No way back for Junk DNA?

With Fresh Funding, ENCODE Team Continues Demolition of "Junk DNA" Myth
Evolution News & Views


Is there treasure in the DNA's so-called "junk" pile? Well, as the first half of a popular saying goes, money talks. The National Institutes of Health (NIH) just funded five centers to explore what the "dark matter genome" (the non-protein-coding part) is doing. Two of the centers will be at the University of California, San Francisco, which describes the new project:

"The Human Genome Project mapped the letters of the human genome, but it didn't tell us anything about the grammar: where the punctuation is, where the starts and ends are," said NIH Program Director Elise Feingold, PhD. "That's what ENCODE is trying to do." [Emphasis added.]
Grammar -- there's an ID-friendly analogy for you. Language students and their teachers don't look for grammar and punctuation in gibberish. The statement implies purpose: functional information that has a beginning and end. Rules that organize information for communication. Genes without grammar are like words without sentences.

Launched in 2003 after the Human Genome Project found that only 2 percent of DNA codes for proteins, ENCODE was tasked "to find all the functional regions of the human genome, whether they form genes or not." Initial results were spectacular, showing that at least 80 percent of DNA is transcribed. This made the #1 spot in our top ten evolution-related stories for 2012 an "easy pick," as Casey Luskin wrote at the time, since it "buries" the "junk DNA" dogma -- the idea that evolution left our genome littered with useless leftovers of mutation and natural selection.

Darwinians don't give up easily, though, as we have often noted. Transcription is not proof of function, they argue. But why use costly resources to transcribe junk for no purpose? In the intervening years, more and more functions have come to light.

The initiative revealed that millions of these noncoding letter sequences perform essential regulatory actions, like turning genes on or off in different types of cells. However, while scientists have established that these regulatory sequences have important functions, they do not know what function each sequence performs, nor do they know which gene each one affects. That is because the sequences are often located far from their target genes -- in some cases millions of letters away. What's more, many of the sequences have different effects in different types of cells.
The new grants from NHGRI [National Human Genome Research Institute] will allow the five new centers to work to define the functions and gene targets of these regulatory sequences.

We anticipate future spectacular discoveries will continue to come from ENCODE. And now researchers have new lights to shine: including faster DNA barcoding and the CRISPR-Cas9 gene-editing tool.

The project's aim is for scientists to use the latest technology, such as genome editing, to gain insights into human biology that could one day lead to treatments for complex genetic diseases.
In addition to the two centers at UCSF, others will be set up at labs including Cornell, Stanford, and Lawrence Berkeley. The National Center for Human Genome Research explains the goals, in which it will invest an initial outlay of $31.5 million for 2017:

At its core, ENCODE is about enabling the scientific community to make discoveries by using basic science approaches to understand genomes at the most fundamental level. Its catalog of genomic information can be used for a variety of research projects -- for example, generating hypotheses about what goes wrong in specific diseases or understanding the processes that determine how the same genome sequence is used in different parts of the body to make cells with specialized functions. More than 1,600 scientific publications by the research community have used ENCODE data or tools.
Other Junk-Busting Research

Meanwhile, labs all over are finding treasure in the formerly dismissed junk. It has become something of a scientific sport these days to get the function ball downfield ahead of other labs.

Enhancer RNAs. Last month, Penn Medicine News threw this touchdown, "'Mysterious' Non-protein-coding RNAs Play Important Roles in Gene Expression." Realizing that transcribing junk didn't make sense, researchers at the University of Pennsylvania suspected that there must be more going on. They asked, Why do body cells turn out so different when they all have the same genome? Seeking function, they learned about the role of enhancer RNAs that regulate which genes get expressed in different types of cells.

DNA repeats. It looks so boring, repetitive DNA. It must be unimportant, right? Not so, found two researchers from Rockefeller University. Writing in PNAS, they discovered that three proteins carefully protect those repeats around centromeres -- the locations on chromosomes where the spindle attaches during cell division. "Our study reveals the existence of a centromere-specific mechanism to organize the repetitive structure and prevent human centromeres from suffering illegitimate rearrangements." Some could lead to cancer and aging. Doesn't the converse, legitimate arrangements, imply complex specified information?

