Chances Are Our Hearing Didn't Evolve "To Do" Anything

[Jud]

Do you understand the discrepancy in the 80% and 9% numbers you've quoted? Most if not all my comments are hints for you to see why the 9% conclusion is invalid -- to the extent that assuming a gene sequence with polymorphisms is less "important". Let me try to explain: suppose the gap has to due with massive redundancy of various types. The evolutionary value of such redundancy *could* allow the genome to survive despite a series of mutations, or it could have other value that you nor I can imagine.

 

Very plainly: the argument that because a gene sequence is not invariant over time, that it is not "important" is invalid. I find the papers that argue this to use trivial and frankly unsophisticated arguments. I've given you counterexample after counterexample so instead I invite you to go back and read every comment I've made and be sure you understand what I am saying. If you have a hard time understanding a specific comment and why it pertains to this argument, please ask and I'll try to explain.

 

Let's start here: suppose my music library is stored on a mirrored volume -- that means it takes up 2x the amount of space -- is that a waste? In the short terms, perhaps yes, but in the long term and statistically, the data is more protected. So I am paying upfront $$ for longer term protection. Evolution is a long term process, so while short term redundancy may result in large numbers of transcriptionally inactive genes, long term is different. -- and this is just one analogy, there are many many other issues.

 

But whether the ENCODE number is 80% or 50% or 95% is not really important in my view. The 9% number is totally irrelevant in my view. I've hardly begun to list the reasons why but think along the lines that mutations are encouraged and desirable in certain situations, that there is a strong evolutionary value in biodiversity. That things which appear to be inefficient in the short term turn out to be essential in the long term. That biology is smarter than we are. etc. etc. etc.

Thanks jabbr, this is helpful. As usual I have lots of questions, but will try to hold them until I've read through more of your references.

[Jud]

I saw it - you might want to try being less of an internet expert in areas you aren't trained in.

 

I would be very happy to. Corrections (here is another term that is more appropriate...) or still better, contributions (the concept is invalid or inappropriate to use in this context, and here's why, or here's a reference...) are gratefully accepted. Of course there are difficulties - we all are busy with other things to do with jobs and real life, I entirely lack fundamental background - but where it is possible to provide information, I'm eager to look at it.

[jabbr]

There probably is a need for a really good book directed at the intelligent lay audience which describe all the frankly amazing discoveries and knowledge about modern molecular genetics/genomics.

 

I think, unfortunately, that most discussions of genes have to do with inheritance and don't properly cover the role of DNA/RNA in modern cell biology.

 

"Lives of a cell" is now too dated.

 

Are there books at this level? I.e. Better than Dawkins and without an agenda other than teaching people about the cool stuff.

 

@Ralf11 is right, the undergrads just start to learn the language that awaits grad level. At least that was the case waay back. Perhaps the undergrads are learning more now. Then again if they can't tell time in @wgscott's class I expect they probably figure the retrotransposon is a fancy time machine more appropriate for "Back To The Future, Part VII"

[Jud]

There probably is a need for a really good book directed at the intelligent lay audience which describe all the frankly amazing discoveries and knowledge about modern molecular genetics/genomics.

 

I think, unfortunately, that most discussions of genes have to do with inheritance and don't properly cover the role of DNA/RNA in modern cell biology.

 

"Lives of a cell" is now too dated.

 

Are there books at this level? I.e. Better than Dawkins and without an agenda other than teaching people about the cool stuff.

 

I'd love to see something like this too. My interest in the topic came through an interest in evolution, so books on topics connected with evolution are by far the greater part of what I've read. This was very good, but it's not what you're asking for (and it's by a science journalist rather than a scientist, albeit a very good one):

 

https://www.amazon.com/dp/B0013TPV7O/ref=dp-kindle-redirect?_encoding=UTF8&btkr=1

[Ralf11]

The problem is that no one is likely to write it. Faculty get no rewards for communicating with the lay public. The only thing that matters is getting research dollars (to support the Dean, and central administration) and getting grad. students out there to perpetuate ideas and directions. They also get no rewards for undergraduate teaching. In fact, I was astounded recently to learn that a professor at a research university was proctoring his own exams.

