Most Ambitious Human Genetics Project To Date

New science is putting the so-called leftovers from our supposed evolutionary past to shame! When the first study of the genome was published about 11 years ago, scientists were surprised to find that only about 3% of it coded for proteins and the rest was considered, “junk DNA.”

Then of course new science discoveries came to be where researchers discovered coded information in the “epigenome,” which includes RNAtranscripts that regulate the code.  New results from the most ambitious human genetics project to date,  show at the least, 80 percent of the genome has a function! A remarkable turnaround in slightly over a decade.

The turnaround has become one of the major stories for science discoveries this year and could be the best breakthrough study out of them all in science for this year as well! Numerous publications have been writing about it. Over 20 papers were published in various publications like Genome Research and Genome Biology, along with reviews in The Journal of Biological Chemistry. Even my local newspaper made this front page news and described what it means for possible future medical uses.

It also has Darwinists putting to rest the notion of  leftovers from our supposed evolutionary past which had been heavily promoted by militant evolutionists who lobby hard against creationism and intelligent design such as  P.Z. Myers, Nick Matzke, Jerry Coyne, Kenneth Miller and British atheist, Richard Dawkins.

It has been part of the creationism model and ID proponents who have argued for years that function will be discovered for much of our DNA that was once considered to be useless with better science and indeed it has!

In an article in Nature

“The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification.”

These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation.

“Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.”  

Was the evolutionary explanation helpful with this discovery? Nope.  In this article in Nature, it says…“Why evolution would maintain large amounts of ‘useless’ DNA had remained a mystery, and seemed wasteful,” Barroso wrote.  “It turns out, however, that there are good reasons to keep this DNA.”

Language like  “evolutionary constraints” and “evolutionarily conserved” used in many of the articles is another indication that evolution was useless when it came to this discovery. Both of those terms of course refer to lack of evolution rather than showing evolution which is why the likes of P.Z. Myers, Nick Matzke, Jerry Coyne, Kenneth Miller and Richard Dawkins advocate junk DNA very heavily! Perhaps it will modify their position, anything left which is considered “junk DNA” they will begin to focus on. Or they could hold the position what New Scientist is now advocating with their skepticism of finding function with non-coding DNA.

“The ENCODE project has revealed that 80 per cent of our genome does something, but doing something is not the same as doing something useful…there are still very good reasons for thinking that most of our DNA is far from essential.”

You can tell that this discovery is not good for evolution when you have a publication like New Scientist that confuses “essential” with “adaptive” and then begs the question whether something useful must be essential. On the other side, ID proponents are jumping for joy, Casey Luskin writes

“We will have more to say about this blockbuster paper from ENCODE researchers in coming days, but for now, let’s simply observe that it provides a stunning vindication of the prediction of intelligent design that the genome will turn out to have mass functionality for so-called “junk” DNA. ENCODE researchers use words like “surprising” or “unprecedented.”

“They talk about of how “human DNA is a lot more active than we expected.” But under an intelligent design paradigm, none of this is surprising. In fact, it is exactly what ID predicted.” 

While this breakthrough in science has caused a problem for the story of evolution, Darwinists have pushed back the idea of forcing the data into their evolutionary framework for future researchers such as in this article, “Evolution and the Code” where one scientist mentions it, but the other three did not which doesn’t mean they didn’t go along with the assumption in the same paper in which they co-wrote together.

Here is a video, where it suggest there might be more than 80 percent function with the genome. “There are probably things that we have no idea what they’re doing and yet they’re going something important.” A logical assumption considering the pattern of discoveries being made so far!

 

Evolution has hurt this part of research for years with its assumption of junk DNA but not anymore. Now researchers are looking for more functions than ever before! Here is more quotes by scientists…

“I don’t think anyone would have anticipated even close to the amount of sequence that ENCODE has uncovered that looks like it has functional importance,” says John A. Stamatoyannopoulos, an ENCODE researcher at the University of Washington, Seattle.  He is referring to researchers who believe in evolution, other scientists have anticipated a lot more sequence that ENCODE.

