We still don’t know what nearly half the chromosome does

_{Denyse O'Leary

November 26, 2016

Genetics, Intelligent Design, News}

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From Robby Berman at BigThink:

While it’s true that every chromosome contains some of 25,000 genes, it now turns out to be the case that this is only a little more than half the story. Computer modeling has revealed that up to 47% of each chromosome is an enigmatic sheath-like substance called the “chromosome periphery,” something about which little is known. That’s because it’s almost impossible to get a good look at in actual chromosomes.

…

It looks like chromatin do make up from 53% to 70% of chromosomes, but the rests is the mysterious chromosome periphery. Earlier research by Booth suggests that the chromosome periphery requires the presence of the protein Ki-67 that’s believed to act as a surfactant that keeps chromosomes from clumping together. This would assign the chromosome periphery a critical job in managing cell division without errors, errors that could result in birth defects and cancer. More.

Would it be rude at this point to bring up the myth of junk DNA?

We don’t even know about half of what the chromosome does? So why do we pay any attention to genetic fundamentalism?

See also: Polyploidy: Genetic fundamentalism is still looking for a job?

and

Life continues to ignore what evolution experts say

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Bob O'H, I know Bob, the answer for Darwinians is always, when faced with a direct contradictions like this, Darwinism evolution can explain completely contradictory results with equal ease.
"Being an evolutionist means there is no bad news. If new species appear abruptly in the fossil record, that just means evolution operates in spurts. If species then persist for eons with little modification, that just means evolution takes long breaks. If clever mechanisms are discovered in biology, that just means evolution is smarter than we imagined. If strikingly similar designs are found in distant species, that just means evolution repeats itself. If significant differences are found in allied species, that just means evolution sometimes introduces new designs rapidly. If no likely mechanism can be found for the large-scale change evolution requires, that just means evolution is mysterious. If adaptation responds to environmental signals, that just means evolution has more foresight than was thought. If major predictions of evolution are found to be false, that just means evolution is more complex than we thought." ~ Cornelius Hunter Who would have thought that it would be biologists that came up with the first Theory of Everything? Biological divergence? Evolution. Biological convergence? Evolution. Gradual variation? Evolution. Sudden variation? Evolution. Stasis? Evolution. Junk DNA? Evolution. No Junk DNA? Evolution. Tree of life? Evolution. No tree of life? Evolution. Common genes? Evolution. Orfan genes? Evolution. Cell with little more than a jelly-like protoplasm? Evolution. Cell filled with countless, highly-specified nano-machines directed by a software code? Evolution. More hardy, more procreative organisms? Evolution. Less hardy, less procreative organisms? Evolution. - Evolution explains everything. - William J Murray
Yet, contrary to what you may religiously believe Bob, such an inability to be falsified by any evidence that may come along is a sure sign that we are dealing with a pseudo-science instead of a real science.
"In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality." Karl Popper - The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge
Further notes:
Atheistic Materialism: An Unscientific House of illusions - video https://youtu.be/e4TfovIU96g The waiting time problem in a model hominin population – 2015 Sep 17 John Sanford, Wesley Brewer, Franzine Smith, and John Baumgardner Excerpt: The program Mendel’s Accountant realistically simulates the mutation/selection process,,, Given optimal settings, what is the longest nucleotide string that can arise within a reasonable waiting time within a hominin population of 10,000? Arguably, the waiting time for the fixation of a “string-of-one” is by itself problematic (Table 2). Waiting a minimum of 1.5 million years (realistically, much longer), for a single point mutation is not timely adaptation in the face of any type of pressing evolutionary challenge. This is especially problematic when we consider that it is estimated that it only took six million years for the chimp and human genomes to diverge by over 5 % [1]. This represents at least 75 million nucleotide changes in the human lineage, many of which must encode new information. While fixing one point mutation is problematic, our simulations show that the fixation of two co-dependent mutations is extremely problematic – requiring at least 84 million years (Table 2). This is ten-fold longer than the estimated time required for ape-to-man evolution. In this light, we suggest that a string of two specific mutations is a reasonable upper limit, in terms of the longest string length that is likely to evolve within a hominin population (at least in a way that is either timely or meaningful). Certainly the creation and fixation of a string of three (requiring at least 380 million years) would be extremely untimely (and trivial in effect), in terms of the evolution of modern man. It is widely thought that a larger population size can eliminate the waiting time problem. If that were true, then the waiting time problem would only be meaningful within small populations. While our simulations show that larger populations do help reduce waiting time, we see that the benefit of larger population size produces rapidly diminishing returns (Table 4 and Fig. 4). When we increase the hominin population from 10,000 to 1 million (our current upper limit for these types of experiments), the waiting time for creating a string of five is only reduced from two billion to 482 million years. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573302/ “Darwinism provided an explanation for the appearance of design, and argued that there is no Designer — or, if you will, the designer is natural selection. If that’s out of the way — if that (natural selection) just does not explain the evidence — then the flip side of that is, well, things appear designed because they are designed.” Richard Sternberg – Living Waters documentary Whale Evolution vs. Population Genetics – Richard Sternberg and Paul Nelson – (excerpt from Living Waters video) https://www.youtube.com/watch?v=0csd3M4bc0Q Haldane's Pre-Cambrian Rabbit plus Natural Selection Falsified by Population Genetics - video https://youtu.be/zlGwjUJLgAE The abject failure of Natural Selection on two levels of physical reality – video (2016) (princess and the pea paradox & quarter power scaling) https://youtu.be/ISu-09yq2Gc
