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13 Oct 2026 01:03:34 EDT (-0400)
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From: Darren New
Subject: Re: Molecular biology
Date: 11 Jan 2011 12:23:23
Message: <4d2c920b@news.povray.org>
Invisible wrote:
> Just about every living organism has homeostasis. I presume you mean 
> *temperature* homeostasis?

Yes.

> Right. So what you're saying is that it's unusual that 5 digits is a 
> conserved feature?

It seems like a very minor and easily-mutated feature, compared to (say) 
bilateral symmetry.

> I suspect what it boils down so is that there's no specific reason why 
> some number other than 5 would be an advantage, so it hasn't changed. 
> (This of course doesn't rule out random "neutral" changes I suppose...)

That's my point. It doesn't rule out neutral changes, yet we don't see 
neutral changes. And people investigating this have found that we don't see 
neutral changes because neutral changes in the gene for finger bones are 
also catastrophically detrimental changes to the reproductive system.

> extremely highly conserved.)

What I've read, which I found interesting, is that five fingers is highly 
conserved not because of itself, but because it's linked to other highly 
conserved genes. That's basically what I'm saying. I.e., something no 
designer would have a reason to do.

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


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From: Jim Henderson
Subject: Re: Molecular biology
Date: 11 Jan 2011 12:33:50
Message: <4d2c947e$1@news.povray.org>
On Tue, 11 Jan 2011 09:20:13 -0800, Darren New wrote:

> Warp wrote:
>> "Observances of the National Day of Prayer took place throughout the
>> U.S. in 2009 and again in 2010.
> 
> OK. But it has been around longer than either of us have been alive;
> it's not something Obama ass-pulled. I'm not sure what "The Obama
> administration" refers to there, but I'm pretty sure it encompasses far
> more than "Obama".

What's more, I would disagree with the court that this is an 
unconstitutional practice.  The first amendment protects against the 
government establishment of a state-sponsored religion.  Setting aside a 
"national prayer day" doesn't violate that unless it also mandates that 
everyone, for example, recite the Lord's Prayer, and establishes 
penalties for those who do not.

I don't think saying "here's a day where if those of you want to focus 
your efforts on praying, you can do so" truly violates that intention in 
the 1st amendment.

But IANAL - nor do I participate in the NDoP.  So far, I've not been 
jailed for it or fined for my non-participation. :-)

Jim


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From: Warp
Subject: Re: Molecular biology
Date: 11 Jan 2011 12:52:50
Message: <4d2c98f1@news.povray.org>
Darren New <dne### [at] sanrrcom> wrote:
> Warp wrote:
> > life on Earth wouldn't exist because
> > all bodies of water would freeze from the bottom up, killing all living
> > organisms.

> Well, unless they evolved in San Diego. ;-)

  The reference is completely lost on me.

-- 
                                                          - Warp


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From: Warp
Subject: Re: Molecular biology
Date: 11 Jan 2011 12:56:45
Message: <4d2c99dd@news.povray.org>
Darren New <dne### [at] sanrrcom> wrote:
> > (Also, most liquids other than water get denser when they
> > solidify, which is a big problem.)

> I'm not sure that's as much of a problem as you think it is for anything 
> other than fish.

  Well, life on Earth was completely in water for the first... what?
3 billion years?

>  Why do you think the fact that it floats is important?

  Because it affects (or in the case of water, doesn't) submarine habitats
quite radically. (As said, it's probably quite difficult for life to form
in non-liquid environments.)

-- 
                                                          - Warp


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From: Warp
Subject: Re: Molecular biology
Date: 11 Jan 2011 13:02:59
Message: <4d2c9b53@news.povray.org>
Darren New <dne### [at] sanrrcom> wrote:
> ID is certainly testable: We've found no irreducibly complex substructures, 

  Even if there *are* irreducibly complex structures in biology (which
I wouldn't be surprised if they existed) it still doesn't mean it could
not have formed by natural means. "Irreducibly complex" does not mean
"impossible to build" (because it would be outright *impossible*, duh).
It simply means that the structure cannot be formed by simply adding each
individual part one at a time. However, it can be built by having additional
helping structures which are later removed as obsolete.

  The classic example is an arc made of stones: Remove even one single
stone, and the whole arc collapses. The arc is irreducibly complex.
However, that doesn't mean the arc is impossible to construct: First
you build a supporting frame, then add the stones, then remove the frame.
Nothing says this cannot happen naturally. (In fact, evolution often gets
rid of parts that become useless over time because they only consume valuable
resources for no benefit. Thus, just because a supporting part is not anymore
there doesn't mean it was never there.)

-- 
                                                          - Warp


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From: Warp
Subject: Re: Molecular biology
Date: 11 Jan 2011 13:06:09
Message: <4d2c9c11@news.povray.org>
Darren New <dne### [at] sanrrcom> wrote:
> Warp wrote:
> > "Observances of the National Day of Prayer took place throughout the
> > U.S. in 2009 and again in 2010.

> OK. But it has been around longer than either of us have been alive; it's 
> not something Obama ass-pulled. I'm not sure what "The Obama administration" 
> refers to there, but I'm pretty sure it encompasses far more than "Obama".

  I think you badly misunderstand.

  The federal judge ruled it unconstitutional for the government to endorse
the national day of prayer, and *regardless of this* Obama decided to
proclaim it. In other words, he willingly broke the first amendment with
complete disregard of the ruling.

-- 
                                                          - Warp


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From: Warp
Subject: Re: Molecular biology
Date: 11 Jan 2011 13:08:44
Message: <4d2c9cac@news.povray.org>
Jim Henderson <nos### [at] nospamcom> wrote:
> What's more, I would disagree with the court that this is an 
> unconstitutional practice.  The first amendment protects against the 
> government establishment of a state-sponsored religion.  Setting aside a 
> "national prayer day" doesn't violate that unless it also mandates that 
> everyone, for example, recite the Lord's Prayer, and establishes 
> penalties for those who do not.

  So as long as no specific religion is explicitly mentioned, any kind of
religious decree is ok?

  I don't think your first amendment says nor means that.

-- 
                                                          - Warp


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From: Jim Henderson
Subject: Re: Molecular biology
Date: 11 Jan 2011 13:16:46
Message: <4d2c9e8e@news.povray.org>
On Tue, 11 Jan 2011 13:08:44 -0500, Warp wrote:

> Jim Henderson <nos### [at] nospamcom> wrote:
>> What's more, I would disagree with the court that this is an
>> unconstitutional practice.  The first amendment protects against the
>> government establishment of a state-sponsored religion.  Setting aside
>> a "national prayer day" doesn't violate that unless it also mandates
>> that everyone, for example, recite the Lord's Prayer, and establishes
>> penalties for those who do not.
> 
>   So as long as no specific religion is explicitly mentioned, any kind
>   of
> religious decree is ok?
> 
>   I don't think your first amendment says nor means that.

