'Junk' DNA Mystery Solved: It's Not Needed

[Desertphile]

'Junk' DNA Mystery Solved: It's Not Needed

http://www.livescience.com/31939-junk-dna-mystery-solved.html

One person's trash may be another person's treasure, but sometimes,
trash is just trash.

So-called junk DNA, the vast majority of the genome that doesn't code
for proteins, really isn't needed for a healthy organism, according to
new research.

[...]


--
"I'm often irrelevant. It confuses people." --- Archie Goodwin

[Richard Norman]

On Sat, 18 May 2013 13:28:36 -0600, Desertphile
<Deser...@spammegmail.com> wrote:

>'Junk' DNA Mystery Solved: It's Not Needed
>
>http://www.livescience.com/31939-junk-dna-mystery-solved.html
>
>One person's trash may be another person's treasure, but sometimes,
>trash is just trash.
>
>So-called junk DNA, the vast majority of the genome that doesn't code
>for proteins, really isn't needed for a healthy organism, according to
>new research.
>

I complain when others post links to news releases or popular magazine
articles without making any contribution of their own. You have done
exactly that, merely cutting and pasting from the article. Sadly, the
"Live Science" publication doesn't even provide a link to the original
publication which can be found at
"Architecture and evolution of a minute plant genome"

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12132.html

(Full text freely available, at least for now)

[wiki trix]

On May 18, 3:55 pm, Richard Norman <r_s_nor...@comcast.net> wrote:
> On Sat, 18 May 2013 13:28:36 -0600, Desertphile
>

I found it interesting. Doubt if any additional/original contribution
by poster would have added much.

[Mitchell Coffey]

I like it when others post links to news releases or popular magazine articles without making any contribution of their own. That way they've made themselves useful by posting material unnoticed by people capable of making contributions of their own, and thus-like furthering the on-topic education of thick-headed swamp-twits like me - God's own dunderfeathers, who know less about evolutionary sciences than, than... well, than any other of God's dunderfeathers!

Desertphile, I thank thee.

Mitchell Coffey

[Ron O]

Fugu have 1/10th the DNA as you or me and some salamanders have 5
times as much. There is no doubt that a lot of the DNA doesn't do
much except keep the chromosomes together.

There are arguments where quantity has it's own quality. Some genes
are huge. A million base-pairs have to be transcribed to make a
14,000 nucleotide mRNA for the Duchene's Muscular Dystrophe gene. It
takes a lot of energy to make such a long transcript and then throw a
million nucleotides away. Fugu have not reduced the size of this gene
to 1/10th like the rest of its genome. This gene is still around
400,000 base-pairs in length in fugu. It could be just chance that it
wasn't reduced in size as much as the rest of the genome, but some
have speculated that the gene just has to be big as part of its
regulation. There are likely multiple failures in completing such a
long transcript, and possibly there would be too many copies if the
gene was as short as it could be. If it is a regulatory mechanism it
is the type of Rube Goldberg type of solution that probably just
worked and then was maintained because the gene obviously does
something important. My guess is that the gene evolved from a very
large stretch of DNA and there has been insufficient selection
pressure to reduce the size of the gene and make, making it more
energy efficient. Tremendous amounts of energy are wasted making RNA
transcripts, and this is just part of the slop that the cell lives
with.

Ron Okimoto

[John Harshman]

On 5/18/13 12:28 PM, Desertphile wrote:
> 'Junk' DNA Mystery Solved: It's Not Needed
>
> http://www.livescience.com/31939-junk-dna-mystery-solved.html
>
> One person's trash may be another person's treasure, but sometimes,
> trash is just trash.
>
> So-called junk DNA, the vast majority of the genome that doesn't code
> for proteins, really isn't needed for a healthy organism, according to
> new research.
>
> [...]
>
>

Two things I find annoying, both typical of science journalism. First,
the overhyping of results, as if this one bit resolves what is at any
rate a non-controversy among evolutionary biologists (though not among
ENCODE authors). Second, the gross misunderstanding of terminology, as
the author equates junk DNA with non-coding DNA.

I also agree with Norman that it would be handy to know Desertphile's
point in posting this, and that the absence of a link to the original
publication is a problem both in the linked article and in Desertphile's
post.

[*Hemidactylus*]

On 05/19/2013 01:54 AM, Mitchell Coffey wrote:

[snip]

> I like it when others post links to news releases or popular magazine articles without making any contribution of their own. That way they've made themselves useful by posting material unnoticed by people capable of making contributions of their own, and thus-like furthering the on-topic education of thick-headed swamp-twits like me - God's own dunderfeathers, who know less about evolutionary sciences than, than... well, than any other of God's dunderfeathers!
>
> Desertphile, I thank thee.

I agree. I had seen some articles via Google News on this topic and
thought about posting one or two, but Desertphile beat me to getting
punched for it. I think posting topical news items with or without any
added personal commentary breaks the typical tropes (or "attractors") of
the group. I was using it as a means of hopefully yanking attention away
from some of our worst trolls in the past. Didn't work.


--
*Hemidactylus*

[*Hemidactylus*]

Jeez, the guy didn't fart in church did he? Posting a link to a recent
and group relevant news item is one of the least offensive things I've
seen done here. Desertphile's intent was from my POV genuine and
positive. It's not his fault what consequences lie waiting for him in
group of grumpy people. At least Ron O posted something about the topic
and not about the poster.


--
*Hemidactylus*

[*Hemidactylus*]

On 05/18/2013 03:28 PM, Desertphile wrote:
> 'Junk' DNA Mystery Solved: It's Not Needed
>
> http://www.livescience.com/31939-junk-dna-mystery-solved.html
>
> One person's trash may be another person's treasure, but sometimes,
> trash is just trash.
>
> So-called junk DNA, the vast majority of the genome that doesn't code
> for proteins, really isn't needed for a healthy organism, according to
> new research.
>
> [...]

Here's an antidote to your revved up detractors:

http://www.youtube.com/watch?v=WY1c7hTmoBE

Switch to Sanka :-)


--
*Hemidactylus*

[Richard Norman]

I indicated in my original complaint (which has been snipped) that I
have done the same to others who post links without any contribution
of their own. It commented about the poster's behavior, not about the
poster's persona.

I have two problems about such posts. First, my library lists some
80+ journals with "evolution" or "evolutionary" in the name. At
least 70 of these are about biological evolution. There are at least
a dozen, probably several dozen, other journals that regularly print
papers dealing with evolution. I would guess there to be probably on
the order of 500 papers related to evolution published every month --
maybe 15 per day. Before being pointed to one particular paper, I
would like some indication of why it is of particular interest.

Second, these posts are invariably from popular sciency magazines and
web sites. To be brutally frank, these almost always are in the
business of selling copies (or advertising hits) more than educating
the public about science. So the more attention they attract the
better. Hence the far too often sensationalist writing and,
especially, catchy headlines. The "scientific" content is ordinarily
taken from the PR office of one of the researchers' institution that
also focuses on glitz and glamor rather than hard science. This
article screams "Junk DNA Mystery Solved!". As John has already
indicated, there is no mystery, this paper about the bladderwort is
about sequencing the entire genome but the genome small size was long
known, and this is not the first or the only example of small genomes
known in plants or animals. Nothing is solved.

John and I are both professional biologists so we have a very
different perspective on what is good and important biology. I assume
he has the same sadness I feel when I see interested "lay" observers
go for the glitz and glamor of presentation rather than the important
matters of content. Readers of this group should realize that both
John and I often provide background and supplementary information
about the content of these papers when they are raised here. I don't
want to discourage people from posting interesting items about science
here but I would like to see at least some personal contribution from
the poster. A brief paraphrase of the key information from the
article rather than a cut and paste of the content would be better in
my opinion.

Yes, I am grumpy and demanding. Yes, I think I have reason to be.

[Roger Shrubber]

Echo echo.
It's a non story other than it being antagonistic to the ENCODE
hype, which is nice, except it gets the definition of junk DNA
wrong, which is bad, in fact very bad. It might have been an
interesting cite in the lines of being another paper that should
not have passed peer review.

Oh, and the Dutch.

[*Hemidactylus*]

Yet this all could have been added without as much preening of ruffled
feathers. Desertphile probably wanted to see this topic addressed by
more knowledgeable posters. If so, that *was* the point of posting.
Ideally we would all be experts in biology that know everything about
every topic. If that were the case, there would be no point in posting
anything at all we would be interconnected via an isomorphic "Jedi mind
meld". But alas the contents of our brains diverge. And many of us have
forgotten much over the years, so refreshers are always welcome.

