded in the DNA. Whoa, talk about another magnitude of complexity in human biology.

    When I was in sicence classes by back in the 60s, it was just a mater of time before our scientists discovered the chemicals that bumped together in a tidal pool just as a jolt of electricity created life. No one talks like that anymore. Since the 1960s, cell biologists have found nothing but more and more complexity. The fools today are those who still think or even talk about creating life in a test tube.

    The complexity, of the human, and most animal cells is mind boggling. The arithmetic chance of it happening at random has reached the miniscule point, much lower than the mathematical possibility that aliens put life on our planet.

    With sicence there is always more to know. It is a certainty that more and more complexity will be found. Nothing is here by accident. And for time to progress forward, the continued growth of entropy is a scientific expectation, till time unravels at the end.

    You know, when I was in science classes by in the 60s, scientists didn’t believe in a beginning or an ending for this existance. Now they do. There is always more to learn. God is playing with you, letting you know so much at a time to see what our corrupt mental capabilities congure up next. I actually enjoy it; read about the new stuff all the time. It’s fascinating. As much as I would love to simply kill all my white adipose cells, we will learn that this is reason for them way beyond the simple storage of energy. Ever growing complexity.

  • Michael B.

    “Here is what I found intriguing as it relates to evolution: Organisms are said to evolve through natural selection; that is, qualities that aid in survival are transmitted to future generations.
    But that assumes the ability to reproduce. And reproduction requires a genetic ability that has to be prior to natural selection. Maybe I’m misunderstanding, or maybe Darwinists have an answer to that. I’d be glad to hear it.”

    Evolution is a theory that explains the diversity of life — not the origin of life. In the Origin of Species, Darwin never claimed to know the origin of life. Currently scientists don’t know the answer. There’s a suggestion that the first reproducing cell might have come from another planet. A religious suggestion is that a supernatural being like a god created it. What’s unsatisfying with both of these suggestions is that they have life coming from another life, so it just raises the question where these other lives come from.

  • Michael B.

    “Here is what I found intriguing as it relates to evolution: Organisms are said to evolve through natural selection; that is, qualities that aid in survival are transmitted to future generations.
    But that assumes the ability to reproduce. And reproduction requires a genetic ability that has to be prior to natural selection. Maybe I’m misunderstanding, or maybe Darwinists have an answer to that. I’d be glad to hear it.”

    Evolution is a theory that explains the diversity of life — not the origin of life. In the Origin of Species, Darwin never claimed to know the origin of life. Currently scientists don’t know the answer. There’s a suggestion that the first reproducing cell might have come from another planet. A religious suggestion is that a supernatural being like a god created it. What’s unsatisfying with both of these suggestions is that they have life coming from another life, so it just raises the question where these other lives come from.

  • Kelly

    @25: “What’s unsatisfying with both of these suggestions is that they have life coming from another life, so it just raises the question where these other lives come from.” The latter shouldn’t be unsatisfying on those grounds, unless you’re somehow thinking of a purely naturalistic “god” who isn’t self-existent. The sensibleness of a self-existent life who is the cause of all other life is why many are theists.

  • Kelly

    @25: “What’s unsatisfying with both of these suggestions is that they have life coming from another life, so it just raises the question where these other lives come from.” The latter shouldn’t be unsatisfying on those grounds, unless you’re somehow thinking of a purely naturalistic “god” who isn’t self-existent. The sensibleness of a self-existent life who is the cause of all other life is why many are theists.

  • Michael B.

    @Kelly

    “The sensibleness of a self-existent life who is the cause of all other life is why many are theists.”

    The strongest argument there has to deal with how perfectly the physical universe appears to be created. Unlike biology, which is a mess, there are constants in the universe that appear to be finely tuned, and if any of them were off by even a slight amount, the universe could not exist. Bear in mind though, these are the more deist arguments. Many theists on the other hand will claim that not only God created the universe, but also will claim to know whom he wants you to vote for, what he wants you to wear, what kind of music he likes, what people will join him in the afterlife, what he wants you to eat, and who he wants you to marry.

  • Michael B.

    @Kelly

    “The sensibleness of a self-existent life who is the cause of all other life is why many are theists.”

    The strongest argument there has to deal with how perfectly the physical universe appears to be created. Unlike biology, which is a mess, there are constants in the universe that appear to be finely tuned, and if any of them were off by even a slight amount, the universe could not exist. Bear in mind though, these are the more deist arguments. Many theists on the other hand will claim that not only God created the universe, but also will claim to know whom he wants you to vote for, what he wants you to wear, what kind of music he likes, what people will join him in the afterlife, what he wants you to eat, and who he wants you to marry.

  • Pingback: Saturday Links: « creationscience4kids

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  • http://www.biblegateway.com/versions/Contemporary-English-Version-CEV-Bible/ sg

    Did anyone else find it cute that Kitty just happened to cite a study of mice?

