Formerly thought “junk DNA,” lncRNA guides development of heart muscle cells

_{Denyse O'Leary

September 13, 2016

'Junk DNA', News}

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long noncoding RNA interacts with a cellular protein to control the development of heart muscle cells. / Jose-Luis Olivares,MIT

Several years ago, biologists discovered a new type of genetic material known as long noncoding RNA. This RNA does not code for proteins and is copied from sections of the genome once believed to be “junk DNA.”

Since then, scientists have found evidence that long noncoding RNA, or lncRNA, plays roles in many cellular processes, including guiding cell fate during embryonic development. However, it has been unknown exactly how lncRNA exerts this influence.

Inspired by historical work showing that structure plays a role in the function of other classes of RNA such as transfer RNA, MIT biologists have now deciphered the structure of one type of lncRNA and used that information to figure out how it interacts with a cellular protein to control the development of heart muscle cells. This is one of first studies to link the structure of lncRNAs to their function. More. Paper. (paywall) – Zhihong Xue et al. A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage. Molecular Cell, September 2016 DOI: 10.1016/j.molcel.2016.08.010

One doesn’t hear so much any more about how “junk DNA” is exactly what we should expect if Darwinism were a correct account of evolution. But finding out that it isn’t junk is, of course, a validation too, right? Some beliefs are just plain immune to the vagaries of evidence.

See also: The latest in functional junk DNA

and these for background:

New York Times science writer defends the myth of junk DNA

Is “dark genome” becoming the new name for junk DNA?

“Researchers say junk DNA plays key role in brain development” and “Non-coding RNAs undermining the junk DNA concept?”

Old concepts die hard, especially when they are value-laden as “junk DNA” has been—it has been a key argument for Darwinism. So even though “dark genome” makes more sense given all the functions now being identified, expect “junk DNA” to be defended in practice.

For an odd example of that, see “Nothing makes sense in evolution except in the light of junk DNA?”: “If ENCODE [a project that identifies functions] is right, then Evolution is wrong.”

And more recently, Furore over no junk DNA?

For background, see Jonathan Wells on the junk DNA myth

Pod: Richard Sternberg on “junk DNA”

