"We Never Said It Was Junk DNA..."

HEAVILY UPDATED with quotes and references! (as of 12:30 pm Sept 6 2012)

Evolution News (September 5, 2012): Junk No More!

Junk No More: ENCODE Project Nature Paper Finds "Biochemical Functions for 80% of the Genome"

An impressive 30 studies have been released and grouped together (mostly through the ENCODE genome sequencing project) in the peer reviewed science magazine "Nature" that has verified a longstanding Intelligent Design hypothesis, that the vast majority of the human genome is NOT "Junk DNA" or "evolutionary garbage" but is in fact functional.

While Intelligent Design scientists are obviously quite enjoying this hugely important vindication of their scientific predictions (a very important part in proving a scientific theory correct), the evolutionists are having to do some serious back pedaling.


A Summary Of "Junk DNA"

"Junk DNA" has been a long standing assumption by evolutionists that most of the genome (in humans as well as all other life) is mostly "left over evolutionary garbage", DNA that we no longer use or need because we've evolved out of needing it. It has been jokingly called "Junk DNA" for many years because of this. 2% of the human genome codes for Proteins, and until recently (and now especially), this tiny drop-in-the-bucket of our total DNA has been considered pretty much "the whole story". The reason this assumption has dominated so strongly and for so long is because evolutionists had convinced themselves (believed whole heartedly) that unless the DNA is being transcoded by RNA (like the 2% of Protein coding DNA), then it is useless or not functional. Because of this belief, 98% of our DNA has largely been ignored except by the occasional study here and there.

For more about "Junk DNA" and the debate over it, see my blog post from June 2012 about this exact issue (before this new comprehensive study came out proving it all true).

As Intelligent Design scientists have been studying and pointing out for well over 10 years now, it turns out that the vast majority of our DNA (ALL of our DNA, including the 98% that has mostly been ignored) is functional (actively used). The studies by the ENCODE project and connected studies released in the peer reviewed science magazine Nature state that at least 80% of our DNA is actually (and surprisingly, to them) functional, and that indications are good that the rest of our DNA is also functional (they just haven't figured out how it's being used yet, though signs indicate that it IS being used). That's a massive blow to a main tenet of Neo-Darwinism and a big boost to Intelligent Design.


Let The Excuses And Falsehoods Fly!

Excuses and falsehoods are already starting to pop up on atheist websites and pro-evolution websites to try and "cover their butts" on this issue. Not surprising considering the huge implications (and embarrassment) of it all, and how dedicated these people are to Neo-Darwinism on the whole.

Here is a list of the things that these folks are likely to say (and starting to say already) in an attempt to pretend that they didn't just get completely outdone by Intelligent Design theory and science.



1) We knew this all along. Nothing to see here folks. All you every day non-scientist types are just catching up to what we've known for a long time...

This is the claim that seems to be the most common so far among evolutionists, that they've actually known this for a long time already. Studies HAVE been coming out for the last 5 years, and even as far back as 10 years ago, that indicated functional properties of DNA that doesn't code directly for Proteins. But the point isn't that SOME studies have found SOME functionality and usage with all this "extra" DNA. The point is that the majority of scientists and especially atheists have been making the claim that "most of it is junk" despite this evidence! But because of their previous dedication to the idea of Junk DNA in the first place, they're STILL very hesitant to accept all this new scientific data.

For example:  At "The Mermaid's Tale" Pro-Evolution Science Blog...
More Advertising, Yet A Lesson To Learn

They confirm our idea that, at its base, DNA controls protein production and perpetuates itself, but through many subtle, complex functional roles.  Many are still to be discovered, but a much larger fraction of the genome is found to have some function, and the protein coding parts have been shown to comprise only a few percent of the whole of our DNA.  Whether ENCODE has actually determined the function of 80% of the genome, as they now claim, is debatable.

Basically, the claim is, "We knew this all along..." PLUS "I highly doubt this study is anything more than hype and promotion anyway and isn't actually saying what it seems to be saying..." That's a great double whamy! First, "We've known this all along." AND "It probably isn't true anyway." WOW! Talk about covering all your bases just in case!