Disordered proteins. Most proteins fold into compact shapes. What are disordered proteins doing, flailing like air dancers in the wind? Canadian researchers publishing in PNAS found one that has a signaling function. It's not alone; intrinsically disordered regions (IDRs) are "widespread" and have "diverse functions," they say. Since they are maintained by "stabilizing selection," they must be doing something important. Oddly, the function remains the same even when the underlying amino acid sequence changes. In one instance in yeast, they found evidence for "selection maintaining this quantitative molecular trait despite underlying genotypic divergence." This could be a major paradigm change, since 40 percent of proteins are predicted to contain "disordered" regions. The one they studied appears to have a signaling function. Now, the hunt is on to find other functions in "disorder" (synonymous with junk).

Accordion genomes. Protein-making is not the only function of DNA. Some of it, we know, provides structural support or anchor points. Researchers at the University of Utah are exploring another mystery: why genomes grow and shrink. By studying the genomes of birds and mammals (including flying mammals, the bats), they speculate that shedding DNA can streamline a bird or bat for flight, but allow other creatures to grow their supply. The stretching and squeezing of genomes they liken to an accordion mechanism. It would seem that extra scaffolding could be jettisoned without harm. Whatever is going on, it doesn't match the old dogmas of neo-Darwinism. "Evolution is often thought of as a gradual remodeling of the genome, the genetic blueprints for building an organism," this article begins. "In some instances it might be more appropriate to call it an overhaul." Since overhauling a genome non-gradually would likely be catastrophic, we suspect scientists will find this process is under careful regulation. "I didn't expect this at all," the lead author remarked. "The dynamic nature of these genomes had remained hidden because of the remarkable balance between gain and loss." Watch this space.


The research strategy of looking for function continues to prove fruitful. It's an attitude that says, If it's there, it's probably doing something important. True, just because some things are designed doesn't imply that everything is designed. But science was hindered for decades by the junk-DNA myth and the vestigial-organs myth, which we now know are being discarded. Science is playing catch-up after years of lazy thinking that reasoned, If it's not doing something I understand right now, it must be junk. It's time now to assume function, until the case is shown to be otherwise. As Paul Nelson says, "If something works, it's not happening by accident."

Darwinism's bridge to nowhere?

Eye Evolution: A Closer Look
Brian Miller

In a  previous article  I described how theories of innovation provide insight into the limits of natural selection. I will now apply those concepts to hypotheses regarding the evolution of the vertebrate eye, a subject that, since the time of Charles Darwin, has been near center of the debate over the creative power of natural selection. As Darwin himself stated in the Origin of Species:

To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree.
He did, however, still believe it could evolve over numerous gradual increments.

Today, evolutionists propose several of the stages in what they believe to be a plausible evolutionary path. Science writer Carl Zimmer outlined the standard story:

In 2007, Trevor Lamb and his colleagues at Australian National University synthesized these studies and many others to produce a detailed hypothesis about the evolution of the vertebrate eye. The forerunners of vertebrates produced light-sensitive eyespots on their brains that were packed with photoreceptors carrying c-opsins. These light-sensitive regions ballooned out to either side of the head, and later evolved an inward folding to form a cup. Early vertebrates could then do more than merely detect light: they could get clues about where the light was coming from...a thin patch of tissue evolved on the surface of the eye. Light could pass through the patch, and crystallins were recruited into it, leading to the evolution of a lens. At first the lens probably only focused light crudely...Mutations that improved the focusing power of the lens were favored by natural selection, leading to the evolution of a spherical eye that could produce a crisp image.
See Wikipedia for a chart illustrating  "Major stages in the evolution of the eye."

To add weight to this narrative, two biologists created a  computer simulation, demonstrating, in their view, the incremental evolution of an eye in fewer than 400,000 generations.

This often-repeated tale sounds impressive at first, but it is not unlike most supposed explanations of the evolution of complex features. It scores high on imagination and flare but low on empirical evidence and thoughtful analysis. It most certainly does not represent a "detailed hypothesis." Likewise, the simulation does an admirable job of describing how a mechanical eye could develop incrementally, but it is completely disconnected from biological reality. In particular, it ignores the details of how a real eye functions and how it forms developmentally. When these issues are examined, the story completely collapses.

