Re: code for 32/64 bit strtoul strtol strtoull strtoll

From	James Kuyper <jameskuyper@verizon.net>
Newsgroups	comp.lang.c
Subject	Re: code for 32/64 bit strtoul strtol strtoull strtoll
Date	2015-03-31 23:33 -0400
Organization	A noiseless patient Spider
Message-ID	<mffota$4pb$1@dont-email.me> (permalink)
References	(10 earlier) <551AF2FC.8080802@verizon.net> <mfeu1b$ulk$1@speranza.aioe.org> <551B09BE.5080109@verizon.net> <76ef08ab-2319-4b5f-a994-5d80e0604aa5@googlegroups.com> <87mw2siup6.fsf@kst-u.example.com>

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On 03/31/2015 08:00 PM, Keith Thompson wrote:
> Malcolm McLean <malcolm.mclean5@btinternet.com> writes:
>> On Tuesday, March 31, 2015 at 9:55:38 PM UTC+1, James Kuyper wrote:
>>> Given that ribosomes translate base pair triplets into amino acids,
>>> there might be some value in wasting a little space encoding only three
>>> base pairs per byte. On the other hand, since a triplet can start with
>>> any given base pair, depending upon where the ribosome starts reading,
>>> that might not be worthwhile (there are particular base pair sequences
>>> that serve to align the ribosomes to the "correct" starting point for a
>>> given gene - there's also some cases where those alignment clues are
>>> missing, where  multiple different proteins are encoded by the same DNA
>>> sequence, depending upon where you start).
>>>
>> There might be a case of an overlapping gene with a different frame
>> somewhere, but it's extremely rare.

Yes, it is, and correspondingly interesting when it happens. I first
read about it in connection with a virus which was carried around in a
structure that was made of a fixed and relatively small number of
protein units arranged in a strict geometric shape. The central part
looked like a geodesic dome, plus there were "legs" and an an injector
that was used to penetrate cell walls. There was only a tiny amount of
room inside that structure for any genetic material, and the structure
was not scalable - any change in it's size would require radical change
to the structure of the proteins that made it up. As a result, there was
strong evolutionary pressure to keep the genetic payload as small as
possible. I believe it was a plasmid - a short circle of RNA. Unlikely
typical human DNA, almost every base pair was used in at least one gene,
and most of them were involved in two, as a result of using an alternate
reading frame. I was very impressed, which is why I still remember the
concept.
The name of virus - that's another matter - that's not nearly as
interesting, and I no longer remember it.

>> If you start transcribing RNA out of frame, it's like taking ascii
>> text and shifting everything along by two bits - the result has to
>> be nonsense, it won't form a functional protein but just a blob
>> with no particular secondary or tertiary structure.

That's what you'd normally expect, which why normal DNA has special
"start" sequences that tell the ribosomes the correct reading frame to
use. The fact that the plasmid I'm talking about made efficient use of
alternate reading frames to encode multiple working genes was what made
it so impressive.
It was only possible because of the redundancy of the genetic code.
There's 64 possible sequences of 3 consecutive base pairs, and only 21
different amino acids that they code for. There's multiple different
encodings for the same amino acid. As a result, the protein encoded when
you use one reading frame does not uniquely determine which protein is
encoded if you use a different reading frame. Without that freedom,
there's no way the plasmid I described would have had any reasonable
chance of evolving.
-- 
James Kuyper