And another pro-evolution blog post regarding the new set of studies...
A Slightly Different Response to Today's ENCODE Hype

The claim that “lots of the genome isn’t junk after all!” is not new — people have been using this straw man for nearly 20 years. What’s novel is that the ENCODE authors are claiming that there is now evidence that 80% of the genome shows signs function, or at least of “specific biological activity”. Many people are not convinced by this, me among them. I am especially unimpressed by this figure when I read the ENCODE project lead’s own words on the subject of “function” and the 80% figure.

Again, "Nothing to see here folks. We've known this all along." PLUS "It probably isn't true anyway. Just a load of hype and show."

Also, the previous linked to article states:

Even after 5 years, $185 million, and a massive study by hundreds of researchers, there still is only evidence of function for 80% of the human genome under the most extremely generous interpretation. That leaves 20% without any signs of function whatsoever.

Oh my! It cost LOTS of money and they didn't figure out what the other 20% of the genome does? That's just terrible!... Come on! You guys were arguing that MOST of the genome is non-functional garbage. Now you're arguing that the functioning of 20% is still unknown, so they're still proven right... Give me a break!

Then that same writer goes into a spout of obfuscation, re-defining terminology and pretending that what was meant by "functional" and "not functional" wasn't really what we think or thought it was.

To get that 80% figure, you have to have a very loose definition of “function” indeed.

Basically, "It's only functional so long as you count ANY function." This is getting very disappointing. Now you're arguing that when you were before saying that "NO function" (as in ANY function AT ALL) existed, you actually meant "no MAJOR function"... *rolls eyes*

Some are undoubtedly functional, but it is quite a stretch to suggest that millions of these elements are needed to regulate our 20,000 genes (but not the 30,000 genes of a pufferfish). As Carl Sagan said, “extraordinary claims require extraordinary evidence”, and so far we simply do not have it when it comes to claiming that the majority of the elements in the genome have a biological function.

"Because we're all just evolved animals and fish, so most of this "extra DNA" is obviously garbage or not that important anyway..." *heavy sigh* They're a dedicated bunch aren't they?


2) We never really MEANT that it was "Junk", just that we didn't yet know any function for it. That's good science, not assuming something until we have solid proof...

The proof has been piling up for many years now, and Intelligent Design scientists have been pointing this out constantly with articles online citing such scientific studies and even publishing entire books about the topic. The proof has been there for quite a while, and the evidence pointing to this reality has been piling up for even longer. "Good science" doesn't consider most of the human genome to be garbage or non-functional just because we don't know the function of it yet. THAT is the key problem here. They assumed that all this DNA was junk, evolutionary left overs, and they stated as much repeatedly over and over again, even using it for a long time as a major argument point against Intelligent Design. "98% of our DNA is non-functional and that's exactly what we'd expect if Evolution were true!"... If they had simply said, "We don't know the function of it yet" or something else similar to that, this whole thing wouldn't be nearly as big of a deal. But that's NOT what they've been saying all this time. They've been mostly argueing that this stuff truely had NO function BECAUSE it was evolutionary junk.


3) We've got scientists who suspected function for some of this "Junk DNA" too!...
Smithsonian.com: Junk DNA Isn't Junk, And That Isn't Really News

Remember in high school or college, when you learned about all that DNA inside of you that was junk? The strings and strings of nonsense code that had no function? A recent blitz of papers from the ENCODE project have the world abuzz with news that would rip that idea apart.
But, like many things that stick around in text books long after science has moved on, the “junk DNA” idea that ENCODE disproved, didn’t really need disproving in the first place.

Yes, there were a few out there who admitted even many years ago that the concept of "Junk DNA" was probably wrong and probably even harmful to the progress of science. But these people were very few and far between and only in very recent years have more scientists finally started to admit that all this DNA does actually have function and is actually being used.