“It’s a treasure trove of information,” says Manolis Kellis, a computational biologist from Massachusetts Institute of Technology (MIT) in Cambridge who analyzed data from the project.

“Regulation is a 3D puzzle that has to be put together,” Gingeras says. “That’s what ENCODE is putting out on the table.”

What an amazing time we live in! Wow! Unless there is a cure for cancer or someone lands on Mars, this is no doubt the science breakthrough for 2012 which confirms creationism and will also help improve the health of mankind!

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10 thoughts on “Most Ambitious Human Genetics Project To Date

  1. As predicted, it didn’t take very long to produce enough creationist material for Michael to know what to think about the ENCODE project results.

    [“Junk DNA”] has been part of the creationism model and ID proponents who have argued for years that function will be discovered for much of our DNA that was once considered to be useless with better science and indeed it has!

    THE FIRST QUESTION to ask is: Why do creationists get their knickers in a twist about “junk DNA”?[1] Because it seems to b a make-or-break proposition for them. If God is competent, then he creates competent designs . Evidence that the genome contains useless crud thus denies the perfection of God. Evolution, on the other hand, allows the possibility of stuff that is useless—or has no current use—but does not require it. Creationists claim that evolution requires non-functional elements in the genome, but this is, and has always been, a lie. Basically, the creationists have to prove that every last drop of DNA has some sort of function; but evolution is indifferent in this matter, so it doesn’t need to prove anything. Further, creationists should have to demonstrate that the function benefits the organism that hosts it. Biology, on the other hand, allows genome elements that may have had a function in an evolutionary ancestor, but has no (or diminished) function.in the organism in which it occurs.[2]

    Despite the efforts of creationists to show that evolution predicts or requires non-functional DNA, evolution allows it, but does not require it. For evolution, it’s optional—but for creationism it’s do or die.

    THE SECOND QUESTION is, did biologists stop studying non-coding DNA because it was mere junk? Obviously not. ALL of the functions discovered in the 60 years since non-coding DNA was discovered have been found by evolutionary biologists, and NONE by creationist investigators.

    Biologists first noticed in the 1960s that genome size does not correlate with number of genes, so researchers wondered what that other stuff does. They put slide to microscope and pen to paper. Ever since, a long list of possible functions has been proposed in the literature. So much so that Gould and Lewontin wrote their famous 1978 “spandrels” paper railing against the apparent tendency of biologists to attribute function to every feature of an organism. Some things, they said, might be there simply because they are good at being there. But functions continued to be found from the1960s to the present in gene regulation, replication initiation, identifying recombination sites, chromosome folding, and more.[3] Some thought that junk DNA was just junk. But many continued to investigate it to discover new functions.

    Now, creationists claim to have “predicted” that junk DNA has some function. But they forget that a prediction must PRECEED the discovery of that which is predicted. In this case, real biologists were researching this subject and finding functions for non-protein-coding DNA ever since anyone knew there was such a thing. So this creationist “prediction” is a bald-faced lie.

    And, to to crown it with chutzpah: Creationists holler up and down about the importance of “junk DNA” yet no creationist biologist has ever lifted a finger to conduct any experiments to discover such functions, nor written any papers to suggest what such functions might be! Can you say “hypocrisy?

    THE THIRD QUESTION is, what is the actual extent of the “function” discovered in the ENCODE project, as reported (and explained/a>) by Ewan Birney? As others have pointed out, the paper’s definition of “function” amounts to “some biochemical activity.”

    This definition of “function” is ridiculously wide, and Birney admits he did it so he could come up with a larger percentage for impressing general audiences. Birney defines “functional” as “having specific biological activity” of some kind. Under this definition, a transposable element is functional—yet its only function is to transose itself from one place to another on a chromosome; it is a DNA parasite of no value whatever to its host organism.[4] A large number of these elements cause disease by their insertion activity—do we really wish to say that disease is a valid “function” of the genome? Other elements exist as millions of copies in the genome, whereas only one or a few copies would have exactly the same function; this inflates a “percentage” measure, but does not add any capability to the organism.[5] Then,as noted above, a large fraction of the non-coding DNA is pseudogenes—replications and broken remnants of genes that have no current biological activity in the genome of the organism that carries them—these too have “function” under Birney’s definition.