Have you read the first amendment to the US Constitution?

"Congress shall make no law respecting an establishment of religion, or 
prohibiting the free exercise thereof; or abridging the freedom of 
speech, or of the press; or the right of the people peaceably to 
assemble, and to petition the Government for a redress of grievances."

Now tell me how a declaration of a National Day of Prayer by the 
executive branch is (a) Congress establishing a law respecting the 
establishment of religion, or (b) prohibits the free exercise thereof.

The way I read it, it actually encourages and promotes the free exercise 
of religion, including the right of one *not* to participate.

Jim


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From: Jim Henderson
Subject: Re: Molecular biology
Date: 11 Jan 2011 13:17:37
Message: <4d2c9ec1@news.povray.org>
On Tue, 11 Jan 2011 13:06:09 -0500, Warp wrote:

> Darren New <dne### [at] sanrrcom> wrote:
>> Warp wrote:
>> > "Observances of the National Day of Prayer took place throughout the
>> > U.S. in 2009 and again in 2010.
> 
>> OK. But it has been around longer than either of us have been alive;
>> it's not something Obama ass-pulled. I'm not sure what "The Obama
>> administration" refers to there, but I'm pretty sure it encompasses far
>> more than "Obama".
> 
>   I think you badly misunderstand.
> 
>   The federal judge ruled it unconstitutional for the government to
>   endorse
> the national day of prayer, and *regardless of this* Obama decided to
> proclaim it. In other words, he willingly broke the first amendment with
> complete disregard of the ruling.

I don't think you understand the text of the first amendment, and I might 
even be so bold as to say that the federal judge also doesn't understand 
it.

Jim


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From: Jim Henderson
Subject: Re: Molecular biology
Date: 11 Jan 2011 13:25:49
Message: <4d2ca0ad$1@news.povray.org>
On Tue, 11 Jan 2011 13:16:46 -0500, Jim Henderson wrote:

> On Tue, 11 Jan 2011 13:08:44 -0500, Warp wrote:
> 
>> Jim Henderson <nos### [at] nospamcom> wrote:
>>> What's more, I would disagree with the court that this is an
>>> unconstitutional practice.  The first amendment protects against the
>>> government establishment of a state-sponsored religion.  Setting aside
>>> a "national prayer day" doesn't violate that unless it also mandates
>>> that everyone, for example, recite the Lord's Prayer, and establishes
>>> penalties for those who do not.
>> 
>>   So as long as no specific religion is explicitly mentioned, any kind
>>   of
>> religious decree is ok?
>> 
>>   I don't think your first amendment says nor means that.
> 
> Have you read the first amendment to the US Constitution?
> 
> "Congress shall make no law respecting an establishment of religion, or
> prohibiting the free exercise thereof; or abridging the freedom of
> speech, or of the press; or the right of the people peaceably to
> assemble, and to petition the Government for a redress of grievances."
> 
> Now tell me how a declaration of a National Day of Prayer by the
> executive branch is (a) Congress establishing a law respecting the
> establishment of religion, or (b) prohibits the free exercise thereof.
> 
> The way I read it, it actually encourages and promotes the free exercise
> of religion, including the right of one *not* to participate.

Not only that, but the judge in the case actually ruled that her ruling 
should not be considered a bar to any prayer days until all appeals are 
exhausted.  So even in the event that the federal judge is correct, she 
herself effectively said her ruling did not impose an injunction or 
prohibition on the President from continuing to do what he has done.

So Obama has not, in fact, broken any law, as the appeals have clearly 
not run out yet.

Jim


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From: Warp
Subject: Re: Molecular biology
Date: 11 Jan 2011 13:43:59
Message: <4d2ca4ef@news.povray.org>
Jim Henderson <nos### [at] nospamcom> wrote:
> Have you read the first amendment to the US Constitution?

> "Congress shall make no law respecting an establishment of religion, or 
> prohibiting the free exercise thereof; or abridging the freedom of 
> speech, or of the press; or the right of the people peaceably to 
> assemble, and to petition the Government for a redress of grievances."

> Now tell me how a declaration of a National Day of Prayer by the 
> executive branch is (a) Congress establishing a law respecting the 
> establishment of religion, or (b) prohibits the free exercise thereof.

  I think that you are falling into interpreting literally the words
rather than wanting to understand the meaning of the text. Or, more
precisely, you are arguing "it doesn't explicitly prohibit this, hence
it allows it".

  The sentiment of the text is quite clearly the same as with most other
constitutions in most other countries: The government shall not endorse
nor prohibit religions.

  If you are trying to argue "but hey, it literally only says that the
government shall not *establish* religions, it doesn't say anything about
the government endorsing *already established* religions" you are
deliberately distorting the meaning of the text by arguing over semantics.

> The way I read it, it actually encourages and promotes the free exercise 
> of religion, including the right of one *not* to participate.

  No, it doesn't. It only says that the government must not endorse nor
prohibit religions. Where exactly do you see the "promotes the free
exercise of religion" part? The government must *allow* it. It doesn't
say it should *promote* it.

  Sheesh, I can't believe a Finn must teach you your own constitution.
(Ok, I don't know if you are a citizen of the US, but I'm assuming you are.)

-- 
                                                          - Warp


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From: Patrick Elliott
Subject: Re: Molecular biology
Date: 11 Jan 2011 14:25:59
Message: <4d2caec7$1@news.povray.org>
On 1/10/2011 3:08 PM, Darren New wrote:
> Patrick Elliott wrote:
>> Yeah, what I was talking about was a programmatic attempt at applying
>> logical reversibility. The stuff you are talking about is completely
>> different.
>
> Logical reversibility hasn't anything to do with saving energy, altho it
> might have something to do with speeding up computations. obviously,
> logical reversibility is a necessary precursor to physical reversibility.
>
Well, in the specific article I read, but don't have anymore, the idea 
was to work out the least costly set of steps, which may include 
reversing them, to produce an equal, or lower, energy state, whenever 
possible, and not using quantum computers either. But, what ever.

-- 
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: 11 Jan 2011 14:47:08
Message: <4d2cb3bc$1@news.povray.org>
On 1/11/2011 11:02 AM, Warp wrote:
> Darren New<dne### [at] sanrrcom>  wrote:
>> ID is certainly testable: We've found no irreducibly complex substructures,
>
>    Even if there *are* irreducibly complex structures in biology (which
> I wouldn't be surprised if they existed) it still doesn't mean it could
> not have formed by natural means. "Irreducibly complex" does not mean
> "impossible to build" (because it would be outright *impossible*, duh).
> It simply means that the structure cannot be formed by simply adding each
> individual part one at a time. However, it can be built by having additional
> helping structures which are later removed as obsolete.
>
>    The classic example is an arc made of stones: Remove even one single
> stone, and the whole arc collapses. The arc is irreducibly complex.
> However, that doesn't mean the arc is impossible to construct: First
> you build a supporting frame, then add the stones, then remove the frame.
> Nothing says this cannot happen naturally. (In fact, evolution often gets
> rid of parts that become useless over time because they only consume valuable
> resources for no benefit. Thus, just because a supporting part is not anymore
> there doesn't mean it was never there.)
>
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. And you are dead wrong on the later, evolution **keeps** 
masses of junk, whether it produces a benefit or not. The reason it does 
has to do with the difference between some single cell organisms, and 
multi-cell organisms. The single cell do not, in general, contain 
mitochondria. 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.