 

Stephen Jay Gould is an exception (he did it anyway, via essays) and even wrote an essay on the above.

 

Actually, you'd enjoy reading his essay jud. Also, he was big on stasis and rejects a lot of adaptationism, so may fit your preconceptions too. Start with "The Panda's Thumb."

[jabbr]

I'd love to see something like this too. My interest in the topic came through an interest in evolution, so books on topics connected with evolution are by far the greater part of what I've read.

 

There is a line of thought that starts with the discovery of reverse transcriptase in 1970, and which has been steadily accelerated that essentially throws traditional dogma of genes as being changed through random DNA mutations on its head. The regions of so-called "junk" DNA have been reconsidered in light of this. So from an evolutionary point of view there is much to be learned.

[Jud]

The problem is that no one is likely to write it. Faculty get no rewards for communicating with the lay public. The only thing that matters is getting research dollars (to support the Dean, and central administration) and getting grad. students out there to perpetuate ideas and directions. They also get no rewards for undergraduate teaching. In fact, I was astounded recently to learn that a professor at a research university was proctoring his own exams.

 

Stephen Jay Gould is an exception (he did it anyway, via essays) and even wrote an essay on the above.

 

Actually, you'd enjoy reading his essay jud. Also, he was big on stasis and rejects a lot of adaptationism, so may fit your preconceptions too. Start with "The Panda's Thumb."

 

I've read a few Gould books, including Panda's Thumb, Mismeasure of Man, Full House, Hen's Teeth and Horse's Toes, and my favorite, Wonderful Life, as well as many of his essays in Natural History magazine. Not the "big one" (The Structure of Evolutionary Theory), though.

 

Someone else whose books I've enjoyed is journalist/non-scientist David Quammen. Song of the Dodo, regarding island biogeography and extinction, is my favorite.

[Jud]

There is a line of thought that starts with the discovery of reverse transcriptase in 1970, and which has been steadily accelerated that essentially throws traditional dogma of genes as being changed through random DNA mutations on its head. The regions of so-called "junk" DNA have been reconsidered in light of this. So from an evolutionary point of view there is much to be learned.

 

There was a New York Times Magazine article (by Carl Zimmer) on this whole kerfuffle, which I thought was balanced in presentation; don't know what you'll think. Can be found here: http://www.nytimes.com/2015/03/08/magazine/is-most-of-our-dna-garbage.html

[jabbr]

There was a New York Times Magazine article (by Carl Zimmer) on this whole kerfuffle, which I thought was balanced in presentation; don't know what you'll think. Can be found here: http://www.nytimes.com/2015/03/08/magazine/is-most-of-our-dna-garbage.html

 

Oh that's where you get some if these ideas. Balanced? It makes it seem like there are two sides to a debate -- and full of internal inconsistencies -- I'd take Francis Collins' view. The people in the field who I know don't debate this -- as I said above there are two kinds of DNA -- folks who think nonfunctional DNA don't have sufficient imaginations

[wgscott]

In fact, I was astounded recently to learn that a professor at a research university was proctoring his own exams.

 

Except for one exam, when I was out of town on an NIH grant review panel, I have proctored every exam I have given for the last 19 years.

[Jud]

Oh that's where you get some if these ideas. Balanced? It makes it seem like there are two sides to a debate -- and full of internal inconsistencies -- I'd take Francis Collins' view. The people in the field who I know don't debate this -- as I said above there are two kinds of DNA -- folks who think nonfunctional DNA don't have sufficient imaginations

 

I'm shocked (not).

 

While Collins certainly has the qualifications, he has a deep religious faith. I don't know whether that predisposes him to favor less junk. Of course there are plenty more scientists who favor the same view as Collins (and you). According to Zimmer's article, that view is currently in the ascendancy (I assume you feel that's something of an understatement).

 

 

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[wgscott]

While Collins certainly has the qualifications, he has a deep religious faith. I don't know whether that predisposes him to favor less junk.