    T. Ryan Gregory, a biologist specializing in genome size evolution at the University of Guelph, estimates that Birney’s 80% number is more like 20%, if functionality is defined more realistically—

    So, even the most rigorous efforts to find function for non-coding DNA in the human genome have come up with a figure of 80% at best, and only when they use a very flexible definition of “function”. 20% remains a more realistic number, and that would leave a heck of a lot of non-functional DNA in the human genome.

    Then, too, creationists must still face the onion problem. Members of the onion family have genomes ranging from 7 picograms(pg) to more than 31 pg. Why do some onions need four and a half times as much DNA as other onions to carry out essentially the same functions at the same level of complexity?[6] And are creationist biologists crowding the lab benches to investigate this apparent problem?[7]

    A large portion of non-coding DNA consists of pseudogenes: unused duplications of genes and pieces of broken genes that once served an evolutionary ancestor. The only function of these pseudogenes seems to be providing raw material for future evolution of the organism. Do creationists really wish to claim that enhancing evolution should be counted as a “function” of non-coding DNA? We’ll see.

    For the present purpose, of course, disputing the exact amount of useless DNA is not very relevant to the creationist claims. “True Junk” DNA is allowed but not required for evolution, but creationism mandates the absence of ANY true junk at all. Unless they can show 0.0% junk, they have lost the argument. And they are still a long way from that goal.

    ===========================

    [1] Well, actually, a preliminary question is; What is “junk DNA”? The scare quotes are used because creationists define this term differently than creationists do. That is, creationists commit the sin of equivocation. In 1972, Susumu Ohno coined the term to include all DNA that does not encode a protein. He used the word “junk” because he found that much of it accumulated from the duplication and inactivation of DNA that that coded in ancestral species, but had broken. Biologists themselves have been occasionally guilty of overapplying it. But the technical meaning still is DNA that does not code for proteins—the opposite of “coding DNA.” You can look it up.

    [2] May of these have in fact been found. They are called “pseudogenes.” Creationists admit that these exist, but conveniently overlook that they are evidence against special creation.

    [3] One of the more interesting uses of junk DNA is to provide raw material for genetic divergence—that is, to provide novel proteins for new evolved functions. Creationists love that one!

    [4] This is like saying that the HIV virus is part of the human body because it lives in our cells.

    [5] Would one claim that a car has a dozen times as much function if it carries twelve spare tires in its trunk instead of just one?

    [6] In comparison, the human genome contains a little over 3 pg of DNA. Onions must have a lot more function than humans, to need all that extra DNA! (Maybe they’re hoarding it for future use against us?)

    [7] No.

  2. Olorin,

    “Creationists claim that evolution requires non-functional elements in the genome, but this is, and has always been, a lie.”

    That is a very harsh statement and very much uncalled for, but you are incorrect and again as you do many times use a strawman’s argument. I named evolutionists who believe “Junk DNA” which are P.Z. Myers, Nick Matzke, Jerry Coyne, Kenneth Miller and British atheist, Richard Dawkins. All of which claim “Junk DNA” is required within the framework of evolution.

    During the 1960s, massive variations within different kinds of species was discovered. To evolutionary scientists, this was a major theoretical dilemma because natural selection would have too many mutations to select over a certain period of time causing calulations within the time frame not to work. More efficiency would be needed to accomplish the task so “neutral evolution” was invented which later became known as “Junk DNA.” This idea would allow natural selection to act upon the important aspects while neutral evolution could act randomly on the rest.

