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Richard Sternberg on “Junk” DNA

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Sternberg needs to write a book debunking junk DNA.

Shoddy Engineering or Intelligent Design? Case of the Mouse’s Eye
By Richard Sternberg

www.evolutionnews.org/2009/04/shoddy_engineering_or_intellig

We often hear from Darwinians that the biological world is replete with examples of shoddy engineering, or, as they prefer to put it, bad design. One such case of really poor construction is the inverted retina of the vertebrate eye. As we all know, the retina of our eyes is configured all wrong because the cells that gather photons, the rod photoreceptors, are behind two other tissue layers. Light first strikes the ganglion cells and then passes by or through the bipolar cells before reaching the rod photoreceptors. Surely, a child could have arranged the system better — so they tell us.

The problem with this story of supposed unintelligent design is that it is long on anthropomorphisms and short on evidence. Consider nocturnal mammals. Night vision for, say, a mouse is no small feat. Light intensities during night can be a million times less than those of the day, so the rod cells must be optimized — yes, optimized — to capture even the few stray photons that strike them. Given the backwards organization of the mouse’s retina, how is this scavenging of light accomplished? Part of the solution is that the ganglion and bipolar cell layers are thinner in mammals that are nocturnal. But other optimizations must also occur. Enter the cell nucleus and “junk” DNA.

…[snip]…

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).

…[snip]…

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.

