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Supposed junk DNA serves as microlens for condensing light

File:DNA simple.svg

A new study, we are told,”turns our picture of the nucleus upside down”:

Eukaryotic chromosomes are built of chromatin, a complex of DNA and associated proteins. Depending on transcriptional activity and degree of compaction, two types of chromatin can be distinguished and these two types are spatially separated within the nucleus. The highly condensed fraction is made up of regions of chromatin that contain few genes and is transcriptionally inactive. It is called heterochromatin, and is located in the periphery of the nucleus, close to the nuclear membrane. Euchromatin, on the other hand, is enriched in genes and corresponds to the active fraction of the genome. It occupies the inner regions of the nucleus, is less densely packed, and therefore more accessible to the protein machineries required for gene expression. This general pattern of genome organization is found in virtually all eukaryotic cell types…

… In rods, the tightly condensed heterochromatin is packed in the interior of the nuclei, while the active euchromatin is localized directly under the nuclear membrane—a unique exception to the general rule. It turned out that the heterochromatin core of rod nuclei serves as a microlens condensing light and thus improving optical properties in the nocturnal retinas….

What organizes the genome in the nucleus?” at Ludwig Maximilian University of Munich

Hat tip: Philip Cunningham

Cunningham notes that Rick Steinberg commented on this kind of thing a decade ago:

Reporting in the journal Cell, Irina Solovei and coworkers have just discovered that, in contrast to the nucleus organization seen in ganglion and bipolar cells of the retina, a remarkable inversion of chromosome band localities occurs in the rod photoreceptors of mammals with night vision (Solovei I, Kreysing M, Lanctôt C, Kösem S, Peichl L, Cremer T, Guck J, Joffe B. 2009. “Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution.” Cell 137(2): 356-368). First, the C-bands of all the chromosomes including the centromere coalesce in the center of the nucleus to produce a dense chromocenter. Keep in mind that the DNA backbone of this chromocenter in different mammals is repetitive and highly species-specific. Second, a shell of LINE-rich G-band sequences surrounds the C-bands. Finally, the R-bands including all examined protein-coding genes are placed next to the nuclear envelope. The nucleus of this cell type is also smaller so as to make the pattern more compact. This ordered movement of billions of basepairs according to their “barcode status” begins in the rod photoreceptor cells at birth, at least in the mouse, and continues for weeks and months. Why the elaborate repositioning of so much “junk” DNA in the rod cells of nocturnal mammals? The answer is optics. A central cluster of chromocenters surrounded by a layer of LINE-dense heterochromatin enables the nucleus to be a converging lens for photons, so that the latter can pass without hindrance to the rod outer segments that sense light. In other words, the genome regions with the highest refractive index — undoubtedly enhanced by the proteins bound to the repetitive DNA — are concentrated in the interior, followed by the sequences with the next highest level of refractivity, to prevent against the scattering of light. The nuclear genome is thus transformed into an optical device that is designed to assist in the capturing of photons. This chromatin-based convex (focusing) lens is so well constructed that it still works when lattices of rod cells are made to be disordered. Normal cell nuclei actually scatter light. So the next time someone tells you that it “strains credulity” to think that more than a few pieces of “junk DNA” could be functional in the cell — that the data only point to the lack of design and suboptimality — remind them of the rod cell nuclei of the humble mouse.

Rick Steinberg (April 29, 2009), “Shoddy Engineering or Intelligent Design? Case of the Mouse’s Eye” at Evolution News and Science Today

Paper. (paywall)

See also: Humans may have only 19,000 coding genes

“Junk DNA” regulates regeneration of tissues and organs

Note: One junk DNA defender just isn’t doing politeness anymore. Hmmm. In a less Darwinian science workplace, that could become more a problem for him than for his colleagues.

Junk DNA can actually change genitalia. Junk DNA played the same role in defending Darwinian evolution as claims that Neanderthal man was a subhuman. did: The vast library of junk genes and the missing link made Darwin’s story understandable to the average person and the missing link even became part of popular culture. With Darwinism so entrenched, the fact that these beliefs are not based on fact will be difficult to root out of the culture. Darwin-only school systems are part of the problem.

Been a while since we’ve heard much about humans as the 98% or 99% chimpanzee. If the human genome is this fuzzy how would we know? And doubtless, things have gotten more complex.

At Quanta: Cells need almost all of their genes, even the “junk DNA”

“Junk” RNA helps regulate metabolism

Junk DNA defender just isn’t doing politeness any more.

Anyone remember ENCODE? Not much junk DNA? Still not much. (Paper is open access.)

Yes, Darwin’s followers did use junk DNA as an argument for their position.

Another response to Darwin’s followers’ attack on the “not-much-junk-DNA” ENCODE findings

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(Solovei I, Kreysing M, Lanctôt C, Kösem S, Peichl L, Cremer T, Guck J, Joffe B. 2009. “Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution.” Cell 137(2): 356-368).

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