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From: scott
Subject: Re: Molecular biology
Date: 11 Jan 2011 06:04:50
Message: <4d2c3952$1@news.povray.org>
> Right. If you accept that our universe is a computer simulation and that
> ID's "designer" is outside out universe, then the theory becomes at
> least logically plausible. (And still not testable.)
>
> That's *a lot* of assumptions just to avoid accepting the vast amount of
> evidence supporting evolution.

If our universe is a kind of computer simulation, that doesn't mean 
evolution didn't or couldn't have happened.  It just means someone or 
something set up the "rules" and the "initial conditions".


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From: Invisible
Subject: Re: Molecular biology
Date: 11 Jan 2011 07:11:22
Message: <4d2c48ea$1@news.povray.org>
On 08/01/2011 04:19 PM, Warp wrote:
> Paul Fuller<pgf### [at] optusnetcomau>  wrote:
>> Makes you wonder what life on a Kuiper Belt Object might be like.
>
>    I don't think it would be physically possible for any kind of life to
> form that far from the Sun.

Certainly life, as we understand the concept, requires energy. Most life 
on *our* planet uses the Sun for that. But not all of it: it's well 
documented that there are organisms fed by chemicals originating from 
the Earth's core, for example. It's plausible that such a thing could 
happen on more distant planets. (Although I have no idea whether the 
chemistry of any /specific/ known planet makes this likely.)

>    It's hard to imagine how life could form without water.

Life, as we understand is, is a dense network of chemical reactions. 
That would logically appear to require some kind of solvent. There's no 
specific reason why it should be water; some scientists have suggested, 
say, ammonia.

More fundamental perhaps is carbon, which is capable of forming very 
complex compounds. (Silicon is also sometimes suggested.)

>    Of course for the water to be any good, it has to be in liquid form.
> If you are too far away from the Sun, all the water will be frozen solid.
> This isn't a very fertile ground for life to form. There are little chemical
> reactions going on, chemicals are not very free to move, and there are
> probably a huge bunch of other properties necessary for *any* kind of
> life to form which just aren't possible with deep-frozen ice.

You're aware that (on Earth) there are organisms that live in solid ice, 
right?

(Of course, further from the Sun, that probably wouldn't be viable.)

Live as it exists on Earth fundamentally requires liquid water, but 
there are reasons to suppose that this isn't necessarily a hard 
requirement for "life" to exist.

>    Now, perhaps if there was a liquid which remains an liquid form at those
> temperatures, it could ostensibly happen. However, such liquids are both
> extremely rare (iow. there wouldn't be enough of it in any given planet),
> and their chemical properties are probably inadequate for any kind of
> lifeforms.

What makes you think that chemicals which are "rare" on Earth would 
necessarily be rare elsewhere?

(E.g., O2 used to be "rare" on Earth - extremely rare, in fact.)

 From what I understand, other planets have been found to have vastly 
different chemistry to Earth.

> (Also, most liquids other than water get denser when they
> solidify, which is a big problem.)

Care to explain why?

>    (Conversely, a planet which is too *close* to the Sun cannot form life
> either, this time because there's no water because it's all vaporized away.
> It also makes forming a viable atmosphere quite hard, making it a very
> hostile environment, where strong radiation hits directly the surface
> of the planet, destroying any complex chemicals that might form by chance.)

I would have thought the biggest problem with living close to the Sun 
would be simply that any complex molecules would get smashed to pieces 
very rapidly.


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From: Paul Fuller
Subject: Re: Molecular biology
Date: 11 Jan 2011 07:53:34
Message: <4d2c52ce@news.povray.org>
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.

The point that some genes are deeply interconnected with others or are 
so important to development or metabolism etc so tend to be highly 
conserved is true.  But as with most things in biology there are more 
things Horatio...