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Comments

A structural argument against a large portions of junk-DNA: Consider this, if an organism contains e.g. 90% junk-DNA, then the DNA-molecule is 90% longer than necessary. Obviously, longer DNA-molecules can more easily get tangled. How can this be "neutral" to an organism? In fact, it is utterly miraculous that DNA doesn't get tangled up all the time:
If you arranged the DNA in a human cell linearly, it would extend for nearly two meters. How do you pack all that DNA into a cell nucleus just five or ten millionths of a meter in diameter? According to the usual comparison it’s as if you had to pack 24 miles (40 km) of extremely thin thread into a tennis ball. Moreover, this thread is divided into 46 pieces (individual chromosomes) averaging, in our tennis-ball analogy, over half a mile long. Can it be at all possible not only to pack the chromosomes into the nucleus, but also to keep them from becoming hopelessly entangled? Obviously it must be possible, however difficult to conceive — and in fact an endlessly varied packing and unpacking is going on all the time. The first thing to realize is that chromosomes do not consist of DNA only. Their actual substance, an intricately woven structure of DNA, RNA, and protein, is referred to as chromatin. Histone proteins, several of which can bind together in the form of an extremely complex histone core particle, are the single most prominent constituent of this chromatin. Every cell contains numerous such core particles — there are some 30 million in a typical human cell — and the DNA double helix, after wrapping a couple of times around one of them, typically extends for a short stretch and then wraps around another one. The core particle with its DNA is referred to as a nucleosome, and between 75 and 90 percent of our DNA is wrapped up in nucleosomes. But that’s just the first level of packing; it accounts for relatively little of the overall condensation of the chromosomes. If you twist a long, double-stranded rope, you will find the rope beginning to coil upon itself, and if you continue to twist, the coils will coil upon themselves, and so on without particular limit, depending on the fineness and length of the rope. Something like this supercoiling happens with the chromosome, mediated in part by the histone core particles. As a result the core particles, and the DNA along with them, become tightly packed almost beyond comprehension, in a dense, three-dimensional geometry that researchers have yet to visualize in any detail. This highly condensed state, characterizing great stretches of every chromosome, contrasts with other, relatively uncondensed stretches known as open chromatin. With that background, we can gain our first glimpse of the concerted dynamism in which genes participate. At any one time — and with the details depending on the tissue type and stage of the organism’s development, among other things — some parts of every chromosome are heavily condensed while others are open. Every overall configuration represents a unique balance between constrained and liberated expression of our total complement of 21,000 genes This is because the transcription of genes generally requires an open state; genes in condensed chromatin are largely silenced. The supercoiling has another direct, more localized role in gene expression. Think again of twisting a rope: depending on the direction of your twist, the two strands of the helix will either become more tightly wound around each other or will be loosened and unwound. (This is independent of the supercoiling, which occurs in either case.) And if, taking a double-stranded rope in hand, you insert a pencil between the strands and force it in one direction along the rope, you will find the strands winding ever more tightly ahead of the pencil’s motion and unwinding behind. Recall, then, that the enzyme (RNA polymerase) responsible for transcribing DNA into RNA must separate the two strands as it moves along a gene sequence. This is much easier if the supercoiling of the chromatin has already loosened the strands — and harder if the strands are tightened. So in this way the variations in supercoiling along the length of a chromosome either encourage or discourage the transcription of particular genes. Moreover, by virtue of its own activity in moving along the DNA and separating the two strands, RNA polymerase (like the pencil) tends to unwind the strands in the chromosomal region behind it, rendering that region, too, more susceptible to gene expression. There are proteins that detect such changes in torsion propagating along chromatin, and they read the changes as “suggestions” about helping to activate nearby genes (Lavelle 2009; Kouzine et al. 2008). Picture the situation concretely. Every bodily activity or condition presents its own requirements for gene expression. Whether you are running or sleeping, starving or feasting, getting aroused or calming down, suffering a flesh wound or recovering from pneumonia — in all cases the body and its different cells have specific, almost incomprehensibly complex and changing requirements for differential expression of thousands of genes. And one thing necessary for achieving this expression in all its fine detail is the properly choreographed performance of the chromosomes. This performance cannot be captured with an abstract code. Interacting with its surroundings, the chromosome belongs as much to a living activity as any other element in its cellular environment. Maybe instead of summoning the image of a rope, I should have invoked a snake, coiling, curling, and sliding over a landscape that is itself in continual movement. Managing the Twists Perhaps none of this helps us greatly to