 

It does, because why would a deity create junk or guide evolution to create junk?

 

Logically, he could be right for the wrong reasons.

[Ralf11]

Except for one exam, when I was out of town on an NIH grant review panel, I have proctored every exam I have given for the last 19 years.

 

At Wisc. the Zool. Dept. only allows full profs. to teach freshmen or used to). It's too bad there is not more emphasis on quality teaching.

 

BTW, Note that I didn't name you.

 

 

Also... why are we allowing chemists to horn in on OUR ribosomes??

[Jud]

It does, because why would a deity create junk or guide evolution to create junk?

 

Logically, he could be right for the wrong reasons.

 

I don't want to presume to read his mind, and he was a witness in favor of science in Kitzmiller, but your reasoning is why I raised the point.

 

As you say, he could be right for the wrong reasons, and there are plenty of other scientists who agree.

 

 

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[Ralf11]

The real question is how much of the junk is junk...

[Jud]

The real question is how much of the junk is junk...

 

Here's a list from the Sandwalk blog that I've referenced a couple of times. I'd be interested to read folks' comments on whether there are particular components of this list you would agree with or dispute, whether you think the whole thing's risible....

 

Junk in Your Genome

 

Transposable Elements: (44% junk)

DNA transposons: active (functional): <0.1%

defective (nonfunctional): 3%

retrotransposons: active (functional): <0.1%

defective transposons (full-length, nonfunctional): 8%

L1 LINES (fragments, nonfunctional): 16%

other LINES: 4%

SINES (small pseudogene fragments): 13%

co-opted transposons/fragments: <0.1% (Co-opted transposons and transposon fragments are those that have secondarily acquired a new function.)

Viruses (9% junk)

DNA viruses active (functional): <0.1%

defective DNA viruses: ~1%

RNA viruses active (functional): <0.1%

defective (nonfunctional): 8%

co-opted RNA viruses: <0.1% (Co-opted RNA viruses are defective integrated virus genomes that have secondarily acquired a new function.)

Pseudogenes (1.2% junk)

(from protein-encoding genes): 1.2% junk

co-opted pseudogenes: <0.1% (Co-opted pseudogenes are formerly defective pseudogenes those that have secondarily acquired a new function.)

Ribosomal RNA genes: essential 0.22% junk 0.19%

Other RNA encoding genes

tRNA genes: <0.1% (essential)

known small RNA genes: <0.1% (essential)

putative regulatory RNAs: ~2% (essential)

Protein-encoding genes: (9.6% junk)

transcribed region: essential 1.8%

intron junk (not included above) 9.6% (Introns sequences account for about 30% of the genome. Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA.)

Regulatory sequences: essential 0.6%

Origins of DNA replication <0.1% (essential)

Scaffold attachment regions (SARS) <0.1% (essential)

Highly Repetitive DNA (1% junk)

α-satellite DNA (centromeres) essential 2.0% non-essential 1.0%

telomeres essential (less than 1000 kb, insignificant)

Intergenic DNA (not included above) conserved 2% (essential)

non-conserved 26.3% (unknown but probably junk)

 

Total Essential/Functional (so far) = 8.7%

 

Total Junk (so far) = 65%

 

Unknown (probably mostly junk) = 26.3%

 

LAST UPDATE: May 10, 2011 (fixed totals, and ribosomal RNA calculations)

[jabbr]

I'm shocked (not).

 

While Collins certainly has the qualifications, he has a deep religious faith. I don't know whether that predisposes him to favor less junk. Of course there are plenty more scientists who favor the same view as Collins (and you). According to Zimmer's article, that view is currently in the ascendancy (I assume you feel that's something of an understatement).

 

 

Uh ... without getting into details of my background that position was assumed by the people I've hung out with for the last 30 years or so to the point where it was never really discussed -- more like : hey isn't this sequence really cool -- wonder what it does?

[jabbr]

It does, because why would a deity create junk or guide evolution to create junk?

 

Logically, he could be right for the wrong reasons.