Now that I've ruffled the feathers of fanboys for two scifi franchises:

http://knowyourmeme.com/memes/jedi-mind-meld


--
*Hemidactylus*

[*Hemidactylus*]

Sometimes, but not always, I find an interesting topical news item via
Google News. I try to find the original abstract and the entire article
(if not paywalled). I might even add some of my own naive or wrongheaded
commentary. Sometimes I do this right after I awake early in the
morning, so it is as if in a hypnapompic trance where the oddest things
seem to make sense at the time. Or I do it late at night before sleep so
it's hypnagogic (thank you Wikipedia!).

Then the howler monkeys attack, rousing me from dogmatic slumber.


--
*Hemidactylus*

[eridanus]

El domingo, 19 de mayo de 2013 16:54:02 UTC+1, *Hemidactylus* escribi�:

some posters that present something, merely want to have the opinions of
other people here, for they assume other people know better than them.
This is the case when I had posted some links here. I was unsure about
the value of the material, then I had not any comment to add, except that
the material of the link impressed me. Perhaps it was a worthless material
but I have not enough information to know it better.
If this confession of my own ignorance is offensive to other I beg
some forgiveness. It is not much begging.

Eridanus

[jillery]

You are conflating multiple issues here. I agree with your comments
about popular science articles generally, and about the specific cited
article specifically. The article's headline is hyperbole, and its
contents convey little of the science contained in the original
article on which it's based. Your comments have to do with the
practice of popular science writing. As that impacts the popular
perception of science, that's also valid topic of discussion within
T.O.

An entirely separate issue you raise is about posting standards in
T.O. You say that you see negative similarities between the OP and
other recent posts. I disagree. Unlike those other posts, the OP
here was not just a raw cite, consisting of a link only. The OP
copied a relevant paragraph as a summary, from which one could decide
whether it was worth the time and risk to click on the link. One
could also reasonably infer that said summary conveys what the OP
believes to be the relevance of the article.

You're correct that the OP didn't elaborate beyond that. But such
elaboration could be better and more appropriately provided as the
topic develops. For example, your criticisms are not about the
scientific issues of the genome mapping itself or the implications of
that research, or even about humped bladderworts, any and all of which
could appropriately develop from the OP.

Your comments above illustrate there are multiple audiences within
T.O.; professionals like yourself, who have ready access to original
articles, and interested amateurs like the OP, who have neither the
time nor resources as you, but still can contribute and initiate
discussions on interesting topics. As a professional, you may be less
aware of what topics are interesting to the unwashed masses. There is
value in providing for both audiences in T.O.

[*Hemidactylus*]

On 05/19/2013 12:33 PM, eridanus wrote:


[snip Google mangled text]

> some posters that present something, merely want to have the opinions of
> other people here, for they assume other people know better than them.
> This is the case when I had posted some links here. I was unsure about
> the value of the material, then I had not any comment to add, except that
> the material of the link impressed me. Perhaps it was a worthless material
> but I have not enough information to know it better.
> If this confession of my own ignorance is offensive to other I beg
> some forgiveness. It is not much begging.

Whether it's being spread thin over many topics and not having an
expert's depth on any or specializing in one branch of knowledge to the
detriment of others, we are all ignorant of much. And by picking the
brains of others posting here, we are not relying exclusively on Google
or the Web.

The more one searches online for answers, the more likely they will land
on a site that zombies their computer, so that's becoming less an
attractive option. The "golden age" of the Web, if there ever was one,
is over, ruined by the miscreant aspects of human nature. It's like
swimming in shark infested waters. One needs a good cage.

Google doesn't seems to be up to par anymore either. Usenet is archaic
(a living fossil) and marginally useful, but I guess it's what one makes
of it. I have diminished expectations.


--
*Hemidactylus*

[*Hemidactylus*]

Excellent points!


--
*Hemidactylus*

[Bob Casanova]

On Sat, 18 May 2013 15:55:31 -0400, the following appeared
in talk.origins, posted by Richard Norman
<r_s_n...@comcast.net>:

>On Sat, 18 May 2013 13:28:36 -0600, Desertphile
><Deser...@spammegmail.com> wrote:
>
>>'Junk' DNA Mystery Solved: It's Not Needed
>>
>>http://www.livescience.com/31939-junk-dna-mystery-solved.html
>>
>>One person's trash may be another person's treasure, but sometimes,
>>trash is just trash.
>>
>>So-called junk DNA, the vast majority of the genome that doesn't code
>>for proteins, really isn't needed for a healthy organism, according to
>>new research.
>>
>
>I complain when others post links to news releases or popular magazine
>articles without making any contribution of their own. You have done
>exactly that, merely cutting and pasting from the article.

I disagree. Posting the link *and* a clear description of
the content which shows how it relates to the newsgroup, is
both necessary and sufficient; a critique is not required.

> Sadly, the
>"Live Science" publication doesn't even provide a link to the original
>publication which can be found at
> "Architecture and evolution of a minute plant genome"
>
>http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12132.html
>
>(Full text freely available, at least for now)

Thanks for researching this.
--

Bob C.

"The most exciting phrase to hear in science,
the one that heralds new discoveries, is not
'Eureka!' but 'That's funny...'"

- Isaac Asimov

[Richard Norman]

On Sun, 19 May 2013 12:51:25 -0400, jillery <69jp...@gmail.com>

I immodestly believe that i do provide information to interested
amateurs. All it takes is some actual input from the interested
party. Something on the order of "Is this really a solution to the
mystery of junk DNA?" Or "My impression was that junk was really
junk so is there a mystery?" Or "My impression was that much junk has
found to be important, so is this true?" Or "What is the current
status of junk DNA?"

[Mike Duffy]

*Hemidactylus* <ecph...@hotmail.com> wrote in
news:t4qdndu2R7aLQAXM...@giganews.com:

> I was using it as a means of hopefully yanking attention
> away from some of our worst trolls in the past. Didn't work.

Perhaps it did. Going back to the original thread subject line, I had the
idea that perhaps DNA which cannot encode proteins is involved somehow in
"coding" behavior (instincts).

If we discuss that possibility, are we not accomplishing your goal of
yanking attention away from the trolls?

--
http://pages.videotron.ca/duffym/index.htm

[Paul J Gans]

One doesn't need personal comments. I rarely post any when I
post a URL to some paper or other.

But one DOES need to explain what the subject of the paper is.
If I don't know that, I often will not pursue the paper.

--
--- Paul J. Gans

[jillery]

On Sun, 19 May 2013 13:36:13 -0400, Richard Norman

I don't imply or suggest otherwise. My point is that the kind of
articles you provide are the only kind appropriate to T.O.

>All it takes is some actual input from the interested
>party. Something on the order of "Is this really a solution to the
>mystery of junk DNA?" Or "My impression was that junk was really
>junk so is there a mystery?" Or "My impression was that much junk has
>found to be important, so is this true?" Or "What is the current
>status of junk DNA?"

Already addressed, as content suitable in follow-up posts.

[Richard Norman]

Your suggestion about DNA "coding" behavior is intriguing but has no
known mechanism, not even a remotely possible mechanism. It is
absolutely clear that the classical mechanisms of DNA, including the
control regions as well as the protein coding regions, are responsible
for producing neural structures including specific neural circuits
which in many invertebrates (and probably vertebrates, too) are
responsible for instinctive behavior. It is absolutely clear that
genetic mutations result in changes to that behavior. But the fact
that humans can engineer DNA sequences to code information does not
even suggest that biology does anything remotely similar with the
non-coding and non-control regions, the "junk" portion, of DNA.

Do you have a citation with more information about that idea? It
certainly is a proper thing to discuss.

[*Hemidactylus*]

Perhaps. But I'm not willing to form an opinion on the present news item
from the OP until Larry Moran gives it to me :-)

I have followed his cogent commentary on ENCODE.


--
*Hemidactylus*

[*Hemidactylus*]

On 05/19/2013 02:40 PM, Richard Norman wrote:
> On Sun, 19 May 2013 18:17:50 +0000 (UTC), Mike Duffy
> <Use.web.form@website_in_sig.com> wrote:
>
>> *Hemidactylus* <ecph...@hotmail.com> wrote in
>> news:t4qdndu2R7aLQAXM...@giganews.com:
>>
>>> I was using it as a means of hopefully yanking attention
>>> away from some of our worst trolls in the past. Didn't work.
>>
>> Perhaps it did. Going back to the original thread subject line, I had the
>> idea that perhaps DNA which cannot encode proteins is involved somehow in
>> "coding" behavior (instincts).
>>
>> If we discuss that possibility, are we not accomplishing your goal of
>> yanking attention away from the trolls?
>
> Your suggestion about DNA "coding" behavior is intriguing but has no
> known mechanism, not even a remotely possible mechanism.