understand how the extraordinarily long chromosome, tremendously compacted to varying degrees along its length, can maintain itself coherently within the functioning cell. But here’s one relevant consideration: there are enzymes called topoisomerases, whose task is to help manage the forces and stresses within chromosomes. Demonstrating a spatial insight and dexterity that might amaze those of us who have struggled to sort out tangled masses of thread, these enzymes manage to make just the right local cuts to the strands in order to relieve strain, allow necessary movement of individual genes or regions of the chromosome, and prevent a hopeless mass of knots. Some topoisomerases cut just one of the strands of the double helix, allow it to wind or unwind around the other strand, and then reconnect the severed ends. Other topoisomerases cut both strands, pass a loop of the chromosome through the gap thus created, and then seal the gap again. (Imagine trying this with miles of string crammed into a tennis ball — without tying the string into knots!) I don’t think anyone would claim to have the faintest idea how this is actually managed in a meaningful, overall, contextual sense, although great and fruitful efforts are being made to analyze isolated local forces and “mechanisms”. [Talbott]
Origenes_{September 19, 2016
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wd400: [Been away from things for about a week]
I’m sure this has been explained previously, but here we go gain. Evolutionary biology says that junk will accumulate in genomes when the cost of an extra sequence is low (i.e. organisms don’t live close to an energetic knife edge) and population sizes are relatively small (since selection is relatively weak in small populations, and will not be able to ‘weed’ out weakly deleterious junk sequences).
So you're making the distinction between "Darwinism," and "evolutionary biology." I suspect this is because of Kimura's Neutral Theory, which, as he tells us, is non-Darwinian: IOW, "selection" is not at play. How do we know "selection" is 'not at play'? Because of the tremendous heterozygosity seen---as I mentioned last time. Now, with "relatively small" populations, given that the equation for "selection" involves the population size, N, directly, means only that "selection" takes place way too slowly. All of this is interpreted by "evolutionary biologist"s as there being, effectively, no "selection pressure." Since "selection pressure" can be, and is (whether or not it is actually true), defined by sequence conservation, all of this simply means that: when 'selection' takes place, it takes place; when 'selection' doesn't take place, it doesn't take place. To which is added: when 'selection' doesn't take place, then "junk" can, and will accumulate. Well, let's get back to Kimura: When he presented his "Neutral Theory" in the 1970's, and with his book (1982?), he was broadly resisted. But, then---as all academics must do---protesting his "belief" in "evolution" (though, obviously non-Darwinian since in his book on NT his calculation of one mutation at a particular site in the elephant genome sequence taking 5, or 7, million years to become "fixed" meant that Darwinism, as it was known then in its "neo-Darwinian" form could not be relied on for "evolution") he was accepted back into the ranks of population geneticists, and "neo-Darwinism" went 'extinct' and "evolutionary biology" came to life. Science 'evolves,' you see! So here you have the failure of a theory becoming somehow, in the minds of the anointed, a victory of sorts. Or else we can look at this way: take the formula of neo-Darwinism: RM + NS = evolution. What modern population genetics has done is to separate these two parts of the formula into two spheres of influence: RM is now the stuff of "neutral molecular evolution," while NS is restricted to those instances of "adaptation" where NS is assumed to be at work. You might say that all is well and good. But here's the problem. Neutral molecular evolution CANNOT explain the Cambrian Explosion (neither can Darwinism itself), and NS can only really explain "adaptation." So, these combined 'spheres' are still not able to explain what we see (and, don't see) in the fossil record. It is not a true theory of the evolution of species. As I've said here over the years countless times: I don't have a problem with a lot of what Darwin wrote. But just call it the "Origin of Adaptation," and NOT "The Origin of Species." Bottom-line: if you run into "junk-DNA," then that's simply the "RM" part of the equation at work; and, if you run into streamlined genomes, like in birds, then that's simply the "NS" part of the equation at work "selecting for" the 'high energy needs' (a knife-like edge) of the organism. You have to marvel: RM + NS can explain anything. You just have to have the right rationalizations for it. Ah, yes. "A sucker is born every minute."PaV_{September 19, 2016
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Anyone who reads the linked thread would be able see my comment comes after many attempts to get you to engage with the biological basis of development, and not your own poor analogy. You only need to read these quotes to see Eric Anderson is demonstrating his own ignorance, rather than reflecting anything I've said.wd400_{September 18, 2016
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In other threads I posed the question:
If most of our genome is junk, then where is the information stored for the (adult) body plan? Where is the information stored for e.g. the brain? And where is the information stored for how to build all this?
Here are the answers by Larry Moran and WD400:
Larry Moran: …. experts do not see a need to encode body plans and brain in our genome …

