[math-fun] Junk DNA allegedly isn't. Big change in standard picture of life.
From: Henry Baker <hbaker1@pipeline.com> Re biological Rube Goldberg: I disagree vehemently. The more I learn of DNA, RNA, proteins, signalling, etc., the more impressed I am. For example, the process of mere _copying_ of DNA operates very close to the thermodynamic limit -- i.e., it would be very difficult to design _any_ system for copying DNA that produced less waste heat than our own DNA copying.
--Exactly wrong. DNA copying is done with rechecking and with use of ATP->AMP not ADP so it can get extra certainty. In other words it intentionally uses both extra energy and extra chemical steps. Many biochemical reactions in fact ARE reversible (e.g. fructose <--> glucose interconversion) and hence consume zero energy. But DNA copying is not one of them.
If our DNA copying were any less thermodynamically efficient, and we continued to copy at the same rate, our dividing cells would fry themselves like a fried egg.
--utter bull. DNA copying is a very small expenditure in human cells compared to other stuff.
Most evolutionary biologists will tell you that _none_ of the DNA is truly "junk". The proof: if it weren't important, it would relatively quickly disappear after a few generations.
--complete bull. DNA actually is expensive in bacteria and viruses, and they have little or no junk. But in eukaryotes like us, DNA is a tiny expenditure relatively speaking so we can afford lots of junk. By the way, you just "proved" microsoft windows is small and compact, not bloated.
Several biologists have proposed that complex organisms have lots of DNA as a form of "diagonalization": all of its siblings with less DNA didn't survive. This is akin to comparing the power of Turing Machines with more or less tape: those with "more" tape can simulate _all_ Turing Machines with "less" tape and do something different.
--you are totally confused. (And if you are right re "several biologists", they are confused too.)
For example, some of our DNA encodes experiences with viruses, some of which may be long extinct or at least dormant. Yet if that virus suddenly shows up, there are at least some fraction of humans that will survive.
--some of our DNA encodes viruses that incorporated themselves into our DNA and are now carried along for the ride for free inside us, where they are incurable since part of us. Further, some our DNA is "self replicating elements" which in fact multiply WITHIN our DNA; they are "out for themselves" not you. Somewhat like cancer but at a smaller size and longer time scale. This is (I suspect) the main reason closely related species have way different amounts of junk and that much of our junk is repeating sequences.
Plants (which typically don't move) seem to require more DNA than animals (which do move). One can speculate that plants have to sit there and take every insult, while animals can avoid the insult by moving and even emigrating when necessary.
--plants do a lot more chemistry than animals, so they need more genes (which describe chemistry). You can't synthesize many amino acids, fats, and vitamins you need because you lack the genes. Plants do not have that luxury. Animals can't do photosynthesis, even though it'd clearly be beneficial if they could. --In this post I am repeating the usual bio- philosophy & refuting weird myths posted by HB. The alleged new "it aint junk" philosophy to some extent must overthrow the old bio philosophy, but I'd like to know what is wrong with the old arguments, because they sure mostly are not wrong.
I don't pretend to know what "junk" DNA is for, but I found it exceedingly arrogant for scientists who didn't know what it might be for to have pronounced it to be purposeless. Reminds me of Crick & Mitchison's pronouncement that dreams are merely the detritus of the psyche. This is possible, but they surely had no evidence for it. It seems far more likely to me that we just don't know yet, and likewise for "junk" DNA. --Dan On 2012-09-06, at 4:54 PM, Warren Smith wrote:
Most evolutionary biologists will tell you that _none_ of the DNA is truly "junk". The proof: if it weren't important, it would relatively quickly disappear after a few generations.
--complete bull. DNA actually is expensive in bacteria and viruses, and they have little or no junk. But in eukaryotes like us, DNA is a tiny expenditure relatively speaking so we can afford lots of junk. By the way, you just "proved" microsoft windows is small and compact, not bloated.
A noticeable fraction (at least a few percent) of our DNA consists of many repetitions of short stretches of 6-25 letters. One might be excused for suspecting it had no important information. Dan> ... exceedingly arrogant for scientists who didn't know ... Fortunately, our scientists are equal to the task, overcoming their natural inborn humility, to better inform us of their discoveries. Rich ----- Quoting Dan Asimov <dasimov@earthlink.net>:
I don't pretend to know what "junk" DNA is for, but I found it exceedingly arrogant for scientists who didn't know what it might be for to have pronounced it to be purposeless.
