Here.
Special Issue on microRNAs – the smallest RNA regulators of gene expression
It is now well recognised that the majority of non-protein-coding genomic DNA is not “junk” but specifies a range of regulatory RNA molecules which finely tune protein expression. This issue of CDD contains an editorial and 5 reviews on a particular class of these regulatory RNAs, the microRNAs (miRs) of around 22 nucleotides, and which exert their effects by binding to consensus sites in the 3’UTRs of mRNAs. The reviews cover the role of miRs from their early association with CLL to other forms of cancer, their importance in the development of the epidermis and their potential as disease biomarkers as secreted in exosomes. In addition, we publish a News and Commentary on CRISPR, a technology which is not only revolutionising genetic manipulation in the lab, but which has the potential to treat genetic disease in vivo.
Oh? Does anyone remember when BioLogos founder Francis Collins was fronting “junk DNA”? So we were all suppose to rush to believe that. But hey, now we aren’t.
Darwinian evolution predicted this, there is no junk, natural selection, random mutation and drift are very efficient unguided processes capable of optimizing the code……
Junk out! That’s what we predicted all along! Darwinism is a fact! And if you deny it you are stupid because a designer would not have done it that way!
I wonder if Biologist Larry Moran will backpedal about junk DNA any more than the way in which he has tried to backpedal on other biologists long help acceptance of “junk” DNA and why it was a prediction of evolution. Junk DNA is both evidence for evolution and mostly functional DNA is also evidence for evolution. Kinda makes me think that evolution is not falsifiable.
Don’t worry, there is still a significant amount of non-coding DNA that is still classified as “junk” and will likely remain so. Yes, the initial “junk” label was probably premature (shame on us!), but there is still a large portion of the genome simply made up of single sequence repeats.
AVS:
“Yes, the initial “junk” label was probably premature”
Yes. Let’s say “premature”. 🙂
“there is still a large portion of the genome simply made up of single sequence repeats.”
I would suggest to avoid making the same “premature” thing twice! That will be shown to be the most important part, sooner or later… 🙂
Next we’ll probably hear that evolutionary biologists are pushing the name of Jonathan Wells as a nobel laureate candidate.
Podcast: Richard Sternberg PhD – ” On Human Origins: Is Our Genome Full of Junk DNA? part 1
http://www.discovery.org/multi.....-junk-dna/
Podcast – Richard Sternberg PhD – On Human Origins: Is Our Genome Full of Junk DNA? Part 2. (Major Differences in higher level chromosome spatial organization)
5:30 minute mark quote: “Basically the dolphin genome is almost wholly identical to the human genome,, yet no one would argue that bottle-nose dolphins are our sister species”
http://www.discovery.org/multi.....-dna-pt-2/
Podcast: Richard Sternberg PhD – ” On Human Origins: Is Our Genome Full of Junk DNA? Part 3″
http://intelligentdesign.podom.....4_33-08_00
Podcast – Richard Sternberg PhD – On Human Origins: Is Our Genome Full of Junk DNA? Part 4
http://www.discovery.org/multi.....-dna-pt-4/
Podcast – Richard Sternberg PhD – On Human Origins: Is Our Genome Full of Junk DNA? Part 5
(emphasis on ENCODE and the loss of the term ‘gene’ as a accurate description in biology and how that loss undermines the modern synthesis of neo-Darwinism)
http://www.discovery.org/multi.....-dna-pt-5/
Biological Information – Not Junk After All 11-29-2014 by Paul Giem – video
https://www.youtube.com/watch?v=xO-7kVBA_JM
In the book “Biological Information: New Perspectives” the chapter entitled “Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information” discusses the various functions of DNA and finds that non-functional DNA is a small minority.
Semi-related: Dr. Giem has a new video uploaded
Overlapping Genetic Codes 12-6-2014 by Paul Giem – video
https://www.youtube.com/watch?v=3WZy0n60_ZU
In the book “Biological Information: New Perspectives” Chapters 6 and 9 (at least) argue that stretches of DNA can have multiple functions encoded into them. We will partially evaluate the strength of the evidence behind that argument.
Easy questions, aren’t they?
🙂
The futile search for the master regulator 🙂
SLT: “When regulators are in turn regulated, what do we mean by “regulate” — and where within the web of regulation can we single out a master controller capable of dictating cellular fates?”
Non-coding DNA has been widely recognised by biologists as having potential function since at least 1971 — before Ohno publicly coined the term “junk DNA”.
Bostock, C. (1971) “Repetitious DNA” Advances in Cell Biology 2: 153-223
Over subsequent decades many, many papers have been written by biologists expanding on this expectation that much “junk” DNA actually had functional activity.
