Jul 18 2017

More on Junk DNA

Junk-VennJunk DNA, put simply, is those parts of the genome (human or otherwise) that have no known function. The human genome has about 19,000 genes. A gene is essentially a sequence of base pairs that code for a protein – there are four difference bases with each triplet being a “word” that either codes for an amino acid or tells the process of transcribing the protein to stop.

Even within genes there are noncoding regions, called introns, which have to be removed from the RNA so that the coding regions can be joined together. Between the genes there are also vast non-coding regions. Some of this non-coding DNA is regulatory and structural – it helps regulate when and how much specific genes are transcribed into proteins.

The burning question is, how much of the non-coding regions between the genes serves any function and how much is completely unnecessary, or “junk”? This is an important question for understanding genetics, but also has implication for creationists. Creationists don’t like the concept of junk DNA because it strongly implies an evolutionary history. Why would a designer sloppily insert so much unneeded junk into our pristine genome? Why are genes clogged with non-coding regions that need to be removed? So they claim that all DNA has function, we just don’t know what it is.

ID proponent Stephen Meyer, for example, said:

“For example, we predicted very early on that the junk DNA was not junk. We did that on the basis of an ID perspective. “

There have been two basic approaches to the question of junk DNA. The first can be characterized as an argument from exclusion. If we don’t know what part of the genome does, we conclude that it probably has no function. But we recognize that these parts of the genome have no known function, and therefore as new discoveries are made some of these parts may flip from unknown to known. Therefore the percentage of the genome that is junk is likely to shrink over time. This doesn’t mean, of course, that it will necessarily shrink to zero.

The second strategy is to look for evidence from which we can reasonably infer that a part of the genome is functional or not. For example, some stretches of DNA appear to be viral DNA that was inserted into the genome, and then became nonfunction through mutations. It is hard to imagine what purpose these viral inclusions serve. Other sections of DNA appear to be copies of known genes that also have mutated and become noncoding, so-called “pseudogenes.” There are also stretches of DNA that are monotonous repeats.

You can further look at DNA to see how often it mutates. Mutations in function DNA has a chance of causing problems, and therefore such mutations are selected against. The more critical the exact structure of a protein is, then the fewer mutations it will accrue over time. Such proteins are said to be highly conserved. This is because any mutation is likely to be fatal. Other proteins can tolerate some mutations.

We also know what the average background mutation rate is. Therefore, if a section of DNA were truly junk, and the sequence of base pairs was of no functional importance, then that region of the DNA should experience the full background mutation rate without any negative selective pressure. Functional parts of the DNA will have less than the full background mutation rate, to whatever extent they are conserved. Using this kind of analysis it seems that at most 20% of our genome is functional – or at least has a function which depends on the genetic sequence.

There is also the ENCODE project which looked at a different piece of information. They analyzed which parts of the human genome are ever transcribed or have regulatory segments bind to them. In other words, they looked for evidence of any activity on the genome. They concluded from their analysis that 80% of the genome is functional. Creationists interestingly celebrated, even though this still left 20% of the genome as junk.

But the conclusions of the ENCODE authors have been soundly criticized. The kinds of activity they found could easily be incidental, and not functional. So they did not demonstrate that 80% of the genome is actually functional.

Currently the consensus is that between 10 and 20% of the human genome is functional, and the rest is junk. Junk does not mean completely inactive. It also does not mean that evolution will not by chance use some of it as raw material. It just means we could live without it, and it is not currently serving any real function.

There is yet another way to approach the question of how much of our genome is junk, called “genetic load.”  Essentially you can calculate how many functional mutations there should be in an individual (developmental load) and over evolutionary time (phylogenetic load).

Evolutionary biologist Dan Graur just published a recent estimate of developmental load, the number of mutations that could be tolerated with each child born, given the known rate of background mutations. He did this in a new way – calculating what the birth rate would have to be in order to maintain population size given the death rate from deleterious mutations. That death rate is determined by the mutation rate and the size of the vulnerable genome. He compared this to historical birth rates and population growth.

From that he calculates that the size of the functional genome is between 10-15% with an upper limit of 25%. This depends on what you accept as the mutation rate, but he considered the range of estimates in his calculation. For example:

“For 80 percent of the human genome to be functional, each couple in the world would have to beget on average 15 children and all but two would have to die or fail to reproduce,” he wrote. “If we use the upper bound for the deleterious mutation rate (2 × 10−8 mutations per nucleotide per generation), then … the number of children that each couple would have to have to maintain a constant population size would exceed the number of stars in the visible universe by ten orders of magnitude.”

This is an interesting line of evidence, and certainly needs to be accounted for, but there are a lot of assumptions and therefore potential for adjustments based on unknown factors. I do think he has convincingly argued that the percentage of the genome that is junk is high, and is almost certainly not zero.

The implications of this, and pretty much all of genetics, is clear – life evolved. The fingerprints of evolutionary history are clearly left behind in all genomes. The molecular evidence for common descent is, in my opinion, an undeniable slam dunk. That does not prevent creationists from denying it, however, with clearly forced intellectual squirming.

 

 

63 responses so far

63 Responses to “More on Junk DNA”

  1. Nidwinon 18 Jul 2017 at 8:33 am

    It’s probably just a matter of time before the pseudos come up with an evidence based therapy of their own, to unlock the use of the remaining 85-75% of junk DNA to heal, proof that goddidit and that psy-chi(ki)-prana is real but you just need to convert a high enough % of junk DNA in chi positive energy inside your body and aura.

