Real Science Friday: "Nature" Confirms Creationist Rejection of Junk DNA

[Jefferson]

"Nature" Confirms Creationist Rejection of Junk DNA

This is the show from Friday, October 5th 2012.

SUMMARY:



* Nature Paper Confirms RSF Rejection of 'Junk' DNA: A landmark study by 440 researchers working in 32 laboratories around the world have so far been able to identify function for 80 percent of the human genome! Real Science Friday co-hosts Bob Enyart and Fred Williams also present six minutes of audio from 1998 when leading evolutionist Eugenie Scott tells Bob that genetic scientists were "over the hump" and affirmatively knew that the pseudogenes had no function and that such junk DNA was therefore evidence against the existence of a Designer. Hear the fundamentalist Bible teacher disagree with the degreed scientist, and guess who science has vindicated?

* Notice the Nucleotides in the Trash Bags: -->

* ENCODE Project Takes Out the Trash: The project leader for ENCODE (the Encyclopedia of DNA Elements) is predicting that eventually we will learn that "100%" of the genome is functional. (ENCODE Consortium, Dunham, et al., Nature, 2012, pp. 57-74). When the scientist finally reaches the summit, he finds the theologian already there.

For this show, RSF recommends
Dr. Don Johnson's Programming of Life DVD!

* Junky Real Science Friday Shows
- "Nature" Confirms Creationist Rejection of Junk DNA (this web page)
- Bob Debates an Evolutionist 1998 DVD (from our archives)
- http://RealScienceFriday.com/ReMine-4RSF: Enyart Exhumes Eugenie Scott (2005 radio program: show summary copied here...)


* RSF: Bob Debates Ph.D. Evolutionist Eugenie Scott: One of the world's leading anti-creationists vs. Bob Enyart. The debate is decided in the first round, by TKO. That’s after Bob asked the well-known scientist for any evidence that any high level function had ever evolved, like eye sight, or hearing, or flight, or mobility in general? Through the hour-long debate, this evolutionist refused to offer any such evidence but finally settled on a claim of evidence against design, which was: junk DNA!

* JUNK DNA: Eugenie Flubs Genetics Prediction, Creationist Hits the Bull's-eye. The negative evidence that Eugenie did offer was Junk DNA. This scientist, from her Darwinist worldview, therefore didn't offer scientific evidence but made this philosophical argument about what a Creator would or would not do; namely, that He wouldn't fill our genome with so much non-protein-coding DNA. While some simple worms have 20,000 genes, it is typically a small portion of DNA that actually codes for proteins. A human has only 20,500 genes, which fills only 2% of our genome. Yet the widespread evolutionary claim for decades (including through the last two decades, and for many, still held today) was that the rest of the genome was left-over evolutionary garbage.

Debating this physical anthropologist, Bob Enyart was just a Christian fundamentalist talk show host who spoke from his biblical worldview. Bob argued that our knowledge of genetics was in its infancy, and that it was too early to make the determination that all those non-coding segments of DNA had no function. After this 1998 debate, the next decade of explosive genetic discoveries overwhelmingly validated this creationist perspective, so much so that aside from coding for 20,500 proteins, it is estimated that the remainder of the genome has approximately four million other functional regulatory segments of DNA. So much for junk. Fulfilled predictions, as the world saw with Einstein's 1919 eclipse prediction, go toward scientific credibility. However, Dr. Scott strongly rejected this creationist prediction making an extraordinary claim, which Bob immediately offered her to retract, that scientists currently knew everything they would ever need to know about genetics to conclusively state that all those regions were useless junk. Bob would love a rematch. But Eugenie Scott, (Ph.D. in Physical Anthropology, leading anti- creationist, and director of the National Center for Science Education), who had just debated evolution on a nation- wide PBS television program, ended this one-hour program with Bob stating, "Well, I don’t debate."



* The Diet Pop Junk DNA Syndrome: The many Darwinists who strongly pushed (and many still do) the Junk DNA claim predicted that nearly 100% of the entire human genome, the portion that was non-coding, was mostly just left-over junk DNA. It's like a diet cola having NO sugar, NO calories, NO cholesterol, NO fiber, NO protein, NO carbs, NO sodium, NO fat. One wonders what in the world gives it its taste. So from the 1970s it's not surprising, assuming as they did that nearly 95% or so of the DNA was junk anyway, that evolutionists could make such sloppy claims about DNA reinforcing the Darwinian tree. However, now, with the List of Genomes that Just Don't Fit, evolutionary geneticists have falsified the claim that DNA confirms Darwinian predictions. And all that progress aside, the canard that there's nearly a 99% similarity between humans and chimps should have been falsified merely by a careful look at differences in brain and overall anatomy.

