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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 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: 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 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();
}

<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 15:08:57
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


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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 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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