 

No deity needed -- how can you ever be sure something is junk? eg might be binding scaffold -- even deciding whether x y or z is junk presupposes we understand what everything does which is just stupid

[jabbr]

Here's a list from the Sandwalk blog that I've referenced a couple of times. I'd be interested to read folks' comments on whether there are particular components of this list you would agree with or dispute, whether you think the whole thing's risible....

 

Junk in Your Genome

 

Transposable Elements: (44% junk)

DNA transposons: active (functional): <0.1%

defective (nonfunctional): 3%

retrotransposons: active (functional): <0.1%

defective transposons (full-length, nonfunctional): 8%

L1 LINES (fragments, nonfunctional): 16%

other LINES: 4%

SINES (small pseudogene fragments): 13%

co-opted transposons/fragments: <0.1% (Co-opted transposons and transposon fragments are those that have secondarily acquired a new function.)

Viruses (9% junk)

DNA viruses active (functional): <0.1%

defective DNA viruses: ~1%

RNA viruses active (functional): <0.1%

defective (nonfunctional): 8%

co-opted RNA viruses: <0.1% (Co-opted RNA viruses are defective integrated virus genomes that have secondarily acquired a new function.)

Pseudogenes (1.2% junk)

(from protein-encoding genes): 1.2% junk

co-opted pseudogenes: <0.1% (Co-opted pseudogenes are formerly defective pseudogenes those that have secondarily acquired a new function.)

Ribosomal RNA genes: essential 0.22% junk 0.19%

Other RNA encoding genes

tRNA genes: <0.1% (essential)

known small RNA genes: <0.1% (essential)

putative regulatory RNAs: ~2% (essential)

Protein-encoding genes: (9.6% junk)

transcribed region: essential 1.8%

intron junk (not included above) 9.6% (Introns sequences account for about 30% of the genome. Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA.)

Regulatory sequences: essential 0.6%

Origins of DNA replication <0.1% (essential)

Scaffold attachment regions (SARS) <0.1% (essential)

Highly Repetitive DNA (1% junk)

α-satellite DNA (centromeres) essential 2.0% non-essential 1.0%

telomeres essential (less than 1000 kb, insignificant)

Intergenic DNA (not included above) conserved 2% (essential)

non-conserved 26.3% (unknown but probably junk)

 

Total Essential/Functional (so far) = 8.7%

 

Total Junk (so far) = 65%

 

Unknown (probably mostly junk) = 26.3%

 

LAST UPDATE: May 10, 2011 (fixed totals, and ribosomal RNA calculations)

 

Do you know what a LINE is?? What is the evidence for and against their functionality? Did you even read the very first reference I quoted?

[wgscott]

Transposable Elements: (44% junk)

 

So is that 44% of the whole genome? If so, dismissing all those transposons as "junk" might be an overstatement.

[wgscott]

Do you know what a LINE is?? What is the evidence for and against their functionality? Did you even read the very first reference I quoted?

 

Retrotransposons are about 20% of the human genome. I believe they have been invoked in explaining generating diversity in developmental neurobiology, but that is kind of getting away from my comfort zone.

[Jud]

Do you know what a LINE is?? What is the evidence for and against their functionality? Did you even read the very first reference I quoted?

 

Yes, I did read it. This isn't my list - I transcribed the list that was on the blog for the purpose of asking for comments in order to continue to learn more about the subject.

[jabbr]

Yes, I did read it. This isn't my list - I transcribed the list that was on the blog for the purpose of asking for comments in order to continue to learn more about the subject.

 

So according to the article: what are LINES involved with?

[Jud]

So is that 44% of the whole genome? If so, dismissing all those transposons as "junk" might be an overstatement.

 

Yes, I believe the 44% is intended to refer to the entire genome. (Sorry, the formatting didn't carry over from the web page, which is at Sandwalk: Theme: Genomes & Junk DNA .)

[Jud]

So according to the article: what are LINES involved with?

 

I took it from the article that LINES may be involved in nuclear architecture and through that functionality.