Thread

code for 32/64 bit strtoul strtol strtoull strtoll jacob navia <jacob@jacob.remcomp.fr> - 2015-03-29 17:33 +0200
  code for 32/64 bit strtoul strtol strtoull strtoll asetofsymbols@gmail.com - 2015-03-29 09:22 -0700
    Re: code for 32/64 bit strtoul strtol strtoull strtoll Barry Schwarz <schwarzb@dqel.com> - 2015-03-29 15:12 -0700
      Re: code for 32/64 bit strtoul strtol strtoull strtoll asetofsymbols@gmail.com - 2015-03-29 23:07 -0700
  Re: code for 32/64 bit strtoul strtol strtoull strtoll Barry Schwarz <schwarzb@dqel.com> - 2015-03-29 09:44 -0700
    Re: code for 32/64 bit strtoul strtol strtoull strtoll jacob navia <jacob@jacob.remcomp.fr> - 2015-03-29 19:05 +0200
      Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-29 12:15 -0700
  Re: code for 32/64 bit strtoul strtol strtoull strtoll Ben Bacarisse <ben.usenet@bsb.me.uk> - 2015-03-30 02:01 +0100
    Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-29 19:48 -0700
      Re: code for 32/64 bit strtoul strtol strtoull strtoll Barry Schwarz <schwarzb@dqel.com> - 2015-03-29 22:08 -0700
        Re: code for 32/64 bit strtoul strtol strtoull strtoll Ben Bacarisse <ben.usenet@bsb.me.uk> - 2015-03-30 12:44 +0100
          Re: code for 32/64 bit strtoul strtol strtoull strtoll Barry Schwarz <schwarzb@dqel.com> - 2015-03-30 09:04 -0700
            Re: code for 32/64 bit strtoul strtol strtoull strtoll Ben Bacarisse <ben.usenet@bsb.me.uk> - 2015-03-30 21:00 +0100
        Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-30 08:24 -0700
      Re: code for 32/64 bit strtoul strtol strtoull strtoll Tim Rentsch <txr@alumni.caltech.edu> - 2015-03-30 07:21 -0700
  Re: code for 32/64 bit strtoul strtol strtoull strtoll Ian Collins <ian-news@hotmail.com> - 2015-03-30 18:02 +1300
    Re: code for 32/64 bit strtoul strtol strtoull strtoll Richard Heathfield <rjh@cpax.org.uk> - 2015-03-30 08:03 +0100
      Re: code for 32/64 bit strtoul strtol strtoull strtoll Ian Collins <ian-news@hotmail.com> - 2015-03-30 20:33 +1300
        Re: code for 32/64 bit strtoul strtol strtoull strtoll Ian Collins <ian-news@hotmail.com> - 2015-03-30 20:35 +1300
  Re: code for 32/64 bit strtoul strtol strtoull strtoll Tim Rentsch <txr@alumni.caltech.edu> - 2015-03-30 07:27 -0700
  Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-30 09:08 -0700
  Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-30 09:29 -0700
  Re: code for 32/64 bit strtoul strtol strtoull strtoll Robert Wessel <robertwessel2@yahoo.com> - 2015-03-30 15:16 -0500
    Re: code for 32/64 bit strtoul strtol strtoull strtoll jacob navia <jacob@jacob.remcomp.fr> - 2015-03-31 00:15 +0200
      Re: code for 32/64 bit strtoul strtol strtoull strtoll Robert Wessel <robertwessel2@yahoo.com> - 2015-03-31 01:42 -0500
    Re: code for 32/64 bit strtoul strtol strtoull strtoll Bartc <bc@freeuk.com> - 2015-03-30 23:39 +0100
      Re: code for 32/64 bit strtoul strtol strtoull strtoll Robert Wessel <robertwessel2@yahoo.com> - 2015-03-31 01:44 -0500
        Re: code for 32/64 bit strtoul strtol strtoull strtoll Bartc <bc@freeuk.com> - 2015-03-31 13:01 +0100
          Re: code for 32/64 bit strtoul strtol strtoull strtoll Malcolm McLean <malcolm.mclean5@btinternet.com> - 2015-03-31 05:13 -0700
          Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-31 08:06 -0700
            Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-31 08:26 -0700
            Re: code for 32/64 bit strtoul strtol strtoull strtoll Richard Heathfield <rjh@cpax.org.uk> - 2015-03-31 16:40 +0100
              Re: code for 32/64 bit strtoul strtol strtoull strtoll Malcolm McLean <malcolm.mclean5@btinternet.com> - 2015-03-31 09:39 -0700
              Re: code for 32/64 bit strtoul strtol strtoull strtoll Kaz Kylheku <kaz@kylheku.com> - 2015-03-31 18:22 +0000
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Richard Heathfield <rjh@cpax.org.uk> - 2015-03-31 19:36 +0100
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-31 12:11 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Kaz Kylheku <kaz@kylheku.com> - 2015-03-31 19:23 +0000