    The less Junk DNA there is, hinders using the explanation of evolution. because it becomes that much more difficult to explain the math when it comes to the evolutionary time frame! Also Junk DNA, is considered evidence for a mindless process because the likes of Dawkins and Myers would argue, an intelligent designer wouldn’t have left junk behind rather a mindless process would…

    According to David Stern, a Princeton professor in the Department of Ecology and Evolutionary Biology, scientists increasingly believe “junk DNA” is crucial for turning the information encoded in genes into useful products. Now scientists look at it as a means of improving quality of people’s lives!

  3. I named evolutionists who believe “Junk DNA” which are P.Z. Myers, Nick Matzke, Jerry Coyne, Kenneth Miller and British atheist, Richard Dawkins. All of which claim “Junk DNA” is required within the framework of evolution.

    Michael, you compound the lie.

    A simple cunterexample: If biologists claim that “junk DNA” is required for evolution, then please consider the following
    (a) All biologists claim that bacteria[1] evolve.
    (b) Bacteria have very small amounts of “junk DNA” Some have none at all..
    (c) All biologists have known (b) for a very long time.
    (d) P.Z. Myers, Nick Matzke, Jerry Coyne, Kenneth Miller and Richard Dawkins are competent biologists.
    Now tell us why it is not a lie that P.Z. Myers, Nick Matzke, Jerry Coyne, Kenneth Miller and Richard Dawkins claim that “junk DNA” is required for evolution..

    Here’s a snippet from The Sensuous Curmudgeon (Nov. 2010),[2] to show that this humble commendatore is not alone in casting aspersions on your already fragile integrity.

    Much of [Francis] Collins’s case for Darwinian evolution is based on so-called “junk DNA.” This is the part of the genome that does not appear to code for the production of proteins. In mammals, the vast majority of DNA has been dismissed as “junk.”

    The case for Darwinian evolution is based on junk DNA? That’s a new one. The Discoveroids are obsessed with junk DNA. To them, it’s a serious affront to the skills of their magical mystery Designer, and they ceaselessly defend his workmanship with the claim that none of the genome is junk. The last time we laughed about that was here: Fearless Predictions of Creation Science.
    ………..

    But the argument from junk DNA — also called “ancient repetitive elements” (AREs) — depends on the premise that no function will ever be discovered for AREs.

    Did you get that? Evolution is based on an “argument from junk DNA.” Actually, it’s not. There was a ton of evidence supporting evolution even before DNA was discovered. Like all new discoveries, DNA could have been a problem for evolution, but it’s not. Indeed, it’s extraordinarily useful in demonstrating common descent. The fact that it’s all junked up wasn’t predicted, and it isn’t essential to the theory, but junk DNA’s existence is a striking rebuke to those who imagine that DNA was intelligently designed.

    So the “argument from junk DNA” is pure Discoveroid fiction. In this context, junk DNA means only that the creationists have a problem explaining its existence. Indeed, it’s the Discoveroids who have the burden of showing that every little scrap of junk DNA serves a purpose. Good luck with that. Evolution could survive with or without the junk, but the junk is incompatible with intelligent design.

    Got it now? The situation is not symmetrical,
    (a) Absence of junk DNA contravenes a fundamental tenet of creationism.
    (b) Presence of “junk DNA” is evidence for evolution, but is not required.

    If you disagree with (b) just above, then you’ll have to explain:
    (a) Which of the several definitions of “junk DNA” you are referring to, and choose only one of them.[3]
    (b) Describe what Myers, et al. claim as to the necessity of this form of “junk DNA”..
    (c) Name which specific aspect of evolution they claim would be affected by total lack of this form of “junk DNA”.
    (d) Explain why they think that evolution depends upon this form of “junk DNA”.

    Then, for extra credit, you can choose an aspect of evolution and describe why you think that this aspect is disproved by absence of t6his form of “junk DNA” in a genome. Be specific.[5]

    I thought not.

    ===============

    [1] The same goes for archea and viruses.

    [2] The interior quotes come from a Discovery Institute blog.

    [3] Equivocation is a primary weapon of creationism.

