Comments on: Genes != Proteins http://www.sciscoop.com/2004-9-20-204150-407.html Scooping up science news and dropping it on your desk Thu, 18 Mar 2010 16:03:57 +0000 http://wordpress.org/?v=2.9.2 hourly 1 By: apsmith http://www.sciscoop.com/2004-9-20-204150-407.html/comment-page-1#comment-4860 apsmith Tue, 28 Sep 2004 20:47:18 +0000 http://localhost/~arielschwartz/wordpress/sciscoop/?p=2183#comment-4860 Yes, I think it's the link between those two things (prokaryote/eukaryote differences in cell structure and in DNA structure) that made me sit up and pay attention. But maybe this is something geneticists have been aware of for years, and is only now reaching a more general public? Any biologists out there to enlighten us? Yes, I think it’s the link between those two things (prokaryote/eukaryote differences in cell structure and in DNA structure) that made me sit up and pay attention. But maybe this is something geneticists have been aware of for years, and is only now reaching a more general public? Any biologists out there to enlighten us?

]]> By: Sweetwind http://www.sciscoop.com/2004-9-20-204150-407.html/comment-page-1#comment-4654 Sweetwind Tue, 28 Sep 2004 09:17:20 +0000 http://localhost/~arielschwartz/wordpress/sciscoop/?p=2183#comment-4654 <a href="http://www.sciam.com/article.cfm?chanID=sa006&colID=1&articleID=00045BB6-5D49-1150-902F83414B7F4945">The Hidden Genetic Program of Complex Organisms</a> The Hidden Genetic Program of Complex Organisms

]]> By: Sweetwind http://www.sciscoop.com/2004-9-20-204150-407.html/comment-page-1#comment-4400 Sweetwind Tue, 28 Sep 2004 09:07:26 +0000 http://localhost/~arielschwartz/wordpress/sciscoop/?p=2183#comment-4400 One thing that struck me in Mattick's thesis was the wide gap between the prokaryotes and the eukaryotes. We learn in secondary school that eukaryotes have a cell nucleus that keeps all the DNA inside, and prokaryotes don't, and there never seemed to be an articulated reason WHY. Mattick's article explains exactly WHY -- prokaryotes do everything directly with proteins, so transcription can occur very simply. Eukaryotes need to perform the DNA transcription inside a nucleus so that the second-level information (in the "junk" DNA) can work in privacy to direct HOW the RNA will be transcribed to proteins once it gets outside the nucleus. One thing that struck me in Mattick’s thesis was the wide gap between the prokaryotes and the eukaryotes. We learn in secondary school that eukaryotes have a cell nucleus that keeps all the DNA inside, and prokaryotes don’t, and there never seemed to be an articulated reason WHY. Mattick’s article explains exactly WHY — prokaryotes do everything directly with proteins, so transcription can occur very simply. Eukaryotes need to perform the DNA transcription inside a nucleus so that the second-level information (in the “junk” DNA) can work in privacy to direct HOW the RNA will be transcribed to proteins once it gets outside the nucleus.

]]> By: Sweetwind http://www.sciscoop.com/2004-9-20-204150-407.html/comment-page-1#comment-4072 Sweetwind Fri, 24 Sep 2004 07:39:00 +0000 http://localhost/~arielschwartz/wordpress/sciscoop/?p=2183#comment-4072 Happy happy, joy joy!<p>But still not online. Happy happy, joy joy!

But still not online.

]]> By: Sweetwind http://www.sciscoop.com/2004-9-20-204150-407.html/comment-page-1#comment-3649 Sweetwind Thu, 23 Sep 2004 08:29:29 +0000 http://localhost/~arielschwartz/wordpress/sciscoop/?p=2183#comment-3649 as of Wednesday's mail. Maybe you live closer to the distributor.<p> On second thought, this happened before, right about the time this site was founded (so it might have been the October 2002 issue). Every other subscriber I knew had gotten their issues three weeks before, so I called the SciAm customer center and they extended my subscription by an issue to make up for it. But before I bought a replacement copy, the subscription copy finally showed up. It was all wrapped in plastic and contained a promotional CD-ROM for genetic therapies or something, so I figured my P. O. didn't like the packaging...<p> Out of pique, today's quote is from the September issue :-) as of Wednesday’s mail. Maybe you live closer to the distributor.