Morphic resonance? A plant guy came up with that idea BTW.

> It is
> absolutely clear that the classical mechanisms of DNA, including the
> control regions as well as the protein coding regions, are responsible
> for producing neural structures including specific neural circuits
> which in many invertebrates (and probably vertebrates, too) are
> responsible for instinctive behavior. It is absolutely clear that
> genetic mutations result in changes to that behavior. But the fact
> that humans can engineer DNA sequences to code information does not
> even suggest that biology does anything remotely similar with the
> non-coding and non-control regions, the "junk" portion, of DNA.
>
> Do you have a citation with more information about that idea? It
> certainly is a proper thing to discuss.

Getting back to a link you provided:

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12132.html

I find this a most interesting part of the summation:

"Furthermore, in contrast to recent publications that highlight a
crucial functional role of non-coding DNA in complex organisms such as
animals24, the necessary genomic context required to make a flowering
plant may not require substantial hidden regulators in the non-coding
�dark matter� of the genome."

24-The ENCODE Project Consortium. An integrated encyclopedia of DNA
elements in the human genome. Nature 489, 57�74 (2012)

If nothing more than to thumb my nose at the people who hyped ENCODE
with regard to the status of junk DNA. I admire Fred Sanford, though I
have found useful things at a junk yard, so maybe that's not the best
metaphor.

[thumbing nose]



--
*Hemidactylus*

[Richard Norman]

>�dark matter� of the genome."

>
>24-The ENCODE Project Consortium. An integrated encyclopedia of DNA

>elements in the human genome. Nature 489, 57�74 (2012)

>
>If nothing more than to thumb my nose at the people who hyped ENCODE
>with regard to the status of junk DNA. I admire Fred Sanford, though I
>have found useful things at a junk yard, so maybe that's not the best
>metaphor.
>
>[thumbing nose]

About morphic resonance: Wikipedia has this to say about Rupert
Sheldrake, the author of that idea: "Sheldrake views the universe as
a swarm of matter waves, spiralling down the gradient of their
synergetic (energetically favourable) constructive interference. When
two matter waves become connected by mutual constructive interference
(quantum entanglement, rapport), they intuit or grok each other.
Intuition interconnects matter waves instantaneously, regardless of
the distance".

Sheldrake was quite right about auxin, the plant hormone, though.

There is nothing bad about junkyards. My grandfather had a junk yard
in Newark NJ back in the 20's to 40's. Or, as I prefer to say, he was
an early environmentalist specializing in ferrous metal recycling.

I personally have no dog in the junk DNA fight. No doubt a
significant amount of non-coding DNA has some function. No doubt a
significant amount of recognizable "binding sites" or "recognition
motifs" really do bind and get recognized but quite possible without
any real function. As a metaphor, people who speak in tongues do
babble in what seems to be language -- it is just that it doesn't mean
anything. Likely a lot of junk that "looks good" is the same.

The fact is that there are a number of complex multicellular plants
and animals with extremely small genomes. They seem to lack most of
the "junk" yet develop and function seemingly quite normally. As
another metaphor, there are minimalist humans, individuals who live
ascetic lives doing without all sorts of things and living perfectly
"normal" lives even revelling in their moral and ethical spirituality.
Meanwhile the rest of us take advantage of all the stuff around us --
we could live without it but enjoy it while it is at hand. Is all of
our "stuff" necessary? We use it but we don't have to. (OK, that is
really pushing the metaphor, but still....)

[jillery]

On Sun, 19 May 2013 14:35:57 -0400, jillery <69jp...@gmail.com>

"are *not* the only kind appropriate to T.O."

<sigh>

[Mike Duffy]

Richard Norman <r_s_n...@comcast.net> wrote in
news:po6ip8t3do61icg76...@4ax.com:

> Do you have a citation with more information about that idea?

None. It is simply a guess on my part.

> It certainly is a proper thing to discuss.

Probably I'm relating it (overly?) to my IT-biased understanding of
systems.

A sophisticated program consists of data structures and program structures.

Ideally, a good "creator" will attempt to delineate the two so that they do
not interfere with each other.

The analogy here is that the "program" portion is an engine to build
various proteins, and the "data" portion is the junk dna which holds
contextual information like templates to aid in making more complicated
structures.

But at the bottom, its all just data (amino acid base pairs) immersed in a
structure that can use the data to self-replicate. This is either a seed, a
zygote, or perhaps a bacterium in an environment it is adapted to.

--
http://pages.videotron.ca/duffym/index.htm

[alias Ernest Major]

The headline is hype.

That organisms of apparently similar complexity vary greatly in genome
size is not new information. (Not even the small size of some
bladderwort genomes is all that new.) From this variation, and from the
observation that most non-coding DNA evolves neutrally, we can infer
(and had inferred) that such DNA has no sequence specific function. No
convincing case has been made for a bulk function either.

The C-value paradox - why this great variation in the amount of
non-coding DNA exists - remains an unsolved mystery.

--
alias Ernest Major

[Richard Norman]

The sad fact is that there are two incredibly wrong-headed and even
destructive notions about DNA and the way molecular biology works. One
is that DNA is a "blueprint" for construction of an organism. The
other is that DNA is a "program" instructing cells how to construct an
organism. I say "destructive" because it impedes understanding just
how cells really work. Unfortunately most people buy into those
stories because they seem so reasonable in terms of what we know about
how humans go about constructing complex objects (blueprints) or how
systems can automatically go about very complex tasks (programs).

The full story is not at all known yet. Still it is very clear that
there is neither blueprint nor instructions on how to "build" a nose,
an arm, or anything specific. Instead you have "instructions" that
say "build this protein with this special piece on the end." That
special piece eventually causes the cell to put that protein in the
cell membrane sticking out. Another "instruction" makes other
proteins that cause the cell to move out in one direction or another.
If that first protein in the membrane happens to come into contact
with another very special protein in another cell then it starts a
signaling system that turns on other parts of DNA to build still other
proteins. The whole thing ends up with arms and noses and stuff but
not at all in the way we think of either blueprints or programs.

It is all just proteins (and some other macromolecules) obeying the
laws of biochemistry and biophysics to either react or change their
shape or create regions that can bind to (or fail to bind to) other
proteins. Basically that is all that cells can do. And all the
equipment that does all this is simply more proteins reacting,
changing shape, or binding/releasing.

The problem of disseminating those evil notions of blueprint and
program is not entirely the fault of journalists and PR people writing
about the science. Far too many scientists take the easy way out to
give out simplistic (and wrong) explanations that keep the public
happy and willing to pay money to hear more stuff that is cleverly and
humorously expressed, especially if gussied up with good visuals and
special effects. Whether it is right or wrong is of lesser value.

But this is just a curmudgeonly old grouch complaining.

So, no, DNA is not separated into program vs. data segments.

[Richard Norman]

On Sun, 19 May 2013 17:13:56 -0400, jillery <69jp...@gmail.com>

wrote:

>On Sun, 19 May 2013 14:35:57 -0400, jillery <69jp...@gmail.com>
>wrote:
>

<snip>

>>I don't imply or suggest otherwise. My point is that the kind of
>>articles you provide are the only kind appropriate to T.O.
>
>
>"are *not* the only kind appropriate to T.O."
>
><sigh>
>

I do that all the time, say or write exactly the opposite of what I
wanted. I got the point even without the correction.

I do understand that the full research paper is far too technical for
most people. They are generally even far too technical for
undergraduates majoring in biology. However some people here do want
to see the real stuff and many if not most can skim the intro and
discussion to pick up some of the basic ideas. The most important
thing, though, is to firmly embed in people minds that the papers
often (usually?) differ strikingly from the press releases about them,
the info on which those magazine and web articles are based.

Incidentally, if anyone here is interested in getting a copy of a
paper behind a paywall just email me with the details of what paper
you want and I will email it back to you. Just delete the two
underscores in my listed email address.

[Mike Duffy]

Richard Norman <r_s_n...@comcast.net> wrote in

news:e9lip8d00vc6b91c1...@4ax.com:

> But this is just a curmudgeonly old grouch complaining.

That should read "explaining". And you have explained it pretty much as I
understand the process. Thanks, it's probable that you have enabled someone
else to get a better idea of the process.

> So, no, DNA is not separated into program vs. data segments.