Comments
Mr DATCG, Next, how many gradual steps by natural selection are required? I'm going to go out on a limb and say very few. It happens in only a very specific cell type, so you are at the end of the line in development. That means that what ever we are doing here doesn't have to get undone in a lot of other places. The essential difference is flipping inside and outside. That might be as simple as modifying one protein from having a slightly positve charge to a slightly negative one, or vice versa. How easy is it, really? We'll have to find the sequence differences, and watch mouse eye tissues develop, and compare with other nocturnal vertebrates and all the rest of that sciency stuff. Sounds fun! Any theory of blind tinkering cannot account for saving any valid core process or data and is utterly unpredictable since inherant to the blind process is non-determination of stability or stasis. Yes. For example, if an ancestral species was diurnal, but then tinkered itself into a nocturnal niche, then tinkered back into a diurnal niche, its time spent in the nocturnal niche might cause it to lose valuable traits such as color vision that are only useful in daylight. Telic, design foresight would be needed to preserve those modules. Otherwise, they would have to be reinvented at great cost upon returning to a daylight niche. Well, did that ever happen? Is the telic design evidence waiting to be found? Perhaps it happened in a special species that the designer cared about more than mice. Actually, no. We privileged humans had an ancestor with tri-chromatic, perhaps even tetra-chomatic vision (like birds). We lost it, probably with a shift to night time living to avoid all those dinosaurs cluttering the planet. Dinos go boom, we take over. Most mammals are still stuck with poor color vision. primates have rebuilt tri-chromic color vision in a variety of ways, and the human way isn't very good. The fairy tale recovery of trichromaticity (old world primate duplication of LWS) is hardly an unmitigated success story. Humans have lost 10 of the 14 ciliary and rhabdomeric opsins present from lamprey to amniote, not to mention oil droplets that refine color vision. The advent of the MWS gene duplicate represents a minor partial recovery of color vision capabilities, though not nearly to that still enjoyed by birds and lizards. However this highly unstable locus experiences chronic non-homologous recombination mishaps, gene conversion erasing critical spectral differences, chimeric single genes, bizarre tandem arrays, leading to dichromatic color vision in perhaps 15% of the population. The locus cannot stabilize itself by translocating away the gene duplication because such an event would not bring along the essential control region, which is tethered upstream to the primary LWS gene. The initial duplication and continuing instability may be driven by flanking Alu units. Recent selective forces acting on the region are difficult to disambiguate from gene conversion homogenization. Howler monkeys independently duplicated LWS and importantly also its LCR control region, perhaps avoiding problems that have plagued anthropoid primates for 35 million years. New world monkeys exhibit a different form of partial recovery (in females) utilizing spectrally significant coding polymorphisms of a single X-linked LWS locus and random X inactivation. So howler monkeys have done a better job than humans, avoiding problems of color blindness. This, my friend, is tinkering.Nakashima
April 30, 2009
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OK, my reading of this goes along these lines: 1. Evolutionists pronounce noncoding DNA is 'junk'/nonfunctional/remnants of evolution. ID proponents argue that it most probably has a function. 2. Another in an increasingly long line of studies shows a case of noncoding DNA having a particular function, in this case for mice. 3. Although the ID prediction is the one supported by this study, the evolutionists claim the evidence supports the 'tinkerbell' of evolution, or is only needed because of supposed bad design. Seems a tad like desparation/shifting of the goalposts.saywhatyouwill
April 30, 2009
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Allen_MacNeill (17) A significant minority of us IDers have looked at the evidence for chimp/human common ancestry and found it to be strong. While I am convinced that some human mutations (such as the HAR1F) are well beyond the reasonable scope of modern evolutionary theory.bFast
April 30, 2009
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Allen, "Sorry, I forgot: the Intelligent Designer works in mysterious ways, and always covers His tracks so that there is never a scrap of empirical evidence that can unambiguously reveal His intervention in nature. After all, if He did, the rest of us would eventually figure out that He cared about some nocturnal mice so much that He arranged the last few billion years of evolution of the eukaryotic genome just for them. My bad." I find your rhetoric to be at a rather junior high level. I think you're a large repository of information, but a rather small shack of actual argument. I'm baffled that you teach at any college, to be honest. I hope you only present information to the students, and not arguments.Clive Hayden
April 30, 2009
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Sorry, I forgot: the Intelligent Designer works in mysterious ways, and always covers His tracks so that there is never a scrap of empirical evidence that can unambiguously reveal His intervention in nature. After all, if He did, the rest of us would eventually figure out that He cared about some nocturnal mice so much that He arranged the last few billion years of evolution of the eukaryotic genome just for them. My bad.Allen_MacNeill
April 30, 2009
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uoflcard in #11: Based on this comment, it is clear that you accept the hypothesis that humans evolved from a simian ancestor, otherwise your comment would make no sense whatsoever. How refreshing! Have you checked out what your fellow ID supporters think about this?Allen_MacNeill