    Sorry but …

  2. BillyJoe7on 18 Jul 2017 at 8:56 am

    “It is hard to imagine what purpose these viral inclusions serve”

    They can serve as memories of previous viral invaders – in the somatic cells of the immune system (enabling it to rapidly respond to a fresh attack) but obviously not in germline cells.

  3. BenEon 18 Jul 2017 at 11:07 am

    “It is hard to imagine what purpose these viral inclusions serve”

    The purpose of these viral inclusions seems obvious if you change the perspective from the human to the virus. The viral code got there because the virus put it there in order to hijack an organism to produce more virus.

    I have a scar on my hand that serves me no purpose. It got there because a cat evolved claws, and said cat purposefully wanted my child self to stop messing with it.

  4. hardnoseon 18 Jul 2017 at 1:33 pm

    You equated ID theorists with creationists, even though ID theorists BELIEVE IN EVOLUTION.

    And there is absolutely no reason to assume any DNA is junk, just because NO ONE KNOWS what it does.

    And junk DNA has nothing to do with evidence for or against evolution.

    How many logical errors can be squeezed into one blog post?

  5. goldmund52on 18 Jul 2017 at 1:36 pm

    Eugene Koonin’s The Logic of Chance* is very good on this topic of junk DNA (and simply a must read on evolution big picture, modern synthesis, natural selection, etc, IMO.) Eukaryotes are a special case because of the elimination of Horizontal Gene Transfer (HGT) and a relatively smaller effective population size (Ne). A couple of quotes:

    “The near elimination of HGT also provides an evolutionary incentive for the extensive gene duplication that is the primary route of innovation in eukaryotes ( Lespinet , et al . , 2002 ) . The population bottleneck caused by the propagation of endosymbionts allowed an explosion of duplications during the stem phase ( Makarova , et al . , 2005 ; see also Chapter 8 ) , but more generally , duplication substitutes for HGT as the main source of novelty throughout the evolution of eukaryotes .”

    “The necessary and possibly sufficient condition for the emergence of complexity was the inefficient purifying selection in populations with small Ne . The inefficient selection provided for the fixation of slightly deleterious features that, in larger populations, would have been eliminated, and for accumulation of junk, some of which was then recruited for diverse functions.”

    *Koonin, Eugene V.. The Logic of Chance: The Nature and Origin of Biological Evolution (FT Press Science) (Kindle Locations 3520-3524). Pearson Education. Kindle Edition.

  6. Steven Novellaon 18 Jul 2017 at 1:52 pm

    HN – the errors are all yours. There is overlap between creationists and ID proponents. You cannot make the blanket statement that ID proponents believe in evolution. You are just demonstrating your stubborn ignorance with that statement.

    While there are many different types of creationism, they common share a belief in a designer, which is also the central point of ID. The commonality of a belief in a designer is the feature relevant to this article.

    I quoted an ID proponent who predicts, based on ID, that junk DNA should not exist. So how can you say junk DNA has nothing to do with this issue. I know they also make claims that are separate from this, but that is irrelevant.

    And, geneticists are beyond assuming DNA is junk simply because we don’t know what it does. I laid out the reasons in this article, which you either didn’t read or didn’t understand, apparently. Nothing new.

  7. BenEon 18 Jul 2017 at 2:12 pm

    “You equated ID theorists with creationists, even though ID theorists BELIEVE IN EVOLUTION.”

    No they don’t. Evolution is the process by which organisms change over time due to genetic mutation and natural selection from a common ancestor.

    What ID religionists believe is that they have a soul and are immortal. What ID religionists deny is the evolution produced us. It’s pretty simple why. You can’t have a soul and its associated immortality otherwise. Souls can’t evolve. What, did some ape get 1% of a soul, then the next generation 2% of a soul, with each successive generation having a larger percentage of it appearing in either heaven or hell? Or did it all happen at once, with some non-souled ape mom raising a fully souled human child having all the pieces needed for immortality? And then who did this individual breed with? This whole paragraph demonstrates the absurdity of discussions attempting to reconcile evolution with the concept of a soul.

    Frankly, protecting that concept of personal immortality is the subconscious barrier that keeps most people from truly understanding evolution and its implications.

  8. hardnoseon 18 Jul 2017 at 3:33 pm

    “Evolution is the process by which organisms change over time due to genetic mutation and natural selection from a common ancestor.”

    NO YOU ARE WRONG. Evolution is known to occur but NO ONE KNOWS how or why it occurs. What you described is a materialist myth, that has no evidence.

    There is evidence for natural selection, and for evolution. There is NO EVIDENCE that evolution is “due to genetic mutation and natural selection.”

  9. BenEon 18 Jul 2017 at 4:02 pm

    [ There is NO EVIDENCE that evolution is “due to genetic mutation and natural selection.” ]

    LOL. What next?

    I suppose there is zero evidence that DNA contains a molecular blueprint for the construction of the human body.

    Also zero evidence that DNA mutates.

    And zero evidence of ionizing radiation.

    And zero evidence of cancer.

    And zero evidence that DNA copying for cell division isn’t 100.00000% accurate.

    All the “evidence” points to a deity going in and personally modifying people’s DNA. Sure.

  10. bachfiendon 18 Jul 2017 at 4:43 pm

    BenE,

    ‘I suppose there is zero evidence that DNA contains a molecular blueprint for the comstruction of the human body.’

    Well, no – the human genome is a recipe not a blueprint for constructing the human body.

    Why take a human centred perspective on evolution? Humans are just one out of perhaps 10 million living species on Earth. The evidence for junk DNA largely comes from the enormous variation in genome size in different species. The marble lungfish for example has a genome around 40 times larger than the human one. Similar species, such as fruit flies, vary in genome size by 30%.