As is the case with poorly "designed" programs. We are not supposed to
write self-modifying code, but it does happen.

(BTW, just so nobody gets the wrong idea, I do not think that DNA was ever
designed; it has evolved.)

DNA is certainly not *organized* into program vs. data segments. But I do
not think it makes the entire process easier to understand if we call the
non-coding parts "junk". Something like "unknown" would be more precise.

Even if we stipulate that most of it serves no purpose, surely parts of it
are used at some point to mediate other processes.

--
http://pages.videotron.ca/duffym/index.htm

[*Hemidactylus*]

I at least still realize the reductionist version of preformation is
wrongheaded and was always more partial to the epigenesis account.

http://plato.stanford.edu/entries/epigenesis/

But although I had some classes in molecular, cell and developmental
biology late last century, I admit my interests have led me away from
that stuff and I'm more interested in higher level phenomena, such as
ethics and morality (almost as departed from physical reality as
ghostbusting and parapsychological resonance theories). But I still must
wonder what "amino acid base pairs" are. I was asleep that day in
Biology class. I do remember three-nucleotide codons which relate
somehow to amino acids.

http://en.wikipedia.org/wiki/Genetic_code#RNA_codon_table


Or maybe it's how amino acids interact with DNA base pairs:

http://www.ncbi.nlm.nih.gov/pubmed/3917212

http://www.nature.com/nature/journal/v326/n6116/abs/326888a0.html


--
*Hemidactylus*

[*Hemidactylus*]

Well it's at least counter-hype. In media accounts hype battles
counter-hype.

What really gets me irate when reading headlines is when the word
"boffin" is used. If Desertphile had found a headline that said "Boffins
salvage junk DNA concept" I might have joined in the blanket party.

--
*Hemidactylus*

[*Hemidactylus*]

What are "amino acid base pairs"?


--
*Hemidactylus*

[Paul J Gans]

Mike Duffy <Use.web.form@website_in_sig.com> wrote:
>Richard Norman <r_s_n...@comcast.net> wrote in
>news:po6ip8t3do61icg76...@4ax.com:

>> Do you have a citation with more information about that idea?

>None. It is simply a guess on my part.

>> It certainly is a proper thing to discuss.

>Probably I'm relating it (overly?) to my IT-biased understanding of
>systems.

>A sophisticated program consists of data structures and program structures.

>Ideally, a good "creator" will attempt to delineate the two so that they do
>not interfere with each other.

Not to start an argument, but while what you say here is true,
it was not known in the Early Days of Computing. Back then
one of the strengths of computers was that they could modify
the program they were running while it was running by actually
changing the code.

The notion of distinct areas for data and programs had to wait
for memory to fall below the $1000 per kilobyte limit -- and
that was in old time prices.

[snip]

[Desertphile]

On Sat, 18 May 2013 15:55:31 -0400, Richard Norman
<r_s_n...@comcast.net> wrote:

> On Sat, 18 May 2013 13:28:36 -0600, Desertphile

> <Deser...@spammegmail.com> wrote:
>
> >'Junk' DNA Mystery Solved: It's Not Needed
> >
> >http://www.livescience.com/31939-junk-dna-mystery-solved.html
> >
> >One person's trash may be another person's treasure, but sometimes,
> >trash is just trash.
> >
> >So-called junk DNA, the vast majority of the genome that doesn't code
> >for proteins, really isn't needed for a healthy organism, according to
> >new research.

> I complain when others post links to news releases or popular magazine
> articles without making any contribution of their own. You have done
> exactly that, merely cutting and pasting from the article.

Ahhh, you poor little baby! I hope you didn't cry and wail and stomp
your wee little foot.

> Sadly, the
> "Live Science" publication doesn't even provide a link to the original
> publication which can be found at
> "Architecture and evolution of a minute plant genome"
>
> http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12132.html
>
> (Full text freely available, at least for now)

--
"I'm often irrelevant. It confuses people." --- Archie Goodwin

[Richard Norman]

My impression is that "amino acid base pairs" is simply an error.

I hate to get all jonathanish about it but the ideas that are behind
complexity theory indicate that a complex feedback system -- genes
producing proteins that either directly or indirectly influence the
expression of genes -- is quite capable of generating complex
patterns.

A truly excellent book, based on really good, solid biology, is "How
the Leopard Changed Its Spots : The Evolution of Complexity" by Brian
Goodwin.

Another excellent book, also based on really good, solid biology, is
"The Evolution of Complexity by Means of Natural Selection" by
John Tyler Bonner.

[Richard Norman]

More important the notion of a Von Neumann computer, a stored program
computer, is that program IS data in a different context. That is
also the basis on which compilers and assemblers work.

[Richard Norman]

On Sun, 19 May 2013 18:43:04 -0600, Desertphile
<Deser...@spammegmail.com> wrote:

>On Sat, 18 May 2013 15:55:31 -0400, Richard Norman
><r_s_n...@comcast.net> wrote:
>
>> On Sat, 18 May 2013 13:28:36 -0600, Desertphile
>> <Deser...@spammegmail.com> wrote:
>>
>> >'Junk' DNA Mystery Solved: It's Not Needed
>> >
>> >http://www.livescience.com/31939-junk-dna-mystery-solved.html
>> >
>> >One person's trash may be another person's treasure, but sometimes,
>> >trash is just trash.
>> >
>> >So-called junk DNA, the vast majority of the genome that doesn't code
>> >for proteins, really isn't needed for a healthy organism, according to
>> >new research.
>
>> I complain when others post links to news releases or popular magazine
>> articles without making any contribution of their own. You have done
>> exactly that, merely cutting and pasting from the article.
>
>Ahhh, you poor little baby! I hope you didn't cry and wail and stomp
>your wee little foot.
>

Nanny did find me on the floor kicking so I didn't get my cookie at
nap time. I am SO upset!

[John S. Wilkins]

Richard Norman <r_s_n...@comcast.net> wrote:

> On Sun, 19 May 2013 18:43:04 -0600, Desertphile
> <Deser...@spammegmail.com> wrote:
>
> >On Sat, 18 May 2013 15:55:31 -0400, Richard Norman
> ><r_s_n...@comcast.net> wrote:
> >
> >> On Sat, 18 May 2013 13:28:36 -0600, Desertphile
> >> <Deser...@spammegmail.com> wrote:
> >>
> >> >'Junk' DNA Mystery Solved: It's Not Needed
> >> >
> >> >http://www.livescience.com/31939-junk-dna-mystery-solved.html
> >> >
> >> >One person's trash may be another person's treasure, but sometimes,
> >> >trash is just trash.
> >> >
> >> >So-called junk DNA, the vast majority of the genome that doesn't code
> >> >for proteins, really isn't needed for a healthy organism, according to
> >> >new research.
> >
> >> I complain when others post links to news releases or popular magazine
> >> articles without making any contribution of their own. You have done
> >> exactly that, merely cutting and pasting from the article.
> >
> >Ahhh, you poor little baby! I hope you didn't cry and wail and stomp
> >your wee little foot.
> >
>
> Nanny did find me on the floor kicking so I didn't get my cookie at
> nap time. I am SO upset!

When my daughter was 2 we used to call these "drop attacks".
--
John S. Wilkins, Associate, Philosophy, University of Sydney
http://evolvingthoughts.net
But al be that he was a philosophre,
Yet hadde he but litel gold in cofre

[John Harshman]

On 5/19/13 5:08 PM, Mike Duffy wrote:
> Richard Norman<r_s_n...@comcast.net> wrote in
> news:e9lip8d00vc6b91c1...@4ax.com:
>
>
>> But this is just a curmudgeonly old grouch complaining.
>
> That should read "explaining". And you have explained it pretty much as I
> understand the process. Thanks, it's probable that you have enabled someone
> else to get a better idea of the process.
>
>> So, no, DNA is not separated into program vs. data segments.
>
> As is the case with poorly "designed" programs. We are not supposed to
> write self-modifying code, but it does happen.
>
> (BTW, just so nobody gets the wrong idea, I do not think that DNA was ever
> designed; it has evolved.)
>
> DNA is certainly not *organized* into program vs. data segments. But I do
> not think it makes the entire process easier to understand if we call the
> non-coding parts "junk". Something like "unknown" would be more precise.

We don't call the non-coding parts "junk". That's one of the big
problems with the OP. Most non-coding DNA, at least in most genomes, is
junk. Junk is DNA without function.

> Even if we stipulate that most of it serves no purpose, surely parts of it
> are used at some point to mediate other processes.