  • http://www.biblegateway.com/versions/Contemporary-English-Version-CEV-Bible/ sg

    Did anyone else find it cute that Kitty just happened to cite a study of mice?

  • WebMonk

    tODD, read a bit more carefully what I’ve been saying.

    I’ve stated elsewhere that yes, the term “junk DNA” is used by scientists, but almost always in colloquial terms and not in scientific papers outside the abstract. The quotes you use back this up. So I’m not sure what your point it – your corrections to what I said are exactly in agreement with what I said. I’m puzzled.

    Francis Crick is a geneticist and he was using the term colloquially, just like I said an expert does. You said I’m wrong and that the truth is … exactly what I had said. Careful, I’ll begin to think you’re a Lutheran or something. ;-)

    And I’m not sure what your objection to my examination of the reporter’s qualifications were. Medical school doesn’t provide much instruction in genetics of this type. I have two friends who have gone through medical school, complete with degrees and are actively working in a hospital who have only a Biology 201 knowledge of genetics. It’s not a topic that is necessarily covered in medical school.

    It’s very much like a software engineer and a mechanical engineer – they may both be engineers but don’t trust a bridge built by a software engineer, and don’t trust a software system written by a mechanical engineer.

    Should we automatically trust the article of a guy who went to medical school 25 years ago but hasn’t practiced medicine of any sort since then, and who referenced nothing of the paper outside what is said in the abstract? (on top of all the additional concerns about accuracy that come with reporting to a general audience on a highly technical field?)

    Sorry. If this were a reporter who had written an article about a paper on adaptive algorithms in disk management, and his qualifications were that he got a masters in mechanical engineering 25 years ago, you’d agree that his base trustworthiness isn’t much/any higher than some other random reporter.

    That’s what this situation is.

    Phew!! *I let out my breath now.* :-D

  • WebMonk

    tODD, read a bit more carefully what I’ve been saying.

    I’ve stated elsewhere that yes, the term “junk DNA” is used by scientists, but almost always in colloquial terms and not in scientific papers outside the abstract. The quotes you use back this up. So I’m not sure what your point it – your corrections to what I said are exactly in agreement with what I said. I’m puzzled.

    Francis Crick is a geneticist and he was using the term colloquially, just like I said an expert does. You said I’m wrong and that the truth is … exactly what I had said. Careful, I’ll begin to think you’re a Lutheran or something. ;-)

    And I’m not sure what your objection to my examination of the reporter’s qualifications were. Medical school doesn’t provide much instruction in genetics of this type. I have two friends who have gone through medical school, complete with degrees and are actively working in a hospital who have only a Biology 201 knowledge of genetics. It’s not a topic that is necessarily covered in medical school.

    It’s very much like a software engineer and a mechanical engineer – they may both be engineers but don’t trust a bridge built by a software engineer, and don’t trust a software system written by a mechanical engineer.

    Should we automatically trust the article of a guy who went to medical school 25 years ago but hasn’t practiced medicine of any sort since then, and who referenced nothing of the paper outside what is said in the abstract? (on top of all the additional concerns about accuracy that come with reporting to a general audience on a highly technical field?)

    Sorry. If this were a reporter who had written an article about a paper on adaptive algorithms in disk management, and his qualifications were that he got a masters in mechanical engineering 25 years ago, you’d agree that his base trustworthiness isn’t much/any higher than some other random reporter.

    That’s what this situation is.

    Phew!! *I let out my breath now.* :-D

  • http://www.biblegateway.com/versions/Contemporary-English-Version-CEV-Bible/ sg

    @29

    The reporter is definitely in the category of well educated lay readers. That is, if he put his mind to actually reading the paper and maybe looking up or following up on a few things, he should be able to understand it and communicate it. So, compare him to a high school student whom so many are just determined should learn complicated theories in high school biology classes. This is why so many complain that the goal is indoctrination not education because some things are beyond the grasp of some x% of folks. So have basic stuff for them and AP classes with all the details for the kids who want to go down that road and quit pretending that teaching certain theories are vital to the average kid’s high school education.

  • http://www.biblegateway.com/versions/Contemporary-English-Version-CEV-Bible/ sg

    @29

    The reporter is definitely in the category of well educated lay readers. That is, if he put his mind to actually reading the paper and maybe looking up or following up on a few things, he should be able to understand it and communicate it. So, compare him to a high school student whom so many are just determined should learn complicated theories in high school biology classes. This is why so many complain that the goal is indoctrination not education because some things are beyond the grasp of some x% of folks. So have basic stuff for them and AP classes with all the details for the kids who want to go down that road and quit pretending that teaching certain theories are vital to the average kid’s high school education.