1974 — E. Southern, “Eukaryotic DNA” in MTP International Review of Science, Biochemistry Series One, Volume 6, Biochemistry of Nucleic Acids, (1974) University Park Press, Baltimore. pp. 101 – 139:
1977 — D.M. Skinner, “Satellite DNAs” BioScience 27 (1977) pp. 790-796:
1980 — Orgel & Crick, Nature (284: 604-607), p. 606:
1982 — R. Lewin, “Repeated DNA still in search of a function” Science 217 (1982) pp. 621-623:
AVS:
And that is junk cuz AVS sez so! All science so far! Unguided evolution cannot explain DNA…
A Short History Of The Junk DNA Argument Of Darwinists
Haldane’s Dilemma
Excerpt: Haldane was the first to recognize there was a cost to selection which limited what it realistically could be expected to do. He did not fully realize that his thinking would create major problems for evolutionary theory. He calculated that in man it would take 6 million years to fix just 1,000 mutations (assuming 20 years per generation).,,, Man and chimp differ by at least 150 million nucleotides representing at least 40 million hypothetical mutations (Britten, 2002). So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (40 million divided by 2), yet natural selection could only have selected for 1,000 of those. All the rest would have had to been fixed by random drift – creating millions of nearly-neutral deleterious mutations. This would not just have made us inferior to our chimp-like ancestors – it surely would have killed us. Since Haldane’s dilemma there have been a number of efforts to sweep the problem under the rug, but the problem is still exactly the same. ReMine (1993, 2005) has extensively reviewed the problem, and has analyzed it using an entirely different mathematical formulation – but has obtained identical results.
John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 159-160
Walter ReMine on Haldane’s Dilemma – interview
http://kgov.com/Walter-ReMine-on-Haldanes-Dilemma
Kimura’s Quandary
Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in response to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most ‘evolution’ must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom’s (neo-Darwinism’s) very validity.
John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 161 – 162
A graph featuring ‘Kimura’s Distribution’ being ‘properly used’ is shown in the following video:
Evolution Vs Genetic Entropy – Andy McIntosh – video
https://vimeo.com/91162565
entire video
http://edinburghcreationgroup.org/video/6
The following video provides a detailed refutation of Fisher’s work, from the 1930’s, in population genetics:
Biological Information – Overlapping Codes 10-25-2014 by Paul Giem – video
https://www.youtube.com/watch?v=OytcYD5791k&index=4&list=PLHDSWJBW3DNUUhiC9VwPnhl-ymuObyTWJ
At the 2:45 minute mark of the following video, the mathematical roots of the junk DNA argument, that is still used by many Darwinists, can be traced through Haldane, Kimura, and Ohno’s work in the late 1950’s, 60’s through the early 70’s:
What Is The Genome? It’s Not Junk! – Dr. Robert Carter – video – (Notes in video description)
http://www.metacafe.com/w/8905583
Carter: Why Evolutionists Need Junk DNA – Robert W. Carter – 2009
Excerpt: Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function, but it is something that is required by evolutionary theory. Mathematically, there is too much variation, too much DNA to mutate, and too few generations in which to get it all done. This was the essence of Haldane’s work. Without junk DNA, evolutionary theory cannot currently explain how everything works mathematically. Think about it; in the evolutionary model there have only been 3-6 million years since humans and chimps diverged. With average human generation times of 20-30 years, this gives them only 100,000 to 300,000 generations to fix the millions of mutations that separate humans and chimps. This includes at least 35 million single letter differences, over 90 million base pairs of non-shared DNA, nearly 700 extra genes in humans (about 6% not shared with chimpanzees), and tens of thousands of chromosomal rearrangements. Also, the chimp genome is about 13% larger than that of humans, but mostly due to the heterochromatin that caps the chromosome telomeres. All this has to happen in a very short amount of evolutionary time. They don’t have enough time, even after discounting the functionality of over 95% of the genome–but their position becomes grave if junk DNA turns out to be functional. Every new function found for junk DNA makes the evolutionists’ case that much more difficult.
Robert W. Carter – biologist
http://creation.com/junk-dna-slow-death
Kimura (1968) developed the idea of “Neutral Evolution”. If “Haldane’s Dilemma” is correct, the majority of DNA must be non-functional.
Susumu Ohno, a leader in the field of genetics and evolutionary biology, explained in 1972 in an early study of non-coding DNA that, “they are the remains of nature’s experiments which failed. The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?”
“The chance of acquiring a new function by unrestricted accumulation of mutations, however, should be as small as that of an isolated population emerging triumphant as a new species. Degeneracy is the more likely fate. The creation of every new gene must have been accompanied by many other redundant copies joining the ranks of silent DNA base sequences, and these silent DNA base sequence may now be serving the useful but negative function of spacing those which have succeeded. Triumphs as well as failures of nature’s past experiments appear to be contained in our genome.”