repost from a few days ago:
A Darwinist putting on a lab coat and performing experiments in a lab does not make him a scientist any more than a man putting on a dress and performing sexual acts on other men makes him a woman. And much like a man having sex with other men will never bear a child to prove that he is, in fact, a woman, Darwinists in lab coats performing experiments in the lab have never bore, and will never bear, fruitful results that will prove Darwinian evolution is, in fact, a real science: (November 2016) ,,,The truth, once you get past all the ‘bluff and bluster’, is that experiments in the lab have never bore, and will never bear, fruitful results that will ever prove Darwinian evolution is, in fact, true: (November 2016) https://uncommondescent.com/biology/coming-soon-design-disquisitions-a-new-id-blog/#comment-621019 One of the main reasons that no one can ever scientifically prove Darwinian evolution is actually true is that Darwinian evolution does not even qualify as a real science in the first place, but is more properly classified as a non-falsifiable pseudo-science: https://uncommondescent.com/biology/coming-soon-design-disquisitions-a-new-id-blog/#comment-620985
bornagain77_{November 28, 2016
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BA77 - The broad sweep answer is that selection pressure vary, so the cost of excess DNA is insufficiently strong to prevent it accumulating. The processes involved in gene expression are more critical, so will be under greater selection pressures.Bob O'H_{November 28, 2016
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BA77 @ 7: Well said.Truth Will Set You Free_{November 28, 2016
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Bob O'H, Exactly how is it that a totally blind process with no goals in mind, that is so inept that it can't, according to Darwinian dogma, prevent 80%-90% junk DNA from accumulating in a genome on the one hand, on the other hand become so intricately precise, and sensitive, so as to create sophisticated control and contouring mechanisms for all that junk?
Scientists' 3-D View of Genes-at-Work Is Paradigm Shift in Genetics - Dec. 2009 Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these 'hot spots'. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory. http://www.sciencedaily.com/releases/2009/12/091215160649.htm Shoddy Engineering or Intelligent Design? Case of the Mouse's Eye - April 2009 Excerpt: -- The (entire) 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 - remind them of the rod cell nuclei of the humble mouse. http://www.evolutionnews.org/2009/04/shoddy_engineering_or_intellig.html
Please note how sensitive it is:
Study suggests humans can detect even the smallest units of light - July 21, 2016 Excerpt: Research,, has shown that humans can detect the presence of a single photon, the smallest measurable unit of light. Previous studies had established that human subjects acclimated to the dark were capable only of reporting flashes of five to seven photons.,,, it is remarkable: a photon, the smallest physical entity with quantum properties of which light consists, is interacting with a biological system consisting of billions of cells, all in a warm and wet environment," says Vaziri. "The response that the photon generates survives all the way to the level of our awareness despite the ubiquitous background noise. Any man-made detector would need to be cooled and isolated from noise to behave the same way.",,, The gathered data from more than 30,000 trials demonstrated that humans can indeed detect a single photon incident on their eye with a probability significantly above chance. "What we want to know next is how does a biological system achieve such sensitivity? How does it achieve this in the presence of noise? http://phys.org/news/2016-07-humans-smallest.html
Second question Bob, exactly how are you able to keep such a deep contradiction in logic, i.e. a process that can't prevent 80%-90% junk and yet can produce a system able to detect a single photon, straight in your head? Most 10 year old children, upon seeing such a deep contradiction, would immediately realize that your preferred explanation, i.e. Darwinian evolution, is total bunk, so why can't you also realize that your explanation is complete bunk?bornagain77_{November 28, 2016
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Reading the comments posted by different folks here in this site one can see how opinions vary on every subject. But that may happen anywhere everywhere. For example, recently the famous Rolling Stones guitarist Keith Richards apparently said to the New York Post: "...all those bastards like Shakespeare ever did was to steal songs and ballads from minstrels [medieval folk singers in England]!” Different strokes for different folks. :)Dionisio_{November 28, 2016
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Would it be rude at this point to bring up the myth of junk DNA?
Please do. The approximate answer to what "about half of what the chromosome does?" is "hold all of that junk DNA together". The details, i.e. how it does it - and also allow access to the DNA for gene expression - are obviously more difficult, and this is what this work is looking at.Bob O'H_{November 28, 2016
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Excellent post and comments/links. Thank you all!Truth Will Set You Free_{November 27, 2016
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Let's be honest. The self-replicating, digital-information-based nanotechnology of life is light years beyond anything we know how to build from scratch. Modern science studying and tinkering with this nanotechnology is like jungle savages working on a computer. Both groups will most certainly screw things up eventually. At least our "expert" savages are finally beginning to realize the danger they place all of life in. See: U.S. Military Preps for Gene Drives Run Amok on the Scientific American web site.harry_{November 27, 2016
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Over the years the periphery was little studied, and its composition was largely undefined [...] [...] it appeared to be simply a thin, amorphous layer sticking to the chromosome.
3D-CLEM Reveals that a Major Portion of Mitotic Chromosomes Is Not Chromatin Daniel G. Booth, Alison J. Beckett, Oscar Molina, Itaru Samejima, Hiroshi Masumoto, Natalay Kouprina, Vladimir Larionov, Ian A. Prior, William C. Earnshaw DOI: http://dx.doi.org/10.1016/j.molcel.2016.10.009 Volume 64, Issue 4, p790–802 http://www.cell.com/molecular-cell/pdf/S1097-2765(16)30632-3.pdf