To fully appreciate why that is so requires a basic understanding of developmental biology. During development, cells divide, migrate, and differentiate into a wide variety of types. Throughout this process, the cells send chemical signals to their neighbors, and these signals cause proteins known as transcription factors (TF) to bind to genes in regulatory regions, which control the corresponding genes' activity. The TFs bind to what are called transcription factor binding sites (TFBS), and the correct binding enables the genes to produce their proteins in the right cells at the right time in the right amount.

The evolution of additional components in the vertebrate eye requires that this network of intercellular signals, TFs, TFBS, chromatin remodeling, as well as many other details be dramatically altered, so that each developmental stage can progress correctly. For instance, the seemingly simple addition of a marginally focusing lens -- that is to say, a lens that directs slightly more light onto a retina -- requires a  host of alterations:

Ectodermic tissue folds into a lens placode, which then forms a lens vesicle.

Cells in the lens vesicle differentiate into lens fibers, which elongate to produce the proper lens shape.

The lens fibers then undergo several key modifications, including tightly binding together, filling almost entirely with special refractive proteins called crystallins, developing special channels to receive nutrients, and destroying their organelles.

All of these steps must proceed with great precision to ensure the end product focuses light in an improved manner. The development of the lens in  all vertebrates  is very similar, and it even resembles that in  other phyla. Therefore, the development of the first lens should have closely followed the steps outlined above with only minor differences, inconsequential to the basic argument.

The challenge to evolution is that, short of completion, most of these changes are disadvantageous. A lens that has not fully evolved through the third step noted above would either scatter light away from the retina or completely block it. Any initial mutations would then be lost, and the process would have to start again from scratch. In the context of fitness terrains, an organism lacking a lens resides near the top of a local peak. The steps required to gain a functional lens correspond to traveling downhill, crossing a vast canyon of visually impaired or blind intermediates, until eventually climbing back up a new peak corresponding to lens-enhanced vision.

Once an organism has a functional lens, natural selection could then potentially make gradual improvements. However, moving from a reasonably functional lens to one that produces a high-resolution image is rather complex. In particular, the refractive index (i.e., crystalline concentration) has to be adjusted throughout the lens to vary according to a precise mathematical relationship. A gradual decrease from the inside to the outside is  needed to prevent spherical aberrations blurring the image.

Even more steps are required for the improved image to be properly interpreted:

Feedback circuitry must be added to allow the lens to automatically refocus  on images at different distances.

The retina has to be completely reengineered to process high-resolution images, including the  addition of circuits  to enable edge and motion detection.

The neural networks in the brain have to be rewired to properly interpret the pre-processed high-resolution images  from the retina.

Higher-level brain functions must be enabled to identify different objects, i.e., dangerous ones such as a shark, and properly respond to them.

Until steps 2 through 4 are completed, a high-resolution image would likely prove disadvantageous, since most of the light would be focused on fewer photoreceptors. In insolation, the alterations of perfecting the lens and those involved in step 1 would hinder the analysis of large-scale changes to the field of view, such as identifying the shadow of a predator. Natural selection would thus remove most of the initial mutations, and evolution of the eye would come to a halt.

The difference between blurry and high-resolution vision is well illustrated by the box jellyfish. It has several eyes around its body. Two have lenses, which can produce highly focused images. However, the focal point is past the retina, so the retinal images are blurry. An ability to focus more clearly than is actually useful seems to be an example of gratuitous design. Zoologist Dan Nilsson comments:

For such a minute eye it is surprising to find well-corrected, aberration-free imaging, otherwise known only from the much larger eyes of vertebrates and cephalopods. The gradient in the upper-eye lenses comes very close to the ideal solution...The sharp image falls well below the retina and it would seem that the sharp focus of the lenses is wasted by inappropriate eye geometry.
However, for the box jellyfish a high-resolution image would be disadvantageous, since its neurology is engineered to respond to such bulky features as the edge of a mangrove. Is this blurry vision the result of the jellyfish not having yet evolved high-resolution vision? No: its neural organization is radically different from that needed for the latter. As Nilsson comments, "Another, more likely, interpretation is that the eyes are 'purposely' under-focused."


"Purposeful"? Yes, it would seem so. The example illustrates that low-resolution vision is not at an inferior point on the same fitness peak as high-resolution vision. Instead, both systems reside near the peaks of separate mountains. For any species, upgrading to high-resolution vision requires massive reengineering in a single step. Such radical innovation, coordinated to achieve a distant goal, is only possible with intelligent design.