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From: Jim Henderson
Subject: Re: Molecular biology
Date: 12 Jan 2011 13:28:17
Message: <4d2df2c1$1@news.povray.org>
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


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From: Patrick Elliott
Subject: Re: Molecular biology
Date: 12 Jan 2011 21:31:27
Message: <4d2e63ff$1@news.povray.org>
On 1/12/2011 2:40 AM, Invisible wrote:
>> This in fact happens. We can even, in many cases, parse out what those
>> *where*, sometimes by finding those extra structures still intact in
>> other species.
>
> More to the point, biological structures can *change purpose* too.
>
>> And you are dead wrong on the later, evolution **keeps**
>> masses of junk, whether it produces a benefit or not.
>
> That too. The human genome has half a dozen broken copies of the globin
> gene, for example. (Plus 4 (?) similar but not identical copies that
> actually work.)
>
>> The single cell do not, in general, contain mitochondria.
>
> False.
>
> Note carefully that "single-celled organisms" covers a vast variety of
> life forms, only some of which are closely related. Many of these
> contain mitochondria, and many do not. The fact that they are
> unicellular does not correlate particularly well with the presence of
> absence of mitochondria.
>
> 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.

>> Their genetics are often **far** more streamlined, because
>> they can't afford to carry junk around, which doesn't do anything, for
>> the reason you describe. It costs resources. Having a sort of "power
>> plant" in the cell, whose genetics are 100% geared at producing excess
>> amounts of energy, over what is absolutely needed by themselves, allows
>> the rest of the genome, in the main cell, to be very sloppy in its
>> operations, copying, cleanup, etc. Anything with such an internal power
>> plant can afford to keep lots of stuff that does nothing at all, and
>> only gets rid of things that are actively defective, usually not by
>> deletion, but just by shutting them off, so they do nothing. This allows
>> for what, in a single cell, would be egregious errors, such as making an
>> exact copy of a sequence, then later having that sequence get mangled
>> into a unique function. Its way harder to manage that if you can't
>> afford extra copies lying around, where your energy input is drastically
>> damaged, if you allow such a copy to happen.
>
> 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.

-- 
void main () {

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

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From: Patrick Elliott
Subject: Re: Molecular biology
Date: 12 Jan 2011 21:54:18
Message: <4d2e695a$1@news.povray.org>
On 1/11/2011 1:57 PM, Jim Henderson wrote:
> On Tue, 11 Jan 2011 13:08:49 -0700, Patrick Elliott wrote:
>
>> The problem with this is that its the **same** excuse that is used by
>> nearly every city council, and other government body, for ***actually***
>> violating the constitution, by having an opening prayer, then babbling
>> about how it just wasn't convenient for them to find a Buddhist that
>> day, or some such, to "flesh out" the roster and make it non-Christian
>> specific. Oh, and of course, they ***never ever*** open without it, so
>> it very much supports religion in general, even when they play lip
>> service to being "fair" about which one of the, maybe 3, they will
>> bother/allow to open the meeting.
>
> I don't entirely disagree with what you've said above.  Having a prayer
> of any sort during government proceedings is a problem for me.
>
> But that's not what we're talking about here.
>
>> Sorry, but Warp is dead right.
>
> I respectfully disagree.  But hey, we can do that.
>
>> The government promoting a day of prayer
>> does not **in any way** imply anything other than an endorsement of
>> religion in general,
>
> Which in and of itself does not violate the the constitution.
> Acknowledging that some people are religions is different from saying
> "You must pray on this day, and if you don't, you're going to jail".
>
>  From a historical context, that's what the founders were dealing with:
> In England, there was a state-sponsored religion, and practicing
> protestants were legally barred from practicing their own non-state-
> sanctioned religion.
>
>> and too often, given the words of those who do such
>> promotion, defend doing so, and get elected on the principle of the
>> "Christian nation" BS, a *specific* one. Its kind of like how federal
>> money gets spent on "faith based initiatives", yet, somehow, 99.9% of
>> all the initiatives getting funded are Christian ones, even when other
>> groups present alternatives, or worse, alternatives that are not "known"
>> to lie, cheat, steal, or fail to provide the things they claim they need
>> the money for (not that we would know, in many cases, since they are
>> often sub-groups of bigger groups, and only the "government" money needs
>> to be accounted for). The 0.1% is pure, 100%, lip service to the
>> principle, and mean jack shit with respect to the idea that the
>> government isn't "endorsing" something.
>
> And those things should be dealt with individually.  That doesn't
> inherently make the NDoP a bad thing or a violation of the US
> Constitution.  Again, this is something entirely different than the
> subject at hand.
>
> Jim
While this is, *technically* true, from a purely literal stance, there 
is often quoted a concept of "spirit of the law". 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. That people might breach the 
spirit of the law, and, being allowed, then breach the law itself, isn't 
an easy thing to recognize, if your goal is to only apply it "loosely". 
The problem is, of course, we *do* see people crossing the line, such as 
one case in the last ten years where a Jewish family was hounded, after 
the city council member that belonged to it said, "Maybe its a bad idea 
to *specifically* open with a prayer to Jesus." In some areas, this is 
all too common, and the excuse is always a) we are allowed to have 
prayers, so the mere accident of who gets prayed to all the time is 
coincidence, b) we would (though not really, see above) allow someone 
else to do it, if we had anyone else around to do so, and c) the 
constitution only says you can't endorse religion, not that we can't 
shove it down everyone's throughts, as long as its "non-sectarian" 
(i.e., being allowed to avoid/not participate in/deal with it, is *not* 
protected, according to this argument).