[From, “So much ‘junk’ DNA in our Genome”, Susumu Ohno, 1972]
Sternberg traces how the junk DNA argument developed through the mid 1970’s to the early 80’s and beyond in the following article:
How The Junk DNA Hypothesis Has Changed Since 1980 – Richard Sternberg – October 8, 2009
Excerpt: Two papers appeared back to back in the journal Nature in 1980: “Selfish Genes, the Phenotype Paradigm and Genome Evolution” by W. Ford Doolittle and Carmen Sapienza and “Selfish DNA: The Ultimate Parasite” by Leslie Orgel and Francis Crick. These laid the framework for thinking about nonprotein-coding regions of chromosomes, judging from how they are cited. What these authors effectively did was advance Dawkins’s 1976 selfish gene idea in such a way that all the genomic DNA evidence available up to that time could be accounted for by a plausible scenario. The thesis presented in both articles is that the only specific function of the vast bulk of “nonspecific” sequences, especially repetitive elements such as transposons, is to replicate themselves — this is the consequence of natural selection operating within genomes, beneath the radar of the cell. These junk sequences, it was postulated, can duplicate and disperse throughout chromosomes because they have little or no effect on the phenotype, save for the occasional mutation that results from their mobility.
http://www.evolutionnews.org/2.....26421.html
Biologists are racking their brains trying to think what useful task this apparently surplus DNA is doing. But from the point of view of the selfish genes themselves, there is no paradox. The true “purpose” of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.
…. “creationists…might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.”
Richard Dawkins – Selfish Gene (mid 1970’s)
http://www.uncommondescent.com.....ent-374475
Selfish DNA: the ultimate parasite. Orgel LE, Crick FH. – 1980
The DNA of higher organisms usually falls into two classes, one specific and the other comparatively nonspecific. It seems plausible that most of the latter originates by the spreading of sequences which had little or no effect on the phenotype.
http://www.ncbi.nlm.nih.gov/pubmed/7366731
Dr. Wells gives some historical background as to why some neo-Darwinists are doing everything they can to discredit the recent (Sept. 2012) ENCODE findings:
Why All the Fuss Over Some Junk? – Jonathan Wells – September 25, 2012
Excerpt: Some historical context might help. After James Watson and Francis Crick discovered the molecular structure of DNA in 1953, Crick announced that they had found “the secret of life,” a popular formulation of which became “DNA makes RNA makes protein makes us.” But biologists discovered that about 98% of our DNA does not code for protein, and in 1972 Susumu Ohno and David Comings independently used the term “junk” to refer to non-protein-coding DNA (though neither man excluded the possibility that some of it might turn out to be functional).
Why didn’t biologists simply call non-protein-coding sequences “DNA of unknown function” rather than “junk DNA?” For some, it was because “junk DNA” seemed more suited to the defense of Darwinism and survival of the fittest. In 1976, Richard Dawkins wrote in The Selfish Gene that “the true ‘purpose’ of DNA is to survive, no more and no less. The simplest way to explain the surplus [i.e., non-protein-coding] DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.”
In 1980, W. Ford Doolittle and Carmen Sapienza wrote in Nature (284:601) that many organisms contain “DNAs whose only ‘function’ is survival within genomes,” and that “the search for other explanations may prove, if not intellectually sterile, ultimately futile.” In the same issue of Nature (284:604), Leslie Orgel and Francis Crick wrote that “much DNA in higher organisms is little better than junk,” and its accumulation in the course of evolution “can be compared to the spread of a not-too-harmful parasite within its host.” Since it is unlikely that such DNA has a function, Orgel and Crick concluded, “it would be folly in such cases to hunt obsessively for one.”
Two biologists then wrote to Nature (285:617,618) expressing their disagreement. Thomas Cavalier-Smith considered it “premature” to dismiss non-protein-coding DNA as junk, and Gabriel Dover wrote that “we should not abandon all hope of arriving at an understanding of the manner in which some sequences might affect the biology of organisms in completely novel and somewhat unconventional ways.” Cavalier-Smith and Dover were not criticizing evolutionary theory; they were merely questioning the claim that non-protein-coding DNA is non-functional.
After the rise of intelligent design (ID) in the 1990s, “junk DNA” became a favorite weapon against ID in the hands of some Darwinists, including Richard Dawkins and the four bloggers mentioned above. According to ID, it is possible to infer from evidence in nature that some features of the world, including some features of living things, are explained better by an intelligent cause than by unguided natural processes. The Darwinists’ argument was that an intelligent designer would not have filled our genomes with so much junk, but that it could have accumulated as an accidental by-product of unguided evolution. In 2004, Dawkins wrote in A Devil’s Chaplain that much of our genome “consists of multiple copies of junk, ‘tandem repeats,’ and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself.” Dawkins suggested that creationists (among whom he included ID advocates) “might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.”
Dawkins continued to rely on junk DNA in his 2009 book The Greatest Show on Earth: The Evidence for Evolution. “It is a remarkable fact,” he wrote, “that the greater part (95 per cent in the case of humans) of the genome might as well not be there, for all the difference it makes.” In particular, pseudogenes “are genes that once did something useful but have now been sidelined and are never transcribed or translated.” Dawkins concluded: “What pseudogenes are useful for is embarrassing creationists. It stretches even their creative ingenuity to make up a convincing reason why an intelligent designer should have created a pseudogene… unless he was deliberately setting out to fool us.”