  • Pingback: What “junk DNA” does | Time For Discernment

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  • http://www.toddstadler.com tODD

    WebMonk (@29), well, that was a waste of a reply.

    I’ll repeat my request (@21), once more:

    Hey, you know what would be great? If you informed us about the topic, rather than spending all your time on ad hominem attacks! Maybe tell us specifically what is wrong in the article. That would be swell. Thx.

    You are repeatedly (and literally) committing the ad hominem fallacy. And you’re failing to educate anybody — if, in fact, you have any ability to educate us on this topic.

    Facts now please. Your conjecture is boring.

  • http://www.toddstadler.com tODD

    WebMonk (@29), well, that was a waste of a reply.

    I’ll repeat my request (@21), once more:

    Hey, you know what would be great? If you informed us about the topic, rather than spending all your time on ad hominem attacks! Maybe tell us specifically what is wrong in the article. That would be swell. Thx.

    You are repeatedly (and literally) committing the ad hominem fallacy. And you’re failing to educate anybody — if, in fact, you have any ability to educate us on this topic.

    Facts now please. Your conjecture is boring.

  • WebMonk

    Ok, I can do a quick breakdown.

    I’ve mentioned this already, but those first two paragraphs give the entirely wrong impression. Scientists don’t use “junk DNA” a tenth as much as the news. For the last twenty years scientists have been actively looking at the non-coding portions of our DNA to find out what they do. For a decade before that, most of them suspected it did stuff, but didn’t have the tools necessary to fully investigate.

    The article’s beginning description – that scientists dismissed 97% of our DNA as junk and are shocked to find that 80% of it actually does something – is extremely false, but it makes for good copy.

    It’s not until the second page that it finally mentions that the “junk” parts have long been suspected to have use. (refer back to my rants about the term ‘junk DNA’)

    You also need to realize what “functional” actually means in the paper. Here’s the quote from the main paper:

    Operationally, we define a functional element as a discrete genome segment that encodes a defined product (for example, protein or non-coding RNA) or displays a reproducible biochemical signature (for example, protein binding, or a specific chromatin structure).

    That may not sound exciting (which is why it isn’t mentioned in news stories), but it shows the bar for “functional” is pretty low. Anything that shows a specific chromatin structure counts, as does anything that gets touched even for non-coding RNA encoding.

    Here’s another quote from the paper:

    The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type.

    Remember, “participating in” is a very broad term, and the RNA/chromatin “associated event” is another very broad term that doesn’t map with what we normally thing of as “function”. An example of this are copying errors that happen frequently and are fixed (usually) but at times remain in the DNA. These chunks are still copied along with the properly-working chunks of DNA, but they are ignored when the DNA is used to do something. These chunks can be passed along and tend to accumulate over time.

    However, those faulty and ignored chunks are still counted in the 80% number – they’re totally ignored when the copied chunk of DNA “does something”, but the mere fact that it is part of the copying process qualifies it for the 80% number.

    That tends to put a bit of a damper on the articles tone of Scientists-shocked-that-the-97%-stuff-they-thought-was-junk-actually-isn’t!!

    Classifying the genomeinto seven chromatin states indicates an initial set of 399,124 regions with enhancer-like features and 70,292 regions with promoter-like features, as well as hundreds of thousands of quiescent regions. High-resolution analyses further subdivide the genome into thousands of narrow states with distinct functional properties.

    (I can’t find where in the paper they clarify the “hundreds of thousands”) Translation: half to a third of the functional parts are parts which don’t seem to have any interaction when the larger chunk is in use.

    These sorts of things make the 80% number a lot more nuanced and tenuous, and therefore a lot less exciting to put into a story for the public.

    There, does that help? Is that at all informative? Does that help to explain why I get torqued when articles like this make these rather overwrought statements?

    Perhaps the author knew all that, and had read the paper himself. I have my doubts, but it’s possible. Do you notice how unexciting my excerpts and clarifications were? If I were writing for a newspaper and were trying to gather as many readers as possible, then I might write the same sort of article as he did.

    It’s the nature of the beast – any science article for the general public is almost guaranteed to be poor as far as accuracy goes. At best it will compose of broad over-generalizations. If that were all, I would shrug. The problem comes when people take the articles as gospel truth and start extrapolating further from the article. Wildly erroneous conclusions are drawn.

  • WebMonk

    Ok, I can do a quick breakdown.

    I’ve mentioned this already, but those first two paragraphs give the entirely wrong impression. Scientists don’t use “junk DNA” a tenth as much as the news. For the last twenty years scientists have been actively looking at the non-coding portions of our DNA to find out what they do. For a decade before that, most of them suspected it did stuff, but didn’t have the tools necessary to fully investigate.

    The article’s beginning description – that scientists dismissed 97% of our DNA as junk and are shocked to find that 80% of it actually does something – is extremely false, but it makes for good copy.