    Why is there such variation in different species if some DNA is doing very little?

    We’ve had arguments with hardnose ad nauseum – he’s managed to derail previous threads on evolution to hideous 1000+ comments lengths with his ridiculous claims that no one knows what causes evolution.

    Evolution is due to populations undergoing a changed environment (changing climate, predators, prey or competitors). One of the mechanisms of evolution is natural selection acting on natural variants within a population, and one mechanism of generating natural variation is ionising radiation (another is random non-directed genetic errors during DNA replication – hardnose is obsessed with mutations being non-random, directed and to the benefit of the organism).

    ID creationists are dreadful liars. ENCODE had released some preliminary results on a very small percentage of the human genome claiming that a large percentage of the genome they’d examined had some sort of function – using a very liberal definition of function to include just being transcribed into RNA even just once – and then Jonathan Wells rushed into print a very short book ‘the Myth of Junk DNA’ in 2011. And the ENCODE released their blizzard of papers, and ID creationists then were able to claim that they’d predicted that junk DNA didn’t exist. It wasn’t a prediction. It was a postdiction.

  11. bachfiendon 18 Jul 2017 at 4:46 pm

    It’s too early in the morning – I meant why is there such variation in different species unless (not if) some DNA is doing very little?

  12. wellerpondon 18 Jul 2017 at 4:48 pm

    @Hardnose

    I’m still trying to parse out how much you think we know and don’t know. *I* would say we know how photosynthesis works because we understand some chemicals and how they react given the same circumstances..

    https://msu.edu/user/morleyti/sun/Biology/photochem.html

    Is your position that we don’t understand photosynthesis because we don’t understand things down to the fundamental particles of the universe? Are you saying we don’t understand ANYTHING or just not everything.

    Where are your lines from what we know, to what we don’t know but might be able to figure out, to what we can’t ever know?

  13. Steven Novellaon 18 Jul 2017 at 4:55 pm

    We don’t know whatever HN doesn’t want us to know, to any arbitrary degree he decides ad hoc, in order to believe whatever bullshit he wants.

  14. Paul Parnellon 18 Jul 2017 at 5:17 pm

    Hardnose,

    You equated ID theorists with creationists, even though ID theorists BELIEVE IN EVOLUTION.

    The first use of “intelligent design” in its current usage was in the book “Of Pandas and People” written by Percival Davis and Dean H. Kenyon. Both young earth creationists. It was part of a legal and political strategy to get creationism into schools. By replacing the word “creationist” with “design proponents” they hoped to create a big tent under which all versions of creationism could gather. And by removing any mention of any particular creation myth they hoped to get past the first amendment. “Creationism” was literally replaced with “design proponent” with a simple search and replace function on an earlier version of the book. This is one of the reasons cited by the judge in the Dover decision when he legally declared it indistinguishable from creationism.

    Next comes Michael Behe. He is a creationist of of the old world type. Being Catholic that was easier for him. He invented the idea of irreducible complexity but in over 20 years since he has not formalized it into a form that can actually be used for anything. Many have pointed out just how impossibly problematic the idea is.

    And then we have Charles Thaxton. Young earth creationist. He invented the term specified complexity. It was as much a failure as irreducible complexity.

    And then there is William Dembski. Young earth creationist. Well, it’s complicated. He has criticized some aspects of YEC but then in 2010 we get:

    https://pandasthumb.org/archives/2010/10/dembski-coming.html

    There is still wiggle room for him but it is clear that his views derive from the bible and not science.

    These are the founders of the ID movement. Creationists one and all and mostly young earth creationists.

  15. BillyJoe7on 18 Jul 2017 at 5:30 pm

    He doesn’t understand this and therefore denies it but what the troll means is that we don’t know everything therefore we know anything

    What the troll means is that we don’t know what the fundamental particles are made of and, if they’re made of vibrating strings, what these vibrating strings are made of. And therefore that any ideas he pulls out of his arse could be true.

    He doesn’t understand that we know the limits of what we don’t know and that those limits already preclude his bullshit.

  16. googolplexbyteon 18 Jul 2017 at 6:04 pm

    There plenty of functions the other ~80% of DNA could serve beside coding;

    It decreases the chance that mutations/viral insertions will affect a section of DNA that’s crucial and delicate.

    It could act as formatting to make the coding DNA easier to read.

    It could act as filler to pack cells out.

    As a guide for folding.

    To make chromosomes bigger so that heat vibration is dampened, or even modulated to be better suited for a specific body temperature. Chromosomes do all happen to be very similarly sized.

    As a reference for DNA repair, or raw material for it.

    A ton of stuff I have no idea about because I’m not a biologist.

    Mitochondrial DNA doesn’t have any Junk DNA, so it’s presence can’t be neutral or they’d be no reason to eliminate it there.

    Also what do creationist have to do with this. Isn’t it evolutionarily reasonable for DNA to be 100% functional? There’s no other situation where biology produces functionless parts. Even things like the appendix turned out to serve some function such as a microbiome reservoir.

  17. hardnoseon 18 Jul 2017 at 7:14 pm

    “Also what do creationist have to do with this. Isn’t it evolutionarily reasonable for DNA to be 100% functional? There’s no other situation where biology produces functionless parts. Even things like the appendix turned out to serve some function such as a microbiome reservoir.”

    Yes. The idea that DNA is mostly garbage is a garbage idea.