But if most of our DNA is functional, as the ENCODE results suggest, then the “junk DNA” argument against ID collapses.
So the four bloggers listed above are doing everything they can to discredit the ENCODE project’s estimate of functional DNA. Yet whatever the estimate may currently be, it is certain to increase with further research. In 2007, the ENCODE pilot project reported on the basis of about 200 datasets that our DNA is “pervasively transcribed,” suggesting functionality. The 2012 results, based on 1,640 datasets, documented that “the vast majority (80.4%) of the human genome” is biochemically functional in at least one cell type. But ENCODE has so far sampled only a fraction of the cell types in the human body.
Clearly, we have a lot more to learn about our genome — but not if we start by assuming that most of it is junk.
http://www.evolutionnews.org/2.....64721.html
In 1994, the authoritative textbook, Molecular Biology of the Cell, co-authored by National Academy of Sciences president Bruce Alberts, suggested (incorrectly!) that introns are “largely genetic ‘junk'”: Unlike the sequence of an exon, the exact nucleotide sequence of an intron seems to be unimportant. Thus introns have accumulated mutations rapidly during evolution, and it is often possible to alter most of an intron’s nucleotide sequence without greatly affecting gene function. This has led to the suggestion that intron sequences have no function at all and are largely genetic “junk”
Soon thereafter, the 1995 edition of Voet & Voet’s Biochemistry textbook explained that “a possibility that must be seriously entertained is that much repetitive DNA serves no useful purpose whatever for its host. Rather, it is selfish or junk DNA, a molecular parasite that, over many generations, has disseminated itself throughout the genome…”
Will Darwinists try to Rewrite the History of Junk-DNA?
In 1996, leading origin of life theorist Christian de Duve wrote: “The simplest way to explain the surplus DNA is to suppose that it is a parasite or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.” (Richard Dawkins makes similar pronouncements that DNA is junk in an article after 1998)
http://www.evolutionnews.org/2.....ull_a.html
Another leading biologist, Sydney Brenner argued in a biology journal in 1998 that:
“The excess DNA in our genomes is junk, and it is there because it is harmless, as well as being useless, and because the molecular processes generating extra DNA outpace those getting rid of it.”
The Unseen Genome, Gems Among the Junk:
“I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century,” Mattick says. “The failure to recognize the full implications of this—particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules—may well go down as one of the biggest mistakes in the history of molecular biology.” (John S. Mattick Scientific American (November, 2003)
http://www.evolutionnews.org/
Casey Luskin response to Farrel – several quotes from Jonathan Wells book – ‘The Myth of Junk DNA’ – May 2011
http://blogs.forbes.com/johnfa.....omment-153
Jonathan Wells on his book, The Myth of Junk DNA – yes, it is a Darwinist myth and he nails it as such – March 2011
Excerpt: Some people revise history by claiming that no mainstream biologists ever regarded non-protein-coding DNA as “junk.”
This claim is easily disproved: Francis Crick and Leslie Orgel published an article in Nature in 1980 (284: 604-607) arguing that such DNA “is little better than junk,” and “it would be folly in such cases to hunt obsessively” for functions in it. Since then, Brown University biologist Kenneth R. Miller, Oxford University biologist Richard Dawkins, University of Chicago biologist Jerry A. Coyne, and University of California–Irvine biologist John C. Avise have all argued that most of our DNA is junk, and that this provides evidence for Darwinian evolution and against intelligent design. National Institutes of Health director Francis Collins argued similarly in his widely read 2006 book The Language of God.
It is true that some biologists (such as Thomas Cavalier-Smith and Gabriel Dover) have long been skeptical of “junk DNA” claims, but probably a majority of biologists since 1980 have gone along with the myth. The revisionists are misinformed (or misinforming).
http://www.uncommondescent.com.....more-18154
Dawkins, 2009: on “junkDNA”
“Junk DNA is just what a Darwinist would expect,”
Dawkins, 2012: on non-junkDNA (after ENCODE)…
“”junk DNA” isn’t junk at all but is instead “exactly what a Darwinist would hope for,”
http://www.evolutionnews.org/2.....64521.html
Richard Dawkins ENCODE 2013 “Junk DNA” – video
http://www.youtube.com/watch?f.....pRB0#t=94s
As some of the outstanding questions get answered, new questions pop up. Kind of like a never-ending story… like the Energizer bunny, which keeps going and going…
🙂
@4 gpuccio
That’s a very wise advice. However, unfortunately some interlocutors won’t heed it. 🙁
On a related note, here’s an interesting comment posted by gpuccio in another thread (post # 805):
http://www.uncommondescent.com.....ent-535236
@5 awstar
Well, perhaps within a hypothetical ‘multiverse’ context that event took place already?
🙂
@10 Box
Interesting observation indeed. Thank you.
Perhaps it would make sense that some parts of the DNA have no beneficial functions, because through history our biological components have been exposed to hostile conditions and processes that could have messed up many parts of the system.