WD400: If it is not clear enough, there is no over-arching “plan” in the genome. There are genes, that have regulatory elements, which produce gene produces respond to environments and influence other genes and so on and so on.
Eric Anderson summarized their position as follows:
Eric Anderson: … this thread may have uncovered at least one aspect of the simplistic thinking that leads a person to believe that most DNA is junk. After all, the thinking goes, all we need to do is specify some parts in the DNA and the machine will build itself all by chemistry. It’s easy! No plan needed. No program required. Just specify some gene products and we’re done. Everything else is probably just junk. Amazing what chemistry can do.
Origenes_{September 17, 2016
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I'm sure this has been explained previously, but here we go gain. Evolutionary biology says that junk will accumulate in genomes when the cost of an extra sequence is low (i.e. organisms don't live close to an energetic knife edge) and population sizes are relatively small (since selection is relatively weak in small populations, and will not be able to 'weed' out weakly deleterious junk sequences). When we look at measures of how junky a genome is (raw size, intron length, repeat content..) we find a pretty good correlation between junkiness and effective population size (eg http://www.yilab.gatech.edu/publications/Yi_Streelman_2005.pdf) and what's more we find particular lineages that have high energetic needs tend to have smaller, less junky genomes that then close relatives (birds, bats and even pterosaurs had small genomes).wd400_{September 17, 2016
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Larry Moran's explanation above turns on the distinction he makes between "evolution" and "Darwinism." As wd400 explains, according to adaptationism, the genome directly interacts with the environment via NS, and organisms that are well-adapted should then now show much heterozygosity. Alas, molecular biology studies of the 60's showed this wasn't so, that heterozygosity is extremely high. It lead to Kimura's "Neutral Theory." Larry Moran invokes this theory, which, as Kimura himself says, is non-Darwinian. Hence the gap that has arisen. So, the 'modern' position is that 'evolution lives,' while 'neo-Darwinism' is dead. Here's the big problem. If 'neo-Darwinism' is dead, then no logical argument exist for how 'evolution' can occur. Evolution is but a house of cards. It simply hangs in the air, just as the fossil record 'hangs in the air' since the Cambrian Explosion reveals that neither NS nor Neutral Theory can explain the large number of body-types that arose in such short order. Just so you know how they're arguing. Curious Cat talks about an "added parameter"; but, it's "adding and subtracting." Darwinism out; Neutral Theory in, so that results can be, as CC says, "explained." I want to know how all those body-types arose in the Cambrian. Any explanations out there?PaV_{September 17, 2016
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wd400:
Moreover our better theory of evolution is also testable. As I said, we can predict where and when junk ought to accumulate.
I, for one, would like to hear more about this "predictive" power. What do you mean?!PaV_{September 17, 2016
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And WD400 just don't seem to understand the fundamental problem. A theory that ends up explaining everything really explains nothing.Andre_{September 15, 2016
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"Moreover our better theory of evolution is also testable. As I said, we can predict where and when junk ought to accumulate." LOL, yeah, the prediction is, if no intelligence was involved in creating life then we should be 100% junk instead of just 90 percent junk!
Can Purifying Natural Selection Preserve Biological Information? - May 2013 - Paul Gibson, John R. Baumgardner, Wesley H. Brewer, John C. Sanford In conclusion, numerical simulation shows that realistic levels of biological noise result in a high selection threshold. This results in the ongoing accumulation of low-impact deleterious mutations, with deleterious mutation count per individual increasing linearly over time. Even in very long experiments (more than 100,000 generations), slightly deleterious alleles accumulate steadily, causing eventual extinction. These findings provide independent validation of previous analytical and simulation studies [2–13]. Previous concerns about the problem of accumulation of nearly neutral mutations are strongly supported by our analysis. Indeed, when numerical simulations incorporate realistic levels of biological noise, our analyses indicate that the problem is much more severe than has been acknowledged, and that the large majority of deleterious mutations become invisible to the selection process.,,, http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0010 Genetic Entropy – references to several peer reviewed papers (via John Sanford and company) http://www.geneticentropy.org/#!properties/ctzx 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/ A Billion Genes and Not One Beneficial Mutation – August 26, 2016 Excerpt: Nature just published results of the Exome Aggregation Consortium (ExAC), the largest survey of human genes to date. (An "exome" is the portion of the genome that codes for proteins.) The exomes from 60,706 individuals from a variety of ethnic groups have been collected and analyzed. If we multiply 60,000 people by the 20,000 genes in the human genome (the lowest estimate), we get a minimum of 1.2 billion genes that have been examined by ExAC for variants.,,, ,,, we search(ed) the paper in vain for any mention of beneficial mutations. There's plenty of talk about disease. The authors only mention "neutral" variants twice. But there are no mentions of beneficial mutations. You can't find one instance of any of these words: benefit, beneficial, fitness, advantage (in terms of mutation),improvement, innovation, invention, or positive selection. They mention all kinds of harmful effects from most variants: missense and nonsense variants, frameshift mutations, proteins that get truncated on translation, and a multitude of insertions and deletions. Quite a few are known to cause diseases. There are probably many more mutations that never survive to birth. As for natural selection, the authors do speak of "negative selection" and "purifying selection" weeding out the harmful mutations, but nowhere do they mention anything worthwhile that positive selection appears to be preserving. http://www.evolutionnews.org/2016/08/a_billion_genes103091.html Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - May 2013 Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11]. 