Mind, "allow" in this context means that the cost gets high enough that 
the cell can't function *with* the change in it, and dies, without 
replicating. Again, if you have something producing *excess* energy for 
you, and nothing but that, you can afford to make single, several, 
dozens, hundreds, of copies, even if they only happen one at a time. The 
result is masses of new functions all derived from the same base code, 
many "irreducible", because over time a) they developed unique 
properties and functions, and b) at some point the support needed to 
make them work at all became redundant and was either deleted, shuffled 
into dead code, or co-opted for/by one of the other copies, which still 
needed it.

In any case, no, evolution doesn't have a garbage collection function, 
as such, and as long as you have all the extra energy resources, doesn't 
delete things in at any major rate. To put it another way... If single 
cell organisms had life cycles like ours, 100 years, and only limited 
offspring, they would "evolve" a lot slower than us. They only reason 
they do evolve faster is *purely* because they produce populations in 
the millions in minutes, or hours, instead of thousands of years. From a 
"cost" standpoint, they can only afford to keep things that actually 
help them, if it involves a new copy of the gene sequence, nor can they 
afford to keep it around, if it stops doing something useful. Most of 
their "changes" are, as a result, point mutation/deletion/addition, not 
the copy of whole sequences.

-- 
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: Jim Henderson
Subject: Re: Molecular biology
Date: 11 Jan 2011 14:52:13
Message: <4d2cb4ed$1@news.povray.org>
On Tue, 11 Jan 2011 13:43:59 -0500, Warp wrote:

> Jim Henderson <nos### [at] nospamcom> wrote:
>> Have you read the first amendment to the US Constitution?
> 
>> "Congress shall make no law respecting an establishment of religion, or
>> prohibiting the free exercise thereof; or abridging the freedom of
>> speech, or of the press; or the right of the people peaceably to
>> assemble, and to petition the Government for a redress of grievances."
> 
>> Now tell me how a declaration of a National Day of Prayer by the
>> executive branch is (a) Congress establishing a law respecting the
>> establishment of religion, or (b) prohibits the free exercise thereof.
> 
>   I think that you are falling into interpreting literally the words
> rather than wanting to understand the meaning of the text. Or, more
> precisely, you are arguing "it doesn't explicitly prohibit this, hence
> it allows it".
> 
>   The sentiment of the text is quite clearly the same as with most other
> constitutions in most other countries: The government shall not endorse
> nor prohibit religions.
> 
>   If you are trying to argue "but hey, it literally only says that the
> government shall not *establish* religions, it doesn't say anything
> about the government endorsing *already established* religions" you are
> deliberately distorting the meaning of the text by arguing over
> semantics.

How much have you actually studied US constitutional law and the US 
constitution?

Moreover, it appears you haven't actually read the decision from the 
federal judge (which I referenced), where she says that her ruling SHOULD 
NOT be taken to mean that the President shouldn't observe the NDoP until 
all appeals have been exhausted.

You do know what an "injunction" is, yes?  There isn't one based on that 
ruling.

>> The way I read it, it actually encourages and promotes the free
>> exercise of religion, including the right of one *not* to participate.
> 
>   No, it doesn't. It only says that the government must not endorse nor
> prohibit religions. Where exactly do you see the "promotes the free
> exercise of religion" part? The government must *allow* it. It doesn't
> say it should *promote* it.
> 
>   Sheesh, I can't believe a Finn must teach you your own constitution.
> (Ok, I don't know if you are a citizen of the US, but I'm assuming you
> are.)

That was uncalled for.  I *could* respond in a similar spirit and say 
that you're not teaching me about the US constitution, only your 
ignorance of it, but I won't do that.

Yes, I'm a US citizen, and I've spent some time (more than most citizens, 
in fact) learning about the constitution and understanding its meaning - 
a meaning that doesn't cherrypick the parts that are relevant to my own 
point of view.

I consider myself pretty non-religious, and yes, I get annoyed with 
things like courthouses posting the 10 Commandments.  That's a little 
different than the President saying "if you believe in prayer, then pray, 
and here's a day for it".  I don't care if it's Obama or Bush saying 
that.  For those who want to pray, knock yourselves out.  I'm not likely 
to join you in doing so, and as long as you don't try to make me pray or 
make those who don't want to do so, hey, that's cool.

Jim


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From: Patrick Elliott
Subject: Re: Molecular biology
Date: 11 Jan 2011 14:56:51
Message: <4d2cb603@news.povray.org>
On 1/11/2011 7:55 AM, Invisible wrote:
>> The difficulty of classifying B in the example also demonstrates the
>> completely fuzzy line between when a species becomes another species.
>> If you trace the ancestry of a modern species back to an ancestral
>> species
>> which spawned one or more other modern species, it's hard to define when
>> exactly the modern species became to exist exactly.
>
> Ring species show fuzziness in the spatial domain, ancestor trees show
> it in the temporal domain. Either way, the problem remains the same: how
> to map discrete names to continuous phenomena?

Seen at least one statement to the effect that "tree" isn't an accurate 
description at all, but rather the complex braiding you see at a river 
delta. It might split off in totally different directions at some 
points, but a lot of stuff close together is prone to flow back and 
forth between channels, maybe even "drifting" back together, when 
previously separate (though, so far we don't see any obvious examples of 
that).