True. Some non-coding DNA is regulatory. But that's a small percentage
of the non-coding DNA, and we don't call that part junk. We also have
pretty good tests for junk DNA, which most certainly do not have
anything to do with "we don't know what that does".

[John Harshman]

They're akin to "heme sequence".

[Mitchell Coffey]

On 5/19/2013 10:14 PM, John S. Wilkins wrote:
> Richard Norman <r_s_n...@comcast.net> wrote:
>
>> On Sun, 19 May 2013 18:43:04 -0600, Desertphile
>> <Deser...@spammegmail.com> wrote:
>>
>>> On Sat, 18 May 2013 15:55:31 -0400, Richard Norman
>>> <r_s_n...@comcast.net> wrote:
>>>
>>>> On Sat, 18 May 2013 13:28:36 -0600, Desertphile
>>>> <Deser...@spammegmail.com> wrote:
>>>>
>>>>> 'Junk' DNA Mystery Solved: It's Not Needed
>>>>>
>>>>> http://www.livescience.com/31939-junk-dna-mystery-solved.html
>>>>>
>>>>> One person's trash may be another person's treasure, but sometimes,
>>>>> trash is just trash.
>>>>>
>>>>> So-called junk DNA, the vast majority of the genome that doesn't code
>>>>> for proteins, really isn't needed for a healthy organism, according to
>>>>> new research.
>>>
>>>> I complain when others post links to news releases or popular magazine
>>>> articles without making any contribution of their own. You have done
>>>> exactly that, merely cutting and pasting from the article.
>>>
>>> Ahhh, you poor little baby! I hope you didn't cry and wail and stomp
>>> your wee little foot.
>>>
>>
>> Nanny did find me on the floor kicking so I didn't get my cookie at
>> nap time. I am SO upset!
>
> When my daughter was 2 we used to call these "drop attacks".

It worked for me until my daughter was 12 or 13.

Mitchell

[jillery]

12 or 13? I bet she found your behavior embarrassing, especially in
front of her friends 8-)

[John S. Wilkins]

It's a father's job to embarass his kids. I failed, alas.

[Paul J Gans]

Richard Norman <r_s_n...@comcast.net> wrote:

[giant snippage]

>I hate to get all jonathanish about it but the ideas that are behind
>complexity theory indicate that a complex feedback system -- genes
>producing proteins that either directly or indirectly influence the
>expression of genes -- is quite capable of generating complex
>patterns.

>A truly excellent book, based on really good, solid biology, is "How
>the Leopard Changed Its Spots : The Evolution of Complexity" by Brian
>Goodwin.

>Another excellent book, also based on really good, solid biology, is
>"The Evolution of Complexity by Means of Natural Selection" by
>John Tyler Bonner.

How do they define "complexity"?

[Paul J Gans]

Richard Norman <r_s_n...@comcast.net> wrote:
>On Mon, 20 May 2013 00:35:40 +0000 (UTC), Paul J Gans
><gan...@panix.com> wrote:

[snippage]

>>Not to start an argument, but while what you say here is true,
>>it was not known in the Early Days of Computing. Back then
>>one of the strengths of computers was that they could modify
>>the program they were running while it was running by actually
>>changing the code.
>>
>>The notion of distinct areas for data and programs had to wait
>>for memory to fall below the $1000 per kilobyte limit -- and
>>that was in old time prices.
>>
>>[snip]

>More important the notion of a Von Neumann computer, a stored program
>computer, is that program IS data in a different context. That is
>also the basis on which compilers and assemblers work.

I may have to grant that since even assemblers had "data" statements.
But I don't think that the distinction was realized back then as being
very sharp. I recall a lot of folks being upset when different
spaces for data and program was introduced.

It took me a while to get over it and even longer to grow to see
the benefits.

But the upset over it rivaled that generated by the deprication and
eventual removal of "go to" from various languages. But we are all
better off for that too.

[Paul J Gans]

You may not have. Only now, with my kids in their 40s, is
the truth coming out about some things... ;-(

[Burkhard]

On 20 May, 07:40, j...@wilkins.id.au (John S. Wilkins) wrote:

> jillery <69jpi...@gmail.com> wrote:
> > On Mon, 20 May 2013 00:45:25 -0400, Mitchell Coffey
> > <mitchell.cof...@gmail.com> wrote:
>
> > >On 5/19/2013 10:14 PM, John S. Wilkins wrote:

Is that one of these lying Greek thingamabobs? Were they dead
embarrassed that you failed in your duty to embarrass them?

[Bob Casanova]

On Mon, 20 May 2013 16:40:53 +1000, the following appeared
in talk.origins, posted by jo...@wilkins.id.au (John S.
Wilkins):

You were never seen in public with them? That's all it
takes, y'know...
--

Bob C.

"The most exciting phrase to hear in science,
the one that heralds new discoveries, is not
'Eureka!' but 'That's funny...'"

- Isaac Asimov

[Richard Norman]

You mean I have to actually put down my laptop, get up off my easy
chair, walk down to the basement, get the books off the shelf, and
then read what they say?

[Richard Norman]

OK, I'm back up from the basement, back on my easy chair.

I do have Bonner who discusses "complexity" in the ordinary language,
common sense meaning: hierarchical levels of organization and
diversity of cell types and morphological structures in large
multicellular organisms. He even goes into ecosystems and behavior as
examples of "complex" systems. However he dismisses all the
mathematical development of his time (preceding "complexity theory")
as unhelpful. More importantly he dismisses the whole
anti-reductionistic arguments of the holists (now called complexity
theory mavens). Instead he describes how cellular and developmental
processes produce complexity of tissue types and morphological
structure and how these cellular and developmental processes evolved
by natural selection. There is no 'measure of complexity', just an
illustration of how what we think of as complex stuff can come about.
And, most definitely, there is no inevitability about it. Complexity
is not a necessary consequent of evolution but merely one possible
result. However since evolution seems to explore all options it
definitely does also procede down the "complexity route".

I do not find Goodwin, probably because it is back in my Arizona home.
He is more of a mathematical biologist although not the evil
theoretician but rather firmly grounded in biological practice.
However he was definitely a systems theory type and anti-reductionist.
That is, the dynamics of the system defines patterns in an otherwise
homogenous field and natural selection (biology) is thus constrained
to create pattern by the underlying system dynamics. I don't find
that anti-reductionistic in the same way that structured sound
production (fundamental and harmonics) of wind blowing across a
cylinder is not anti-reductionistic. The solutions to the
fundamental differential equations have eigenvalues and eigenfunctions
and so anything that obeys physical laws expressed by those equations
must then be organized into "complex patterns" (the eigenfunctions).
He was a founding member of the Santa Fe Institute and therefore a
bona fide complexity theorist. However he applied mathematics to
biology appropriately and with understanding of the underlying
biology.

[J. J. Lodder]

John S. Wilkins <jo...@wilkins.id.au> wrote:

Doesn't matter,
as long as you didn't fail in your core task:
to corrupt their minds,

Jan

[J. J. Lodder]

Paul J Gans <gan...@panix.com> wrote:

Why would there be a need to 'define' it?

Jan

[James Beck]

Does it always mean the same thing?

[alextangent]

On May 20, 1:35�am, Paul J Gans <gan...@panix.com> wrote:
> Mike Duffy <Use.web.form@website_in_sig.com> wrote:

> >Richard Norman <r_s_nor...@comcast.net> wrote in

> >news:po6ip8t3do61icg76...@4ax.com:
> >> Do you have a citation with more information about that idea?
> >None. It is simply a guess on my part.
> >> It certainly is a proper thing to discuss.
> >Probably I'm relating it (overly?) to my IT-biased understanding of
> >systems.
> >A sophisticated program consists of data structures and program structures.
> >Ideally, a good "creator" will attempt to delineate the two so that they do
> >not interfere with each other.
>
> Not to start an argument,

Too late!

> but while what you say here is true,
> it was not known in the Early Days of Computing. �Back then
> one of the strengths of computers was that they could modify
> the program they were running while it was running by actually
> changing the code.
>
> The notion of distinct areas for data and programs had to wait
> for memory to fall below the $1000 per kilobyte limit -- and
> that was in old time prices.

Hmm.

Self modifying code reduced in popularity because many early high
level programming languages (such as the still popular C) didn't
permit it. It's also of benefit if your program is to be in read only
memory (ROM); it's much cheaper than dynamic RAM.

For RAM machines, chip designers found that it was possible to get
increases in speed if code didn't modify itself; the pressure for
performance and code clarity (it can make life difficult) still make
it a technique to avoid.