But jumping into conclusions prematurely is not prudent.
Researchers work hard trying to figure out how things work and what they do.
Dionisio: Researchers work hard trying to figure out how things work and what they do.
And nearly all of those hard workers in biology support evolutionary theory. In any case, one way to determine whether a sequence is neutral or not is to look at its history. If it is not under selection, then it will drift at a known rate.
I bet they cannot reference this alleged theory.
@21 Zachriel
How do you know what nearly all of them really support?
FYI – The serious ones don’t have time to squander on the type of discussions we see here and in other blogs out there.
They have challenging issues to resolve.
The Polish, Scandinavian and Spanish scientists I know personally are serious biologists who don’t seem to care much about any evolutionary theory, because they are working (sometimes outside their original countries) on leading-edge biomedical research in order to understand and find cures for diseases that affect many people. They analyze the current system in front of them, using the available technology and information, in order to answer many questions they have. At least that’s the impression I got when I spoke to them and they told me about the work they do. I don’t recall them making any reference to any evolutionary theory at all. Obviously when they explained their work to me, they knew they had to make their explanation understandable to an ignorant like me. 🙂
However, in some occasions they humbly admitted to not knowing where to find the answers to some of my questions.
BTW, in my professional field, software development, I don’t recall ever meeting anyone who would say they don’t know where to find the answers to any serious questions related to the given profession. All the answers are written somewhere out there. Perhaps some of the proprietary information is confidential, hence unavailable to some of us, but it is there.
My biologist friends confessed that the answers to some fundamental questions in their profession aren’t known to anyone yet. That’s why they have to work so hard.
BTW, those friends and I may not be necessarily on the same page regarding worldview positions. Actually, probably we are pretty far apart in some philosophical/theological areas. But those differences did not hinder our friendly conversations.
🙂
No one ever claimed that there was any such thing as junk DNA.
AVS @3:
Wishful thinking by mental midgets.
Premature? It’s just plain stupid. How much do you want to bet that junk DNA is a superstitious Darwinist myth through and through. There never was such a thing. It’s in the same category as “random mutations”, the flat earth hypothesis and the tooth fairy.
have not been as extensively studied?
Why?
Mung 24
Evolutionists predict that whatever they say about DNA will be fully correct until or unless they say something different about it in the future.
@24 Mung
Well, the concept seems related to the biblical claim of the spiritual fall of mankind at the beginning of human history and the mess that followed, hence maybe the name was coined by some religious people to prove their case? 🙂
@25 Mapou
Well, my children claim that they had tangible evidences that the tooth fairy was real. 🙂
Is most of the genome functional, or is biological function restricted to tiny islands of sequence space?
Given how mutations we each have it can’t be both.
Dionisio: My biologist friends confessed that the answers to some fundamental questions in their profession aren’t known to anyone yet. That’s why they have to work so hard.
Your biologists friends, who may work in tangentially related fields, who didn’t even express an opinion, is your authoritative source?
Dionisio: BTW, in my professional field, software development, I don’t recall ever meeting anyone who would say they don’t know where to find the answers to any serious questions related to the given profession.
That’s the difference between engineering and science. Engineers apply existing knowledge. Scientists extend it.
@31 Zachriel
authoritative source of what?
Dionisio: authoritative source of what?
You noted the many hardworking biologists. We pointed out that nearly all of those hardworking biologists support evolutionary theory. For some reason, you then brought up your biologist friends, who haven’t expressed an opinion on the subject.
@31 Zachriel
What do you mean by “Scientists extend it“?
Can you provide an example as illustration?
How does that relate to what I wrote?
Dionisio: What do you mean by “Scientists extend it“?
Engineers apply known science. Scientists work on the edges of knowledge in order to increase the sphere of what is known.
Dionisio: Can you provide an example as illustration?
Darwin’s studies when he circumnavigated the globe. Shubin’s adventures in the Canadian Arctic. Taking close-up pictures of a comet. Lenski’s E. coli long-term evolution experiment.
Dionisio: How does that relate to what I wrote?
Dionisio: BTW, in my professional field, software development, I don’t recall ever meeting anyone who would say they don’t know where to find the answers to any serious questions related to the given profession.
Software development is a field within engineering. Nothing wrong with that, but the purpose of engineering isn’t to extend human knowledge, but to apply what is already known. They’re professional interest isn’t in finding unanswered scientific questions.
@33 Zachriel
Well, first, I don’t recall seeing your answer to my question in post #23:
How do you know what nearly all of them really support?
Second, why did you write “We” instead of “I” in the above quoted sentence that starts “We pointed out that…”?
Third, how do you know that my friends haven’t expressed an opinion on the subject?
Dionisio: How do you know what nearly all of them really support?
We could start with scientists named Steve.
http://ncse.com/taking-action/project-steve
Dionisio: how do you know that my friends haven’t expressed an opinion on the subject?
Dionisio: I don’t recall them making any reference to any evolutionary theory at all.
@35 Zachriel
They’re?