However this is a classic case of "We're always right, even when we're wrong." Basically they point out evolutionists that DID get this right even from early on, and claim that this is proof that evolutionism didn't get it wrong. Sorry, but you can't constantly argue the complete opposite and then turn around and say you were right all along because of a few open-minded scientists that didn't follow the mainstream belief. Just because a very small minority of evolutionists didn't get hoodwinked by this bad Neo-Darwinist assumption doesn't mean that the rest of you guys didn't get completely blown apart. You guys are all about "consensus" until the "consensus" gets found out to be completely wrong, and then you shout, "not following the consensus is good science!" This is classic stance jumping, basically, "We're always right, even when we're wrong." As long as ONE scientist SOMEWHERE suggested that there MIGHT be function to SOME of this other DNA, then they claim that the scientific community as a whole didn't grossly screw this up. Sorry, but those smart few people who weren't blinded by Neo-Darwinism are the clear exception to the rest of you.


4) The STUDY is Junk! The scientists are lying!

Michael Eisen, a science writer, on his Twitter feed says about the study:

"measurable biochemical activity" is a meaningless measure of functional significance.

Just like from "The Mermaid's Tale", this science writer who has dedicated himself to the evolutionism debates says that the comprehensive study by the best genome sequencing and analysis project on the planet consisting of hundreds of top scientists is wrong and blowing things way out of proportion. They're basically lying to make the news... Denial at it's finest. These guys constantly argue that science is above hype, promotion, half-truths and lies, and then when it doesn't agree with them that's exactly what they claim the science is. Oi!


Closing

Those are just a few claims that the evolutionists are already starting to make, and likely to continue making for weeks and months (even years) to come. This has all been done before repeatedly as evolutionism has gotten things very wrong and had to completely change its stance and pretend like it never actually did so. All in all it always comes down to, "We might have gotten that one thing wrong, but we're right about everything else, so trust us. Even if something is currently wrong, we'll eventually get it right anyway. Good science goes in the direction that the evidence points, even when the evidence contradicts long held scientific beliefs."

That's very true, but sooner or later it just becomes ridiculous the amount of effort that goes into "covering the trail" of complete missteps that the scientific community have taken based entirely on the assumption that Neo-Darwinist evolution is true. It gets to the point where it's obvious that no matter HOW wrong they are on even MAJOR issues, they simply re-warp the evolutionary system to accommodate it.

This is NOT science, it's desperate blind religion and faith. Science is falsifiable. If a bunch of theories are being overturned then the basis for those bad theories is probably wrong too, otherwise they wouldn't keep getting these big issues wrong in the first place. Intelligent Design didn't get this wrong. So why did evolutionism? But that doesn't matter to evolutionists who are drinking the evolution kool aid. They KNOW in their heart of hearts that evolution must be true so no matter what the evidence says, they believe Neo-Darwinism, even if they have to re-write their core theories every 5 or 10 years in order to still make it work.

Not Junk DNA

Roughly 2% of our human DNA codes for Proteins (think of Proteins like the microscopic parts that are bodies are made of) and the other 98% of our DNA has often casually been called “Junk DNA”, or “non-functional DNA”. Evolutionists for a long time have considered this 98% to be unimportant evolutionary left-overs, so called “Junk DNA”, that has accumulated across hundreds of millions of years of evolution, but is now, for the most part, garbage and unimportant. This belief, however, is being absolutely destroyed by modern genetics.

There’s a very common myth out there that the human genome (genetic code) is 98% similar to that of Chimpanzee monkeys, which according to evolutionists is a huge proof that humans evolved from monkeys. What usually gets left out of such statements is that the 98% similarity is only a miniscule section of the human and chimpanzee DNA. Basically, scientists have run the genetic sequences of about 2% of the human and chimpanzee genome, the part of the genome that codes for Proteins. That’s only 2%! Then scientists have taken the genetic sequences of that 2% and re-arranged the genes (chunks of DNA) because the chimp and human genomes are in a very different order. Without this purposeful re-arrangement by scientist, the genes simply would not match up side by side. Then the scientists chopped away the parts of this 2% that do not match, and compared only the parts that do closely match each other, and declared that human and chimpanzee DNA is 98% the same between us and them…