            Re: code for 32/64 bit strtoul strtol strtoull strtoll Bartc <bc@freeuk.com> - 2015-03-31 16:52 +0100
              Re: code for 32/64 bit strtoul strtol strtoull strtoll glen herrmannsfeldt <gah@ugcs.caltech.edu> - 2015-03-31 17:54 +0000
                Re: code for 32/64 bit strtoul strtol strtoull strtoll raltbos@xs4all.nl (Richard Bos) - 2015-03-31 18:51 +0000
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Richard Heathfield <rjh@cpax.org.uk> - 2015-03-31 20:05 +0100
                Re: code for 32/64 bit strtoul strtol strtoull strtoll James Kuyper <jameskuyper@verizon.net> - 2015-03-31 15:18 -0400
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Richard Heathfield <rjh@cpax.org.uk> - 2015-03-31 20:49 +0100
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Malcolm McLean <malcolm.mclean5@btinternet.com> - 2015-03-31 13:06 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll raltbos@xs4all.nl (Richard Bos) - 2015-04-06 13:03 +0000
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Bartc <bc@freeuk.com> - 2015-04-06 14:27 +0100
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Richard Heathfield <rjh@cpax.org.uk> - 2015-04-06 17:01 +0100
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Malcolm McLean <malcolm.mclean5@btinternet.com> - 2015-04-06 11:25 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll James Kuyper <jameskuyper@verizon.net> - 2015-04-06 23:34 -0400
                Re: code for 32/64 bit strtoul strtol strtoull strtoll glen herrmannsfeldt <gah@ugcs.caltech.edu> - 2015-04-07 03:46 +0000
                Re: code for 32/64 bit strtoul strtol strtoull strtoll James Kuyper <jameskuyper@verizon.net> - 2015-04-08 11:05 -0400
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Malcolm McLean <malcolm.mclean5@btinternet.com> - 2015-04-08 08:31 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll glen herrmannsfeldt <gah@ugcs.caltech.edu> - 2015-03-31 19:54 +0000
                Re: code for 32/64 bit strtoul strtol strtoull strtoll James Kuyper <jameskuyper@verizon.net> - 2015-03-31 16:55 -0400
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Bartc <bc@freeuk.com> - 2015-03-31 22:20 +0100
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-31 14:36 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Malcolm McLean <malcolm.mclean5@btinternet.com> - 2015-03-31 14:55 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-31 17:00 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Bartc <bc@freeuk.com> - 2015-04-01 01:24 +0100
                Re: code for 32/64 bit strtoul strtol strtoull strtoll James Kuyper <jameskuyper@verizon.net> - 2015-03-31 23:33 -0400
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Richard Heathfield <rjh@cpax.org.uk> - 2015-04-01 04:42 +0100
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Bartc <bc@freeuk.com> - 2015-03-31 20:26 +0100
            Re: code for 32/64 bit strtoul strtol strtoull strtoll Ian Collins <ian-news@hotmail.com> - 2015-04-01 10:33 +1300
              Re: code for 32/64 bit strtoul strtol strtoull strtoll Robert Wessel <robertwessel2@yahoo.com> - 2015-04-01 04:33 -0500
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Bartc <bc@freeuk.com> - 2015-04-01 12:43 +0100
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Robert Wessel <robertwessel2@yahoo.com> - 2015-04-02 01:02 -0500
                Re: code for 32/64 bit strtoul strtol strtoull strtoll asetofsymbols@gmail.com - 2015-04-01 23:57 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Robert Wessel <robertwessel2@yahoo.com> - 2015-04-03 00:29 -0500
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Malcolm McLean <malcolm.mclean5@btinternet.com> - 2015-04-02 09:01 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-04-02 14:30 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Robert Wessel <robertwessel2@yahoo.com> - 2015-04-03 00:39 -0500
                Re: code for 32/64 bit strtoul strtol strtoull strtoll glen herrmannsfeldt <gah@ugcs.caltech.edu> - 2015-04-01 15:55 +0000

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