Did you mean Their?
@37 Zachriel
When I asked them directly to explain how we humans and the rest of the living creatures we see around got here, they humbly admitted they don’t have any coherent comprehensive explanation.
Most probably you and your comrades would have answered very differently, but that’s expected.
BTW, humility is a rare virtue, very much appreciated in many circles, including scientific ones. It may go along with honesty and courage too.
🙂
Dionisio: When I asked them directly to explain how we humans and the rest of the living creatures we see around got here, they humbly admitted they don’t have any coherent comprehensive explanation.
That’s not what you indicated above. What are their specialties, by the way?
We’d be happy to look at their published research debunking evolutionary theory. If they just mean there are unanswered questions, then sure, there are plenty of unanswered questions when determining historical events.
@37 Zachriel
What is that web site supposed to tell me?
Dionisio,
The first paragraph describes it pretty well — it’s a response to a particularly silly creationist gambit.
If you want something less tongue in cheek, then ~97% of scientists agree that humans evolved, 87% that we did so “due to natural processes”
We have to see this alleged evolutionary theory first. Darwin’s contribution, natural selection, has proven to be impotent and nothing else has been offered as a materialistic alternative. So what is there to debunk?
Ah yes. The experiment that demonstrates the severe limits of evolutionary change. That is some great evidence that unguided evolution cannot get past prokaryotes given starting populations of prokaryotes. Not sure why you brought that up.
As for Shubin if the tetrapod tracks that were found in Poland were found before Shubin started planning his trip, according to him he wouldn’t have gone to where he found Tiktaalik. Either that or Tiktaalik would have been dated to 400+ million years ago…
wd400- Is science done via consensus or evidence? You can have all of the scientists and it wouldn’t give you any supporting evidence for evolutionism.
Obviously, evolutionary science is now done by consensus, however it’s not a simplistic democratic vote, but rather a carefully managed process by the de facto elite in the field, who carefully fit any new discoveries into the continually evolving theory of evolution—a very demanding process that requires the best minds in science!
However, there’s an evolving grass roots movement that asserts that what was formerly considered junk DNA, is actually junk after all! Here’s why this is necessary.
Firstly, according to Dr. Ohno, the presence of “junk” DNA is actually evidence for evolution. That non-coding DNA is actually a “fossil record” of evolution, thus vital for the theory.
Secondly, if all DNA were functional, then any mutations would most likely be deleterious. You need non-coding DNA to serve both as a scratch pad and a buffer against excessive changes.
This proves that a significant portion of DNA must undeniably be junk, regardless of apparent evidence to the contrary.
😉
-Q
@33 Zachriel
why did you write “We” instead of “I” in the above quoted sentence?
Are you one person or a group of people?
That’s not why junk DNA exist, because mutation rates are pre-site and not per-replication you can’t have a “scratch pad”. But the fact we have ~50 mutations but are not dead is strong evidence that much of our genomes are junk. The other possibility is that biological function are easy to come by in sequence space.
@40 Zachriel
Do you have reading comprehension problems?
Where did I write that they debunked any theory?
Dionisio to Zacky:
He’s been doing this for a while. It’s an “us vs. them” thing for Zacky.
Dionisio, to Zachriel:
I explained that to tjguy on another thread:
@40 Zachriel
What historical events are you talking about?
My questions were about biology, not history. I simply requested a description of any hypothetical processes that could have brought us here. Signaling pathways, regulatory networks and the whole nine yard. That’s all, buddy. Leave history alone. Think pure science. Just biochemistry, biology, physics. They couldn’t provide any or point to any document that could explain it. They just claimed that’s not their area of interest. They work on stem cell research, etc. No time for entertainment or speculative discussions. Got it now?
“My questions were about biology, not history. I simply requested a description of any hypothetical processes that could have brought us here.”
Oh, Dio. You’ve never heard of “natural history” have you?
@33 Zachriel
why did you write “We” instead of “I” in the above quoted sentence?
Are you one person or a group of people?
@40 Zachriel
What historical events are you talking about?
My questions were about biology, not history. I simply requested a description of any hypothetical processes that could have brought us here. Signaling pathways, regulatory networks and the whole nine yard. That’s all, buddy. Leave history alone. Think pure science. Just biochemistry, biology, physics. They couldn’t provide any or point to any document that could explain it. They just claimed that’s not their area of interest. They work on stem cell research, etc. No time for entertainment or speculative discussions. Got it now?
Zachriel
Apparently your comrades and fellow travelers have come to give you a hand (@42, 50, 52).
Now I understand why you wrote ‘we’ in lieu of ‘I’.
Ciao!
🙂
Zachriel @40
What historical events are you talking about?
My questions were about biology, not history. I simply requested a description of any hypothetical processes that could have brought us here. Signaling pathways, regulatory networks and the whole nine yard. That’s all, buddy. Leave history alone. Think pure science. Just biochemistry, biology, physics. They couldn’t provide any or point to any document that could explain it. They just claimed that’s not their area of interest. They work on stem cell research, etc. No time for entertainment or speculative discussions. Got it now?