Darwinian Logic: The Latest on Chimp and Human DNA  (by Jonathan Wells, October 27 2011)

http://www.evolutionnews.org/2011/10/the_latest_on_chimp_and_human052291.html

www.EvolutionNews.org

But why only compare the 2% (or so) of the genome that specifically codes for Proteins? What about the other 98%? That’s what is off-handedly called “Junk DNA”. It’s DNA that does not code specifically for Proteins, and thus, has been considered “junk” or genetic garbage. Remember folks, this is 98% of our DNA! Over the last 20 years (and especially the last 10 years), scientists are discovering that this “junk DNA” is actually vital to exactly how our genes are expressed, how our cells do what they do. “Junk DNA”, by and large, seems to actually tell the Protein coding genes how to function (what to do), when to do it, how long to do it for, how and when to change things up, and how best to use what has been built off the blue print of our DNA. Basically, as it’s turning out, the “junk DNA” is the bulk of our genetic code. More and more signs and studies are showing us that most of it has important, even critically important, functions and purpose. It is NOT junk or left-over evolutionary garbage, as some of the most enthusiastic atheistic apologists have claimed over the years.

“If Junk DNA Is Useful, Why Is It Not Shared More Equally?”

ScienceDaily (Jan. 31, 2011)

www.sciencedaily.com/releases/2011/01/110131133137.htm

“DNA was originally thought to have a single function: to help cells make the proteins they need. Any DNA that is not immediately required to produce proteins was written off as "junk" and deemed unworthy of study. Recently, however, it has become clear that junk DNA performs a wide range of important tasks.”

Evgeniy S. Balakirev, and Francisco J. Ayala, Pseudogenes, "Are They "Junk" or Functional DNA?," Annual Review of Genetics, Vol. 37:123--51 (2003)

“pseudogenes that have been suitably investigated often exhibit functional roles.”

THEY MISSED THE MOST IMPORTANT PART!

One of my many hobbies is computer programming. DNA is very similar to a computer programming language, one that is highly complex and sophisticated unlike anything mankind has ever programmed before. It puts our most incredible complicated computer programs to shame. There is a very serious flaw in the assumption that the “Junk DNA” (98% of our DNA) is not really that important. To show exactly what I mean when I say that “They Missed The Most Important Part”, I want to describe this scenario by using a few metaphorical examples to help get the point across.

The Food Recipe

Imagine that the 2% of DNA that codes for Proteins in our bodies is a rather non-specific set of ingredients for making a particular meal for supper. You’ve got beef, a bunch of spices, a bunch of vegetables, and a few other ingredients. Now you’re told to cook a very specific kind of meal with these ingredients, but not given any instructions on how to do it. No specific portion sizes, no instructions on the order in which the ingredients should be added, the timing of adding each ingredient, how they are to be cooked, prepared or combined… Nothing! To make matters worse, the person who is cooking this meal has no cooking experience or knowledge at all. All of the instructions, experience and knowledge that goes into making the meal is equivalent to the 98% of our DNA that does not code for Proteins. That’s pretty important stuff, isn’t it?

The Math Equation

How about another example, this time one from math. Let’s say that X = 5 and Y = 4. Those are two set values and they won’t change no matter what we do with them. But here comes the important part. How are those variables (X and Y) arranged in a math equation? Does it make any different to the answer you get, the end result? Do the instructions (the equation) matter?

If we make the equation X + Y = Z, we know that it’ll turn out like this: 5 + 4 = 9. But if you change that “+” operator to a “-“, the equation becomes 5 – 4 = 1, a completely different answer. And what if you make it a big long equation but still only using the X and Y variables? How about, X(Y) + (X / Y) – (Y^X) = Z … Yikes, that’s getting kind of complicated isn’t it?

The point I’m trying to make is this. The instructions or operational actions (or controls) are what give you the answers. Different instructions (layouts and equations) will give you different results, different answers. So if X and Y, which represent 5 and 4, are the Protein coding part of our DNA, then the other 98% of the DNA is telling the cells of our body exactly how to use and handle X and Y. These instructions, these operators, are essential to everything working like it’s supposed to. The slightest change and the answer in the equation can be VERY different, despite using the exact same numbers (5 and 4).