April 30, 2009
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And, while we're at it, stephenB (I know you're out there), were the biologists who discovered the inversion of the vertebrate retina and the cooption of for light pipes in some mice motivated to do so by their Christian convictions that God (aka the Intelligent Designer) must have done something just like this for His favorite clade of mammals?Allen_MacNeill
April 30, 2009
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Just out of curiosity, does anyone here want to hazard a guess as to why comparative anatomists declared that the vertebrate retina was "inverted", and how it probably got that way? After all, the retinas of cephalopods, are strikingly similar, except that their retinas aren't inverted. Once again, was this all part of the Grand Plan to make the world a better place for those cute little rodents? Just curious...Allen_MacNeill
April 30, 2009
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Let me see if I get this straight: the Intelligent Designer put all that non-coding DNA into the genomes of every eukaryote in order to make it possible for a few restricted clades of nocturnal mice to be able to see better in the dark, right? Or, the Intelligent Designer put all of that non-coding DNA in the genomes of every eukaryote in order to make it possible for it to eventually be activated as regulatory regions in some eukaryotes (and differently in each major clade), right? And the Intelligent Designer did this by designing DNA polymerase billions of years ago so that it would "skip-duplicate" randomly when it hits certain repeated nucleotide sequences (such as those in the ALU regions of the eukaryote genome), thereby making it possible for a few restricted clades of nocturnal mice a few billion years later to be able to see better in the dark, right? And the Intelligent Designer also crafted some of the non-coding sequences to look exactly like degenerate transposon sequences and retroviral cDNA sequences and randomly retrotransposed RNA sequences, so that at some point He (of course the Intelligent Designer can't possibly be a She; after all, that would mean He has a Vulva, not a Penis)...anyway, so that He could eventually make those sequences work as "light pipes" for a few restricted clades of mice, right? J.B.S. Haldane got it wrong: the Intelligent Designer doesn't have an inordinate fondness for beetles, He has crafted the vast majority of the eukaryotic genome to benefit those little rodents. Holy Mice Eyes, Batman! (Wait, those would be Fledermice, wouldn't they, and the Intelligent Designer crafted the pinnae of mammals so that, in the fullness of time they could be modified into wave-guides for ultrasound, right?) At what point does one stop and ask if all this teleology run wild makes any kind of realistic sense...unless, of course, one is an ID supporter like Richard Sternberg, in which case every single characteristic of every single living organism has been expressly created "in order to" do something or other, regardless of who benefits from such intervention and regardless of whether there is even the tiniest scrap of empirical evidence that this might, indeed, the case. And you criticize evolutionary biologists for practicing "faith-based" science...Allen_MacNeill
April 30, 2009
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Mr JGuy, The inversion applies to all vertebrates, humans, mice, chickens, fish, etc. After having gotten off to a bad start a few hundred million years ago, it is not surprizing that the vertebrate eye has picked up a number of helpful adaptations which it wouldn't need at all if not for the fact that it was inverted in the first place. Turning glial nerves into light pipes is clever tinkering, but unecessary if the glial cells weren't out front getting in the way. Eyes, like flight, have been invented many times. Each time using the cell histories available.Nakashima
April 30, 2009
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Also, I think this topic is a good time to remind everyone of the bad design of the "inverted" human retina that Dawkins touted in some of his writings. Many years later (relatively recently), it wase discovered that there were cells acting as perfect fiber optics transmiting light through the layers of the retina to the photosenesitive cells. Reminiscent of what Sternberg is arguing of regarding mouse eyes. http://www.detectingdesign.com/humaneye.html#Optical Also, this reminds me of Walter ReMine's comments that roughly decalred that the half life of evolutionists latest & greatest evidences of evolution have a half life of about 15 years. Refuted arguments against the supposedly "bad design" of the human retina will be considered one of the classic examples.JGuy
April 30, 2009
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Slightly OT, but interesting: Scientists Revive Dormant, HIV-Fighting Genes Interesting quote:
A group of scientists noticed that our simian ancestors expressed a protein called retrocyclin that essentially renders them immune to HIV. Hoping to find a way to introduce the same immunity to humans, the group discovered that we too had the same genetic ability to create retrocyclin, but that it was turned into junk DNA long ago for no discernable reason.
Whattaya know, our ancestors were "more fit" than us. And there is a very discernable reason, in light of ID or genetic entropy: neo-Darwinian evolution doesn't build proteins, it destroys them. Probably slowly over time, but it is inevitable that small, non-lethal mutations will build up in genes coding for proteins in an entire population, until the genes start to fail universally, not just in select individuals.uoflcard
April 30, 2009