Read this a few weeks ago and thought I would share as it is on topic:
No junk: Long RNA mimics DNA, restrains hormone responses
Excerpt:
“Unlike many genes scientists are familiar with, GAS5 does not encode a protein. It gets transcribed into RNA, like other genes, but with GAS5 the RNA is what’s important, not the protein. The RNA accumulates in cells subjected to stress and soaks up steroid hormone receptors, preventing them from binding DNA and turning genes on and off.”
Also:
“There are thousands of long non-coding RNAs that play critical roles in gene regulation, and little data to tell us how they are functioning or where they came from,” says lead author graduate student Will Hudson. “We took a deep dive into looking at the interaction of the Gas5 RNA with steroid hormone receptors, and we think this work may serve as a model to understand how lincRNAs interact with other proteins.”
Interesting stuff.
@57 bw
Agree, it is very interesting. Thank you for sharing it here.
Querius: Obviously, evolutionary science is now done by consensus …
No, but Dionisio brought up hardworking scientists, so we thought he considered them a valid authority.
Dionisio: Where did I write that they debunked any theory?
So your scientific friends didn’t express an opinion on evolution, it’s not their area of expertise, but did say there are unanswered questions. Sounds reasonable. Not sure why you brought it up.
Dionisio: What historical events are you talking about?
Turns out that there has been life on Earth for billions of years, and life today is not like life of yesteryears.
http://static.guim.co.uk/sys-i.....il-001.jpg
Dionisio: I simply requested a description of any hypothetical processes that could have brought us here.
That’s an historical question, obviously. The basic process is branching descent with modification. Adaptation is guided by natural selection.
wd400,
You ask some decent questions regarding mutations in our DNA, but the questions are based on an invalid premise – that our DNA is not designed, and especially not superlatively designed.
First of all, consider the relative amount of mutation before stuff breaks, not the absolute. While there may be a large number of mutations in every person’s DNA, as a percentage of the DNA the number is pretty small – smaller than, say, the % difference between a human and a chimp (wink). And we know that this (tiny) percentage of mutations IS damaging – hence the well-known deleterious impacts of in-breeding, for example. Or the many known damaging defects of chromosomal mutations. To your point – if so much of our DNA is junk, why does it take so little mutation (relatively) to cause bad things? The fairly obvious logical conclusion is that our DNA isn’t mostly junk.
So, if we thus assume that the clear majority of our genome is functional in some manner, how can we have so many mutations (numerically) without obvious deleterious effects? If we take the approach of assuming the DNA is designed, there are some pretty simple possibilities:
1) Some sections are not always “On”/Used. We know that some areas of DNA are only active under certain environmental stimuli. If mutations occur in a section of code that is not “mission-critical” to daily operation, it may not present itself as damaging. By analogy, think of a congenital heart defect that only causes problems in professional athletes.
2) Over-design. Using the same congenital heart-defect analogy – if the DNA was designed to be robust in its production, genetic defects can be “hidden” by the excess or “safeties” built in to the final product. Many people are unaware that one of their two bilateral organs is “defective” for most/all of their lives.
3) Redundant Systems. Staying with the bilateral organ example – if we assume designed DNA, it is very likely that redundancy is built in to the DNA. Experiments with eyeless fruit-flies suggest that they can re-gain sight over multiple generations of interbreeding – in turn suggesting that there is some kind of “eye backup” built in to fruit-fly DNA that can fix a busted eye gene. Consider that your DNA may be like a RAID array – multiple mutations across redundant data only causes issues when it shows up in both copies (another reason not to in-breed!)
Personally – if someone told me that even just 2% of my DNA was “non-functional” or “neutral” mutations, and offered to excise that portion for me? I’d pass.
drc466,
If every base is functional, then it absolutely is the absolute number that matters.
We know some mutations are damaging, but most of us aren’t dead. If we each had 50 mutations in a genome completely full of function it’s hard to see how we could survive. (FWIW, using 50 mutations as a rough number we end up with 50 mutations * 3% protein-coding * 3/4 non-synonymous ~ 1 protein-coding mutation per live birth).
All of your proposed work-arounds require some sort of redundancy to shield mutated sequences from the effects of their mutation. But that doesn’t work. Being sheilded from the effects of mutation means those sequences are shielded from purifying selection, the mutations they accrue will gradually spread through the population and the “back up” will no longer work.
I would be surprised if more than about 20% of genome was functional at the sequence level.
wd400:
“I would be surprised if more than about 20% of genome was functional at the sequence level.”
You will be surprised.
“We know some mutations are damaging, but most of us aren’t dead. If we each had 50 mutations in a genome completely full of function it’s hard to see how we could survive.”
Why? Only rarely functional mutations are incompatible with life, even in protein coding genes.
And you always avoid the problem that there is functional diversity. All humans are not the same, We are not the same as chimps. And so on.
Life and death are not the only things in the game.