-- 
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: 11 Jan 2011 15:08:54
Message: <4d2cb8d6$1@news.povray.org>
On 1/11/2011 12:52 PM, Jim Henderson wrote:
> On Tue, 11 Jan 2011 13:43:59 -0500, Warp wrote:
>
>> Jim Henderson<nos### [at] nospamcom>  wrote:
>>> Have you read the first amendment to the US Constitution?
>>
>>> "Congress shall make no law respecting an establishment of religion, or
>>> prohibiting the free exercise thereof; or abridging the freedom of
>>> speech, or of the press; or the right of the people peaceably to
>>> assemble, and to petition the Government for a redress of grievances."
>>
>>> Now tell me how a declaration of a National Day of Prayer by the
>>> executive branch is (a) Congress establishing a law respecting the
>>> establishment of religion, or (b) prohibits the free exercise thereof.
>>
>>    I think that you are falling into interpreting literally the words
>> rather than wanting to understand the meaning of the text. Or, more
>> precisely, you are arguing "it doesn't explicitly prohibit this, hence
>> it allows it".
>>
>>    The sentiment of the text is quite clearly the same as with most other
>> constitutions in most other countries: The government shall not endorse
>> nor prohibit religions.
>>
>>    If you are trying to argue "but hey, it literally only says that the
>> government shall not *establish* religions, it doesn't say anything
>> about the government endorsing *already established* religions" you are
>> deliberately distorting the meaning of the text by arguing over
>> semantics.
>
> How much have you actually studied US constitutional law and the US
> constitution?
>
> Moreover, it appears you haven't actually read the decision from the
> federal judge (which I referenced), where she says that her ruling SHOULD
> NOT be taken to mean that the President shouldn't observe the NDoP until
> all appeals have been exhausted.
>
> You do know what an "injunction" is, yes?  There isn't one based on that
> ruling.
>
>>> The way I read it, it actually encourages and promotes the free
>>> exercise of religion, including the right of one *not* to participate.
>>
>>    No, it doesn't. It only says that the government must not endorse nor
>> prohibit religions. Where exactly do you see the "promotes the free
>> exercise of religion" part? The government must *allow* it. It doesn't
>> say it should *promote* it.
>>
>>    Sheesh, I can't believe a Finn must teach you your own constitution.
>> (Ok, I don't know if you are a citizen of the US, but I'm assuming you
>> are.)
>
> That was uncalled for.  I *could* respond in a similar spirit and say
> that you're not teaching me about the US constitution, only your
> ignorance of it, but I won't do that.
>
> Yes, I'm a US citizen, and I've spent some time (more than most citizens,
> in fact) learning about the constitution and understanding its meaning -
> a meaning that doesn't cherrypick the parts that are relevant to my own
> point of view.
>
> I consider myself pretty non-religious, and yes, I get annoyed with
> things like courthouses posting the 10 Commandments.  That's a little
> different than the President saying "if you believe in prayer, then pray,
> and here's a day for it".  I don't care if it's Obama or Bush saying
> that.  For those who want to pray, knock yourselves out.  I'm not likely
> to join you in doing so, and as long as you don't try to make me pray or
> make those who don't want to do so, hey, that's cool.
>
> Jim
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.

Sorry, but Warp is dead right. The government promoting a day of prayer 
does not **in any way** imply anything other than an endorsement of 
religion in general, 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.

-- 
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: Warp
Subject: Re: Molecular biology
Date: 11 Jan 2011 15:08:57
Message: <4d2cb8d9@news.povray.org>
Patrick Elliott <sel### [at] npgcablecom> wrote:
> Seen at least one statement to the effect that "tree" isn't an accurate 
> description at all, but rather the complex braiding you see at a river 
> delta. It might split off in totally different directions at some 
> points, but a lot of stuff close together is prone to flow back and 
> forth between channels, maybe even "drifting" back together, when 
> previously separate (though, so far we don't see any obvious examples of 
> that).

  It's quite probable that many species divided (usually geographically)
into two isolated groups and started to drift genetically apart from each
other but then joined again before they drifted too much, and the gene pool
got intermixed once again, stopping the speciation that was happening.
(I don't know if there are concrete examples of this.)

-- 
                                                          - Warp


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From: Patrick Elliott
Subject: Re: Molecular biology
Date: 11 Jan 2011 15:14:34
Message: <4d2cba2a@news.povray.org>
On 1/11/2011 5:53 AM, Paul Fuller wrote:
> Replying to Invisible but some comments on what Darren kicked off about
> fingers.
>
> On 8/01/2011 5:05 AM, Darren New wrote:
>  >
>  > I remember reading somewhere that there's a gene that controls how many
>  > fingers you have *and* something about the reproductive system, so any
>  > mutation in that gene tends to keep you from reproducing for entirely
>  > unrelated reasons. Hence the reason why everything from fish to bats to
>  > birds to people have five finger bones.
>  >
>
> On 11/01/2011 8:54 PM, Invisible wrote:
>>
>> I suspect what it boils down so is that there's no specific reason why
>> some number other than 5 would be an advantage, so it hasn't changed.
>> (This of course doesn't rule out random "neutral" changes I suppose...)
>>
>
> Given the enormous range of limb variations it is surprising that the
> number 5 is so common. Sure some of the digits might be fused or reduced
> to almost nothing.
>
> However I don't think it is true that *all* tetrapods have 5 digits.
>
> Snakes are tetrapods. While some snakes have vestigial hind legs, I
> don't know that they actually have digits. Most snakes have no remaining
> legs to speak of - maybe a bump where the legs might have been but no
> identifiable limbs and certainly no digits.
>
> Similar with whale hind limbs I think. Some species have vestigial
> pelvis and hind limbs. Usually within their bodies. Occasionally some
> individuals have some protrusion. Maybe digits are present during
> development of the foetus but as far as I know there are not actual
> digits by the time they are born. Could be wrong on that but in any case
> they are well on the path to losing them altogether.
>
> The limb changes here might start out as 'the limb genes are still there
> but the gene(s) controlling their size, placement, function etc cause
> them to get smaller, relocated or stop working'. Given enough time
> though, genes that generate something that is irrelevant tend to
> accumulate changes and either become 'broken' or can be co-opted for
> something else.
>
> Then going the other way there are animals with more than 5 digits on
> one or more limbs. Some people for instance - see 'polydactylism'. Some
> of the pictures out there are fake but it is a real condition. Most
> common is 6 fingers or toes instead of 5. It may be a quite harmless
> single gene mutation or part of a more severe complex. As far as I know
> the milder form doesn't render the individual prematurely dead or
> infertile.
>
> There is a breed or at least a population of 'polydactyl cats' that have
> more than the usual number of toes on their front legs, back legs or
> both. They even apparently can be more dextrous than normal so that
> might confer an advantage in some ways but there may be some
> disadvantages as well. Again, I don't think that the genetic change that
> causes this is fatal. It certainly does not prevent development from egg
> to adult because these cats are real.
>
Its a single point mutation in a stop Cordon, which causes the 
"paw/hand/foot" to go Index, second, third, pinkie, extra (woops), Stop, 
now make the thumb. Since its specific to those digits, in this case, it 
doesn't effect anything else.

Oh, and in the case of snakes, during very early development, as I 
understand it, they do form limbs, but then those are reabsorbed, before 
they form fully, the "code" turning off, and other code scavenging the 
remains for other purposes.

-- 
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: Warp
Subject: Re: Molecular biology
Date: 11 Jan 2011 15:19:00
Message: <4d2cbb34@news.povray.org>
Jim Henderson <nos### [at] nospamcom> wrote:
> Yes, I'm a US citizen, and I've spent some time (more than most citizens, 
> in fact) learning about the constitution and understanding its meaning - 
> a meaning that doesn't cherrypick the parts that are relevant to my own 
> point of view.