There are programming languages where data is program and program is
data; Lisp for one. This ability to inspect and modify programs in the
same way as data is called reflection. Reflective languages generally
avoid self-modifying code by having a layer of abstraction, a virtual
machine, that runs on the real hardware. That VM code can be freely
modified, as the hardware sees it as data, not code.

[Paul J Gans]

No. Don't bother. It is my impression that complexity is
no more complex to define than is the term "life".

I just wanted to know how the undefinable evolves by means
of natural selection.

Chemistry is SO much easier.

[Paul J Gans]

Because I want to know what it is the evolves by natural
selection in the book by Bonner.

Maybe it is one of those "I know it when I see it" things.

[Paul J Gans]

Now that's a complex question.

[Richard Norman]

I am too lazy to look up the details and the history but my impression
is that when computers became large and powerful enough to allow
multitasking between different users, it became absolutely necessary
to implement hardware security features to protect access to
particular segments of memory. One essential protection is
designation of memory as non-executable because embedding virus or
trojan code into data is a preferred hacking method. So there are
hardware methods built into "modern" CPUs to separate data from
executable code and rather high level privileges are needed to control
these.

PC's with 8 bit CPUs and even early 16 bit CPUs didn't have that but
now all systems do. Whether the operating system takes full advantage
of these controls is another issue.

Incidentally I have done a substantial amount of ROM-based programming
for embedded systems. Putting data into ROM obviously fails but
putting executable code into RAM (which really should be called RWM)
was never a problem. Debugging methods often implement breakpoints
simply by overwriting the instruction at the desired location with an
operating system call, usually a special interrupt instruction. You
do not want to try to debug programs if you can't modify the code in
this way and are denied breakpoints. Of course the idea of a virtual
machine requires treating code as data.

[Richard Norman]

On Mon, 20 May 2013 23:09:49 +0000 (UTC), Paul J Gans

Actually "I know it when I see it" is far more fun to read (and view!)
than is Bonner's book.

[Paul J Gans]

Richard Norman <r_s_n...@comcast.net> wrote:
>On Mon, 20 May 2013 15:24:02 -0700 (PDT), alextangent
><bl...@rivadpm.com> wrote:

>>On May 20, 1:35?am, Paul J Gans <gan...@panix.com> wrote:
>>> Mike Duffy <Use.web.form@website_in_sig.com> wrote:
>>> >Richard Norman <r_s_nor...@comcast.net> wrote in
>>> >news:po6ip8t3do61icg76...@4ax.com:
>>> >> Do you have a citation with more information about that idea?
>>> >None. It is simply a guess on my part.
>>> >> It certainly is a proper thing to discuss.
>>> >Probably I'm relating it (overly?) to my IT-biased understanding of
>>> >systems.
>>> >A sophisticated program consists of data structures and program structures.
>>> >Ideally, a good "creator" will attempt to delineate the two so that they do
>>> >not interfere with each other.
>>>
>>> Not to start an argument,
>>
>>Too late!
>>
>>> but while what you say here is true,

>>> it was not known in the Early Days of Computing. ?Back then

I think that's right, but the large and powerful machines came
along well after computers were introduced.

>PC's with 8 bit CPUs and even early 16 bit CPUs didn't have that but
>now all systems do. Whether the operating system takes full advantage
>of these controls is another issue.

Yes.

>Incidentally I have done a substantial amount of ROM-based programming
>for embedded systems. Putting data into ROM obviously fails but
>putting executable code into RAM (which really should be called RWM)
>was never a problem. Debugging methods often implement breakpoints
>simply by overwriting the instruction at the desired location with an
>operating system call, usually a special interrupt instruction. You
>do not want to try to debug programs if you can't modify the code in
>this way and are denied breakpoints. Of course the idea of a virtual
>machine requires treating code as data.

I agree with this too. No more debugging from core dumps!

[Paul J Gans]

I can believe that.

But my question was (half) serious. We get into dangerous ground
at times. There is no question that they are onto something with
"complexity", but I'll be danged if I can pinpoint it.

[John S. Wilkins]

Paul J Gans <gan...@panix.com> wrote:

Both of them swear I failed. Not for lack of trying.

[John S. Wilkins]

J. J. Lodder <nos...@de-ster.demon.nl> wrote:

> John S. Wilkins <jo...@wilkins.id.au> wrote:
>

...

> >
> > It's a father's job to embarass his kids. I failed, alas.
>
> Doesn't matter,
> as long as you didn't fail in your core task:
> to corrupt their minds,
>

Well spotted. That I succeeded in.

[Paul J Gans]

There's an upside to that too.

[Richard Norman]

On Tue, 21 May 2013 02:35:40 +0000 (UTC), Paul J Gans

John is from the antipodes. Wouldn't that be a downside for him?

[John S. Wilkins]

This again? It's you bastards that are upside down:

http://flourish.org/upsidedownmap/

[alextangent]

On May 21, 12:18嚙窮m, Richard Norman <r_s_nor...@comcast.net> wrote:
> On Mon, 20 May 2013 15:24:02 -0700 (PDT), alextangent
>
>
>
>
>
>
>
>
>

> <b...@rivadpm.com> wrote:

> >On May 20, 1:35嚙窮m, Paul J Gans <gan...@panix.com> wrote:
> >> Mike Duffy <Use.web.form@website_in_sig.com> wrote:
> >> >Richard Norman <r_s_nor...@comcast.net> wrote in
> >> >news:po6ip8t3do61icg76...@4ax.com:
> >> >> Do you have a citation with more information about that idea?
> >> >None. It is simply a guess on my part.
> >> >> It certainly is a proper thing to discuss.
> >> >Probably I'm relating it (overly?) to my IT-biased understanding of
> >> >systems.
> >> >A sophisticated program consists of data structures and program structures.
> >> >Ideally, a good "creator" will attempt to delineate the two so that they do
> >> >not interfere with each other.
>
> >> Not to start an argument,
>
> >Too late!
>
> >> but while what you say here is true,

> >> it was not known in the Early Days of Computing. 嚙畿ack then

Yes, qv Multics. Code was not allowed to be self modifying -- and the
languages used helped in that goal, as did the virtual memory
segmentation model. But then IBM took a different approach; the
operating systems for the S/360 through to the present day Z/ allow
it. I blame COBOL; it had a number of self-modifying features built
into the language. Although IBM boxes now have an NX (no execute)
feature at the page level, it can be turned on and off for that memory
that is in the user's control. The same is true of Windows.

(An aside; the IBM instruction set has an operation that has the
effect of modifying another operation for a single execution. It's an
oddity.)

> One essential protection is
> designation of memory as non-executable because embedding virus or

> trojan code into data is a preferred hacking method. 嚙磅o there are

> hardware methods built into "modern" CPUs to separate data from
> executable code and rather high level privileges are needed to control
> these.

Not if it's memory the user is in charge of. For instance, the stack
in Windows is marked NX as it is a common virus vector, but there's a
non-privileged (i.e. available at the lowest level of security) call
to turn this off.

>
> PC's with 8 bit CPUs and even early 16 bit CPUs didn't have that but

> now all systems do. 嚙磕hether the operating system takes full advantage

> of these controls is another issue.

Virus writers seem to have got round the protection. It's an arms
race.

>
> Incidentally I have done a substantial amount of ROM-based programming

> for embedded systems. 嚙瞑utting data into ROM obviously fails but

> putting executable code into RAM (which really should be called RWM)

It was named after its major feature; random access. The W in RWM is
redundant; it really isn't memory if you can't write to it at least
once. ROM is the wrong 'un and should really be called WORM for write
once, read many.

> was never a problem. 嚙瘩ebugging methods often implement breakpoints

> simply by overwriting the instruction at the desired location with an

> operating system call, usually a special interrupt instruction. 嚙磐ou

> do not want to try to debug programs if you can't modify the code in

> this way and are denied breakpoints. 嚙瞌f course the idea of a virtual

> machine requires treating code as data.

Not all virtual machines treat code as data; VMware, VirtualBox, BOCHS
and so on treat code as code. They execute code directly on the
hardware, but maintain control by requiring the hardware to interrupt
on privileged operations and other exceptions. These are then emulated
by the VM; sometimes the hardware can assist the VM with special
instructions available only to it. Software VMs (JavaVM, CLR etc)
generally emulate all of an instruction set which may not be the
native instruction set of the processor. In general they need an OS to
support them.

Debugging is better done by setting control registers, of which modern
processors have many. They can watch memory for changes, trap on
execution and so on.