  18. bachfiendon 18 Jul 2017 at 7:15 pm

    googleplexbyte,

    ‘There’s no other situation where biology produces functionless parts. Even things like the appendix turned out to serve some function such as a microbiome reservoir.’

    Why be human centred? Humans are just one species out of millions of living species. Functionless parts are part and parcel of evolution including verstigial eyes in blind cave dwellers.

    There are many hypotheses for the small size of the human appendix. The one I find most appealing is that as the hominid brain grew larger, the hominid gut grew smaller (the large amounts of energy required to maintain a large gut digesting low energy plant food went to maintain a larger brain which was able to acquire higher energy animal food). And the appendix is part of the gut, and shared in its decrease in size.

    There are many hypotheses for the existence of junk DNA in eukaryotes. The simplest one is that it just happens, because there’s no mechanism in eukaryotes to get rid of extraneous viral insertions and DNA duplications, unlike in prokaryotes, which reproduce so rapidly that not all of its DNA is replicated before the cell divides. This results in bacteria cleaning their genomes of junk DNA. Any vital genes that are lost in the same process can be regained as as result of bacterial conjugation.

    If junk DNA had a function, then why does the size of genomes, even similar ones, vary so markedly? In the same way that the size of the human appendix also varies in size ranging from a thin vestigial thread to a wide one which coils around the abdominal cavity. There doesn’t appear to be an optimum size for the size of the genome in species, nor for the size of the human appendix.

  19. Willyon 18 Jul 2017 at 8:10 pm

    Off topic, yet still relevant:

    Three New York surgeons were playing golf together and discussing surgeries they had performed.
    One of them said, ‘I’m the best surgeon in the state. In my favorite case, a concert pianist lost seven fingers in an accident; I re-attached them, and 8 months later he performed a private concert for the Queen of England.’

    The second surgeon said, ‘That’s nothing. A young man lost an arm and both legs in an accident; I reattached them, and 2 years later he won a Gold Medal in track and field events in the Olympics.’

    The third surgeon said, ‘You guys are amateurs. Several years ago a man was high on cocaine and marijuana and he rode a horse head-on into a train, travelling 80 miles an hour. All I had left to work with was the man’s blonde hair and the horse’s ass. I was able to put them together and now he’s president of the USA!’

  20. mumadaddon 19 Jul 2017 at 3:15 am

    LOL – thanks, Willy.

  21. BillyJoe7on 19 Jul 2017 at 6:46 am

    “The idea that DNA is mostly garbage is a garbage idea”

    The idea that DNA is mostly garbage is a garbage idea is a garbage idea.
    Now that was easy!

  22. SteveAon 19 Jul 2017 at 10:38 am

    googolplexbyte: “Isn’t it evolutionarily reasonable for DNA to be 100% functional? There’s no other situation where biology produces functionless parts.”

    I take your point, but the reverse is also true. Isn’t it equally reasonable to suppose that if the accumulation of ‘junk’ DNA poses a minimal burden (if any) to an organism, then it simply doesn’t matter if it’s accumulated or not?

    As to functionless; polyploidy might count. Having multiple copies of the same gene coding for the same things seems pretty redundant.

  23. hardnoseon 19 Jul 2017 at 10:53 am

    It is ARROGANT to think that if you don’t understand the purpose of something, it must have no purpose.

    But arrogance is really at the center of this human-centered materialist ideology.

    And I don’t blame this entirely on Old White Men.

  24. Pete Aon 19 Jul 2017 at 1:13 pm

    Willy, LOL! Many thanks indeed for your comment.

    I’m surprised that the commentator “Echo” — who has self-reported to be qualified in ‘English’ — didn’t (or hasn’t yet) admonished you for the punctuation and grammar.

    To me, the punctuation and grammar in your reported story adds much to its hilarity: within the context of the recent deluge of long posts by said commentator.

    “The third surgeon said, ‘You guys are amateurs. Several years ago a man was high on cocaine and marijuana and he rode a horse head-on into a train, travelling 80 miles an hour. …'”

    Which implies that the horse and rider, not the train, were travelling at 80 miles per hour. Perhaps the expected recollection of a rider who was/is high on narcotics; or a rider who was/is feeling particularly high on their hobby horse of bashing skeptics plus everyone who does not abide by their ‘rules’ for US English 🙂

  25. Echoon 19 Jul 2017 at 1:32 pm

    When you look at beautiful painting do you scoff at it’s lack of realism? When you listen to music, do you complain that the lyrics aren’t logical? Do all stand up comedians just sound like gibberish to you?

    Actually Pete, it’s incredibly obvious to anyone that the implied meaning of the sentence is that the train was the thing traveling at 80 miles and hour. Instead of attacking hardnose why don’t you come and take on someone your own size? I notice you dodged my recent replies to you among other things.

    http://theness.com/neurologicablog/index.php/the-fragility-of-truth/#comment-350646

  26. Pete Aon 19 Jul 2017 at 2:06 pm

    Echo,

    You have made it blindingly obvious that you are incapable of firstly understanding, then appreciating, British satire.

    Hence the hilarity of this part of your reply: “Do all stand up comedians just sound like gibberish to you?”