On second thought, this happened before, right about the time this site was founded (so it might have been the October 2002 issue). Every other subscriber I knew had gotten their issues three weeks before, so I called the SciAm customer center and they extended my subscription by an issue to make up for it. But before I bought a replacement copy, the subscription copy finally showed up. It was all wrapped in plastic and contained a promotional CD-ROM for genetic therapies or something, so I figured my P. O. didn’t like the packaging…

Out of pique, today’s quote is from the September issue :-)

]]> By: Anonymous http://www.sciscoop.com/2004-9-20-204150-407.html/comment-page-1#comment-3110 Anonymous Wed, 22 Sep 2004 07:47:57 +0000 http://localhost/~arielschwartz/wordpress/sciscoop/?p=2183#comment-3110 I mentioned in a commentary on the Sweet Fat story that over evolutionary time biomacromolecules have developed more and more toggles and switches for regulatory integration. This is readily seen in the proteins- forms not only get bigger with time and end up with all sorts of bits and pieces that stick out waiting for interaction, but through RNA editing one can have many variant final protein products from the same underlying DNA. And of course genes duplicate and then diversify their products at the DNA level as well.<p> t-RNA's have diverse covalently modified forms as well, which may allow tweaking of their activity in different environmental and physiological conditions. <p> "Junk DNA" regulation just seems to be the natural extension of these regulatory adaptations to the genetic storage forms, just as extra loop material on RNA is. <p> We're already well aware of the base encoding which allows conversion of nucleic acid sequences to protein, and I mentioned in the Sweet Fat comment the possibility of a state-space sugar code. Why could there not also be an internal nontranscriptional/translational code in the DNA sequencing itself? Partially based on relative position in the strand, partially on tension, shape, and solubility effects at the local level, and of course partially dependent on actual transcript coding sequences as well as the introns.<p> By the way- the lipid membranes themselves, an assemblage of polymers though not a classical polymer itself, might also exhibit some sort of shape-charge-solubility code at some level. We already know that varying the membrane content of lipids (which tend to zip around rather rapidly) changes the properties of the membrane (melting temperature/glass transition analog, etc.).<p> Biopolymers have two foci when it comes to purely physical interactions- those they have with themselves (Double helices in nucleic acids- either straight or loopy, secondary and tertiary structure in protein, and so on), and those they have with others of the same or different type.<p> It all may seem like a mess as new data comes in, but I'm betting not only is the evolved systematicity of the inner workings of living cells NOT a kluge, but should be in many ways iconically based, and any arbitrary symbolicity should be traceable back to original iconicity.<p> Codemaniac I mentioned in a commentary on the Sweet Fat story that over evolutionary time biomacromolecules have developed more and more toggles and switches for regulatory integration. This is readily seen in the proteins- forms not only get bigger with time and end up with all sorts of bits and pieces that stick out waiting for interaction, but through RNA editing one can have many variant final protein products from the same underlying DNA. And of course genes duplicate and then diversify their products at the DNA level as well.

t-RNA’s have diverse covalently modified forms as well, which may allow tweaking of their activity in different environmental and physiological conditions.

"Junk DNA" regulation just seems to be the natural extension of these regulatory adaptations to the genetic storage forms, just as extra loop material on RNA is.

We’re already well aware of the base encoding which allows conversion of nucleic acid sequences to protein, and I mentioned in the Sweet Fat comment the possibility of a state-space sugar code. Why could there not also be an internal nontranscriptional/translational code in the DNA sequencing itself? Partially based on relative position in the strand, partially on tension, shape, and solubility effects at the local level, and of course partially dependent on actual transcript coding sequences as well as the introns.

By the way- the lipid membranes themselves, an assemblage of polymers though not a classical polymer itself, might also exhibit some sort of shape-charge-solubility code at some level. We already know that varying the membrane content of lipids (which tend to zip around rather rapidly) changes the properties of the membrane (melting temperature/glass transition analog, etc.).

Biopolymers have two foci when it comes to purely physical interactions- those they have with themselves (Double helices in nucleic acids- either straight or loopy, secondary and tertiary structure in protein, and so on), and those they have with others of the same or different type.

It all may seem like a mess as new data comes in, but I’m betting not only is the evolved systematicity of the inner workings of living cells NOT a kluge, but should be in many ways iconically based, and any arbitrary symbolicity should be traceable back to original iconicity.

Codemaniac

]]> By: apsmith http://www.sciscoop.com/2004-9-20-204150-407.html/comment-page-1#comment-2360 apsmith Tue, 21 Sep 2004 14:00:38 +0000 http://localhost/~arielschwartz/wordpress/sciscoop/?p=2183#comment-2360 It came last Saturday - sorry :-) It came last Saturday – sorry :-)

]]> By: Sweetwind http://www.sciscoop.com/2004-9-20-204150-407.html/comment-page-1#comment-1335 Sweetwind Tue, 21 Sep 2004 13:45:35 +0000 http://localhost/~arielschwartz/wordpress/sciscoop/?p=2183#comment-1335 ...and it isn't in my mailbox yet, either! So, apsmith, did you buy it off the newstand (where it usually appears first)? Cuz if you got your subscription copy in the mail AND you've already had time to read an article from it, I'm jealous! :-) …and it isn’t in my mailbox yet, either! So, apsmith, did you buy it off the newstand (where it usually appears first)? Cuz if you got your subscription copy in the mail AND you’ve already had time to read an article from it, I’m jealous! :-)

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