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If one could calculate the information content of the physical architecture of the cell (minus the DNA), and compare it to the staight forward information of human DNA (6 billion nucleotides?)... I suspect the total information content of the cell strucutre dwarfs the information capacity of DNA. That is, if you count the arrangement of molecules or atomic bonds between the two as a type of information. Unless DNA has some kind of "super duper" data compression scheme that hasn't been discovered yet.JGuy
April 30, 2009
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Along the same lines I would really like to hear the evolutionists explain how the scapula of a quadriped animal (which has no body attachment via ligament) migrated from the left and right side of the rib cage to a position where both scapula are now on one side fo teh rib cage? How ddi this happen AND form a body attachement via ligament? The reason I ask is that when scapular dyskenisis occurs in my patients we see everything from impingement to rotator cuff tears to bicep tendon tears to labral fraying all because the position of the scapula isn't where it's suppose to be. It's seems to me that a body part or system would have to go from functional to dysfunctional before going back to functional again IF evolution were true.wagenweg
April 30, 2009
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Nakashima, Not sure I understand all your statements. "What would confirm whether this tinkering was a design choice or a random improvement?" I would consider modularity, compression and shared data space overlapping, a design choice. Why? Because that is what we do in software design on hardware platforms. What we design today by intelligence we discovered in genetic transcription factors. I then ask, what would confirm it is random improvement period without broad speculation? The only thing so far the Darwinist have is "Time" and "Randomness" can produce anything. Anything remotely probable is thus possible. But, if that is true, then design is probable and inherant in their arguments of ramdom tinkering. They are not allowed to shut out intelligent tinkering based upon random mutation because intelligent foresight can allow for random variation based upon external stimuli as input. Next, how many gradual steps by natural selection are required? How many coordinated genes and transcription factors are involved for regulatory processes of such optimal development in this one area for the mouse? How many critical overlaps of data in genes are there that other phenotypic processes share? "This is a better 'evolution the blind tinkerer' story." I'm assuming that statement is sarcasm. But the point of the article is not to blow away the entire process of Darwinian theory. But to show evolutionist were wrong in their previous assumptions and blind tinkerer sub-optimal statements in regards to the mouse eye. In this particular case, Sternberg answered critics succinctly and rebutted accurately the wrong assumptions made by Darwinian materialist. Assumptions based upon the faulty logic of an outdated research methodology enshrined long ago a priori by a materialist-only approach. A now virtually dead theory except in high school textbooks. This dead theory gave rise to many false leads, wasted time and imaginary phylogentic trees based upon false assumptions. As a result, JUNK DNA is becoming, or has become another failed prediction by strict Darwinian materialist. How much critical time has been wasted on dead end predictions? As to your question on confirmation one way or the other. There's an interesting Nature Research Highlight out recently promoting Systems Genetics research on fruit flies I do not have access to the full paper. If someone does, I think it would be fascinating reading and supports the Design position vs the blind tinkerer story. Quotes from the highlight...
There was a high degree of correlation between the variably expressed transcripts. The authors were able to group these transcripts into 241 modules, with each module consisting of a separate cluster of highly interconnected genes." "The systems genetics approach used in this study is a powerful method for identifying novel candidate genes for complex traits and for determining the relationships between these genes. Notably, most of the candidate transcripts identified were unexpected based on previous mutational analyses of the traits.
a key bold point: "... previous mutational analyses of the traits" What failed in past mutational analyses? Could it be the failed Darwinian paradigm? Some quotes of the abstract from original research paper by Aryoles, et al: "Regressions of organismal phenotypes on transcript abundance implicate several hundred candidate genes that form modules of biologically meaningful correlated transcripts affecting each phenotype. Overlapping transcripts in modules associated with different traits provide insight into the molecular basis of pleiotropy between complex traits." For readers, from Wiki:
"'Pleiotropy' is the multiple effects of a single gene. In other words, it is when a single gene controls several phenotype traits. These traits may be seemingly unrelated."
Essentially, this is shared data space using the same data for different outcomes and regulations. Software programmers do this daily. There are core data that does not change and there is mixed fields that can vary dependent upon interaction with input. Random tinkering does not predict this. It predicts JUNK DNA. Design does predict this based upon forethought and knowledge of future events for variable responses and outcomes. Design also inhibits certain change to core processes due to recognizable limitations that lead to catostrophic failure rates. Natural Selection cannot think ahead. Design can. Design leads to a theory of Core Process Design network with designated overflow areas and interchangeable variation fields. Design also leads to highly compressed fields of shared space between other sub-routines, or program calls. Any theory of blind tinkering cannot account for saving any valid core process or data and is utterly unpredictable since inherant to the blind process is non-determination of stability or stasis. Blind tinkering cannot account for highly coordinated instructed programs to share modular data space either. Also, the article seems to account for larger leaps of funtional outcomes(variation) through organized clusters of modular, shared component space. This is favorable to a Design model instead of many small, gradual steps for a Darwinist model. It appears to weaken the gradualist model. If so, it then explains the fossil record for lack of transitionals and rapid appearances of highly complex life forms. I'm curious what Gil would think of this paper.DATCG