1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696. 2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19. 3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358. 4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144. 5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47. 6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. 7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117. 8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526. 9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685. 10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079. 11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006
Moreover, anyone who believes that an organism of a billion-trillion protein molecules can come about by a process that, by their own estimation, produces 90% junk DNA, is not a person that is dealing with a full deck~
HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE - Stephen L. Talbott - May 2012 Excerpt: “If you think air traffic controllers have a tough job guiding planes into major airports or across a crowded continental airspace, consider the challenge facing a human cell trying to position its proteins”. A given cell, he notes, may make more than 10,000 different proteins, and typically contains more than a billion protein molecules at any one time. “Somehow a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places”. And further: “It’s almost as if every mRNA [an intermediate between a gene and a corresponding protein] coming out of the nucleus knows where it’s going” (Travis 2011),,, Further, the billion protein molecules in a cell are virtually all capable of interacting with each other to one degree or another; they are subject to getting misfolded or “all balled up with one another”; they are critically modified through the attachment or detachment of molecular subunits, often in rapid order and with immediate implications for changing function; they can wind up inside large-capacity “transport vehicles” headed in any number of directions; they can be sidetracked by diverse processes of degradation and recycling . . . and so on without end. Yet the coherence of the whole is maintained. The question is indeed, then, “How does the organism meaningfully dispose of all its molecules, getting them to the right places and into the right interactions?” The same sort of question can be asked of cells, for example in the growing embryo, where literal streams of cells are flowing to their appointed places, differentiating themselves into different types as they go, and adjusting themselves to all sorts of unpredictable perturbations — even to the degree of responding appropriately when a lab technician excises a clump of them from one location in a young embryo and puts them in another, where they may proceed to adapt themselves in an entirely different and proper way to the new environment. It is hard to quibble with the immediate impression that form (which is more idea-like than thing-like) is primary, and the material particulars subsidiary. Two systems biologists, one from the Max Delbrück Center for Molecular Medicine in Germany and one from Harvard Medical School, frame one part of the problem this way: "The human body is formed by trillions of individual cells. These cells work together with remarkable precision, first forming an adult organism out of a single fertilized egg, and then keeping the organism alive and functional for decades. To achieve this precision, one would assume that each individual cell reacts in a reliable, reproducible way to a given input, faithfully executing the required task. However, a growing number of studies investigating cellular processes on the level of single cells revealed large heterogeneity even among genetically identical cells of the same cell type. (Loewer and Lahav 2011)" ,,, And then we hear that all this meaningful activity is, somehow, meaningless or a product of meaninglessness. This, I believe, is the real issue troubling the majority of the American populace when they are asked about their belief in evolution. They see one thing and then are told, more or less directly, that they are really seeing its denial. Yet no one has ever explained to them how you get meaning from meaninglessness — a difficult enough task once you realize that we cannot articulate any knowledge of the world at all except in the language of meaning.,,, http://www.netfuture.org/2012/May1012_184.html#2
Verse and Quote:
Psalms 139:14 I praise you, for I am fearfully and wonderfully made. Wonderful are your works; my soul knows it very well. Mathematician Alexander Tsiaras on Human Development: "It's a Mystery, It's Magic, It's Divinity" - March 2012 Excerpt: 'The magic of the mechanisms inside each genetic structure saying exactly where that nerve cell should go, the complexity of these, the mathematical models on how these things are indeed done, are beyond human comprehension. Even though I am a mathematician, I look at this with the marvel of how do these instruction sets not make these mistakes as they build what is us. It's a mystery, it's magic, it's divinity.' http://www.evolutionnews.org/2012/03/mathematician_a057741.html
bornagain77_{September 15, 2016
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Well, you'd have to ask Larry, but I really don't think he is saying the the discovery of junk DNA confirmed his view. Just that it is compatible with it. I think this is actually a good example of how testibility works. Junk DNA is not compatible with a strict Darwinian view of evolution, so those hyper-adaptationist theories were found wanting. But the discover of junk didn't change the evidence for common descent or re-write what we already knew about natural selection. So the baby doesn't need to be thrown out with the bathwater. Moreover our better theory of evolution is also testable. As I said, we can predict where and when junk ought to accumulate.wd400_{September 15, 2016
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redwave @12:
1. Is there a “decorum”, however unwritten and unenforceable, expected from a Professor and an expectation that PhDs exhibit a higher degree of communicative skill over an ochlocratic dissonance? NO. Obviously. You may expect it, but that's your personal opinion. There are no absolute rules in this spiritually dead world to require what you expect. :) 2. Is your language an integral part of a “serious scientific debate”? NO. If you don't like it, that's your problem. :) 3. Are pejoratives really necessary? NO. But everybody is free to say them if they want to. If you don't like them, that's your problem. :) 4. If so, what are the reasons, since I am not familiar with the idea that a serious scientific debate is a brawl among men? The reason is simple: everybody says whatever they want to anytime. If you don't like it, that's your problem. :) 5. For what “ideals” of thought and experience are you fighting? No one is fighting. Just saying what they want. If you don't like it, that's your problem. :) 6. Are there truths, right thinking, or correct knowledge for which you find pejoratives, superlatives, and derogatives necessary? No. This world recognizes relative truths, relative self-righteousness, relative correctness. That's all. Nothing is necessary. Everybody say whatever they want. If you don't like it, too bad. That's your problem. Chill out! :)
In this spiritually egocentric dead world, the only acceptable rule is Frank Sinatra's song "My way" and the only hope is expressed in John Lennon's song "Imagine" (specially the first line). Everything else is irrelevant. Fortunately, in the current age of grace God is keeping things from getting much worse. However, we know this age will come to an end. Things will get really ugly before Christ's return. When He comes back, every knee will bow and every tongue will confess that He is Lord. But then it will be too late for many to get reconciled with their Creator. I believe we all were made by our Creator in IMAGO DEI, hence we all have dignity. Every person is special in the mind of our Creator. Besides, Christ demands from us that we love our neighbors as ourselves. When asked to clarify what is a neighbor, He said the story of the good Samaritan who helped a Jew after two Jews had refused to help. Those two ethnicities -Samaritans and Jews- disliked each other. Very shocking example. It sends a very strong message. That means that even if we are treated bad, we still respond gracefully and respectfully. However, we keep presenting what we believe is true. That's what makes some folks angry to the point that they express themselves in not so nice terms. I had an interesting experience with professor L.M. of the U. of T. in Canada here in this blog a while back. I asked him a few simple (yes/no) questions, but he did not like them and accused me of asking dishonest questions. I can provide the link to the thread where he posted those comments. Definitely he knows more biology than I ever will learn, but unfortunately sharing his knowledge in a friendly chat does not seem to satisfy him. I pray for professor Moran, because I'm sure that God loves him. I know it because God has proven to me that He loves me, and I'm much worse a person than professor Moran. Who knows? Maybe some day he will surprise us with a nicely written comment and will be willing to discuss in friendly terms some fundamental issues of biology. The threads "Mystery at the heart of life" and "third way of evolution" have over 2,500 posts with references to interesting biology-related research papers we could discuss for mutual benefit.Dionisio_{September 15, 2016
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wd400 #19 Now, that's the heart of the problem. We should not use "updating a theory" as a slogan for scientific progress. Here, the update is, as you have also pointed above, adding another parameter to the model (theory) so that model explains the data. Now, that's always possible to rescue a model from being rejected. Sometimes, this has merits, to extend the lifespan of a useful theory. Sometimes, it is problematic, it just fits (and explains) the data at hand, but cannot make any reliable predictions. I guess the distinction here again lies in the predictive power of the theory, but again there's the same problem. In the future, in a similar instance, in which the current evolution paradigm (Darwinian, or "pluralistic", or whatever) encounters a problem, which will not predicted but also not be inconsistent with the theory, this same strategy will be applied. Another parameter will be added to the model, and theory will go on living.CuriousCat_{September 15, 2016
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wd400,
The discovery of junk DNA did require revision of our theory of evolution. It was part of a slew of results and theoretical papers that showed us that much of molecular evolution is not effected by natural selection.
Translation: Advances in the mathematics of population genetics cast natural selection, which was Charles Darwin's main claim to fame, and which was the supposed 'designer substitute', to be cast under the bus. Now the more 'enlightened' Darwinists, such as wd400 and Moran, who know the theoretical (and empirical) failings of natural selection, cling to neutral theory as the main driver of Darwinian evolution. Although Moran has switched back and forth, between selection and neutral theory, depending on who's eyes he is trying to pull the wool over on.
"many genomic features could not have emerged without a near-complete disengagement of the power of natural selection" Michael Lynch The Origins of Genome Architecture, intro "the uncritical acceptance of natural selection as an explanatory force for all aspects of biodiversity (without any direct evidence) is not much different than invoking an intelligent designer" Michael Lynch The Origins of Genome Architecture, p 368 "a relative lack of natural selection may be the prerequisite for major evolutionary advance" Mae Wan Ho Beyond neo-Darwinism “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 Majestic Ascent: Berlinski on Darwin on Trial - David Berlinski - November 2011 Excerpt: The publication in 1983 of Motoo Kimura's The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura's theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism. "A critique of neo-Darwinism," the Dutch biologist Gert Korthof boasted, "can be incorporated into neo-Darwinism if there is evidence and a good theory, which contributes to the progress of science." By this