> I consider myself pretty non-religious, and yes, I get annoyed with 
> things like courthouses posting the 10 Commandments.  That's a little 
> different than the President saying "if you believe in prayer, then pray, 
> and here's a day for it".  I don't care if it's Obama or Bush saying 
> that.  For those who want to pray, knock yourselves out.  I'm not likely 
> to join you in doing so, and as long as you don't try to make me pray or 
> make those who don't want to do so, hey, that's cool.

  Well, look at it like this: You (and by that I mean the USA) have
basically two options:

  1) Keep the government separate and completely neutral with respect to
religion, taking no stance on it whatsoever (as long as they don't break
the law, of course), like any other civilized country.

  2) Keep arguing about the wording of your constitution, and the government
proclaiming religious events, and praying before state senate meetings, and
causing all kinds of controversy and legal battles over the matter.

  Which one of the two choices seems more practical in the long run?

-- 
                                                          - Warp


Post a reply to this message

From: Patrick Elliott
Subject: Re: Molecular biology
Date: 11 Jan 2011 15:46:25
Message: <4d2cc1a1$1@news.povray.org>
On 1/11/2011 1:08 PM, Warp wrote:
> Patrick Elliott<sel### [at] npgcablecom>  wrote:
>> Seen at least one statement to the effect that "tree" isn't an accurate
>> description at all, but rather the complex braiding you see at a river
>> delta. It might split off in totally different directions at some
>> points, but a lot of stuff close together is prone to flow back and
>> forth between channels, maybe even "drifting" back together, when
>> previously separate (though, so far we don't see any obvious examples of
>> that).
>
>    It's quite probable that many species divided (usually geographically)
> into two isolated groups and started to drift genetically apart from each
> other but then joined again before they drifted too much, and the gene pool
> got intermixed once again, stopping the speciation that was happening.
> (I don't know if there are concrete examples of this.)
>
Hmm. Human and Neanderthal, at least from the genetics data? But, yeah, 
it would be hard to pin down unless you had a case like that, where 
there where clear markers that couldn't arise otherwise, in some 
sub-group of the survivor, while the main group those markers came from 
went extinct. In most cases, the result would homogenize the gene pool, 
erasing, over time, any evidence.

-- 
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: Jim Henderson
Subject: Re: Molecular biology
Date: 11 Jan 2011 15:52:45
Message: <4d2cc31d$1@news.povray.org>
On Tue, 11 Jan 2011 15:19:00 -0500, Warp wrote:

> Jim Henderson <nos### [at] nospamcom> wrote:
>> Yes, I'm a US citizen, and I've spent some time (more than most
>> citizens, in fact) learning about the constitution and understanding
>> its meaning - a meaning that doesn't cherrypick the parts that are
>> relevant to my own point of view.
> 
>> I consider myself pretty non-religious, and yes, I get annoyed with
>> things like courthouses posting the 10 Commandments.  That's a little
>> different than the President saying "if you believe in prayer, then
>> pray, and here's a day for it".  I don't care if it's Obama or Bush
>> saying that.  For those who want to pray, knock yourselves out.  I'm
>> not likely to join you in doing so, and as long as you don't try to
>> make me pray or make those who don't want to do so, hey, that's cool.
> 
>   Well, look at it like this: You (and by that I mean the USA) have
> basically two options:
> 
>   1) Keep the government separate and completely neutral with respect to
> religion, taking no stance on it whatsoever (as long as they don't break
> the law, of course), like any other civilized country.

Declaring a national day of prayer does not have the government taking a 
stance on religion.  Just like a declaration of a National Day of 
Twinkies doesn't mean that everyone should go out and buy Twinkies if 
they don't want to.

"Shall make no law respecting the establishment of a religion" does not 
mean that it prohibits people who work in government from ever talking 
about religion.

>   2) Keep arguing about the wording of your constitution, and the
>   government
> proclaiming religious events, and praying before state senate meetings,
> and causing all kinds of controversy and legal battles over the matter.
> 
>   Which one of the two choices seems more practical in the long run?

It's not really a matter of practicality, it's a matter of law.  Sadly, 
the two don't always go hand in hand.

Jim


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From: Jim Henderson
Subject: Re: Molecular biology
Date: 11 Jan 2011 15:57:12
Message: <4d2cc428@news.povray.org>
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


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From: Paul Fuller
Subject: Re: Molecular biology
Date: 11 Jan 2011 16:32:25
Message: <4d2ccc69$1@news.povray.org>
On 12/01/2011 7:14 AM, Patrick Elliott wrote:
>
> Oh, and in the case of snakes, during very early development, as I
> understand it, they do form limbs, but then those are reabsorbed, before
> they form fully, the "code" turning off, and other code scavenging the
> remains for other purposes.
>

Well yes.  During early development you and I formed gills but before 
they were fully formed they were reabsorbed or scavenged for other purposes.

You wouldn't say that all tetrapods possess gills today though would you?


Post a reply to this message

From: Warp
Subject: Re: Molecular biology
Date: 11 Jan 2011 17:04:42
Message: <4d2cd3fa@news.povray.org>
Jim Henderson <nos### [at] nospamcom> wrote:
> >   1) Keep the government separate and completely neutral with respect to
> > religion, taking no stance on it whatsoever (as long as they don't break
> > the law, of course), like any other civilized country.

> Declaring a national day of prayer does not have the government taking a 
> stance on religion.

  Of course it is. It's an implicit encouragement from the government for
people to follow a religious custom.

> "Shall make no law respecting the establishment of a religion" does not 
> mean that it prohibits people who work in government from ever talking 
> about religion.

  Of course they are free to do whatever they want, but not officially
on behalf of the government. The government has certain responsibilities
and duties towards their citizens.

  When the president speaks to the country on a televised official ceremony,
that's quite different from the president talking with a friend.

-- 
                                                          - Warp


Post a reply to this message

From: Warp
Subject: Re: Molecular biology
Date: 11 Jan 2011 17:06:58
Message: <4d2cd482@news.povray.org>
Paul Fuller <pgf### [at] optusnetcomau> wrote:
> On 12/01/2011 7:14 AM, Patrick Elliott wrote:
> >
> > Oh, and in the case of snakes, during very early development, as I
> > understand it, they do form limbs, but then those are reabsorbed, before
> > they form fully, the "code" turning off, and other code scavenging the
> > remains for other purposes.
> >

> Well yes.  During early development you and I formed gills but before 
> they were fully formed they were reabsorbed or scavenged for other purposes.

> You wouldn't say that all tetrapods possess gills today though would you?

  AFAIK snakes have vestigial limbs (usually quite obvious when looking
at their skeletons).

-- 
                                                          - Warp


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From: Jim Henderson
Subject: Re: Molecular biology
Date: 11 Jan 2011 17:33:30
Message: <4d2cdaba$1@news.povray.org>
On Tue, 11 Jan 2011 17:04:42 -0500, Warp wrote:

> Jim Henderson <nos### [at] nospamcom> wrote:
>> >   1) Keep the government separate and completely neutral with respect
>> >   to
>> > religion, taking no stance on it whatsoever (as long as they don't
>> > break the law, of course), like any other civilized country.
> 
>> Declaring a national day of prayer does not have the government taking
>> a stance on religion.
> 
>   Of course it is. It's an implicit encouragement from the government
>   for
> people to follow a religious custom.