Reminds me of Crick & Mitchison's pronouncement that dreams are merely the detritus of the psyche.
This is possible, but they surely had no evidence for it.
It seems far more likely to me that we just don't know yet, and likewise for "junk" DNA.
--Dan
On 2012-09-06, at 4:54 PM, Warren Smith wrote:
Most evolutionary biologists will tell you that _none_ of the DNA is truly "junk". The proof: if it weren't important, it would relatively quickly disappear after a few generations.
--complete bull. DNA actually is expensive in bacteria and viruses, and they have little or no junk. But in eukaryotes like us, DNA is a tiny expenditure relatively speaking so we can afford lots of junk. By the way, you just "proved" microsoft windows is small and compact, not bloated.
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You've never heard of "loop-unrolling" ?? :-) It is conceivable that these stretches might act as some sort of "spacers", whose size/number might be more important than their content. One of the articles about this DNA map also indicated that portions of DNA that are far from one another in the linear sequence may end up near to one another when the DNA is in its normal folded state. Changes in the size/number of such stretches might mess up this folded alignment. At 07:08 PM 9/6/2012, rcs@xmission.com wrote:
A noticeable fraction (at least a few percent) of our DNA consists of many repetitions of short stretches of 6-25 letters. One might be excused for suspecting it had no important information.
There have been a lot of claims about junk DNA in this thread that are simply wrong. Rather than enumerate them, I'll just direct you to the blog of Toronto biologist Larry Moran, who has a number of posts about junk DNA, as well as a number of posts illustrating why the latest news has been oversold. http://sandwalk.blogspot.ca/
I must have missed something (a lot of somethings?) on this blog. I couldn't find much detail on it at all. All he seems to say is that at least 80% of the DNA is functional, and probably 100%. I agree with this assessment. Is there more detail somewhere else? Perhaps you have a better link? At 03:13 AM 9/7/2012, Jeffrey Shallit wrote:
There have been a lot of claims about junk DNA in this thread that are simply wrong.
Rather than enumerate them, I'll just direct you to the blog of Toronto biologist Larry Moran, who has a number of posts about junk DNA, as well as a number of posts illustrating why the latest news has been oversold.
Indeed, you have missed almost everything. It is Larry Moran's position that 90% of DNA has no function. You can start with http://sandwalk.blogspot.ca/2011/10/myth-of-junk-dna-by-jonathan-wells.html which is easily findable with a google search. On 9/7/12 6:52 AM, Henry Baker wrote:
I must have missed something (a lot of somethings?) on this blog. I couldn't find much detail on it at all.
All he seems to say is that at least 80% of the DNA is functional, and probably 100%. I agree with this assessment.
Is there more detail somewhere else?
Perhaps you have a better link?
At 03:13 AM 9/7/2012, Jeffrey Shallit wrote:
There have been a lot of claims about junk DNA in this thread that are simply wrong.
Rather than enumerate them, I'll just direct you to the blog of Toronto biologist Larry Moran, who has a number of posts about junk DNA, as well as a number of posts illustrating why the latest news has been oversold.
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Well, I believe that he's wrong, but I probably won't live long enough to see him debunked. Of course, some of this controversy depends upon the definition of "junk". If you consider all the extra bits in random codes to be "junk", then so be it. They are there to increase the coding distance, but don't add any information, per se. There is a _huge_ reservoir of resilience built into living beings; there has to be, given that those organisms that didn't have this resilience didn't survive to the present. As I mentioned before in my Microsoft Windows analogy, you can't possibly understand why 90% of the code in Windows is there until you see the test suite for Windows, which rigorously checks that every "corner case" is properly handled -- even "corner cases" that many/most of us would now consider to be "bugs". This is due to the requirement for "backwards compatibility". And of course, DNA is by definition "backwards looking", in that it "remembers" insults/challenges from the past that may or may not ever re-occur. If these insults/challenges never re-occur, then is any DNA that is required to meet these challenges considered to be "junk DNA" ? If so, then a significant fraction of the items in your computer's cache memory are also "junk", since these cache lines will be evicted before ever being used again. At 07:03 AM 9/7/2012, Jeffrey Shallit wrote:
Indeed, you have missed almost everything. It is Larry Moran's position that 90% of DNA has no function.
You can start with
http://sandwalk.blogspot.ca/2011/10/myth-of-junk-dna-by-jonathan-wells.html
which is easily findable with a google search.