  27. Echoon 19 Jul 2017 at 2:42 pm

    @Pete A: Hide behind a false comedic pretense now, because that’s realistic given your recent behavior. You have shown multiple times that you take things way too literally, you’ve lost it over my use of gravity waves. Meanwhile someone as laid back, as you now are clearly just pretending to be, would have seen that many journalists who made the same error in reference to LIGO, in fact it’s such a common mistake/inaccuracy that when one googles “gravity waves” you get results for LIGO and the wiki page for gravitational waves, not the wiki page for “gravity waves,” which you linked to. This makes you a pedantic whiny loser. And this is saying nothing of your recent illogical rant on programing languages, in reference to my justified objection with someone using quotation marks to **paraphrase** my work. OH and this is also ignoring the time, quite recently, where you literally, in response to a one-liner by hardnose, DUG UP HIS COMMENTS FROM TWO YEARS AGO… Yeah, you are right, I don’t understand your satire at all, you wound-collecting, vindictive, sociopathic troll.

    http://theness.com/neurologicablog/index.php/the-fragility-of-truth/#comment-350230

  28. bachfiendon 19 Jul 2017 at 4:20 pm

    Hardnose,

    ‘It is ARROGANT to think that if you don’t understand the purpose of something, it must have no purpose’.

    You’re confusing ‘purpose’ and ‘function’. The function of the heart is to pump blood. The purpose of the heart in an elite marathon runner is to allow the runner to do a sub-2 hour 5 min marathon. Function is something that truly exists. A vestigial structure may lose its original function and become functionless – or it may acquire new functions, such as the human appendix might become a refuge for the normal commensal bacterial flora of the gut. Purpose is a human teleological invention – the claim that what sommethng is being used for now was the intention all the way along.

    Echo,

    ‘When you listen to music, do you claim that the lyrics aren’t logical?’ I had a good answer for that, but they just played the 18th variation of Rachmaninov’s ‘Rhapsody on a Theme of Paganini’ and it completely went out of my head.

  29. Pete Aon 19 Jul 2017 at 4:30 pm

    Echo,

    Please continue writing comments which are based in your claim of gaining a qualification in ‘English’. It’s hilarious to observe your comments within the context of your claim. Just as it was hilarious with the previous commentator(s) who claimed similarly. Two of whom spring to mind are the commentators: “cozying”; “Sophie”.

    You have overtly revealed both your general modus operandi, and your utter contempt for my personhood, by writing the following using your self-proclaimed qualification in the English language:

    “I notice you dodged my recent replies to you among other things.”

    Well, guess what: I became aware, ages ago, that you regard me as a “thing”; and that you, and many others, will continue to regard me as simply a “thing” which needs to be attacked.

    Notes to the readers:
    I deliberately avoided highlighting the grammatical errors made by the commentators “cozying”, “Sophie”, and “Echo”, because it would spoil the fun of observing the strong correlation between the comments made by the three pseudonyms;

    I shall leave it to the readers to decide whether or not, in this case, the commonality shown is simply a chance correlation, or if it is becoming an increasingly-thinly-obfuscated causation.

  30. Willyon 19 Jul 2017 at 5:02 pm

    Pete A: You’re welcome! As to the content, I just cut and pasted it from an e-mail. I think the tears in my eyes prevented me from seeing any errors…

  31. Pete Aon 19 Jul 2017 at 5:24 pm

    Willy, It was some while after clearing away the tears of laughter from my first read of it that it dawn on me the added hilarity of a horse managing to achieve a speed of 80 miles per hour 🙂

  32. BillyJoe7on 19 Jul 2017 at 5:35 pm

    Echo,

    “Instead of attacking hardnose why don’t you come and take on someone your own size?”

    Great take down of the troll. 😀
    Small guy with a small mind and a “flat learning curve”.

    (Just in this thread he made an obviously false statement and had it corrected by the author by referencing the contents of the post that the troll obviously hasn’t bothered reading before commenting. Then what does the troll do? He just repeats the same obviously false statement!)

  33. Echoon 19 Jul 2017 at 6:51 pm

    @Pete A: re:

    Please continue writing comments which are based in your claim of gaining a qualification in ‘English’. It’s hilarious to observe your comments within the context of your claim. Just as it was hilarious with the previous commentator(s) who claimed similarly. Two of whom spring to mind are the commentators: “cozying”; “Sophie”.

    What in the actual… This Steve Cross stuff again? Errr… Umm?.. Ah… Uh… Please, don’t let me stop you, I want to learn more. Continue with these theories and elaborate, I require some more information before I can best form a response. I’m not sure where to begin at this point.

    Specifically, I just want to know where exactly does it appear that I claimed to have a “qualification in ‘English.'” I’m a student, I have not graduated yet. I never claimed to have a degree, or anything, I don’t think I ever expressed that I’m qualified in anything? I never claimed to be a qualified professional, and have repeatedly described myself as an outsider. Previously however, I did for sure, definitely concede that I write in an unprofessional style using informal language. I also had no problem admitting that I routinely make grammatical errors. Additionally I admitted to using slang and non-words for emphasis or emotional expression. So I have literally no earthly idea what you are talking about.

    I mean for someone like you, who holds the English language as sacred, and loves nitpicking grammar and implied meanings of informal writing, why is that you write stuff like this:

    (Pete A): … It was some while after clearing away the tears of laughter from my first read of it that it dawn on me the added hilarity of a horse managing to achieve a speed of 80 miles per hour 🙂

    It’s a sentence that might be missing at least a comma, and a definitely a period. Your use of “first read of it that it” sounds clunky to me at the very least, if it’s not outright incorrect, I dunno I’m not an english major. Also, I don’t understand your consciously applied bold emphasis on “speed,” is that another one of your obsessions with taking things literally? You think it’s funny that whoever crafted the original informal line misused the word “speed,” instead of the physics term “velocity,” or something?

    So if a cop pulls you over, and explains he is going to give you a ticket for “speeding,” or exceeding the “speed” limit, are you going to laugh and protest the language?