* Tossing the Wright Brothers Materials and Tools: Consider the significance of the four million regulatory regions of the human genome as compared to the relatively tiny portion that codes for proteins. The creationist Wright Brothers' design, that is, their regulatory input, so-to-speak, dwarfed the importance of the particular kinds of materials and tools that built their airplane. Other tools and materials could suffice. But all the tools and materials in the world assembled for workers who had no design to begin with would not produce an airplane. Thus the regulatory portion of the genome, including that in epigenetics, very possibly may be the more significant part. And similarly, the design concept of a nucleus itself is far more important than what specific chemistry will implement it.

* Can Evolution Proceed One Small Step at a Time? If it is true that there are no "small steps," logically or physically, between monochromatic and dichromatic vision, then at least for this wildly complex vision-system upgrade, Richard Dawkins' Mt. Improbable must be scaled in one huge step. And scaling such a complexity cliff in one step, he himself admits, would be very difficult to advocate. There are no Darwin-friendly small steps between eukaryote (nucleus) and prokaryote (no nucleus), nor between invertebrate and vertebrate, nor between monochromatic and dichromatic vision. Whether you are an extinct fossil or a living species, you either have a backbone or you don't; you either have a nucleus or you don't, you might have monochromatic or dichromatic vision, or not, but you don't have something in between.

Post-show Note: Illustrating this nicely the Wikipedia article on transposons states, ironically that transposition elements, "are often considered 'junk DNA'. In Oxytricha... they play a critical role..." And from Scientific American, "The term 'junk DNA' repelled mainstream researchers from studying noncoding genetic material for many years."



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[Daedalean's_Sun]

We've known that much of non-coding DNA has had function for quite some time. It being evidence doesn't rest upon it being entirely non-functional. Non-coding DNA would still have function in numerous arrays, however the specific arrays we find still points to Evolutionary lineage through descent with modification of this non-coding DNA.

 

[Nick M]

We've known that much of non-coding DNA has had function for quite some time.

So you knew and didn't tell the professor with the PhD?

 

[Daedalean's_Sun]

So you knew and didn't tell the professor with the PhD?

As far as I can tell she has never made a claim to the contrary.

 

[Frayed Knot]

This web page from a working geneticist explains a lot about the headlines regarding the ENCODE work and "junk" DNA. It's a very good read and should give you the idea of where the science actually stands.

The section headings of the essay are titled:

ENCODE says what?
The human genome has a lot of junk DNA
Noncoding DNA is part junk, part regulatory, part unknown
ENCODE’s definition of “functional” includes junk

The key point is that we know that the human genome is at least 50% of what a reasonable person would term "junk." But the people who summarized the ENCODE project used a very unusual definition of "functional," so they got a percentage that's way higher than what most people who know the details would say.

Some highlights:

Genome size varies a lot. You might think that apparently more complex organisms like human would have more DNA than simpler organisms like single-celled amoebae but that turns out not to be true. Salamanders have 10-fold more DNA than us; lungfish, about 30-fold more.

So maybe we don’t really know how to define or measure “complexity”; maybe we’re just being anthropocentric when we think of ourselves as complex. Who’s to say that amoebae are less complex than humans? Ever looked at an amoeba? (They’re pretty awesome.) Still. The key observation isn’t just that very different creatures have very different genome sizes; it’s that similar species can have very different genome sizes. This fact, surprising at the time, begged a good explanation. If two species are similar, yet their genomes are 10x different in size, what’s all that extra DNA doing?

This observation about genome sizes raised the idea that maybe genomes could expand (and shrink) rapidly (on an evolutionary timescale) as a result of some neutral (non-adaptive) processes — that maybe organisms could tolerate DNA that didn’t have a direct functional effect on the organism itself, but was instead was being created and maintained by neutral or even parasitic mechanisms of evolution. Somebody dubbed this “junk” DNA, and that was probably an unfortunate term, because it’s incited people’s anger from the day it was coined. It’s not polite to tell someone their beautiful house is full of junk. Even if it is.

A key discovery that satisfactorily explained the C-value paradox was the discovery that genomes, especially animal and plant genomes, contain large numbers of transposable (mobile) elements that replicate all by themselves, often at the (usually slight) expense of their host genome. For instance, about 10% of the human genome is composed about a million copies of a small mobile element called Alu. Another big fraction of the genome is composed of a mobile element called L1. Transposons are related to viruses, and we think that for the most part they are parasitic in nature. They infect a genome, replicating, spreading, and multiplying; eventually they die, mutate, and decay away, leaving their DNA sequences. Sometimes when an Alu replicates and hops into a new place in our genome, it breaks something. Usually (partly because the genome is mostly nonfunctional) a new Alu just hops somewhere else in the junk, and has no appreciable effect on us.