On 9/7/12 6:52 AM, Henry Baker wrote:
I must have missed something (a lot of somethings?) on this blog. I couldn't find much detail on it at all.
All he seems to say is that at least 80% of the DNA is functional, and probably 100%. I agree with this assessment.
Is there more detail somewhere else?
Perhaps you have a better link?
At 03:13 AM 9/7/2012, Jeffrey Shallit wrote:
There have been a lot of claims about junk DNA in this thread that are simply wrong.
Rather than enumerate them, I'll just direct you to the blog of Toronto biologist Larry Moran, who has a number of posts about junk DNA, as well as a number of posts illustrating why the latest news has been oversold.
Clone someone using a starting cell with all the "junk" removed and I doubt the conclusion will be that it has no function ;) On 7 Sep 2012, at 15:59, Henry Baker wrote:
Well, I believe that he's wrong, but I probably won't live long enough to see him debunked.
Of course, some of this controversy depends upon the definition of "junk".
If you consider all the extra bits in random codes to be "junk", then so be it. They are there to increase the coding distance, but don't add any information, per se.
There is a _huge_ reservoir of resilience built into living beings; there has to be, given that those organisms that didn't have this resilience didn't survive to the present.
As I mentioned before in my Microsoft Windows analogy, you can't possibly understand why 90% of the code in Windows is there until you see the test suite for Windows, which rigorously checks that every "corner case" is properly handled -- even "corner cases" that many/most of us would now consider to be "bugs". This is due to the requirement for "backwards compatibility".
And of course, DNA is by definition "backwards looking", in that it "remembers" insults/challenges from the past that may or may not ever re-occur. If these insults/challenges never re-occur, then is any DNA that is required to meet these challenges considered to be "junk DNA" ? If so, then a significant fraction of the items in your computer's cache memory are also "junk", since these cache lines will be evicted before ever being used again.
At 07:03 AM 9/7/2012, Jeffrey Shallit wrote:
Indeed, you have missed almost everything. It is Larry Moran's position that 90% of DNA has no function.
You can start with
http://sandwalk.blogspot.ca/2011/10/myth-of-junk-dna-by-jonathan-wells.html
which is easily findable with a google search.
On 9/7/12 6:52 AM, Henry Baker wrote:
I must have missed something (a lot of somethings?) on this blog. I couldn't find much detail on it at all.
All he seems to say is that at least 80% of the DNA is functional, and probably 100%. I agree with this assessment.
Is there more detail somewhere else?
Perhaps you have a better link?
At 03:13 AM 9/7/2012, Jeffrey Shallit wrote:
There have been a lot of claims about junk DNA in this thread that are simply wrong.
Rather than enumerate them, I'll just direct you to the blog of Toronto biologist Larry Moran, who has a number of posts about junk DNA, as well as a number of posts illustrating why the latest news has been oversold.
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The meaning and purpose of life is to give life purpose and meaning. The instigation of violence indicates a lack of spirituality.
Clone someone using a starting cell with all the "junk" removed and I doubt the conclusion will be that it has no function ;)
I don't think that's the right test. Suppose things believed to be "junk" were entirely without function 99.99% of the time, but important the remaining times. Then such a clone would presumably be nonviable (lacking thousands of important elements) even though the "junk" classification was essentially accurate. Further it seems that this test has been done, though removing only a portion of the junk DNA: http://www.ncbi.nlm.nih.gov/pubmed/15496924 Their conclusion: "Some of the deleted sequences might encode for functions unidentified in our screen; nonetheless, these studies further support the existence of potentially 'disposable DNA' in the genomes of mammals." Charles Greathouse Analyst/Programmer Case Western Reserve University On Sat, Sep 8, 2012 at 6:00 AM, David Makin <makinmagic@tiscali.co.uk> wrote:
Clone someone using a starting cell with all the "junk" removed and I doubt the conclusion will be that it has no function ;)
On 7 Sep 2012, at 15:59, Henry Baker wrote:
Well, I believe that he's wrong, but I probably won't live long enough to see him debunked.
Of course, some of this controversy depends upon the definition of "junk".
If you consider all the extra bits in random codes to be "junk", then so be it. They are there to increase the coding distance, but don't add any information, per se.
There is a _huge_ reservoir of resilience built into living beings; there has to be, given that those organisms that didn't have this resilience didn't survive to the present.