Why? Only rarely functional mutations are incompatible with life, even in protein coding genes.
Then why is there so little diversity in protein-coding sequences compared with introns?
And you always avoid the problem that there is functional diversity. All humans are not the same, We are not the same as chimps. And so on.
Yeah, so the only way out for non-junkers is to claim that biological functions are not restricted to small islands of sequence space. But that’s not exactly the standard ID/Creationist position…
I would be surprised if any of DNA was functional.
wd400:
“Yeah, so the only way out for non-junkers is to claim that biological functions are not restricted to small islands of sequence space. But that’s not exactly the standard ID/Creationist position…”
It seems that you are the only one to see that point. Functional islands are small and rare. That does not mean that they cannot present engineered variation, or that they cannot be rather robust to limited random error.
Synonymous mutations are neutral in protein coding genes. What is the reason for that neutrality? The redundancy of the genetic code, a specific property of the coding sequences. If we did not understand the way that genes code for proteins, we would not understand why synonymous mutations are well tolerated in that kind of sequence.
In the same way, if we do not understand the functional role of non coding genes, we cannot understand what kind of variation they can tolerate, or not tolerate.
And we cannot understand what kind of variation is functionally engineered to provide functional diversity.
Diversity can in itself be a functional goal. We have many examples of that in human engineering and in human creations, including art.
But we’d see very clearly that some positions could chagne, and others were conserved, within populations and between spcies. There is no such conservation, within or between, for the vast majority of human genome. If those bases are functional, then function must be very easy to come by because it looks like any old sequence will do it.
wd400:
Evolutionarily Conserved Noncoding DNA
http://www.els.net/WileyCDA/El.....06126.html
Abstract:
Just an example of a recent approach.
wd400:
From the above paper, about repeats:
Evolutionary conservred non-coding DNA adds up to less than 10% of the genome. Repeats get co-opted into functional sequences of course, but they weren’t functional before they copied themselves into the new structure.
wd400:
“Repeats get co-opted into functional sequences of course, but they weren’t functional before they copied themselves into the new structure.”
Unless their function was exactly to help generating the new functional structures.
drc466:
Ha! Ain’t that the truth! I’ll just hang onto my “junk” DNA if it’s all the same to you.
Unless their function was exactly to help generating the new functional structures.
And we are back to the fact you can’t maintain something for future use without having it be subject to the deleterious effects of mutation. Unless you think mutations are directed, in which case you have a fresh set of evidence against you.
wd400, just what do you think the function of DNA consists of? What does it do?
I don’t understand the question Mung — are you quibbling about a precise meaning or do have a substantive point to make?
Oh don’t all of a sudden be coy now wd400. You’re the one who is making the argument.
wd400 @ 30:
By “most of the genome” do you mean DNA? Will it help you if I ask you “what is the function of the genome”?
What if the question you pose is a false dichotomy?
wd400 @ 30:
Sure it can.
wd400 @ 47:
Well there you have it. You’re talking about DNA. When you say DNA you mean genome and when you say genome you mean DNA. So why is it so hard to understand what I asked?
wd400 @ 47:
Or you could be equivocating and presenting a false dichotomy.
wd400 @ 61:
Every base in DNA? What is the “function” of a base in DNA?
wd400 @ 61:
A genome “completely full of function”? What does that even mean?
wd400 @ 63:
Again I ask you, what is the biological function of DNA? What’s so difficult about that? It seems to comprise a large part of your argument, so you must know what you’re talking about.
wd400 @ 66:
What is the function of a base in DNA?
wd400 @ 69:
See, you’re talking about DNA. And equating it with the genome. DNA which is composed ob sequences of bases. the function of which, or lack thereof, is crucial to your argument.
So again I ask, what is the function that you’re referring to? If you can’t say, then you really don’t have an argument.
So you don’t understand the question and I don’t understand how you can not understand the question.
All through this thread you’ve been making an argument about DNA/GENOME/BASES and their FUNCTION. So I ask what is their function. Does that help?
wd400 @ 74:
Am I quibbling about a precise meaning of function? Hardly.
Let me try again.
You claim the genome/DNA/a base [as far as I can tell you you use these terms interchangeably in this thread] have or do not have a function. For those that have a function, what is their function? For those that do not, what function do they lack?
Your argument is that this as yet unidentified and unspecified function is easily found.
What does it even mean to say that a base is functional or to deny that a base is functional? When you say that function must be easy to come by what do you mean?
It’s your argument. When you say FUNCTION what do you mean?
Different parts of the functional subset of our DNA have different functions. For instance, a ribosomal RNA forms part of the ribosome, and thus facilitates the expression of protein-coding genes.
Typically, we consider “functional sequences” to be those that contribute to some part of the organism’s normal activities. A 50 million year old broken transposon almost certainly doesn’t do that, a ribosomal RNA does.
Before you embark on some philosophical exploration of the word “function”, I’d remind you any argument as the the amount of junk DNA requires a definition of biological funciotn.