Anyhow, interesting though this is, it's seriously OT for T.O.

[J. J. Lodder]

John S. Wilkins <jo...@wilkins.id.au> wrote:

> J. J. Lodder <nos...@de-ster.demon.nl> wrote:
>
> > John S. Wilkins <jo...@wilkins.id.au> wrote:
> >
> ...
> > >
> > > It's a father's job to embarass his kids. I failed, alas.
> >
> > Doesn't matter,
> > as long as you didn't fail in your core task:
> > to corrupt their minds,
> >
> Well spotted. That I succeeded in.

As some mahematician once said:
My attempts at education have been largely in vain,
except for a few happy cases in which they were not needed,

Jan

[Richard Norman]

On Mon, 20 May 2013 23:34:51 -0700 (PDT), alextangent
<bl...@rivadpm.com> wrote:

<snip because of the following true statement>

>Anyhow, interesting though this is, it's seriously OT for T.O.
>

Very much so, but thank you for educating me on details about
something for which I had only limitedl knowledge.

[jillery]

On Mon, 20 May 2013 22:46:09 -0400, Richard Norman

It's relative.

[hersheyh]

On Sunday, May 19, 2013 11:17:50 PM UTC-4, John Harshman wrote:
> On 5/19/13 5:08 PM, Mike Duffy wrote:
>
> > Richard Norman<r_s_n...@comcast.net> wrote in
>
> > news:e9lip8d00vc6b91c1...@4ax.com:
>
> >
>
> >
>
> >> But this is just a curmudgeonly old grouch complaining.
>
> >
>
> > That should read "explaining". And you have explained it pretty much as I
> > understand the process. Thanks, it's probable that you have enabled someone
> > else to get a better idea of the process.
>
> >
>
> >> So, no, DNA is not separated into program vs. data segments.
>
> >
>
> > As is the case with poorly "designed" programs. We are not supposed to
> > write self-modifying code, but it does happen.
>
> >
>
> > (BTW, just so nobody gets the wrong idea, I do not think that DNA was ever
> > designed; it has evolved.)
>
> >
>
> > DNA is certainly not *organized* into program vs. data segments. But I do
> > not think it makes the entire process easier to understand if we call the
> > non-coding parts "junk". Something like "unknown" would be more precise.
>
>
>
> We don't call the non-coding parts "junk". That's one of the big
> problems with the OP. Most non-coding DNA, at least in most genomes, is
> junk. Junk is DNA without function.
>
Well, at least without sequence-specific function. I don't want to automatically
rule out some bulk-related function in all cases. Other than that tiny nit, I
certainly concur that most non-coding DNA is, indeed, junk and without
evolutionarily relevant function. Such sequence-non-specific DNA is dispensable
and changes at the expected rate for selective neutrality.
>
> > Even if we stipulate that most of it serves no purpose, surely parts of it
> > are used at some point to mediate other processes.
>
>
>
> True. Some non-coding DNA is regulatory. But that's a small percentage
> of the non-coding DNA, and we don't call that part junk. We also have
> pretty good tests for junk DNA, which most certainly do not have
> anything to do with "we don't know what that does".

[Bob Casanova]

On Mon, 20 May 2013 22:27:15 +0200, the following appeared
in talk.origins, posted by nos...@de-ster.demon.nl (J. J.
Lodder):

There wouldn't, unless there was a desire to create it as a
word (as it has been), or to discuss it (as is done here).
Or did you mean that there's no need since it's already
defined unambiguously and consistently? If so, where?

[eridanus]

El martes, 21 de mayo de 2013 18:53:31 UTC+1, Bob Casanova escribi�:

I do not think that it exists a universal definition of Nature.
Most of all, because we have only a limited knowledge of it.
Then, we consider all that is around us, all that can be seen
directly, with our eyes, or indirectly with instruments, like
photography or radio sensors, or other devices, gives us an
amplified vision of nature, or the Universe, as it is called
nature when we consider things outside this planet.

But on the whole, our vision and knowledge of nature is very
limited. Then it makes not any sense to post some questions
over matter we ignore, like "is the universe finite or infinite?"
Of course someone can try to answer this question, but I consider
this an absurd. We can easily be wrong with the things we think
we know. Then, what is the meaning of going farther and ask
questions over matters we clearly ignore?

Eridanus

[J. J. Lodder]

Seems they are all like that, down there,

Jan

[J. J. Lodder]

Bob Casanova <nos...@buzz.off> wrote:

> On Mon, 20 May 2013 22:27:15 +0200, the following appeared
> in talk.origins, posted by nos...@de-ster.demon.nl (J. J.
> Lodder):
>
> >Paul J Gans <gan...@panix.com> wrote:
> >
> >> Richard Norman <r_s_n...@comcast.net> wrote:
> >>
> >> [giant snippage]
> >>
> >> >I hate to get all jonathanish about it but the ideas that are behind
> >> >complexity theory indicate that a complex feedback system -- genes
> >> >producing proteins that either directly or indirectly influence the
> >> >expression of genes -- is quite capable of generating complex
> >> >patterns.
> >>
> >> >A truly excellent book, based on really good, solid biology, is "How
> >> >the Leopard Changed Its Spots : The Evolution of Complexity" by Brian
> >> >Goodwin.
> >>
> >> >Another excellent book, also based on really good, solid biology, is
> >> >"The Evolution of Complexity by Means of Natural Selection" by
> >> >John Tyler Bonner.
> >>
> >> How do they define "complexity"?
> >
> >Why would there be a need to 'define' it?
>
> There wouldn't, unless there was a desire to create it as a
> word (as it has been), or to discuss it (as is done here).
> Or did you mean that there's no need since it's already
> defined unambiguously and consistently? If so, where?

The idea that you can't talk about something scientifically
without 'defining' it first is silly,

Jan

[Paul J Gans]

Almost certainly.

The amazing thing is that most children survive and thrive
in spite of our best efforts.

[Paul J Gans]

Of course it's again. Do you think there are any new
threads on talk.origins.

Nevertheless the view of the "other" is always a subject
of dispute.

I cite Burns:

"O wad some Power the giftie gie us To see oursels as ithers see us!"

Why do I cite Burns? I like his poetry.

[Richard Norman]

On Tue, 21 May 2013 22:28:12 +0000 (UTC), Paul J Gans

Being unpoetic myself, I did a scientific experiment. I asked
everyone on t.o. to point "up" and took the vector sum of the
responses. The response was overwhelmingly in favor of the "true up."
OK, what I really did was I alphabetized the respondents and got bored
after finally getting through to S-T-U-V when the statistical
signifcance was so overwhelming. So there was no reason even to
catalog the W-X-Y-Z responses.

[John S. Wilkins]

Richard Norman <r_s_n...@comcast.net> wrote:

> On Tue, 21 May 2013 22:28:12 +0000 (UTC), Paul J Gans
> <gan...@panix.com> wrote:
>
> >John S. Wilkins <jo...@wilkins.id.au> wrote:
> >>Richard Norman <r_s_n...@comcast.net> wrote:
> >
> >>> On Tue, 21 May 2013 02:35:40 +0000 (UTC), Paul J Gans
> >>> <gan...@panix.com> wrote:

...

> >>> >
> >>> >There's an upside to that too.
> >>>
> >>> John is from the antipodes. Wouldn't that be a downside for him?
> >
> >>This again? It's you bastards that are upside down:
> >
> >>http://flourish.org/upsidedownmap/
> >
> >Of course it's again. Do you think there are any new
> >threads on talk.origins.
> >
> >Nevertheless the view of the "other" is always a subject
> >of dispute.
> >
> >I cite Burns:
> >
> > "O wad some Power the giftie gie us To see oursels as ithers see us!"
> >
> >Why do I cite Burns? I like his poetry.
>
> Being unpoetic myself, I did a scientific experiment. I asked
> everyone on t.o. to point "up" and took the vector sum of the
> responses. The response was overwhelmingly in favor of the "true up."
> OK, what I really did was I alphabetized the respondents and got bored
> after finally getting through to S-T-U-V when the statistical
> signifcance was so overwhelming. So there was no reason even to
> catalog the W-X-Y-Z responses.

Argumentum ad gentium! The facts clearly state that the Antarctic is up.
AFter all the north pole is just frozen dihydrogen monoxide.

[John S. Wilkins]

You wee mousie, you.

[Paul J Gans]

You want a degree in psychology from a university in the
Netherlands?

No, I'm not being snarky. Three guys from the NYU medical
school got busted a couple of days ago for taking bribes.
And no, I don't know the details.