standard, if the Archangel Gabriel were to accept personal responsibility for the Cambrian explosion, his views would be widely described as neo-Darwinian. http://www.evolutionnews.org/2011/11/berlinski_on_darwin_on_trial053171.html (With the adoption of the 'neutral theory' of evolution by prominent Darwinists, and the casting aside of Natural Selection as a major player in evolution),,, "One wonders what would have become of evolution had Darwin originally claimed that it was simply the accumulation of random, neutral variations that generated all of the deeply complex, organized, interdependent structures we find in biology? Would we even know his name today? What exactly is Darwin really famous for now? Advancing a really popular, disproven idea (of Natural Selection), along the lines of Luminiferous Aether? Without the erroneous but powerful meme of “survival of the fittest” to act as an opiate for the Victorian intelligentsia and as a rationale for 20th century fascism, how might history have proceeded under the influence of the less vitriolic maxim, “Survival of the Happenstance”?" - William J Murray Junk DNA Argument Of Darwinists - a short history https://docs.google.com/document/d/14-TXfGxPu-3YeCHtLmxTmL4UZN90Odt135c59yTIFsw/edit The mathematics of population genetics has not been kind to Darwinian claims in the least. Three devastating problems are revealed by population genetics. The Waiting Time problem, Natural selection is ineffective, and all of our perceptions of reality become illusory. (July 2016) https://uncommondescent.com/intelligent-design/81705/#comment-613650 Haldane's Pre-Cambrian Rabbits 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
bornagain77_{September 15, 2016
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Don’t you just hate scientific fields that update when new data comes to light!
Not as much as modern day pseudoscientific phlogiston theories ;)Vy_{September 15, 2016
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wd400 #15 The discovery of junk DNA did require revision of our theory of evolution. It was part of a slew of results and theoretical papers that showed us that much of molecular evolution is not effected by natural selection. That’s why Larry said junk DNA is not compatible with strict Darwinism. The part I referred to was after Dr. Moran said "Junk DNA is inconsistent with strict Darwinism. That’s why most Darwinists opposed it." I believe you are confused about the succession of the arguments. Dr. Moran did not say "as a result of this we changed the theory" or something. What Dr. Moran said referred to was his initial pluralistic views and the view he still held after the observations. The thing I would like to emphasize is that his pluralistic view frees evolution theory from the burden of being testable.CuriousCat_{September 15, 2016
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Don't you just hate scientific fields that update when new data comes to light!wd400_{September 15, 2016
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Andre, that is not what I am saying. At all. What are you on about?
Hmm...
The discovery of junk DNA did require revision of our theory of evolution.
In simple terms: The ~~myth~~ theory of ~~evodelusion~~ evolution evolves to fit the data.Vy_{September 15, 2016
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Andre, that is not what I am saying. At all. What are you on about?wd400_{September 15, 2016
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What WD400 is really saying is Darwinian evolution really explains everything. He is really punting for the idea that evidence for or against Darwinian evolution does not really matter because whatever it is, it is Darwinian.Andre_{September 15, 2016
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CuriousCat, The rest of Larry's comment makes this pretty clear, but to expand a little: The discovery of junk DNA did require revision of our theory of evolution. It was part of a slew of results and theoretical papers that showed us that much of molecular evolution is not effected by natural selection. That's why Larry said junk DNA is not compatible with strict Darwinism. Our improved theories of evolution have helped us predict when we expect junk DNA to accumulate. So it's not the case that evolution predicts junk always, only in some special cases.wd400_{September 15, 2016
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Surprise Grows Over Importance of Previously Dismissed Portions of the Genome – Sept. 15, 2016 Excerpt: Don't Vary the Repeats News from Duke University announces, "Variation in 'Junk' DNA Leads to Trouble." Trouble, indeed: "unstable genomes, cancer, and other defects." That's what they found can happen when apparently worthless repetitive sequences around centromeres are varied.,,, Glimpsing a Multi-Functional lncRNA Long non-coding RNAs (lncRNA) used to be on the genetic junk pile. As we have seen before, they can be indispensable.,,, The current study, therefore, is another "tip of the iceberg" case that has implications for all lncRNAs. In this case, the researchers from University of North Carolina at Chapel Hill identified "complex well-defined secondary structure domains" in this 18,000-base RNA molecule that are related to specific functions.,,, http://www.evolutionnews.org/2016/09/surprise_grows103142.html
bornagain77_{September 15, 2016
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Those of us who subscribe to a more pluralistic view of evolution know that junk DNA is consistent with that view but none of us ever said that junk DNA is what we “expect” if evolution were true. Dr. Moran, but as far I as I can see (I'll try to keep your original wording as much as I can, so that there might be no significant change in the meaning), you do not expect junk DNA, but at the same time you do not find the existence of junk DNA to be inconsistent with your "pluralistic" view. My question is as follows: Could you please give me an example similar to the that given above, i.e. (using my own wording) "the positive outcome is NOT predicted by the theory, but the positive outcome IS consistent with the theory" with the additional assumption that "the current theory needs NO revision in the light of these findings", in physics or chemistry? Thanks in advance.CuriousCat_{September 15, 2016