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From: scott
Subject: Re: Molecular biology
Date: 11 Jan 2011 08:19:48
Message: <4d2c58f4@news.povray.org>
>    Water would be the liquid of choice because it has two very special
> properties that basically no other liquid has: It's extremely common,
> and its solid form has lessed density than its liquid form. Without these
> two properties there would be no life on Earth (or anywhere else). (There
> are probably also many other necessary properties, related to solubility
> and how water reacts chemically with other compounds, but I do not know
> enough about chemistry to say anything about that.)
>
>    It's hard to imagine how life could form without water.

How come?  Didn't life as we know it develop because there was plenty of 
water around?  On planets or moons much further away where another 
liquid is in plentiful supply (eg methane) couldn't some kind of life 
develop that uses that instead?  What's the general definition of life 
(without referencing the specific life we have on Earth)?


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From: Warp
Subject: Re: Molecular biology
Date: 11 Jan 2011 08:38:57
Message: <4d2c5d70@news.povray.org>
Invisible <voi### [at] devnull> wrote:
> >    Of course for the water to be any good, it has to be in liquid form.
> > If you are too far away from the Sun, all the water will be frozen solid.
> > This isn't a very fertile ground for life to form. There are little chemical
> > reactions going on, chemicals are not very free to move, and there are
> > probably a huge bunch of other properties necessary for *any* kind of
> > life to form which just aren't possible with deep-frozen ice.

> You're aware that (on Earth) there are organisms that live in solid ice, 
> right?

  They did not originate in ice. The simply adapted to it afterwards.

> >    Now, perhaps if there was a liquid which remains an liquid form at those
> > temperatures, it could ostensibly happen. However, such liquids are both
> > extremely rare (iow. there wouldn't be enough of it in any given planet),
> > and their chemical properties are probably inadequate for any kind of
> > lifeforms.

> What makes you think that chemicals which are "rare" on Earth would 
> necessarily be rare elsewhere?

  There would have to be a significantly different process that formed
those rare elements than here on Earth. What would that process be?

  Heavy elements are formed when stars explode. After that the only way
for one element to change into another is by radioactive decay, and there's
only so much that will be formed that way.

> (E.g., O2 used to be "rare" on Earth - extremely rare, in fact.)

  O2 is not essential for life (unlike eg. water).

> > (Also, most liquids other than water get denser when they
> > solidify, which is a big problem.)

> Care to explain why?

  If water had a higher density when it freezes (as happens with the vast
majority of other chemical compounds), life on Earth wouldn't exist because
all bodies of water would freeze from the bottom up, killing all living
organisms. Water having a lower density when it freezes happens to create
a nice protective "shell" on top of bodies of water when they freeze,
insulating it from the cold. (That's why eg. lakes don't freeze solid
throughout, they only get a relatively thin layer of ice. Relative to
the entire depth of the lake, of course.)

  (Although I don't know this for certain, I'm pretty sure that if the
Earth was closer to the Sun so that it would never experience ice ages
or the like, it would be too close for life to form for other reasons.)

-- 
                                                          - Warp


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From: Warp
Subject: Re: Molecular biology
Date: 11 Jan 2011 08:42:04
Message: <4d2c5e2c@news.povray.org>
scott <sco### [at] scottcom> wrote:
> How come?  Didn't life as we know it develop because there was plenty of 
> water around?  On planets or moons much further away where another 
> liquid is in plentiful supply (eg methane) couldn't some kind of life 
> develop that uses that instead?  What's the general definition of life 
> (without referencing the specific life we have on Earth)?

  Do other liquids have the same chemical properties advantageous to the
forming of life?

  Also, other liquids often require such cold temperatures that the planet
may be uninhabitable for that reason: It doesn't receive enough energy from
the Sun to form or sustain life.

  Also, if the liquid gets a higher density when it freezes, it can become
a problem with respect to forming life.

-- 
                                                          - Warp


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From: scott
Subject: Re: Molecular biology
Date: 11 Jan 2011 08:55:09
Message: <4d2c613d$1@news.povray.org>
>>> (Also, most liquids other than water get denser when they
>>> solidify, which is a big problem.)
>
>> Care to explain why?
>
>    If water had a higher density when it freezes (as happens with the vast
> majority of other chemical compounds), life on Earth wouldn't exist because
> all bodies of water would freeze from the bottom up, killing all living
> organisms.

