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From: Jim Henderson
Subject: Re: Molecular biology
Date: 13 Jan 2011 18:02:37
Message: <4d2f848d$1@news.povray.org>
On Thu, 13 Jan 2011 20:52:18 +0000, Stephen wrote:

> On 13/01/2011 8:38 PM, Jim Henderson wrote: ...
>>
>> Jim
> 
> Mornington Crescent! :-P

It's about time! :-)

Jim


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From: Darren New
Subject: Re: Molecular biology
Date: 13 Jan 2011 18:09:11
Message: <4d2f8617$1@news.povray.org>
Warp wrote:
>   The offspring must be fertile. Ligers and tigons aren't.

How often do they have to be fertile for it to count. If 10% of the 
offspring are viable, is that enough? 1%?

Also, there are some tree species[*] C that's a cross between species A and 
species B. It won't fruit except in the presence of A or B. I.e., the 
offspring are fertile with their parents, but not with each other. Does that 
count?

And, has been mentioned, men are not the same species as other men, so it's 
difficult to understand exactly how to apply this definition to individuals.


[*] I thought it was tangelos, but wikipedia doesn't mention that on their page.

-- 
Darren New, San Diego CA, USA (PST)
   Serving Suggestion:
     "Don't serve this any more. It's awful."


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From: Darren New
Subject: Re: Molecular biology
Date: 13 Jan 2011 18:11:03
Message: <4d2f8687$1@news.povray.org>
Warp wrote:
>   It's just that defining "species" in terms of behavior is ludicrous.

Well, give a definition that shows two men are the same species, that a 
bacteria's descendants are the same species, and that these two populations 
of fruit flies are the same species.  What exactly has to be in the genetics?

-- 
Darren New, San Diego CA, USA (PST)
   Serving Suggestion:
     "Don't serve this any more. It's awful."


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From: Patrick Elliott
Subject: Re: Molecular biology
Date: 13 Jan 2011 23:17:22
Message: <4d2fce52$1@news.povray.org>
On 1/13/2011 2:49 AM, Invisible wrote:
>>> The distinction you're looking for is between eukaryotes and
>>> non-eukaryotes.
>>>
>> Uh, yeah. Couldn't think of the proper term though. But, the rest is
>> correct. If you don't have excess resources to waste on messing with
>> extra baggage, you don't live long if you have it. If you do have the
>> "power plants", you can afford to waste more space in the genome on
>> things that don't work, duplicate results, etc.
>
>>> I'm not sure I actually agree with this assessment.
>>>
>> http://scienceblogs.com/pharyngula/2010/12/how_to_afford_a_big_sloppy_gen.php
>>
>>
>> As to the cite for prokaryotes not having as many copy errors, I think
>> it would be more accurate to say, "They don't *preserve* as many." If
>> they did, they would have way more junk DNA, which is precisely what
>> they can't afford to have laying around in the first place. The actual
>> number of such errors that happen is likely the same, but, when it comes
>> to costs, if you can't afford them, you don't see those copied chunks
>> sticking around long.
>
> I think we need to distinguish between DNA that isn't used for anything,
> and DNA which actually produces proteins, but they don't do anything
> really useful.
>
> Just having a sequence in your genome doesn't really cost that much.
> Synthesizing it into a protein is much more expensive.
>
> It wouldn't surprise me if non-eukaryotes have fewer genes turned on,
> and possibly smaller genomes, but I doubt that they have radically
> "cleaner" genomes.
You are forgetting that you *still* have to copy all that extra stuff, 
when ever you divide the cell, so there is still a cost to synthesize 
all the copies, before the cell splits to form new cells. Also, its not 
a simple case of, "just ignore the stuff I don't use", something has to 
run through the pattern, decide what needs to be unfolded, or folded, 
jump past any stuff that is folded into an unusable state, etc.

And, most of the code, unlike in multi-celled organisms, is going to be 
"on". There is no reason to turn parts off, except for mitosis, and the 
like, if you are not differentiating the cells, which requires shutting 
off the parts you don't need running at all. Something that has a mess 
of extra code is going to have a lot of stuff the maneuver around to get 
anything done, and those that don't, are not likely to have a lot of 
inactive code, which isn't doing synthesis, more or less massively 
parallel, constantly.