  34. Paul Parnellon 19 Jul 2017 at 6:58 pm

    Keeerriiiist people! You argue like a bunch of old married people.

  35. Echoon 19 Jul 2017 at 7:04 pm

    @Paul Parnell: Watch out! Pete A, will run you over for daring to use such a non-literal analogy. All while heading down the road at a tremendous “velocity.”

  36. Pete Aon 19 Jul 2017 at 7:04 pm

    Echo,

    QED. ‘Nuf said. So STFU.

  37. hardnoseon 19 Jul 2017 at 8:18 pm

    [Small guy with a small mind and a “flat learning curve”.]

    When you don’t have any logical arguments, just call your opponent stupid.

  38. bachfiendon 19 Jul 2017 at 8:38 pm

    Hardnose,

    When your ‘opponent’ doesn’t answer your logical arguments, you’re perfectly entitled to call him ‘stupid’.

  39. mumadaddon 20 Jul 2017 at 1:27 am

    Wait, I thought it was known that some genomes do contain actual junk? The example that springs to mind was the chicken genome containing sections that would code for teeth if activated. Didn’t some researchers actually reactivate thus section in an experiment? So the genome can contain sections that previously did code for protein but are no longer expressed — if this isn’t “junk” then don’t know what would qualify.

  40. bachfiendon 20 Jul 2017 at 2:59 am

    mumadadd,

    A better example are olfactory receptor genes. All mammals (perhaps I should have stated all placental mammals? I’m not certain about monotremes – they’re so strange genetically) contain about 1,000 genes for olfactory receptors.

    In humans, only about 1/3 are expressed. The other 2/3 have acquired mutations rendering them inactive. In whales and dolphins, they’re all inactive, with mutations preventing them from ever expressing functional olfactory receptor proteins, regardless of whether some genetic manipulation causes them to transcribe mRNA.

    Now, that’s what I’d call ‘junk’ DNA (there’s are other types, of course).

  41. Nidwinon 20 Jul 2017 at 4:45 am

    May be it’s a bit like grandma, keeping everything just in case it could be needed in the future. And our ladies our going to hate me for this but aren’t our girls bying hundreds of pair of shoes to make sure to have one available to fit a special, new or specific outfit, just in case?

    I’ve only a very global knowledge about genetics. I’m although wondering if it’s possible, theory or even proven to be able to, active genetic “components” in grown living lifeforms.

  42. bachfiendon 20 Jul 2017 at 6:37 am

    Nidwin,

    If you’re suggesting that junk DNA is there because it’s being retained just in case at some undefined point in the future it might turn out to be useful, the answer is ‘no’.

    Retaining junk DNA in case it becomes useful would be like the dodo on Mauritius retaining the power of flight in case Dutch and English sailors appeared there in the 17th century. It might have been useful, but it didn’t happen.

    You’ve fallen for the temptation of teleological thinking. Evolution doesn’t have goals and future plans. Its only concerns are in the present.

  43. BillyJoe7on 20 Jul 2017 at 6:49 am

    bachfiend and mumadadd,

    I’m sure, despite your efforts on top of those by Steven Novella, that small guy with the small mind and the “flat learning curve” will be back with his brain dead refrain.

  44. Nidwinon 20 Jul 2017 at 7:27 am

    Bachfiend,

    I didn’t suggest that at all and the chances that grandma’s stockpile and our girls 300+ pairs bought/stocked-away shoes would ever find a use are probably as high or low as junk DNA in the near future. I only pointed out that grandma, the ladies and e.g. humans have a crapload of stockpiled stuff that doesn’t seem to have any use. And that’s it from my side.

    Evolution doesn’t have concerns btw. It would be actually frightning if it did have concerns, especially in the present.

  45. Yehouda Harpazon 20 Jul 2017 at 8:42 am

    > # bachfiendon 19 Jul 2017 at 8:38 pm
    > Hardnose,

    > When your ‘opponent’ doesn’t answer your logical arguments, you’re perfectly
    > entitled to call him ‘stupid’.

    No, you are not.

    Calling people ‘stupid’ is almost always wrong. It is reasonable only if you have
    evidence that the person you call ‘stupid’ does badly on virtually any complex mental task.

    Posting BS on blogs is very far from being such evidence. And not
    answering your logical arguments doesn’t count as BS.

  46. SteveAon 20 Jul 2017 at 8:48 am

    Yehouda Harpaz: “Calling people ‘stupid’ is almost always wrong. It is reasonable only if you have
    evidence that the person you call ‘stupid’ does badly on virtually any complex mental task.”

    Odd definition. I’d count myself of average intelligence, but if I walked into the road without checking for traffic first I’d happily own up to being ‘stupid’.

  47. Yehouda Harpazon 20 Jul 2017 at 9:00 am

    > # SteveAon 20 Jul 2017 at 8:48 am

    > Odd definition. I’d count myself of average intelligence, but if I walked into
    > the road without checking for traffic first I’d happily own up to being ‘stupid’.

    ‘Being ‘stupid” and ‘stupid are quite different things. ‘Being ‘stupid” is time variable,
    as in your example. ‘stupid’ is not.

  48. mumadaddon 20 Jul 2017 at 9:40 am

    I also wonder if we’ve learned anything about junk DNA from knock out mice, though I think it would probably be an inappropriate use of funding to knock out sections of the genome thought to be “junk”. Plenty of other sections to target first I would think.

  49. hardnoseon 20 Jul 2017 at 12:03 pm

    [Small guy with a small mind and a “flat learning curve”.]

    I have a f”lat learning curve” because his illogical and incoherent arguments did not convince me.