April 30, 2009
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Not that I agree or disagree with SalGal, but small correction to Pav: BIOS is itself a program too. The rest of your analogy is a bit off, too, although I think your overall point may be valid despite this.William Wallace
April 30, 2009
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hi jerry,
I have a question. Is Sternberg saying that the DNA in certain cells rearranges itself in the genome after the embryo starts to form.
No. What he is saying is, the DNA is arranged differently within the nucleus in nocturnal vs diurnal mammals.Dave Wisker
April 30, 2009
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jerry: Sternberg is saying that the chromosomes---wherein, of course, the DNA lies---assumes certain shapes (the eucchromatin and the heterochromatin) AND assumes certain positions within the cell nucleus itself. The G-band and the R-band (associated w/"junk DNA") segregate differently, some going to the very center of the nucleus(chromocenters), and some to the very edge of the nuclear envelope. Thus there is a gap between the center and the edge through which the nucleus is ablt to 'focus' photons onto the edges of the rod cells. This discovery (having come sooner than I expected! validates the predictions of ID, which assumes efficiency and purpose to be elements of design. OTOH, evolutionists use the 'bad design' of the vertebrate eye to make an argument that the design hypothesis is foolish. And yet, ID predictions come true, and confound the argument put forth by evolutionists. What will be their reaction? "You see how clever NS is!" Darwinism---a theory that can never be disproved. As to what SalGal wrote, it is not 'science fiction'. The genetic code is exactly that: a code,'programmed' to produce certain molecules and to perform certain tasks. But it is a program which, like all 'programs' has to be 'run' by some kind of machinery. In this case, the machinery is the cell. In particular, if you built your own computer---motherboard, disk drives, memory, power supply, hard drive---unless there was a communication system that allowed these elements to interact, nothing would happen. In your everyday computer, it's called BIOS; that is, 'basic input output system'. The "BIOS" sets up a priority system (roughly speaking what we call the 'registry') for how these various components can, and should interact. Without the BIOS, you could never get your computer program onto your hard disk. Nothing would happen. Most computer users never even fiddle with the BIOS, but it's the backbone of the computer. SalGal's point is that this "BIOS", by necessity, must be located in the cell itself. If it weren't, then simply combining the DNA, as happens at fertilization, would provide for large amounts of information, but information that could not be processed and used. Her's is a perfectly valid point. The cell also happens to be the repositor of all of the 'hardware' that is needed to 'run a program'. Hence, when the proverbial question is asked: 'which came first, the chicken or the egg', the answer has to be the 'egg'.PaV
April 30, 2009
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I have a question. Is Sternberg saying that the DNA in certain cells rearranges itself in the genome after the embryo starts to form.jerry
April 30, 2009
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Hmmm, what would confirm whether this tinkering was a design choice or a random improvement? Dr Sternberg seems to be arguing "old PC as doorstop = design!" This is a better "evolution the blind tinkerer" story. I think he'd be better off arguing that the position of junk DNA in the normal nuclear architecture shows function as some kind of protection for the protein coding DNA.Nakashima
April 30, 2009
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Is Sal Gal looking for a career as a science fiction writer? It looks like a whole lot of new theory is evolving. The DNA is the design of the cell " No, the cell actively operates upon the DNA, and a great deal of what the cell does is not specified in any sense by the DNA." Is it specified by the "Cell Fairy?"jerry
April 30, 2009
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I believe that the notion that the DNA runs the cell is an unfortunate remnant of the neo-Darwinian paradigm. Every organism begins life as a functioning cell, and uses DNA in various ways. One of those ways is as a nonvolatile store of data. As a computer scientist, I cannot see a prokaryotic bud that has just separated from its parent as supplying a "bootstrap procedure" that gets the "genetic program" up and running. (And let's recall that prokaryotes account for most of the earth's biomass.) No, the cell actively operates upon the DNA, and a great deal of what the cell does is not specified in any sense by the DNA. The only sane evolutionary perspective is that relatively simple uses of DNA arose prior to the complex processes of transcription and translation we observe today. I speculate that some of the present functions of DNA predate storage of protein templates. I'm glad to learn that a multicellular eukaryote has evolved a remarkable use for DNA. The finding lends credence to the notion that there was a time when rudimentary organisms used DNA in ways that we cannot guess today.Sal Gal
April 29, 2009
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