As I mentioned before in my Microsoft Windows analogy, you can't possibly understand why 90% of the code in Windows is there until you see the test suite for Windows, which rigorously checks that every "corner case" is properly handled -- even "corner cases" that many/most of us would now consider to be "bugs". This is due to the requirement for "backwards compatibility".
And of course, DNA is by definition "backwards looking", in that it "remembers" insults/challenges from the past that may or may not ever re-occur. If these insults/challenges never re-occur, then is any DNA that is required to meet these challenges considered to be "junk DNA" ? If so, then a significant fraction of the items in your computer's cache memory are also "junk", since these cache lines will be evicted before ever being used again.
At 07:03 AM 9/7/2012, Jeffrey Shallit wrote:
Indeed, you have missed almost everything. It is Larry Moran's position that 90% of DNA has no function.
You can start with
http://sandwalk.blogspot.ca/2011/10/myth-of-junk-dna-by-jonathan-wells.html
which is easily findable with a google search.
On 9/7/12 6:52 AM, Henry Baker wrote:
I must have missed something (a lot of somethings?) on this blog. I couldn't find much detail on it at all.
All he seems to say is that at least 80% of the DNA is functional, and probably 100%. I agree with this assessment.
Is there more detail somewhere else?
Perhaps you have a better link?
At 03:13 AM 9/7/2012, Jeffrey Shallit wrote:
There have been a lot of claims about junk DNA in this thread that are simply wrong.
Rather than enumerate them, I'll just direct you to the blog of Toronto biologist Larry Moran, who has a number of posts about junk DNA, as well as a number of posts illustrating why the latest news has been oversold.
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The meaning and purpose of life is to give life purpose and meaning.
The instigation of violence indicates a lack of spirituality.
_______________________________________________ math-fun mailing list math-fun@mailman.xmission.com http://mailman.xmission.com/cgi-bin/mailman/listinfo/math-fun
With suspecting, there's nothing to forgive. With acting certain -- when we just don't know -- and announcing it to the world, that's not so forgivable. --Dan On 2012-09-06, at 7:08 PM, rcs@xmission.com wrote:
A noticeable fraction (at least a few percent) of our DNA consists of many repetitions of short stretches of 6-25 letters. One might be excused for suspecting it had no important information.
Well, I don't agree at all. There are *good reasons* to believe that much of the genome is junk (see, for example, the experiments referred to on Larry Moran's blog) and it is completely reasonable to deduce this from what is currently known. Could the junk proponents be wrong? Of course - all science is provisional. Nevertheless, that is what the evidence currently says. I strongly recommend reading blogs written by actual biologists who have studied the area for years. Another good one is Genomicron, written by U. Guelph biologist T. Ryan Gregory: http://www.genomicron.evolverzone.com/category/junk-dna/ On 9/7/12 11:03 AM, Dan Asimov wrote:
With suspecting, there's nothing to forgive.
With acting certain -- when we just don't know -- and announcing it to the world, that's not so forgivable.
--Dan
I will read them. Thanks for the links! At 08:50 AM 9/7/2012, Jeffrey Shallit wrote:
I strongly recommend reading blogs written by actual biologists who have studied the area for years. Another good one is Genomicron, written by U. Guelph biologist T. Ryan Gregory:
From a system standpoint it makes sense that the genome would accumulate a lot of junk. Simple natural selection preserves [currently] essential components of the genome; errors and omissions would mostly negatively impact the probability of survival of progeny. Since errors and omissions are unavoidable given limited resources, some level of functional redundancy is preserved as well. This redundancy may include both duplicate pieces of genome as well as pieces that code alternative methods for producing the same function. But the ability to adapt to inevitably changing conditions over time is essential to preserving a genomic lineage, and so the reproduction mechanism needs to produce "errors" and duplicates at some frequency, and to preserve the resulting "junk" (which it doesn't really know is junk). In the absence of the "junk" turning into nonjunk, by acquiring some role, whether positive or negative, evolution will just carry the junk along and continue to mutate it. Only if the junk interferes with the nonjunk, or when the burden of carrying all that extra DNA is sufficiently large, will natural selection tend to eliminate it. A sufficiently intelligent life form, if one ever evolves, might eliminate the need for this genomic-based adaptation mechanism. --ms On 07-Sep-12 11:50, Jeffrey Shallit wrote:
Well, I don't agree at all. There are *good reasons* to believe that much of the genome is junk (see, for example, the experiments referred to on Larry Moran's blog) and it is completely reasonable to deduce this from what is currently known. Could the junk proponents be wrong? Of course - all science is provisional. Nevertheless, that is what the evidence currently says.