    I am “small” because I do not belong to the intellectually superior, big-brained, “skeptic” tribe.

  50. BillyJoe7on 20 Jul 2017 at 3:18 pm

    Yahouda,

    You said “almost always”. Above you have an obvious exception to your rule. If you’re not convinced, follow him for a while. I promise it won’t take long. He is a prime example of the arrogance of ignorance, believing what you want to be true, and an inability to understand logic and counter-argument.

  51. Sylakon 21 Jul 2017 at 7:15 pm

    I can totally see that. After epigenetic, “unlock your hiddens ancestral genes”, “awake long lost potential”. I can also picture bad scifi actions movies. Instead of “the 10% of the brain” stupid gimmick, it can be “hidden” ability in the genes. A little Like the awful and cheesy Sens8 excuse of “homo sensorium”. It’s just a matter of time.

  52. hfern1on 24 Jul 2017 at 11:36 am

    I’m not concerned with the ID vs evolution argument, but that the science of the paper described is faulty, in my opinion. Graur does not make a good case for 75% of the genome being junk. He does if protein coding genes were the only DNA that has any function. He completely ignores non-coding DNA; Steven writes more about it here than Graur does in his paper. While a single base mutation in a coding sequence can completely knock out the expression of a gene, non-coding regions have much higher tolerances for mutations. In his paper, he doesn’t even use the term non-coding (or noncoding) once, when the main argument between him and those at ENCODE centres around this specific point. I admit ENCODE’s definition of “functional” is too broad, equally his is FAR too narrow, and all his calculations in this paper stem from an overly narrow definition of function. He doesn’t consider the essential functions that non-coding RNA play in gene regulation, let alone in processes as diverse as, for example, maintenance of heterochromatin structure. For him to write a paper proclaiming 75% of the genome is junk, while not even mentioning the word non-coding once, confirms to me my previous opinion that he is one of those stubborn, close-minded, ignorant, overly dogmatic scientists that stifle scientific progress. Add to that the arrogant notion that “i don’t know what it does, so it must not do anything”.

  53. bachfiendon 25 Jul 2017 at 4:26 pm

    hfern1,

    You’re being far too human centred. The best evidence for the existence of junk DNA is the fact that the size of the genome over different eukaryote species, even very similar ones, varies so much without other reasons.

    The fruit fly genome varies by around 30% in different species. The marble lungfish has a genome 40 times larger than the human one. Some single-celled amoeba have even larger genomes, so the extra DNA isn’t there to regulate genes to make bodies.

    The best explanation for the existence of the extra DNA in eukaryotes is not that most of it has a function, but rather that eukaryotes lack a mechanism to rid themselves of functionless DNA, unlike prokaryotes, which do.

  54. Aceofspades25on 26 Jul 2017 at 9:51 am

    Hi Steve

    Genetic load is one of the arguments for junk DNA but there are also many other lines of evidence that point to us carrying a significant amount of Junk DNA.

    One example of these is the Onion Test: Genome size varies enormously among species.

    For example, a human genome contains eight times more DNA than that of a pufferfish but is 40 times smaller than that of a lungfish. The genomes of Salamanders are between four and 35 times larger than the human genome. The domestic onion has a genome which is five times larger than the human genome and this is where we derive the name of the test from.

    Other lines of evidence concern things like genome composition (which you mentioned), looking at conserved sequences (which you mentioned), Genetic load (which Graur’s paper is about) and an understanding that transcription is inherently noisy.

    This is an excellent paper on the case for Junk DNA:

    http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004351

  55. SteveAon 27 Jul 2017 at 11:17 am

    Aceofspades25

    Great paper. Thanks for the link.

    “The domestic onion, Allium cepa, is a diploid plant (2n = 16) with a haploid genome size of roughly 16 billion base pairs (16 Gbp), or about five times larger than humans. Although any number of species with large genomes could be chosen for such a comparison, the onion test simply asks: if most eukaryotic DNA is functional at the organism level, be it for gene regulation, protection against mutations, maintenance of chromosome structure, or any other such role, then why does an onion require five times more of it than a human? Importantly, the comparison is not restricted to onions versus humans. It could as easily be between pufferfish and lungfish, which differ by ∼350-fold, or members of the genus Allium, which have more than a 4-fold range in genome size that is not the result of polyploidy.”

  56. hfern1on 27 Jul 2017 at 11:42 am

    bachfiend, I’m not arguing that junk DNA doesn’t exist, of course it would, with plenty of evidence for it including what you mentioned. All I’m saying is that Graur is so vocally for it making up 75% or more of the genome, and in his paper calculates this using protein coding sequences, while completely ignoring proven functional non-coding DNA, which do have essential functions as well. Maybe functional non-coding DNA only makes up a small amount more of non-junk DNA, but Graur completely ignores its existence in his latest paper, which is just poor science, considering that the only argument for less junk DNA than he says, is the presence of functional (by anyone’s definition) noncoding DNA, such as those I mentioned.

  57. SteveAon 27 Jul 2017 at 11:47 am

    After reading the PLOS paper linked to by Aceofspades25 (above), I had a mooch through the site and came across this: ‘A misdiagnosed infection mimicking “tree man disease”’.

    http://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0005543

    There’s a happy ending. Hooray for science-based medicine.

  58. bachfiendon 27 Jul 2017 at 4:14 pm

    hfern1,

    Graur is making a very good case for at least 75% of the human genome being junk DNA (in other species, such as the marble lungfish, it would be much higher). It’s a fact that functioning genes account for 1.5% of the human genome, and another few percent are strongly conserved, so that mutations are ‘punished’ by natural selection and eliminated.