Its like telling someone, "You need to use turn signals, but not on 
parking lots", pretty soon people are making jokes, like locally here, 
in the vein of, "When you move here they inject you with a virus, which 
makes you forget where the turn signals are." Enforcement *only* 
happens, as it is, if someone sues, and in many places, everything from 
homogenization of the assumption that there is nothing wrong with their 
purely sectarian support, to even fear of what would happen *if* someone 
protested, results in *no* enforcement. And, you can't take something on 
a "case by case" basis, if no one will recognize there *is* problem, 
admit it needs to be fixed, or actively do something about it.

If the rules was "never", this wouldn't be a problem. Instead, we have, 
"Well, you are not supposed to, but....", and a near infinite list of 
exclusions and exceptions. So, unless someone crosses a line by a 
provable amount, nothing happens, and even if they do, they pay a fine, 
maybe lose some government endorsement (unless they are the government), 
and next week the are doing the same thing again.

-- 
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();
}

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3D Content, and 3D Software at DAZ3D!</A>


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From: Patrick Elliott
Subject: Re: Molecular biology
Date: 12 Jan 2011 22:07:56
Message: <4d2e6c8c$1@news.povray.org>
On 1/12/2011 8:53 AM, Warp wrote:
> Darren New<dne### [at] sanrrcom>  wrote:
>> Warp wrote:
>>>    Of course it is. It's an implicit encouragement from the government for
>>> people to follow a religious custom.
>
>> Does this mean Black History Month implies you should go out and be Black
>> for a few weeks?
>
>    How exactly does "Black History" imply "you should *be* black"?
>
>    It implies that people should study and consider the history of black
> people, doesn't it? So yes, it is quite a similar thing.
>
>    Likewise "national day of prayer" promotes prayer. Not all people are
> either firm believers or firm unbelievers. There *are* impressionable
> people who may follow authority in these matters, and it's certainly *not*
> the place for a secular government to promote religion.
>
Yes, this is precisely the point being missed by others. "Black History 
Month", doesn't imply you should examine Chinese Immigrants, American 
Indians, or some UFO nuts "Reptiloid aliens living in the center of the 
Earth.". It means they look at "Black History". Someone calls for a day 
of prayer, it doesn't mean, "How about buying a lot of lattes, watching 
more TV, going to dance clubs, nude bicycling, or 5 billion other things 
you might opt to do." It means, "We would like to encourage you to do 
something specifically religious, not not just religious, but specific 
to a specific 'set' of religions, since some don't." To me, this is a 
huge, Duh! I literally don't get why others can't see what is wrong with it.

-- 
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: Jim Henderson
Subject: Re: Molecular biology
Date: 13 Jan 2011 01:27:19
Message: <4d2e9b47@news.povray.org>
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


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From: Jim Henderson
Subject: Re: Molecular biology
Date: 13 Jan 2011 01:28:23
Message: <4d2e9b87$1@news.povray.org>
On Wed, 12 Jan 2011 20:07:50 -0700, Patrick Elliott wrote:

>  It means, "We would like to encourage you to do
> something specifically religious, not not just religious, but specific
> to a specific 'set' of religions, since some don't."

No, really, it doesn't.  At least not to me.

Jim


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From: Invisible
Subject: Re: Molecular biology
Date: 13 Jan 2011 04:49:23
Message: <4d2ecaa3$1@news.povray.org>
>> 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.


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From: Warp
Subject: Re: Molecular biology
Date: 13 Jan 2011 06:45:32
Message: <4d2ee5dc@news.povray.org>
Invisible <voi### [at] devnull> wrote:
> On 12/01/2011 04:12 PM, Warp wrote:
> > Invisible<voi### [at] devnull>  wrote:
> >> If you can't, take a look at dogs. Some kinds can't interbreed with each
> >> other, if only due to huge differences in size. Humans did that.
> >
> >    I don't think that is what defines a species. It's about genetics.

> How about this: There are two species of grasshopper that never 
> interbreed. The females of species A ignore the songs of males of 
> species B. However, if you mute the male and play back a recording of a 
> male of species A, the two will mate, and produce viable offspring. It's 
> just that this only ever happens in the lab.

  The definition of species is related to genetics, not to behavior.

> Similarly, there are probably classes of birds where you could do the 
> same thing by putting coloured visors over the bird's eyes, or moths 
> where you could mask one chemical pheromone with another. Are these 
> separate species?

  It's about genetics, not about behavior.

> You can apparently mate a lion with a tiger, producing either a "liger" 
> or a "tiglon". (Go look them up.) But this never happens in the wild (as 
> far as we know). Are these separate species?

  The offspring must be fertile. Ligers and tigons aren't.

-- 
                                                          - Warp


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From: Invisible
Subject: Re: Molecular biology
Date: 13 Jan 2011 06:58:42
Message: <4d2ee8f2$1@news.povray.org>
>    The definition of species is related to genetics, not to behaviour.

I disagree.

By human intervention, you can cause all kinds of matings to occur that 
would never, ever happen in nature. That does /not/ mean that all 
animals are of the same species.

>    The offspring must be fertile. Ligers and tigons aren't.

Apparently it was long thought that ligers and tiglons were infertile, 
but apparently they have in a few rare cares produced long-lived offspring.

But in any case, yes, I agree that the offspring must be fertile.


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From: Warp
Subject: Re: Molecular biology
Date: 13 Jan 2011 07:00:34
Message: <4d2ee962@news.povray.org>
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.

-- 
                                                          - Warp


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