    [5] Hint: The first sentence in your penultimate paragraph is factually incorrect. The second sentence addresses only why “junk DNA” is required by creationism, not why it might be essential to evolution.

    The less Junk DNA there is, hinders using the explanation of evolution. because it becomes that much more difficult to explain the math when it comes to the evolutionary time frame! Also Junk DNA, is considered evidence for a mindless process because the likes of Dawkins and Myers would argue, an intelligent designer wouldn’t have left junk behind rather a mindless process would…

    You would do better to start over from scratch..

  4. Oops. Mixed up a negative in the above comment—

    Got it now? The situation is not symmetrical,
    (a) Absence of junk DNA contravenes a fundamental tenet of creationism.
    (b) Presence of “junk DNA” is evidence for evolution, but is not required.

    In (a), “Absence” should read “Presence.”

  5. The less Junk DNA there is, hinders [sic] using the explanation of evolution. because it becomes that much more difficult to explain the math when it comes to the evolutionary time frame!

    Michael, I have no clue what you are talking about here. Why on earth—or in heaven—would junk DNA have anything to do with an evolutionary time frame? And in what way—too short, too long, what? What math are you talking about—scientific math or creationist math?

  6. According to David Stern, a Princeton professor in the Department of Ecology and Evolutionary Biology, scientists increasingly believe “junk DNA” is crucial for turning the information encoded in genes into useful products.

    This is entirely irrelevant to the question of whether or not evolution requires junk DNA. In what way would this discovery have shown that these fruit flies did not evolve?

    Moreover, the genetic material Stern speaks of are gene regulators, just like many other already known non-coding regulators. Others had previously thought that these additional copies of the regulators were too far from their genes to have much functional effect. Stern found that in fact they could perform at least some regulation of the gene from 1,000 base-pairs away. Other researchers had already hypothesized that these regions had some function, and called them “shadow enhancers.” Stern merely tested this hypothesis, finding that deletion of a few of them affected survival, altho only in extreme conditions.

    However, this function has nothing to do with evolution, and certainly nothing to do with whether or not evolution requires junk DNA.

    Query for Michael: Go look up the press reports for any discovery of a function for DNA previously thought to be useless junk. Did any of the reports mention any negative impact of the discovery on whether the genome or the organism had evolved? No.

    ————————————————-
    SIDEBAR

    In fact, as mentioned previously, recent discoveries have shown that pseudogenes have a positive use for evolution. These mutated, broken pieces of genes can serve as partly-processed material for the evolution of new proteins for novel capabilities. Not essential, but useful. Analogize to the smelting of aluminum. The Hall process requires great gobs of electricity to separate the metal from the ore. BUT, if we recycle our aluminum cans, we can save much of the electricity. That is, recycling is useful, but not essential.

    For example, the large group of pseudogenes for olfactory receptors (ORs) in metazoans may be resurrectable. A cluster of human ORs which contains 16 OR genes and 6 OR pseudogenes on chromosome 17 appears to have been subjected to about 20 gene resurrection conversions over the course of primate evolution. (Genomics 61 (1): 24–36; Oct. 1999)

    .———————————————

    The existence of pseudogenes cannot be explained by creationism, but can be easily explained for evolution. It is easy to see that pseudos’ sequences are similar to fully functional genes—all the way from fully functional duplicates to frame shifts to missing stops to deletions/insertions to barely recognizable versions. The degree of similarity matches distance in the evolutionary phylogeny. Where could the pseudos have come from, other than from evolutionary ancestors? Certainly the creationists can’t tell us.

    ———————————————-

    Would not pseudogenes accumulate to the point where the genome can no longer support all that bulk? The material I’ve read indicates that formation rate is low—only several new ones since the divergence between humans and chimps 6 million years ago. Also, genomes have mechanisms for deleting material. One paper estimates that generation and deletion rates are about the same.