IF THEY BELIEVE IN IT.  It's not saying "even if you don't believe in it, 
give it a try, you might like it".

>> "Shall make no law respecting the establishment of a religion" does not
>> mean that it prohibits people who work in government from ever talking
>> about religion.
> 
>   Of course they are free to do whatever they want, but not officially
> on behalf of the government. The government has certain responsibilities
> and duties towards their citizens.

Of course they do.  And encouraging people to practice their beliefs - 
whatever those beliefs are - isn't advocating for a particular religion.  
It doesn't establish a state-sponsored religion at all.  It says "hey, if 
you believe in this, practice it".  Simple.  Not advocating for Jesus, 
not advocating for the Pope, just simply saying "if you believe this, do 
it."

>   When the president speaks to the country on a televised official
>   ceremony,
> that's quite different from the president talking with a friend.

Sure.  And saying "if you believe in this, here's an opportunity to 
practice it" is different from saying "if you don't, we'll fine you or 
lock your ass up in jail."

The former is not establishment of a state-sponsored religion.  The 
second is.  Note the differences.

Jim


Post a reply to this message

From: Darren New
Subject: Re: Molecular biology
Date: 11 Jan 2011 17:35:33
Message: <4d2cdb35$1@news.povray.org>
Warp wrote:
> Darren New <dne### [at] sanrrcom> wrote:
>> Warp wrote:
>>> life on Earth wouldn't exist because
>>> all bodies of water would freeze from the bottom up, killing all living
>>> organisms.
> 
>> Well, unless they evolved in San Diego. ;-)
> 
>   The reference is completely lost on me.

Water outside doesn't freeze in San Diego. It rarely goes below freezing 
here, let alone long enough to make water freeze solid outdoors.

-- 
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: 11 Jan 2011 17:37:01
Message: <4d2cdb8d$1@news.povray.org>
Warp wrote:
> helping structures which are later removed as obsolete.

That too. :-)

-- 
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: 11 Jan 2011 17:38:42
Message: <4d2cdbf2$1@news.povray.org>
Warp wrote:
> (I don't know if there are concrete examples of this.)

It's trivial to do in a lab. Take any experiment that speciates fruit flies, 
for example. Stop it half way through and let them mix together again. 
Bingo, it happened. :-)

-- 
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: 11 Jan 2011 17:40:05
Message: <4d2cdc45$1@news.povray.org>
Jim Henderson wrote:
> Now tell me how a declaration of a National Day of Prayer by the 
> executive branch is (a) Congress establishing a law respecting the 
> establishment of religion, or (b) prohibits the free exercise thereof.

I'll just point out again that it wasn't the executive branch, but the 
congress, that declared a national day of prayer.

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


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From: Jim Henderson
Subject: Re: Molecular biology
Date: 11 Jan 2011 17:42:19
Message: <4d2cdccb@news.povray.org>
On Tue, 11 Jan 2011 14:40:03 -0800, Darren New wrote:

> Jim Henderson wrote:
>> Now tell me how a declaration of a National Day of Prayer by the
>> executive branch is (a) Congress establishing a law respecting the
>> establishment of religion, or (b) prohibits the free exercise thereof.
> 
> I'll just point out again that it wasn't the executive branch, but the
> congress, that declared a national day of prayer.

Somehow I missed that, but at the same time, I fail to see how telling 
people "if you believe in something, practice it" comes even close to 
establishing a state-sponsored religion (especially the way the founders 
were viewing it as it occurred in England).

Jim


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From: Darren New
Subject: Re: Molecular biology
Date: 11 Jan 2011 17:44:01
Message: <4d2cdd31$1@news.povray.org>
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?

(Sorry. Just being silly.)

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


Post a reply to this message

From: Darren New
Subject: Re: Molecular biology
Date: 11 Jan 2011 17:45:49
Message: <4d2cdd9d$1@news.povray.org>
Warp wrote:
> he willingly broke the first amendment with
> complete disregard of the ruling.

Yep. Just like the last 60 years or so. :-) Plus, of course, the judge said 
"I think it's unconstitutional, but let's push it all the way up before we 
actually prohibit it." So he didn't break the law. He broke the law as 
interpreted by one judge who admitted her interpretation might not be correct.

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


Post a reply to this message

From: Darren New
Subject: Re: Molecular biology
Date: 11 Jan 2011 17:48:16
Message: <4d2cde30$1@news.povray.org>
Jim Henderson wrote:
> On Tue, 11 Jan 2011 14:40:03 -0800, Darren New wrote:
> 
>> Jim Henderson wrote:
>>> Now tell me how a declaration of a National Day of Prayer by the
>>> executive branch is (a) Congress establishing a law respecting the
>>> establishment of religion, or (b) prohibits the free exercise thereof.
>> I'll just point out again that it wasn't the executive branch, but the
>> congress, that declared a national day of prayer.
> 
> Somehow I missed that, 

Yeah. NDoP was established back when we were fighting the godless communists 
in the 1950's.

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


Post a reply to this message

From: Jim Henderson
Subject: Re: Molecular biology
Date: 11 Jan 2011 17:56:05
Message: <4d2ce005$1@news.povray.org>
On Tue, 11 Jan 2011 14:48:14 -0800, Darren New wrote:

> Jim Henderson wrote:
>> On Tue, 11 Jan 2011 14:40:03 -0800, Darren New wrote:
>> 
>>> Jim Henderson wrote:
>>>> Now tell me how a declaration of a National Day of Prayer by the
>>>> executive branch is (a) Congress establishing a law respecting the
>>>> establishment of religion, or (b) prohibits the free exercise
>>>> thereof.
>>> I'll just point out again that it wasn't the executive branch, but the
>>> congress, that declared a national day of prayer.
>> 
>> Somehow I missed that,
> 
> Yeah. NDoP was established back when we were fighting the godless
> communists in the 1950's.

Yes, back in 1952, but such a thing did actually exist off and on going 
back to the 1700s in the US.  The Continental Congress declared an NDP 
back in 1775, and Washington proclaimed a day of public thanksgiving and 
prayer back in 1795.  (Obviously, the 1775 reference predates the US 
Constitution).  President Madison also declared an observance around 1813 
as well.

So did Lincoln back in 1863.

Jefferson opposed it the idea in 1808.

The law as it stands today, just requires the President select a day for 
NDP - it doesn't really say anything about what such prayer should be or 
which denomination/religion/belief system should be the basis for such 
selection.

