“Junk” DNA: Darwinism’s Last Stand?

Here Jonathan Wells writes about the junk that turned out not to be.

Suppose your genome was your late great aunt's attic. You think the stuff in her attic is all just a load of junk. But unknown to you, her great-great grandma's Georgian dressing table is worth US$50 000 on the museum market, and archivists would kill for her great-grandpa's letters from the front.

Darwinists assumed that everything that wasn't being used now was junk, but apparently they were wrong - because they neglected the value of information generally, and stored information in particular. They truly believe in randomness, not information. Anyway, here's Wells:

We are often told that the evidence for evolution is “overwhelming.” If “evolution” is defined as “change over time” or “minor changes within existing species,” this is a truism. But what if “evolution” means Charles Darwin’s theory? According to Darwin, all living things are descendants of a common ancestor that have been modified by unguided processes such as random variation and natural selection.

Despite the hype from Darwin’s followers, the evidence for his theory is underwhelming, at best.

Natural selection—like artificial selection—can produce minor changes within existing species. But in the 150 years since the publication of Darwin’s Origin of Species by Means of Natural Selection, no one has ever observed the origin of a new species by natural selection—much less the origin of new organs and body plans.

As a result, the only evidence that all living things are biologically descended from a common ancestor comes from comparisons of the similarities and differences among fossil and living species. When making such comparisons, however, Darwinists start by assuming common ancestry. Then they try to fit similarities and differences into the branching-tree pattern that would result from it, and they ignore the glaring inconsistencies that often remain.

Read the rest here at Evolution News and Views

See also Wells's book Politically Incorrect Guide to Darwinism and Intelligent Design (Regnery, 2006)

Find out why there is an intelligent design controversy:

Now junk DNA "assists" evolution

Some excerpts from a recent Science Alert:

"Current theory doesn't tally with fossil evidence"

"Dr Greene, a Senior Lecturer in Molecular Genetics, said current evolutionary theory, which assumed biological lineages evolved by the slow accumulation of adaptive mutations, did not tally with the fossil record.

"However, the “Genomic Drive” theory provided a significant explanation for the way new species arose abruptly and periodically.

"The theory also fitted with fossil records which showed intermittent and long periods of stasis – where many species stood still or remained the same."

Here's Princeton:

Now researchers from Princeton University and Indiana University who have been studying the genome of a pond organism have found that junk DNA may not be so junky after all. They have discovered that DNA sequences from regions of what had been viewed as the "dispensable genome" are actually performing functions that are central for the organism. They have concluded that the genes spur an almost acrobatic rearrangement of the entire genome that is necessary for the organism to grow.

Remember when junk DNA "proved" Darwin's theory by being junk? It's not safe to forget that, because you have to believe two contradictory things at once for now.

More stories here at the Post-Darwinist on junk DNA.

See especially:

Junk DNA: Sorting through the trash

Junk DNA: I told you, keep those documents in the packaging ... are you listening NOW?

Junk RNA just like junk DNA? Stuff you should NOT have thrown out with the packaging?

Intelligent design vs. Darwinism: Junk DNA as the genes' antique shop?

By the way, junk DNA is the new vestigial organs - the ones you supposedly didn't need, but actually do.

Junk DNA: Sorting through the trash

From the evil Discos:

When "Junk DNA" Isn't Junk: Farewell to a Darwinist Standard Response
Richard Sternberg, research scientist at the Biologic Institute supported by the Center for Science and Culture, is now blogging at Evolution News & Views, weighing in on the latest research showing that so-called “Junk DNA,” which Darwinists have discounted as “rubbish,” are actually “anything but that.”

Sternberg writes:

In the Darwinist repertoire, a standard response to evidence of design in the genome is to point to the existence of “junk DNA.” What is it doing there, if purposeful design really is detectable in the history of life’s development? Of course this assumes that the “junk” really is junk. That assumption has been cast increasingly into doubt. New research just out in the journal Nature Genetics finds evidence that genetic elements previously thought of as rubbish are anything but that. The research describes tiny strands of RNA, previously thought to be junk, that now turn out to play a role in gene expression. Another finding by Dr. Geoff Faulkner shows that “retrotransposons,” a further variety of “junk” as the dogma previously taught, play a similar role.