    It’s not until the second page that it finally mentions that the “junk” parts have long been suspected to have use. (refer back to my rants about the term ‘junk DNA’)

    You also need to realize what “functional” actually means in the paper. Here’s the quote from the main paper:

    Operationally, we define a functional element as a discrete genome segment that encodes a defined product (for example, protein or non-coding RNA) or displays a reproducible biochemical signature (for example, protein binding, or a specific chromatin structure).

    That may not sound exciting (which is why it isn’t mentioned in news stories), but it shows the bar for “functional” is pretty low. Anything that shows a specific chromatin structure counts, as does anything that gets touched even for non-coding RNA encoding.

    Here’s another quote from the paper:

    The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type.

    Remember, “participating in” is a very broad term, and the RNA/chromatin “associated event” is another very broad term that doesn’t map with what we normally thing of as “function”. An example of this are copying errors that happen frequently and are fixed (usually) but at times remain in the DNA. These chunks are still copied along with the properly-working chunks of DNA, but they are ignored when the DNA is used to do something. These chunks can be passed along and tend to accumulate over time.

    However, those faulty and ignored chunks are still counted in the 80% number – they’re totally ignored when the copied chunk of DNA “does something”, but the mere fact that it is part of the copying process qualifies it for the 80% number.

    That tends to put a bit of a damper on the articles tone of Scientists-shocked-that-the-97%-stuff-they-thought-was-junk-actually-isn’t!!

    Classifying the genomeinto seven chromatin states indicates an initial set of 399,124 regions with enhancer-like features and 70,292 regions with promoter-like features, as well as hundreds of thousands of quiescent regions. High-resolution analyses further subdivide the genome into thousands of narrow states with distinct functional properties.

    (I can’t find where in the paper they clarify the “hundreds of thousands”) Translation: half to a third of the functional parts are parts which don’t seem to have any interaction when the larger chunk is in use.

    These sorts of things make the 80% number a lot more nuanced and tenuous, and therefore a lot less exciting to put into a story for the public.

    There, does that help? Is that at all informative? Does that help to explain why I get torqued when articles like this make these rather overwrought statements?

    Perhaps the author knew all that, and had read the paper himself. I have my doubts, but it’s possible. Do you notice how unexciting my excerpts and clarifications were? If I were writing for a newspaper and were trying to gather as many readers as possible, then I might write the same sort of article as he did.

    It’s the nature of the beast – any science article for the general public is almost guaranteed to be poor as far as accuracy goes. At best it will compose of broad over-generalizations. If that were all, I would shrug. The problem comes when people take the articles as gospel truth and start extrapolating further from the article. Wildly erroneous conclusions are drawn.

  • WebMonk

    If you look down into the paper itself, you’ll see that it breaks up the 80% number with a lot more clarity. If you look for what qualifies as “functional” in the way the term is usually understood by people, you’ll find that the exons, DNaseI portions, binding motifs, DNA:protein touching, etc (which make up what most closely matches people’s concept of “functional”) add up to about 20% of the DNA.

    If you take the term “functional” the way it is defined in the paper, then the previous understanding of DNA by scientists would define 60% as “functional”. They’ve found another 20 percentage points of “function” beyond what had been previously found – when “function” is defined broadly and beyond most people’s conception of the term.

    That’s way too boring to make an exciting story, though. The reporters use the 80% number from the abstract without checking what the 80% number actually means.

  • WebMonk

    If you look down into the paper itself, you’ll see that it breaks up the 80% number with a lot more clarity. If you look for what qualifies as “functional” in the way the term is usually understood by people, you’ll find that the exons, DNaseI portions, binding motifs, DNA:protein touching, etc (which make up what most closely matches people’s concept of “functional”) add up to about 20% of the DNA.

    If you take the term “functional” the way it is defined in the paper, then the previous understanding of DNA by scientists would define 60% as “functional”. They’ve found another 20 percentage points of “function” beyond what had been previously found – when “function” is defined broadly and beyond most people’s conception of the term.

    That’s way too boring to make an exciting story, though. The reporters use the 80% number from the abstract without checking what the 80% number actually means.

  • http://www.biblegateway.com/versions/Contemporary-English-Version-CEV-Bible/ sg

    I think that also included in the 80% are repeats. That is genes that are repeats of another. So and organism with one copy of a gene displays a different trait or degree of a trait or a different distribution of a trait than one that has two or three repeats because of how many repeats it has.

  • http://www.biblegateway.com/versions/Contemporary-English-Version-CEV-Bible/ sg

    I think that also included in the 80% are repeats. That is genes that are repeats of another. So and organism with one copy of a gene displays a different trait or degree of a trait or a different distribution of a trait than one that has two or three repeats because of how many repeats it has.


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