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Larry Moran @6. "Alex Palazzo and Ryan Gregory are friends of mine. They never said any such thing. What they said is that the presence of large amounts of junk DNA does not conflict with the modern understanding of evolution even though it is inconsistent with Darwinism. ... That is not the same as saying that evolution SHOULD produce junk DNA and it’s very different from what Denyse O’Leary said." Your correction, in the precise use of terminology, of the National Geographic writers' review is well-taken. "Should" from the Old English sceolde: past of shall and "shall" from the Old English sceal, of Germanic origin; related to Dutch zal and German soll, from a base meaning 'owe' (OED, 2014) do suggest causation rather than correlation. Larry Moran @11. "I agree completely. That would be very stupid behavior. It is definitely not science. Anyone who believes that’s the way science works is an idiot or an IDiot." Exactly what is "an IDiot"? I had assumed from the comments of others that you are a Professor and note that you hold a PhD in Biochemistry. Is there a "decorum", however unwritten and unenforceable, expected from a Professor and an expectation that PhDs exhibit a higher degree of communicative skill over an ochlocratic dissonance. Is your language an integral part of a "serious scientific debate"? Are pejoratives really necessary? If so, what are the reasons, since I am not familiar with the idea that a serious scientific debate is a brawl among men? For what "ideals" of thought and experience are you fighting? Are there truths, right thinking, or correct knowledge for which you find pejoratives, superlatives, and derogatives necessary?redwave_{September 15, 2016
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See what I mean the Prof just could not resist.Andre_{September 14, 2016
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However, declaring something ‘nonfunctional’ just because we don’t know what it does or what it is for doesn’t seem like a scientific approach.
I agree completely. That would be very stupid behavior. It is definitely not science. Anyone who believes that's the way science works is an idiot or an IDiot.Larry Moran_{September 14, 2016
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Andre @7: They can resolve it as a domestic issue between fellow Canadians. :)Dionisio_{September 14, 2016
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After the first humans decided to make Frank Sinatra's song "My way" our own hymn, history has been continuously filled with so much greed that led to total disregard for the healthy care of our bodies and the surrounding environment. One could argue that's the price to pay for increasing material comfort and conveniences, but I believe that's the price to pay for rebelling against our wonderful Maker, ignoring His caring instructions and underappreciating the marvelous initial environment we were supposed to live in. As result of all that mess we have created through our foolishness, our biological bodies have been negatively affected at physiological, cellular, biochemical and molecular levels. Hence, the presence of some 'junk DNA' should not be a surprise to anyone. Despite all that mess we have brought ourselves into after rejecting God's gracious conditions, humanity has amazingly survived and reproduced, which clearly testifies that our complex biology is quite robust. That robustness may be related -at least in part- to the observed complex complexity of our biological bodies, as professor Denis Noble has indicated. However, declaring something 'nonfunctional' just because we don't know what it does or what it is for doesn't seem like a scientific approach. We need more research -in both wet and dry labs- to decipher the outstanding biological mysteries. We should encourage more young people to pursue STEM careers, specially biology. Here in this blog we should engage in serious discussions about fundamental topics of modern science, specially biology-related issues. Those who don't want to do it should consider going back to their natural habitats in the beautiful Norwegian fjords. :)Dionisio_{September 14, 2016
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Denyse See what you have done now Prof Moran is upset and for weeks we are going to read about the IDiot's that don't understand evolution and that only Prof Moran does.Andre_{September 14, 2016
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Palazzo and Gregory, on the other hand, argue that evolution should produce junk.
Alex Palazzo and Ryan Gregory are friends of mine. They never said any such thing. What they said is that the presence of large amounts of junk DNA does not conflict with the modern understanding of evolution even though it is inconsistent with Darwinism. That is not the same as saying that evolution SHOULD produce junk DNA and it's very different from what Denyse O'Leary said.
Genetic material derisively called “junk” DNA because it does not contain the instructions for protein-coding genes and appears to have little or no function is actually critically important to an organism’s evolutionary survival, according to a study conducted by a biologist at UCSD.
Popular science websites like Science Daily make these kind of mistake all the time. Unfortunately, some scientists make the same mistake. It's just plain wrong. We've known for over 40 years about non-coding regions that are very functional. These include genes for functional RNAs such as tRNA and ribosomal RNA (and many others), centromeres, telomeres, and regulatory sequences. Anyone, in the past 40 years, who said that all non-coding regions are junk is stupid. Knowledgeable scientists would never say such a thing.Larry Moran_{September 14, 2016
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Larry Moran is still thinking in 19th century linear terms, while he should know, as a biochem-prof and because I have informed him several times, that biological systems operate in redundancy networks. The knockout experiments designed to unravel functions of single components of such networks have already been shown to be doomed in the 90th of the past century: no-phenotype knockouts are the rule not the exception. That also holds for the finetuning-functions of thousands of lncRNAs. A Darwinian, Moran will never understand biology. But let's wait for the book he is writing and find out if he has original ideas.Peer_{September 14, 2016
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