-- 
void main () {

     if version = "Vista" {
       call slow_by_half();
       call DRM_everything();
     }
     call functional_code();
   }
   else
     call crash_windows();
}

<A HREF='http://www.daz3d.com/index.php?refid=16130551'>Get 3D Models, 
3D Content, and 3D Software at DAZ3D!</A>


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From: Patrick Elliott
Subject: Re: Molecular biology
Date: 13 Jan 2011 23:39:36
Message: <4d2fd388@news.povray.org>
On 1/13/2011 5:00 AM, Warp wrote:
> Darren New<dne### [at] sanrrcom>  wrote:
>> Surprisingly enough, it really is trivial.
>
>> http://en.wikipedia.org/wiki/Speciation#Artificial_speciation
>
>    It talks about preference, not about capability. Just because some man will
> not mate with fat women doesn't make the man a different species.
>
But, by the same token, just because a species has developed to "prefer" 
their own species, doesn't mean its 100% impossible for an impregnation 
to happen, it just isn't too common. The question then is, are the rest 
of the genes compatible at all. The answer is, "Depends". For common 
things, like insulin, the genome doesn't much care, as long as its 
"close enough". Basically, you have these barriers:

1. Pheromone response.
2. Reproductive compatibility (fusion will happen).
3. Number of chromosomes, though a difference of 1-2 may *not* be a big 
deal, as long as there are parallels, or the two available fill in any gaps.
4. Immune response - does the host mother's immune system see the cell 
as a problem?
5. Hormonal issues - the wrong levels "may" effect development, if far 
enough off.

Most of these are not likely to be surmountable by species in nature, 
short of a lot of very unusual mutations all coinciding. In principle, 
we could take steps to eliminate most of them, but no one is likely to 
do that (at least not in legit labs, in first, or probably even second, 
world countries). However, that the odds of a pure chance combination of 
factors resulting in a combination working being low doesn't mean 
"impossible". That is the problem. Of course, one big difference also 
comes down to the fact that "preference" in this case is *not* the same 
thing at all. For a fruit fly, preference means, short of outside 
intervention, its almost 100% certain they will never mate with a 
different species. The more complex the organism, the greater the odds 
it will "override" that preference, by self choice. Which is why you 
don't see, say, birds trying to mate spiders, but its not unheard of for 
dogs to try to mate with sheep, etc., or apes to mate with everything 
from frogs, to anything else that can't get away, mostly purely to "got 
off", which most simpler species don't do at all either. But, at that 
level of complexity, the number of barriers in place to prevent cross 
over is *very* high, even if they develop some truly odd preferences.

-- 
void main () {

     if version = "Vista" {
       call slow_by_half();
       call DRM_everything();
     }
     call functional_code();
   }
   else
     call crash_windows();
}

<A HREF='http://www.daz3d.com/index.php?refid=16130551'>Get 3D Models, 
3D Content, and 3D Software at DAZ3D!</A>


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From: Patrick Elliott
Subject: Re: Molecular biology
Date: 13 Jan 2011 23:49:48
Message: <4d2fd5ec$1@news.povray.org>
On 1/12/2011 11:27 PM, Jim Henderson wrote:
> On Wed, 12 Jan 2011 19:54:12 -0700, Patrick Elliott wrote:
>
>> And, I would, and many
>> others have, that if you do not enforce the matter strictly, you lend
>> yourself to a slow erosion of principle, in which the number of people
>> trying to actively violate it, or find ways around it, or even
>> repeal/change it, increases, as more and more succeed in finding such
>> loopholes. We often have difficulty seeing this, for much the same
>> reason the other side can't imagine every problem being solved from
>> guns, or prayer, or capitalism, or what ever combination of notions they
>> think are king of the hill at the time.
>
> My word, that's a very long run-on sentence. ;-)
>
> But it boils down to the "slippery slope" argument, and while I have been
> guilty of using it myself in the past, in more recent times, I've not
> really been convinced of it.
>
> Both ideologies use the argument when it suits them.
>
> I'm not really sure what the rest of what you wrote was, because it was
> so difficult to read.  Sorry.
>
> Jim
Well, the reason both sides make the argument is that its correct. If 
you don't enforce absolute moral codes, and arrest, hang, burn, or 
whatever, anyone you catch at it, you end up finding that some of the 
stuff you think is wrong becomes "normal", for everyone except your 
group. The flaw in the ointment is that they assume they *know* the 
answer, and what the consequences are, even when they have no evidence. 
I would say that, while this *sometimes* happens with the other side, 
most of the arguments *tend* to be backed by, "We tried that, it didn't 
work, made things worse, or nothing bad happened when no one followed 
it." All of them much more sane arguments than, "The world will come to 
an end if we let X people do Y thing! Someone told me, though I have 
know idea on what page, that the Babble says so!!!"