    It’s been conservatively estimated that as much as 20% of the human genome might have a function (even before ENCODE) with little supporting evidence. Graur’s calculation of 25% supports this estimate. Just because he doesn’t specifically mention functional non-coding DNA in the paper, it’s included in the 25%. Any mutation that reduces ‘fitness’ is punished by natural selection and removed.

    Functioning genes and regulatory regions of the genome make up very little of the human genome (around 5%), and that’s all we definitely know isn’t junk DNA in the human genome. The argument is about how much of the remaining 95% isn’t junk.

  59. hfern1on 28 Jul 2017 at 2:22 am

    bachfiend,
    Graur only included protein coding genes in his calculations, if I read it correctly. Even if he did include (known) functional non-coding DNA, mutations in functional non-coding DNA do not have the same effects as those in coding regions, so how can they be treated the same? A mutation in functional non-coding regions could have minimal or no effect, but the same mutation could completely knock out the expression of a protein. While the majority of lncRNAs have not been ascribed a function, how can someone conclude with absolute certainty that a particular lncRNA does not have a function under ANY condition, tissue type or developmental stage? Hence I don’t think we can accurately estimate an upper limit on “non-junk” non-coding DNA. I’m not saying that even a majority of DNA is functional, I’m just of the opinion we are far from working this out, and I just don’t agree with Graur’s limitations and perceived (to me) overly dogmatic blinkered opinions. And the vehemence with which he has expressed his opinions in the past just brings to mind the phrase “shouting something doesn’t make it true”.

  60. bachfiendon 28 Jul 2017 at 3:40 am

    hfern1,

    You’re not getting the point. Functioning genes (coding DNA) make up just 1.5% of the human genome. ONE POINT FIVE PER CENT of the human genome. That’s a long way short of Graur’s calculation of non-junk DNA being no more than 25% of the human genome.

    So what makes up the other 22.5% of Graur’s functional DNA? A few percent will be regulatory stretches of DNA, as shown by being conserved.

    ‘A mutation in functional non-coding regions could have minimal or no effect, but the same mutation could completely knock out the expression of a protein’. How do you know this? Actually, about a third of point mutations in genes are neutral in the expression of genes. The genetic code is redundant so that the same amino acid is encoded by more than one triplet with the nucleotide in the third position not mattering. Do you have any examples of mutations in functional non-coding DNA not having any effect? Or are you just sucking this out of your thumb?

    But still the same. The strongest evidence for the existence of junk DNA in eukaryotes is that the size of the genome varies so much across species, even in similar species.

    ID proponents don’t like the idea of junk DNA because they don’t think the Intelligent Designer would have created a bad design (Stephen Meyer gave the game away in ‘Darwin’s Doubt’ when he admitted that the Intelligent Designer is God).

    The existence or non-existence of junk DNA is irrelevant for science. Evolution could have resulted in some mechanism allowing the editing of genomes to get rid of non-functional DNA such as the thousands of broken genes, including the 700 or so non-functional genes for olfactory receptor proteins and the broken genes involved in vitamin C synthesis in humans, which would have been favoured by natural selection.

    But it didn’t. Or couldn’t.

  61. hfern1on 28 Jul 2017 at 11:30 am

    bachfiend,
    I understand how codons work, and about multiple codons per amino acid, I didn’t miss that class in undergrad. I was referring to an insertion, in a protein coding gene, that introduces a premature stop codon. A single base insertion in a non-coding RNA COULD stop its function, but doesn’t necessarily, e.g. shRNA molecules can tolerate a single base insertion depending on where it is. There are probably hundreds to thousands of examples of functional non-coding RNA that can tolerate a base insertion, but you know so much about codons and amino acids you don’t need me to find them for you.

    You are missing my point, I’m not saying junk DNA doesn’t exist, it obviously does, it’s just the amount that is the question and I think it is premature to be able to set limits at this point when there is so much we don’t know yet. And Graur’s adamance about the figure is what irritates me. I am in NO WAY an ID proponent.

    I’ll be happy to admit Graur is right if you can refer me to a paper of transcriptomic or genomic sequencing that details the reasons why there cannot be more than 25% non-junk DNA, rather than just “estimated” percentages based on incomplete/as yet not fully defined criteria. I assume since Graur had to publish this theoretical paper that one doesn’t exist yet.

  62. hfern1on 28 Jul 2017 at 11:44 am

    sorry, meant to say “siRNA” rather than “shRNA”

  63. bachfiendon 28 Jul 2017 at 4:22 pm

    hfern1,

    You still don’t get the point. Functional genes – the coding DNA – makes up 1.5% of the human genome.

    What is it other than non-coding DNA that makes up the remainder of up to 25% that Graur calculates to be non-junk DNA?

    ENCODE had asserted that 80% of the human genome is functional, using a definition of ‘functional’ that’s so liberal it’s useless. We actually know that less than 5% of the human genome is functional (functional genes and conserved regions of the genome). Graur’s calculation sets an upper limit to the percentage of functional DNA in the human genome of 25%. It could be much less – 10 or 15% – without being much of a burden on a cell preparing to divide. Other species do just fine replicating much larger genomes.

    You’re quibbling when you dismiss Graur’s paper just because the terminology of non-coding DNA isn’t specifically mentioned.

    Junk DNA exists in humans because junk DNA exists in other eukaryote species, often in much larger proportions, as in the marble lungfish. Eukaryotes just don’t have a mechanism allowing them to edit their genomes to remove junk DNA, unlike prokaryotes.

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