appeared to be simply [...]? appeared ? simply ? Well, sometimes appearances can be deceiving, can't they? :) Could it be that their wrong biased presuppositions sometimes make them see complex things as "simply unimportant irrelevant stuff" not worth additional investigation? Haven't we seen this problem in other biology research papers too? We need humble open-minded thinking out of pre-established boxes. Let's test everything and hold what is good. Always let's keep in mind that biology deals with complex complexity. :) BTW, there are situations where appearances are not deceiving. Now we know that many things that appear 'designed' in biology are in most cases really designed.Dionisio_{November 27, 2016
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News, Thank you for posting this reference to such an interesting article. Here's a reference to the original report:
[...] chromatin makes up a surprisingly small percentage of the total mass of metaphase chromosomes. [...] the detailed organization of mitotic chromosomes remains a mystery. This first application of 3D-CLEM analysis yielded the remarkable, and surprising, conclusion that a very large percentage of the total volume of mitotic chromosomes is not composed of chromatin, but is instead in the periphery compartment. The behavior of this compartment, for example, whether it is liquid-like, and how it influences the structural changes in the chromatin during the transition from interphase to mitosis will now become a much more active area of study. 3D-CLEM Reveals that a Major Portion of Mitotic Chromosomes Is Not Chromatin Daniel G. Booth, Alison J. Beckett, Oscar Molina, Itaru Samejima, Hiroshi Masumoto, Natalay Kouprina, Vladimir Larionov, Ian A. Prior, William C. Earnshaw DOI: http://dx.doi.org/10.1016/j.molcel.2016.10.009 Volume 64, Issue 4, p790–802 http://www.cell.com/molecular-cell/pdf/S1097-2765(16)30632-3.pdf
surprising? Every new discovery is bad news for our politely dissenting interlocutors. Poor things. We ain't seen nothing yet. :)Dionisio_{November 26, 2016
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