Or, Rand's book said so, or the wild guess I pulled out of my ass 
yesterday says so, or I find it icky, so it must be so, etc., ad nauseum.

Someone quoted the thinking behind some of this stuff as, "Credo quia 
absurdum" : 'I believe *because* the idea is absurd.'

-- 
void main () {
   If Schrödingers_cat is alive or version > 98 {
     if version = "Vista" {
       call slow_by_half();
       call DRM_everything();
     }
     call functional_code();
   }
   else
     call crash_windows();
}

<A HREF='http://www.daz3d.com/index.php?refid=16130551'>Get 3D Models, 
3D Content, and 3D Software at DAZ3D!</A>


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From: Patrick Elliott
Subject: Re: Molecular biology
Date: 14 Jan 2011 00:37:59
Message: <4d2fe137$1@news.povray.org>
On 1/12/2011 11:28 AM, Jim Henderson wrote:
> On Wed, 12 Jan 2011 11:01:50 -0500, Warp wrote:
>
>> Jim Henderson<nos### [at] nospamcom>  wrote:
>>> I fail to see how telling
>>> people "if you believe in something, practice it" comes even close to
>>> establishing a state-sponsored religion
>>
>>    For fair balance, shouldn't there be a "Nation Day of Atheism"? You
>>    can
>> make the exact same arguments: It's not promoting atheism nor forcing
>> anybody to be atheist. You can be atheist if you want, but it's your
>> choice.
>
> Actually, there is one - and it's usually (now) held on the same day as
> the NDP IIRC.
>
> Jim
I also here there is a "national body awareness day", AKA, "national 
nude day", but I don't see anyone in congress, or the president, 
standing up and declaring *either* a NBAD day, *or* a, "national day of 
keep your clothes on". The people *in* the government are far more 
Christian, usually, than the ones that elected them. Few, if any, are 
anything else, with the exception of some Jewish people. The presidents 
have *all* been Christian. It is irrelevant if the "indended" result 
isn't sectarian. You might as well go to Africa and not complain when 
the local president, with great cheers from everyone else in the 
government, and a lot of stupid speeches about the "blackness" of 
Africa, declared a, "National day of not being white."

What matters is the result, the perceived support it lends to the 
majority religion, the very narrow list of "faiths" that tend to get 
mentioned, and that it *supports*, how ever unintended, the position of 
people who *literally* believe that the government *can* be totally 
Christian, supporting it, endorsing it, etc., just so long as they 
"allow" everyone else to worship as they please (just not marry, have 
sex in certain ways, dress, look, speak, think, sell, buy, own, or 
publicly display what they wish, if it offends the sort of Christians 
that those people believe qualify).

Its this thinking, and the inadvertent support for it, which makes the 
national day of prayer a problem. For them, it *does* endorse it, and 
they quite clearly do not think that "endorsing" religion, even their 
own, is a problem, only denying others their own (save, again, for any 
conflicts in expression, in which case their own overrides the "wrong" one).

We see it all the damn time, in everything from the 100% church driven 
drive to get Prop 8 passed, to violence against minority religions, 
which gets brushed off as, "Well, its a small town, so.. And they won 
the case, even if they lost their business, home, etc., due to having to 
move.", to you name it. Its the same argument some atheists give 
"against" those they call "accommidationists". If you give ground, you 
find yourself not addressing one clear issue, you find that the issue 
gets buried under a dozen stray men, 50 irrelevant issues, and 100 
unrelated cases/assertions. Even if you win, you lose, since merely 
trying to win will result in cries of persecution. Nah, merely 
suggesting that you might have a relevant point about *any* religion 
does, even from the people that don't follow it.

The whole "Nation day of Atheism" thing is precisely what they would 
like to see atheists do, or anyone else with the "wrong religion", or 
who doesn't pray. We do our thing, you do yours, just so long as its out 
of sight, in the basement, with the door locked, and we don't hear any 
of it. After all, we outnumber you, and most of us are *sure* God = 
Jesus. Suggesting otherwise is persecution, and how dare you do that on 
the "national day of prayer".