    But then there are a lot of recognizable pseudos in may genomes, so the selection pressure against increased size appears to be very weak. Retrotransposons, for example, are invaders from the outside, yet they persist in the genome for eons, despite the facts that they use energy, and in some cases even cause disease.

    ———————————————-

    We also always come bck to the question of why no creationist has ever lifted a finger to find a function for genetic material that some biologists call “junk.” Here’s why: Creations do not operate from curiosity as scientists do, but from fear. What if they’re wrong? What if they cannot find a function for the subjects of their experiments? This would be evidence against creationism. Moreover, creationism cannot tell them what to look for. Evolution, on the other hand, provides both incentive and guide for research in this area.

    .

  7. Why does Michael continue to claim that evolution requires junk DNA?

    This is an easy one. Michael claims it because the Discovery Institute and Answers in Genesis say it, and Michael’s belief have destroyed his independent judgment.

    OK, so why do the DI and AiG make that claim?

    Here we have yet another example of the creationists’ favorite weapon, the false dichotomy. Many of their claims presuppose that, if any aspect of evolution can be shown to be incorrect, then the world was created in six days, starting on a Monday morning, 6006 years ago. This is, of course, a logical fallacy, because it by no means exhausts the possibilities.

    The junk-DNA claim is a little more convoluted. That’s why the creationists are so proud of it. They take the true statement “creationism prohibits junk DNA” and derive from it “THEREFORE evolution requires junk DNA.”

    This is more clever than their usual effort, because it contains TWO false oppositions:
    > First, creationism/evolution is a false dichotomy, because other possibilities exist: space aliens, for example, or Sheldrake’s morphogenetic fields.
    > Second, “require” is not the opposite of “prohibit.” The opposite of “prohibit” is “allow.” Evolution “allows” junk DNA, but does not require it.

    It seems that creationists are counting on us not to be able to unravel two logical errors in the same proposition. What say you? Have they underestimated us?

    Watch how Michael employs this double-shuffle:

    I named evolutionists who believe “Junk DNA” which are P.Z. Myers, Nick Matzke, Jerry Coyne, Kenneth Miller and British atheist, Richard Dawkins. All of which [sic] claim “Junk DNA” is required within the framework of evolution.

    First sentence is not far off: All of the named worthies do in fact think (not “believe”) that some junk DNA will be found in many genomes, especially mammalian. But it does not logically follow from this that they claim that junk DNA is required. This is an unpowered flight of fancy that only creationists are capable of.

    Just one more reason that scientists laugh at creationists.

  8. It’s time to move on, Michael. You have not managed to advance any reasons to counter my claim that absence of junk DNA does not falsify evolution.

    So it’s time for that time-honored creationist response—CHANGE THE SUBJECT.

    Let’s see. Michael has alr4eady “falsified” evolution six times within the past month. One might think it would roll over and die from Michael’s multiple wounds. But, so far…..

    Why doesn’t he try another subject? He’s only attacked the teaching of evolution once, and only “disproved” the 4.5-billion year age of the universe once. No attacks on the horrors of embryonic stem-cell research. No falsifications of the geologic column. Nothing about creationism’s uneasy ally, intelligent design.

    There must be something else in the recent literature from those respected journals Answers in Genesis and Creation Science Research Quarterly that will tell Michael what to think about some other area of recent scientific research.

    Wait for it…….

  9. For a non-technical summary of the mishandling of the “junk DNA” aspect of the ENCODE project, see “Most of what you read was wrong: how press releases rewrote scientific history” in Ars Technica, Sept. 10, 2012.

    Yet the third sentence of the lead ENCODE paper contains an eye-catching figure that ended up being reported widely: “These data enabled us to assign biochemical functions for 80 percent of the genome.” Unfortunately, the significance of that statement hinged on a much less widely reported item: the definition of “biochemical function” used by the authors.

    This was more than a matter of semantics. Many press reports that resulted painted an entirely fictitious history of biology’s past, along with a misleading picture of its present. As a result, the public that relied on those press reports now has a completely mistaken view of our current state of knowledge

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