The Computer Code

All computer programs are essentially made up of the exact same things, variables and computer code. Let’s imagine that the 2% of our DNA that codes for Proteins are variables. Now, knowing this, that all computer programs use variables and programming language instructions to make them work the way they’re supposed to, you brazenly announce to the world that, “All computer programs are 98% the same!”… Such an exclamation is of course ridiculous, right? Because you’re only comparing one very general aspects of what a program is and has within it. You’re completely ignoring exactly what those variables contain, how many variables there are, and ALL of the instructions or code that makes each program do what it does. You see, the instructions are the difference between a computer program used for reading your email or playing a fast paced 3D game where you blow away fictional bad guys with guns. Both use variables, probably even the same kinds of variables (numbers, strings of text) but HOW they are used makes ALL the difference.

CONCLUSION

The Protein Coding part of our DNA (2% of our DNA) is basically the tiny set of instructions for building the little bits and pieces that our body uses to do most of what it does. They are the “Lego blocks”, the “ingredients”, the materials, the tools. The other 98% is the instructions for how to use those parts and tools. That 98% controls how much of this stuff works, when it works, in what way it works, and has tons of important (even critical) information within it to make sure the whole complicated system works like it’s supposed to. That 98% of our DNA (the so called “Junk DNA”) runs and controls the whole show! These instructions are the key to what makes the vast majority of life forms on our planet so incredibly different and unique from each other, and yet so much of this DNA was until recently shrugged off as “not that important”.

To ignore this fact is like claiming that volleyball and ballet are essentially the exact same thing because both are a physical work out. No, they’re not anywhere close to being “the same thing”. You’re ignoring the huge amount of details that make them so different from each other!

The “human and chimp DNA almost identical comparison” is basically a massive case of extreme selective statistics filtering, especially when every day we’re discovering more and more about that other 98% of the genome that was ignored in that study. As more and more of the incredible importance of this “Junk DNA” is coming into the light of cutting edge modern science, scientists are finally discovering just how very different and unique we are. It’s blowing a lot of evolutionary thought and assumptions right out of the water. This, however, is no surprise at all to people who believe that God created, designed and wrote this genetic code into all living things, and that except for parts of it that have broken down over the many centuries since creation, it’s all functional and important.

The Changing Face of Pseudo Genes

http://www.truthinscience.org.uk/tis2/index.php/component/content/article/277.html

Quick Extra Points:  Why "Junk DNA"?

Part of the reason for the myth of “Junk DNA” is that some of this “Junk” looks almost identical to actual Protein coding genes, yet scientists found that this DNA (often called Pseudo Genes) was not being coded into Proteins. Since the belief was that Protein Coding genes are the important part, the fact that these other genes were not being used that way made the scientists think they were broken duplicates of the working genes, evolutionary screw ups. Though some of these Pseudo Genes could very well be no longer fully functional broken genes, scientists are now finding that many of these “Pseudo Genes” are actually being used in connection with the Protein coding genes that look so similar to them. So what’s going on here? It’s becoming clear that these “Pseudo Genes” are like identifiers, a bit like a website’s URL address. They basically contain the instructions for how to use the target gene. In other words, the part of these genes that look so similar to the functional protein coding genes are actually saying, “Do this with this target DNA.”

Why the quickly shifting perspective on Pseudo Genes and “Junk DNA”? One reason is the many studies that are discovering important functions for this DNA that were never tested or recognized before. Our modern technology allows us to study all this stuff in far more detail. The second big reason is that it makes absolutely no sense at all for biological life forms to hold onto (store and continue to pass along through successive generations) all of this genetic data if it’s “evolutionary garbage”. The amount of energy and resources it takes to keep this genetic library going is huge, and there would be no reason for life to hold onto it all if it were simply completely broken, non-functional, or junk. The fact that life does go through so much effort to preserve this vast amount of DNA (98% in humans compared to the 2% that codes for Proteins), even under pressure to get rid of it, strongly indicates that this DNA is very important and functional after all.