This is the logic we are trying to deal with here. What is "intended", 
never mind "legal" doesn't mean jack, if 10% of the people think its 
about *them*, 60% of them don't give a shit, as long as you *are* 
praying, and everyone that isn't is seen as stupid, abnormal, wrong 
headed, or even Un-American, for not "joining in", and the 20% that 
don't care *also* don't care to try to change the situation. Its about 
perception, not strict legality. And, just as you can't cry "fire" in a 
crowded theater, it is not appropriate to cry, "All you people are 
special, if you are one of the ones that prays", in a nation where most 
of them see it as reflecting one religion, some see it as *only* about 
that one religion, and it actively excludes those that do not believe in 
doing it at all, including other religions.

-- 
void main () {
   If Schrödingers_cat is alive or version > 98 {
     if version = "Vista" {
       call slow_by_half();
       call DRM_everything();
     }
     call functional_code();
   }
   else
     call crash_windows();
}

<A HREF='http://www.daz3d.com/index.php?refid=16130551'>Get 3D Models, 
3D Content, and 3D Software at DAZ3D!</A>


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From: Stephen
Subject: Re: Molecular biology
Date: 14 Jan 2011 03:08:07
Message: <4d300467@news.povray.org>
On 13/01/2011 11:02 PM, Jim Henderson wrote:
> On Thu, 13 Jan 2011 20:52:18 +0000, Stephen wrote:
>
>> On 13/01/2011 8:38 PM, Jim Henderson wrote: ...
>>>
>>> Jim
>>
>> Mornington Crescent! :-P
>
> It's about time! :-)
>

How many words?


-- 
Regards
     Stephen


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From: Invisible
Subject: Re: Molecular biology
Date: 14 Jan 2011 04:27:55
Message: <4d30171b$1@news.povray.org>
>> I think we need to distinguish between DNA that isn't used for anything,
>> and DNA which actually produces proteins, but they don't do anything
>> really useful.
>>
>> Just having a sequence in your genome doesn't really cost that much.
>> Synthesizing it into a protein is much more expensive.
>>
>> It wouldn't surprise me if non-eukaryotes have fewer genes turned on,
>> and possibly smaller genomes, but I doubt that they have radically
>> "cleaner" genomes.

> You are forgetting that you *still* have to copy all that extra stuff,
> when ever you divide the cell, so there is still a cost to synthesize
> all the copies, before the cell splits to form new cells.

Yes, there is a cost. What I'm saying is that it's a very small cost.

> Also, its not
> a simple case of, "just ignore the stuff I don't use", something has to
> run through the pattern, decide what needs to be unfolded, or folded,
> jump past any stuff that is folded into an unusable state, etc.

It's not like a computer, doing a linear scan of the entire genome 
looking for active genes. It doesn't work like that.

As far as I know (and I'm not an expert on the subject), having extra 
inactive genes imposes very little penalty for transcription.

> And, most of the code, unlike in multi-celled organisms, is going to be
> "on". There is no reason to turn parts off, except for mitosis, and the
> like, if you are not differentiating the cells

False.

Unicellular organisms might not build colonies of differentiated cells, 
but that does *not* mean that all genes are switched on, all the time.

There are organisms that can metabolise both aerobically and 
anaerobically. That's two different metabolic pathways, involving 
different sets of proteins. Many if not most organisms can utilise more 
then one food source. That's different sets of proteins. Many organisms 
have a life-cycle more complex them just "grow, divide, grow, divide". 
That requires different sets of proteins. Some cells even signal each 
other, and undergo limited differentiation under certain conditions. 
More sets of genes. Then there are genes only used in response to attack 
or damage. And so forth.

Seriously. Few if any organisms go around with *all* their genes 
switched on all the time.


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From: scott
Subject: Re: Molecular biology
Date: 14 Jan 2011 05:09:49
Message: <4d3020ed@news.povray.org>
> It means that the value you are measuring is not determined until you
> measure it. Hence, as far as we will ever be able to know without
> divine(*) intervention, yes, it's random.

OK, but that was my point, it could be controlled by something 
*impossible* for us to find out.  The same way as an artificial brain 
simulation running on one of our computers would find it impossible to 
find out about our universe.


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