I strongly recommend reading blogs written by actual biologists who have studied the area for years. Another good one is Genomicron, written by U. Guelph biologist T. Ryan Gregory:
http://www.genomicron.evolverzone.com/category/junk-dna/
On 9/7/12 11:03 AM, Dan Asimov wrote:
With suspecting, there's nothing to forgive.
With acting certain -- when we just don't know -- and announcing it to the world, that's not so forgivable.
--Dan
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Neither Internet Explorer nor Firefox shows anything but the first snippet of each entry in this blog, and there is no place to click to expand the entries. Clearly, this fellow understands more about biology than about software. At 08:50 AM 9/7/2012, Jeffrey Shallit wrote:
I strongly recommend reading blogs written by actual biologists who have studied the area for years. Another good one is Genomicron, written by U. Guelph biologist T. Ryan Gregory:
You just click on the title of each article. Seems kind of obvious to me. Sorry it was so difficult for you to figure that out. On 9/7/12 4:15 PM, Henry Baker wrote:
Neither Internet Explorer nor Firefox shows anything but the first snippet of each entry in this blog, and there is no place to click to expand the entries.
Clearly, this fellow understands more about biology than about software.
At 08:50 AM 9/7/2012, Jeffrey Shallit wrote:
I strongly recommend reading blogs written by actual biologists who have studied the area for years. Another good one is Genomicron, written by U. Guelph biologist T. Ryan Gregory:
Yes, but the only thing that "lights up" when you "mouse over" it is the "..." (dot dot dot) at the end, but when you click on that "...", nothing happens. Very poor GUI design. At 04:54 AM 9/8/2012, Jeffrey Shallit wrote:
You just click on the title of each article. Seems kind of obvious to me. Sorry it was so difficult for you to figure that out.
On 9/7/12 4:15 PM, Henry Baker wrote:
Neither Internet Explorer nor Firefox shows anything but the first snippet of each entry in this blog, and there is no place to click to expand the entries.
Clearly, this fellow understands more about biology than about software.
At 08:50 AM 9/7/2012, Jeffrey Shallit wrote:
I strongly recommend reading blogs written by actual biologists who have studied the area for years. Another good one is Genomicron, written by U. Guelph biologist T. Ryan Gregory:
http://selab.janelia.org/people/eddys/blog/?p=683 I certainly hope this is readable by everyone, and passes the test for good user interface. But if anyone needs step-by-step instructions on how to read it, perhaps a small child nearby can help.
Regarding http://www.genomicron.evolverzone.com/category/junk-dna/ With javascript enabled, I am asked to install "missing plugins" (apparently Flash, a hallmark of poorly done web pages). Looking at the source, there is a lot of scripting (including special treatment of Internet Explorer, by versions). The <noscript></noscript> missing for all but one trivial case. The headlines are set to NOT change appearance with mouse-over (terminally stupid!). So, yes, poor design (technical, not talking eye candy) indeed. Certainly in good company with very many "shiny defeats function" pages that use god-awful scripting where one line of HTML would have done. I have seen the "forever rotating dots" phenomenon (apparently described by Henry) with very many web pages, but, for the record, not with this one. http://validator.w3.org/ gives, for this page, 204 Errors and 288 warnings, see http://validator.w3.org/check?uri=http%3A%2F%2Fwww.genomicron.evolverzone.co... Browsers have to be exceedingly forgiving to show anything at all for such an utterly broken page. Best, jj * Jeffrey Shallit <shallit@uwaterloo.ca> [Sep 09. 2012 07:56]:
http://selab.janelia.org/people/eddys/blog/?p=683
I certainly hope this is readable by everyone, and passes the test for good user interface. But if anyone needs step-by-step instructions on how to read it, perhaps a small child nearby can help.
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Doesn't clicking on each headline work? --Dan On 2012-09-07, at 1:15 PM, Henry Baker wrote:
Neither Internet Explorer nor Firefox shows anything but the first snippet of each entry in this blog, and there is no place to click to expand the entries.
Clearly, this fellow understands more about biology than about software.
At 08:50 AM 9/7/2012, Jeffrey Shallit wrote:
I strongly recommend reading blogs written by actual biologists who have studied the area for years. Another good one is Genomicron, written by U. Guelph biologist T. Ryan Gregory:
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Mike Speciner -
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Warren Smith