[Paul J Gans]

I think it is louse, actually.

[Paul J Gans]

But what about the east pole and the west pole? Would
Winnie-ther-Po lie?

[John S. Wilkins]

Undertake an expotition to find out.

[John S. Wilkins]

Paul J Gans <gan...@panix.com> wrote:

> John S. Wilkins <jo...@wilkins.id.au> wrote:
> >Paul J Gans <gan...@panix.com> wrote:
>
> >> John S. Wilkins <jo...@wilkins.id.au> wrote:
> >> >Richard Norman <r_s_n...@comcast.net> wrote:
> >>
> >> >> On Tue, 21 May 2013 02:35:40 +0000 (UTC), Paul J Gans
> >> >> <gan...@panix.com> wrote:
> >> >>
> >> >> >John S. Wilkins <jo...@wilkins.id.au> wrote:
> >> >> >>Paul J Gans <gan...@panix.com> wrote:
> >> >> >
> >> >> >>> John S. Wilkins <jo...@wilkins.id.au> wrote:
> >> >> >>> >jillery <69jp...@gmail.com> wrote:
> >> >> >>>
> >> >> >>> >> On Mon, 20 May 2013 00:45:25 -0400, Mitchell Coffey
> >> >> >>> >> <mitchel...@gmail.com> wrote:
> >> >> >>> >>
> >> >> >>> >> >On 5/19/2013 10:14 PM, John S. Wilkins wrote:
> >> >> >>> >> >> Richard Norman <r_s_n...@comcast.net> wrote:
> >> >> >>> >> >>
> >> >> >>> >> >>> On Sun, 19 May 2013 18:43:04 -0600, Desertphile
> >> >> >>> >> >>> <Deser...@spammegmail.com> wrote:
> >> >> >>> >> >>>
> >> >> >>> >> >>>> On Sat, 18 May 2013 15:55:31 -0400, Richard Norman
> >> >> >>> >> >>>> <r_s_n...@comcast.net> wrote:
> >> >> >>> >> >>>>

...

OK: wee timorous lousie

[Bob Casanova]

On Tue, 21 May 2013 23:07:56 +0200, the following appeared

I disagree, at least insofar as actual communication of
ideas is considered to be desirable. Of course, YMMV if you
consider a "discussion", *especially* a supposedly
scientific one, in which the participants are talking past
each other to be profitable. And the more ambiguous the
subject (life, complexity, etc,) the greater the need for an
agreed-upon definition, at least for the course of the
discussion.

[Walter Bushell]

In article <kngruc$4rr$1...@reader1.panix.com>,

Survive yes. Thrive???

--
Gambling with Other People's Money is the meth of the fiscal industry.
me -- in the spirit of Karl and Groucho Marx

[Walter Bushell]

In article <kngsds$4rr$3...@reader1.panix.com>,

There isn't any other. The Universe is one process. Selecting subsets
to be considered as objects is just a convenience for porpoises of
anal lysis and hence is not objective.

[Paul J Gans]

OK! I'm off to the 100 aker wood.

[Paul J Gans]

The poem is "To A Louse, On Seeing One on a Lady's Bonnet at Church".
It was composed at roughly the same time as "To a Mouse", which begins,
as John said:

"Wee, sleekit, cow'rin, tim'rous beastie,
O, what a panic's in thy breastie!"

My thanks to Google for quotations. But most of you knew that.

[Mark Isaak]

That's a silly argument. Yes, there is a mass of rock at the south
pole, but that is what drags it *down*.

You might, in rebuttal, point out that most continental mass is still in
the northern hemisphere, even if not at the pole. There is a very good
argument against that point. I don't know what it is, but since I know
I am right, I know there must be one.

--
Mark Isaak eciton (at) curioustaxonomy (dot) net
"It is certain, from experience, that the smallest grain of natural
honesty and benevolence has more effect on men's conduct, than the most
pompous views suggested by theological theories and systems." - D. Hume

[Paul J Gans]

I dunno. Anal lysis sounds unpleasant to me.

[John S. Wilkins]

This discussion is getting heavy.

[hersheyh]

On Wednesday, May 22, 2013 1:44:42 PM UTC-4, Walter Bushell wrote:
> In article <kngruc$4rr$1...@reader1.panix.com>,
>
> Paul J Gans <gan...@panix.com> wrote:
>
>
>
> > Richard Norman <r_s_n...@comcast.net> wrote:
>
> > >On Tue, 21 May 2013 02:35:40 +0000 (UTC), Paul J Gans
>
> > ><gan...@panix.com> wrote:
>
> >
>
> > >>John S. Wilkins <jo...@wilkins.id.au> wrote:
>
> > >>>Paul J Gans <gan...@panix.com> wrote:
>
> > >>

[snip]

>
> >
>
> > The amazing thing is that most children survive and thrive
> > in spite of our best efforts.
>

That depends greatly on time and place (think Darfur and Somalia and
the late but not so great 1800s almost anywhere or the fun mid 1300s in
Europe). And if you start "childhood" at fertilization rather than birth, it
most likely isn't true even now.

[Paul J Gans]

hersheyh <hers...@yahoo.com> wrote:
>On Wednesday, May 22, 2013 1:44:42 PM UTC-4, Walter Bushell wrote:
>> In article <kngruc$4rr$1...@reader1.panix.com>,
>>
>> Paul J Gans <gan...@panix.com> wrote:
>>
>>
>>
>> > Richard Norman <r_s_n...@comcast.net> wrote:
>>
>> > >On Tue, 21 May 2013 02:35:40 +0000 (UTC), Paul J Gans
>>
>> > ><gan...@panix.com> wrote:
>>
>> >
>>
>> > >>John S. Wilkins <jo...@wilkins.id.au> wrote:
>>
>> > >>>Paul J Gans <gan...@panix.com> wrote:
>>
>> > >>
>[snip]
>>
>> >
>>
>> > The amazing thing is that most children survive and thrive
>> > in spite of our best efforts.
>>
>That depends greatly on time and place (think Darfur and Somalia and
>the late but not so great 1800s almost anywhere or the fun mid 1300s in
>Europe). And if you start "childhood" at fertilization rather than birth, it
>most likely isn't true even now.

I'm an "at birth" sort of person. Why? It is a far more obvious
and certain point than counting weeks from an uncertain origin.

[hersheyh]

I agree. But I do like to point out that the biggest abortionist of
all is the same God some believers claim hates abortion. If He did
hate abortion, you might think He could do more to prevent
them, perhaps by using the same method these believers think He
uses to prevent pregnancy after 'legitimate' rape, whatever that is.

[Ron O]

On May 25, 9:29 pm, hersheyh <hershe...@yahoo.com> wrote:
> On Friday, May 24, 2013 2:07:14 PM UTC-4, Paul J Gans wrote:

> > hersheyh <hershe...@yahoo.com> wrote:
>
> > >On Wednesday, May 22, 2013 1:44:42 PM UTC-4, Walter Bushell wrote:
>

> > >> In article <kngruc$4r...@reader1.panix.com>,

>
> > >>  Paul J Gans <gan...@panix.com> wrote:
>

> > >> > Richard Norman <r_s_nor...@comcast.net> wrote:
>
> > >> > >On Tue, 21 May 2013 02:35:40 +0000 (UTC), Paul J Gans
>
> > >> > ><gan...@panix.com> wrote:
>

> > >> > >>John S. Wilkins <j...@wilkins.id.au> wrote:
>
> > >> > >>>Paul J Gans <gan...@panix.com> wrote:
>
> > >[snip]
>
> > >> > The amazing thing is that most children survive and thrive
>
> > >> > in spite of our best efforts.
>
> > >That depends greatly on time and place (think Darfur and Somalia and
>
> > >the late but not so great 1800s almost anywhere or the fun mid 1300s in
>
> > >Europe).  And if you start "childhood" at fertilization rather than birth, it
>
> > >most likely isn't true even now.
>
> > I'm an "at birth" sort of person.  Why?  It is a far more obvious
> > and certain point than counting weeks from an uncertain origin.
>
> I agree.  But I do like to point out that the biggest abortionist of
> all is the same God some believers claim hates abortion.  If He did
> hate abortion, you might think He could do more to prevent
> them, perhaps by using the same method  these believers think He
> uses to prevent pregnancy after 'legitimate' rape, whatever that is.

You get into issues of freewill etc. A better example would have been
the flood and all the existing babies and small children along with
the pregnancies that were terminated, Sodom and Gomorrah, the conquest
of the promised land, etc..

Ron Okimoto