Click here to read more

See also these stories abut supposed "junk" DNA.

Find out why there is an intelligent design controversy:

Junk DNA: I told you, keep those documents in the packaging ... are you listening NOW?

Commenting, I gather on this post, a reader writes,

This morning I had a guest speaker giving a run down on DNA diagnostic technology to a Medical Science class and almost as a throw-away line he commented on part of the DNA which doesn't code for proteins and virtually dismissed the use of the term Junk DNA and confirmed it afterwards in a brief conversation.

See also:

Junk RNA just like junk DNA? Stuff you should NOT have thrown out with the packaging?

Intelligent design vs. Darwinism: Junk DNA as the genes' antique shop? Find out who honestly believed it was junk and went on record ...

Find out why there is an intelligent design controversy:

Junk RNA just like junk DNA? Stuff you should NOT have thrown out with the packaging?

Casey Luskin of the Discovery Institute, writes:

When large-scale function was detected for non-coding DNA (once called "junk" DNA) Darwinists, knowing that their viewpoint had long boasted that junk-DNA was evidence for common ancestry and that they were losing that argument, responded in one of two ways: Some sought to rewrite history by claiming that evolutionary biology predicted all along that we'd find function for junk-DNA. Others, however, pushed the "junk" back to RNA. They effectively argued, "Sure, we know that most of the genome is being transcribed into RNA, but that doesn't mean that the RNAs have function. Much of the transcriptome might in fact be junk."

Evolutionist biochemist Larry Moran, for example, argued that either "[t]he so-called transcripts are just noise from accidental transcription" or "[t]he regions of junk DNA could be transcribed regularly but the transcripts are rapidly degraded. They do not have a biological function. They are junk RNA." Intelligent design (ID) proponents were quick to predict the demise of that argument, and if a recent paper in Nature is any indication, "junk RNA" may have the same fate as "junk DNA."

Larry Moran? Sounds vaguely familiar. A biochem prof at the University of Toronto. Now and then he mentions me in his online gossip column.

I'd rather he didn't, really, but I am glad to say that the Internet is - with all its faults - a free country. That part I like.

Here's a podcast on the new "junque RNA."

Intelligent design vs. Darwinism: Junk DNA as the genes' antique shop?

Scene: The antiques road show: "You're telling me this old book is worth $10 000 to a collector?" (Faints)

One often hears the claim that researchers' belief in the myth of junk DNA (the garbage heap of evolution that most of our genes supposedly are, because they do not apparently code for anything) did not retard scientific progress.

Usually, the claim shores up Darwinism (or neo-Darwinism), which the junk factor was said to demonstrate. Devout Catholic Darwinist Kenneth Miller, for example, called it "a sea of nonsense."

From a design perspective, that idea is highly suspect.

Richard Dawkins has also called it that.

A friend points me to this startling admission:

“Although catchy, the term ‘junk DNA’ for many years repelled mainstream researchers from studying noncoding DNA. Who, except a small number of genomic clochards, would like to dig through genomic garbage? However, in science as in normal life, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. Because of them, the view of junk DNA, especially repetitive elements, began to change in the early 1990s. Now, more and more biologists regard repetitive elements as a genomic treasure ( 4, 5).” (Wojciech Makalowski, “Not Junk After All,” Science, Vol. 300(5623): (May 23, 2003). )

So swearing allegiance to Darwin, vs. design, wasted a lot of time.

Here's an explanation of how junk became junque.

Now, can anyone point to ID-friendly or non-Darwinian scientists who had the confidence to make this prediction before it was confirmed? If they didn't, it shows how lack of confidence can lead to lost opportunities.

Find out why there is an intelligent design controversy:

Junk reclaimed: Junk DNA now hailed as "powerful regulator"

Yes! See here:

Large swaths of garbled human DNA once dismissed as junk appear to contain some valuable sections, according to a new study by researchers at the Stanford University School of Medicine and the University of California-Santa Cruz. The scientists propose that this redeemed DNA plays a role in controlling when genes turn on and off.