So it turns out that when we look at all these different genome sizes, almost all of the puzzling size variation is explained by genomes having different “loads” of transposable elements. Some creatures, like pufferfish, have only low loads of transposons. Some creatures, like salamanders, lungfish, amoebae, corn, and lilies, are loaded with massive numbers of transposons. As it happens, the human genome is annotated as about 50% transposon-derived sequence — right at that 50/50 borderline where someone can say “the human genome is mostly junk” and someone else can say “the human genome is mostly not junk”.

About 1% of it is coding. Something like 1-4% is currently expected to be regulatory noncoding DNA given what we know (and our knowledge about regulatory sites is especially incomplete). About 40-50% of it is derived from transposable elements, and thus affirmatively already annotated as “junk” in the colloquial sense that transposons have their own purpose (and their own own biochemical functions and replicative mechanisms), like the spam in your email. And there’s some overlap: some mobile-element DNA has been co-opted as coding or regulatory DNA, for example.

But as far as questions of “junk DNA” are concerned, ENCODE’s definition isn’t relevant at all. The “junk DNA” question is about how much DNA has essentially no direct impact on the organism’s phenotype – roughly, what DNA could I remove (if I had the technology) and still get the same organism.

 

[lucaspa]

"Nature" Confirms Creationist Rejection of Junk DNA

* Nature Paper Confirms RSF Rejection of 'Junk' DNA: A landmark study by 440 researchers working in 32 laboratories around the world have so far been able to identify function for 80 percent of the human genome! Real Science Friday co-hosts Bob Enyart and Fred Williams also present six minutes of audio from 1998 when leading evolutionist Eugenie Scott tells Bob that genetic scientists were "over the hump" and affirmatively knew that the pseudogenes had no function and that such junk DNA was therefore evidence against the existence of a Designer.

Jefferson, this is nice bait and switch, but really bad science. I also think it is bad Christian morals, but that is another topic. "junk" DNA was the whimsical name given to DNA that did not directly code for proteins. That was it: the DNA was not translated to proteins. That never meant it had NO function whatsoever, like the name "junk" implies. Instead, even at the time, it was known that long stretches of DNA before the coding regions were used for transcription control: to determine when the coding region was transcribed to messenger RNA and how many copies were transcribed.

Over the years, it has become that much of the non-coding DNA is subject to natural selection.
Alexey S. Kondrashov. Evolutionary biology: Fruitfly genome is not junk Nature Volume 437: 1106 Oct 20, 2005
"A comparison of two fruitfly genomes shows that much of their non-coding DNA is controlled by either negative or positive selection,"

It also turns out that DNA that doesn't code for proteins can also code for microRNA that have regulatory functions within the cell.

However, notice that Enyart's discussion of the paper said they found a function for 80% of the genome. That leaves 20% without a function.

Pseudogenes are something else. Once upon a time they were part of the "non-junk" or coding DNA. That is, they coded for proteins. But, in mutations or gene duplication they lost the ability to be transcribed to messenger RNA: http://www.pseudogene.org/background.php, http://en.wikipedia.org/wiki/Pseudogene. (BTW, when you can accurately use Wikipedia to refute Enyart, then it tells you that he just isn't paying attention.)

The classic example of a pseudogene is the enzyme L-gulono-γ-lactone oxidase (GULO) in primates. It is an essential enzyme in the synthesis of ascorbic acid (vitamin C). In all mammals except guinea pigs and primates, vitamin C is not a vitamin. It is made in adequate quantities by the individual and they don't have to get it from their diet like we do.

In primates, the DNA sequence to code for the enzyme is still there, but it is disabled, thus the pseudogene. So yes, Eugenie Scott was correct that pseudogenes have no function. The new data does not alter that. And yes, it is a theological argument against God directly designing humans: if God was the Designer, then God deliberately disabled a gene that would make ascorbic acid -- a chemical essential to our health -- and condemned countless people thru history to the disease scurvy. That's a cruel sadistic god that isn't worthy of worship.

This is one area where evolution by natural selection rescues God from creationism. Now God is not the direct designer of pseudogenes: evolution is. Evolution gets God off the hook for being cruel and sadistic. It's why Christians were so quick to ditch creationism/ID when evolution was discovered.