Jim


Post a reply to this message

From: Jim Henderson
Subject: Re: Molecular biology
Date: 11 Jan 2011 17:57:08
Message: <4d2ce044$1@news.povray.org>
On Tue, 11 Jan 2011 14:43:59 -0800, Darren New 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?
> 
> (Sorry. Just being silly.)

Silliness is a good thing. :-)

Maybe if more people went out and stood in the shoes of minorities, 
though, they'd have a better appreciation for what being a minority in 
the US is really like.

Jim


Post a reply to this message

From: Darren New
Subject: Re: Molecular biology
Date: 11 Jan 2011 18:46:09
Message: <4d2cebc1$1@news.povray.org>
Warp wrote:
>   When the president speaks to the country on a televised official ceremony,
> that's quite different from the president talking with a friend.

Apparently, the Congress requires the President to announce the national day 
of prayer. Obama is the most atheist-friendly president we've ever had, afaik.

"""
The Congress, by Public Law 100-307, as amended, has called on the President 
to issue each year a proclamation designating the first Thursday in May as a 
"National Day of Prayer."
"""

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


Post a reply to this message

From: Paul Fuller
Subject: Re: Molecular biology
Date: 11 Jan 2011 20:52:28
Message: <4d2d095c@news.povray.org>
On 12/01/2011 9:06 AM, Warp wrote:
>
>    AFAIK snakes have vestigial limbs (usually quite obvious when looking
> at their skeletons).
>

Yes.  I said as much.  Vestigial.

Snakes are tetrapods and yet you cannot find 5 digits on the end of a 
limb in the vast majority of individuals.  Some individuals may have 
more evidence than the average.  Rarely a quite recognisable but non 
functional leg.  All may have some relic or indication of where limbs 
existed in ancestral forms.

The original assertion that 'fingers' always number 5 in tetrapods is 
not totally correct.

There is a strong connection between limb development and the overall 
foetal development path.  And genital development is a big part of that 
as well.  The 'Homeobox' or 'Hox' genes are what Darren had read about 
and the gist of what he said is true enough.  All tetrapods (as far as 
is known) have 5 'buds' or zones per limb during development that are 
eligible to become fingers / toes.

But there are variations in the Hox genes that alter limb development 
and are not fatal.  There can be other genes involved that modify the 
basic structures and even cause them to disappear as the foetus develops.

As shown by polydactylism in humans and cats there can be more than 5 
fully formed functional digits on each limb.  From what I've read, the 
mechanism leading to this is duplication of one of the existing digits 
rather than a completely new type of digit.  Having an exact copy of a 
digit alongside the original doesn't seem to have enough advantage to 
overcome the associated risks to the rest of the development process.

Evolutionary development can proceed from a duplicate gene.  So long as 
it isn't fatal the possibility exists that some other mutation or gene 
variant will modify the duplicate some time in the future to be actually 
useful.

As a conjecture, there is probably selection for mechanisms that provide 
genetic flexibility.  A species that has a certain degree of variablity 
is more likely to have individuals within it that can survive some 
change in the environment than one that doesn't.  So evolving the 
ability to have mutations and carry variations has its own advantage. 
On the flip side, really optimising for a niche may come at the cost of 
that variability.  Evolution of the mechanism of evolution!


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From: Le Forgeron
Subject: Re: Molecular biology
Date: 12 Jan 2011 02:08:52
Message: <4d2d5384$1@news.povray.org>
Le 11/01/2011 23:35, Darren New a écrit :
> Warp wrote:
>> Darren New <dne### [at] sanrrcom> wrote:
>>> Warp wrote:
>>>> life on Earth wouldn't exist because
>>>> all bodies of water would freeze from the bottom up, killing all living
>>>> organisms.

I would ponder to "all massive living organisms".
Bacteria & such would be still be fine.
Can a cloud/colony of bacteria develops as an intelligent
being/population and make something fancy ?

>>
>>> Well, unless they evolved in San Diego. ;-)
>>
>>   The reference is completely lost on me.
> 
> Water outside doesn't freeze in San Diego. It rarely goes below freezing
> here, let alone long enough to make water freeze solid outdoors.
> 


If you compress it hard enough, even in San Diego, even oxygen could
freeze...

Water is paradoxal in that at high pressure the more compact form is
liquid rather than solid.


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From: scott
Subject: Re: Molecular biology
Date: 12 Jan 2011 03:27:42
Message: <4d2d65fe$1@news.povray.org>
>> but maybe that's just because we haven't figured out yet what is
>> driving those events, so they just *appear* random to us.
>
> FWIW, the answer to this speculation is "no, we have proven that's not
> the case." :-)

Really?  How?


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From: Invisible
Subject: Re: Molecular biology
Date: 12 Jan 2011 04:06:39
Message: <4d2d6f1f$1@news.povray.org>
On 12/01/2011 07:08 AM, Le_Forgeron wrote:

> Water is paradoxal in that at high pressure the more compact form is
> liquid rather than solid.

Water is unusual in having half a dozen distinct phases rather than just 
3...


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From: Invisible
Subject: Re: Molecular biology
Date: 12 Jan 2011 04:15:11
Message: <4d2d711f@news.povray.org>
>> I'm not sure that's as much of a problem as you think it is for anything
>> other than fish.
>
>    Well, life on Earth was completely in water for the first... what?
> 3 billion years?

Wikipedia (which is always right) asserts that "life" began 3.8 billion 
years ago, and land plants appeared 475 million years ago.

3,800 - 475 = 3,325 million years = 3.3 billion years with no life on land.


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From: Invisible
Subject: Re: Molecular biology
Date: 12 Jan 2011 04:29:30
Message: <4d2d747a$1@news.povray.org>
>> ID is not testable. It's so vague that any time someone falsifies it,
>> the proponents can just claim that the theory says something slightly
>> different, and hence is not falsified.
>
> That's a different problem. Denying the evidence of the failed tests
> doesn't mean that it passed the tests. It only means the proponents are
> pushing the concept regardless of whether it has failed the tests.

No, I'm saying that the ID people keep changing their minds about which 
theory is the one they're advocating.

You don't change the theory half way through the experiment. That's not 
how science works. If your theory is so inadequately specified that you 
can change your mind about it every second Thursday, you're doing it wrong.

(But yes, the ID people *also* deny the evidence too...)

> ID is certainly testable: We've found no irreducibly complex
> substructures, we have overwhelming evidence of evolution, etc.

Correction: "Irreducibly complex" merely means that removing a single 
component makes the thing stop working. We've found *plenty* of things 
that are irreducibly complex. The point is, the ID people argue that 
"irreducibly complex" = "cannot evolve", which is false.

All of which is window dressing, really. All of the "evidence for ID" is 
actually "evidence against evolution". That's not how science works. 
Einstein didn't overturn Netwon's highly successful theory of motion by 
saying "hey, I think this is wrong". He did it by offering something 
better. ID rests on the sadly mistaken belief that "evolution is wrong" 
is the same thing as "ID is right". That's not how it works.