...

It turns out that most of the segments described in the research paper cluster near genes that play a carefully orchestrated role during an animal's first few weeks after conception. Bejerano and his colleagues think that these sequences help in the intricate choreography of when and where those genes flip on as the animal lays out its body plan. In particular, the group found the sequences to be especially abundant near genes that help cells stick together. These genes play a crucial role early in an animal's life, helping cells migrate to the correct location or form into organs and tissues of the correct shape.

The intelligent design advocates have long maintained that junk DNA would not turn out to be junk, so this should be a score for their side, but watch fora ll sorts of people to deny that. For an interesting discussion of that problem, go here, but you have to hunt and peck on "junk" DNA.

Why is there an intelligent design controversy? Read By Design or by Chance?, my overview of the intelligent design controversy.

Richard Sternberg, vindicated, publishes paper on "junk DNA"

Well, as you've probably heard, Richard Sternberg wasn't wrong when he figured his bosses at the Smithsonian were out to get him, after he permitted the publication of a peer-reviewed ID-friendly paper in a Smithsonian journal. As David Klinghoffer recounts in National Review, Office of Special Counsel attorney James McVay has found that (August 5, 2005):

Our preliminary investigation indicates that retaliation [against Sternberg by his colleagues] came in many forms. It came in the form of attempts to change your working conditions...During the process you were personally investigated and your professional competence was attacked. Misinformation was disseminated throughout the SI [Smithsonian Institution] and to outside sources. The allegations against you were later determined to be false. It is also clear that a hostile work environment was created with the ultimate goal of forcing you out of the SI.

Klinghoffer's piece is a well-written summary of a persecution campaign that should embarrass the scientists involved.

Interestingly, Sternberg has never claimed to be an ID supporter, but he enjoys considering new ideas. As he told Michael Powell of the Washington Post, ""I loathe careerism and the herd mentality," he said. "I really think that objective truth can be discovered and that popular opinion and consensus thinking does more to obscure than to reveal." Powell's excellent piece on Sternberg reveals the shameful role that National Center for Science Education, a seriously mission-challenged organization, played in promoting the persecution. NCSE's alleged purpose is to promote Darwinism in the public school system, not hound a productive scientist at a research institution. (Note: For an interview with Sternberg, go here.)

But the most encouraging news is, Sternberg has just co-authored a paper. (Note: If you click this link, you may not be able to get back using the back browser button. ) So they didn't ruin his career after all. Here's the abstract:

Why repetitive DNA is essential to genome function
Biol. Rev. (2005), 80, pp. 227–250. f 2005 Cambridge Philosophical Society 227 doi:10.1017/S1464793104006657

James A. Shapiro 1,* and Richard von Sternberg 2,3

There are clear theoretical reasons and many well-documented examples which show that repetitive DNA is essential for genome function. Generic repeated signals in the DNA are necessary to format expression of unique coding sequence files and to organise additional functions essential for genome replication and accurate transmission to progeny cells. Repetitive DNA sequence elements are also fundamental to the cooperative molecular interactions forming nucleoprotein complexes. Here, we review the surprising abundance of repetitive DNA in many genomes, describe its structural diversity, and discuss dozens of cases where the functional importance of repetitive elements has been studied in molecular detail. In particular, the fact that repeat elements serve either as initiators or boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the repetitive component of the genome plays a major architectonic role in higher order physical structuring. Employing an information science model, the ‘functionalist ’ perspective on repetitive DNA leads to new ways of thinking about the systemic organisation of cellular genomes and provides several novel possibilities involving repeat elements in evolutionarily significant genome reorganisation. These ideas may facilitate the interpretation of comparisons between sequenced genomes, where the repetitive DNA component is often greater than the coding sequence component.

While we are at it, what about the ID-friendly paper that NCSE and the Smithsonian boffins tried to ruin his career over?

Apparently, it has received way more publicity than it ever would have otherwise.

Good thing, too. Now that the bullies are (we hope) leaving town by a slow train, maybe we can start to have reasonable discussions about the way in which the Cambrian explosion fails to support the predictions of classical Darwinism.