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From: Invisible
Subject: Re: Molecular biology
Date: 12 Jan 2011 04:40:08
Message: <4d2d76f8$1@news.povray.org>
> 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.

> 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.

> Most of
> their "changes" are, as a result, point mutation/deletion/addition, not
> the copy of whole sequences.

You got a citation for that?


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From: Invisible
Subject: Re: Molecular biology
Date: 12 Jan 2011 04:52:50
Message: <4d2d79f2$1@news.povray.org>
On 11/01/2011 07:56 PM, Patrick Elliott wrote:

> Seen at least one statement to the effect that "tree" isn't an accurate
> description at all, but rather the complex braiding you see at a river
> delta. It might split off in totally different directions at some
> points, but a lot of stuff close together is prone to flow back and
> forth between channels, maybe even "drifting" back together, when
> previously separate (though, so far we don't see any obvious examples of
> that).

The tree metaphor doesn't account for "horizontal gene transfer".

Bacteria reproduce asexually. However, they sometimes two cells will 
hook up and swap genes with each other (without producing offspring).

Viruses, plasmids and other "transposable elements" can move genes from 
cell to cell. (This is how genetic engineering works.)

The human genome actually contains several (mostly broken) viral genomes 
within it. Usually a virus infects a cell, gets copied, and the cell 
dies. At some point, an egg or sperm cell was infected, and the 
infection became permanent. (And, presumably, not too detrimental.)

There's even some suggestion that these virii's ability to evade the 
immune system might be how viviparous animals were able to evolve. 
(I.e., how an embryo evades the mother's immune system.)

Then of course, the dynamic, ever-changing face of geology and geography 
is such that there is an almost never-ending stream of habitats 
appearing and disappearing all the time. Lakes dry out and become 
multiple lakes, only to later reflood and become a single lake again. 
Hydrothermal sea vents spring up, develop their own local tribe of 
organisms, and then shut down, while new nearby vents appear.

Heck, black people and white people marrying, anyone?

It must surely happen all the time. It doesn't even require physical 
separation. Just any time one group happens to not interact with another 
group, and then later starts interacting again.


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From: Warp
Subject: Re: Molecular biology
Date: 12 Jan 2011 10:30:41
Message: <4d2dc921@news.povray.org>
Darren New <dne### [at] sanrrcom> wrote:
> It's trivial to do in a lab. Take any experiment that speciates fruit flies, 
> for example. Stop it half way through and let them mix together again. 
> Bingo, it happened. :-)

  Can you actually speciate two groups of fruit flies in the lab so much
that they can't reproduce anymore with each other, hence making them two
different species?

-- 
                                                          - Warp


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From: Invisible
Subject: Re: Molecular biology
Date: 12 Jan 2011 10:34:44
Message: <4d2dca14$1@news.povray.org>
On 12/01/2011 03:30 PM, Warp wrote:
> Darren New<dne### [at] sanrrcom>  wrote:
>> It's trivial to do in a lab. Take any experiment that speciates fruit flies,
>> for example. Stop it half way through and let them mix together again.
>> Bingo, it happened. :-)
>
>    Can you actually speciate two groups of fruit flies in the lab so much
> that they can't reproduce anymore with each other, hence making them two
> different species?

I should imagine so.

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.


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From: Warp
Subject: Re: Molecular biology
Date: 12 Jan 2011 10:49:02
Message: <4d2dcd6e@news.povray.org>
Jim Henderson <nos### [at] nospamcom> wrote:
> >   Of course it is. It's an implicit encouragement from the government
> >   for
> > people to follow a religious custom.

> IF THEY BELIEVE IN IT.  It's not saying "even if you don't believe in it, 
> give it a try, you might like it".

  Yeah, like there were only two types of people: Those who firmly believe
and those who firmly don't believe. There is nothing in between. Like,
I don't know, impressionable children? Yeah, they don't exist.

  It's not the place for the government to tell people, even indirectly,
that a religion has a sound basis. There *are* impressionable people out
there who will believe something more easily if a high authority promotes
it. There is already enough misinformation out there. The government
shouldn't be encouraging it.

> >> "Shall make no law respecting the establishment of a religion" does not
> >> mean that it prohibits people who work in government from ever talking
> >> about religion.
> > 
> >   Of course they are free to do whatever they want, but not officially
> > on behalf of the government. The government has certain responsibilities
> > and duties towards their citizens.

> Of course they do.  And encouraging people to practice their beliefs - 
> whatever those beliefs are - isn't advocating for a particular religion.  

  Ah, so you want to nitpick between "advocating for a *particular* religion"
vs. "advocating religion". The government can be as religious as they want
as long as they don't advocate any particular religion.

  No, and a thousand times no. It's not the place for the government to
take any stance whatsoever on religion (or non-religion). It doesn't matter
if they differentiate between religions or not. That's not the issue.

  If you ask a government official, in an official setting, "what's the
government's position on religion?", the correct answer is "no comment".

> It doesn't establish a state-sponsored religion at all.  It says "hey, if 
> you believe in this, practice it".  Simple.

  A "national day of prayer" is certainly not a neutral proclamation of
religious freedom, "if you want to do something religious, just do it,
we won't stop you".

  Just think about it like this: Why exactly do you need a "national day
of prayer"? What's so special about that particular day? What purpose does
it serve? Why does the government have to declare a special day for that?

  If you think about the answer, you'll see that the government is not
being neutral and impartial in this matter, as they should.

>  Not advocating for Jesus, 
> not advocating for the Pope

  Advocating prayer. What's the difference, exactly?

> >   When the president speaks to the country on a televised official
> >   ceremony,
> > that's quite different from the president talking with a friend.

> Sure.  And saying "if you believe in this, here's an opportunity to 
> practice it" is different from saying "if you don't, we'll fine you or 
> lock your ass up in jail."

  You don't seem to understand the difference between promoting and forcing.

  You claim is "they are not promoting religion" and your argument for that
is "they are not forcing religion to be practiced". A fallacious argument if
I ever saw one.

-- 
                                                          - Warp


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From: Warp
Subject: Re: Molecular biology
Date: 12 Jan 2011 10:53:15
Message: <4d2dce6b@news.povray.org>
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.

-- 
                                                          - Warp


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From: Warp
Subject: Re: Molecular biology
Date: 12 Jan 2011 10:55:54
Message: <4d2dcf0a@news.povray.org>
Darren New <dne### [at] sanrrcom> wrote:
> Apparently, the Congress requires the President to announce the national day 
> of prayer. Obama is the most atheist-friendly president we've ever had, afaik.

> """
> The Congress, by Public Law 100-307, as amended, has called on the President 
> to issue each year a proclamation designating the first Thursday in May as a 
> "National Day of Prayer."
> """

  Ok, I retract my allegation that it was Obama's own decision to announce
the day. It might well be that he had not much choice (lest he cause even
*more* unneeded controversy).

-- 
                                                          - Warp


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