Is it a requirement of life to have frozen water around?  Couldn't life 
start on a planet where there were areas that never froze (or at least 
didn't freeze for long enough for life develop sufficiently)?


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From: Warp
Subject: Re: Molecular biology
Date: 11 Jan 2011 09:03:28
Message: <4d2c632f@news.povray.org>
Invisible <voi### [at] devnull> wrote:
> Evolution asserts that species are not fixed; they /change/. And so the 
> species we see today were not always there. And, in particular, not so 
> much evolution itself, but molecular evidence says that all life on 
> Earth has a single common ancestor.

  Actually the definition of "species" is a hard one.

  By definition two animals are of different species if they cannot produce
fertile offspring. However, this definition is lacking.

  It's lacking because the definition implies transitivity: If A can reproduce
with B (thus A and B are of the same species), and B can reproduce with C
(thus B and C are of the same species), by definition A and C should be of
the same species (and hence able to reproduce). However, there are eg.
so-called ring species (look it up) where this doesn't happen: It may be
that A and C cannot reproduce, making them by definition members of
different species, even though B can reproduce with either A or C. This
makes a clear definition of B's species rather difficult.

  (And with ring species we are not necessarily talking here about some
weird obscure unicellular organisms living in the depths of the ocean
which defy all classification. We are talking about regular everyday
animals, such as certain species of seagull.)

  A ring species is actually an excellent demonstration of how speciation
can happen gradually, unlike the straw man that some creationists present
of "a species suddenly transforming into another": Yes, it *is* possible
for a subgroup of a species to *slowly* transform into a different species
over time, and during this period the ability of procreation between the
two groups gradually becomes less and less possible (the probability of
a successful fertilization becomes smaller and smaller because of the
constantly increasing differences in genes). If this subgroup further
spawns an even more isolated sub-subgroup, we may end up precisely in the
situation where a member of group A can procreate with a member of group
B, and a member of B with a member of C, but a member of A cannot procreate
with a member of C.

  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. By definition every
offspring is of the same species has its parents, but if you continue
this back long enough, you end up with animals that are so different from
the modern equivalents that they cannot be considered of the same species
anymore (if that ancient species was brought back to life today, it would
be unable to reproduce with its modern descendant). However, drawing the
dividing line where the ancient species became the modern one is impossible.
It's a fuzzy line.

-- 
                                                          - Warp


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From: Warp
Subject: Re: Molecular biology
Date: 11 Jan 2011 09:08:58
Message: <4d2c6479@news.povray.org>
Darren New <dne### [at] sanrrcom> wrote:
> Warp wrote:
> >   (I read somewhere that recently Barack Obama decided to announce the
> > National Day of Prayer, or something like that, 

> The "national day of prayer" has been around since we were fighting the 
> godless communists (I kid you not) in the 1950's, passed by Congress at the 
> time. That's the same time we got "under god" added to "one nation under 
> god" in the pledge of allegiance.  Given that Obama keeps referring to 
> atheists in all his speeches (which ticks off the religious folks) I would 
> guess (without a cite) this is at least as much a lie as half the other 
> things said about him.

  Well, perhaps this will do for a citation:

http://www.snopes.com/politics/obama/prayerday.asp

"Observances of the National Day of Prayer took place throughout the
U.S. in 2009 and again in 2010. The status of the National Day of
Prayer is currently somewhat uncertain, though, as on 15 April 2010 a
federal judge ruled in favor of a challenge brought by the Freedom
from Religion Foundation and held that the National Day of Prayer is
unconstitutional. The Obama administration was actually the defendant
in that suit, arguing in favor of retaining the National Day of
Prayer."

-- 
                                                          - Warp


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From: Warp
Subject: Re: Molecular biology
Date: 11 Jan 2011 09:18:58
Message: <4d2c66d1@news.povray.org>
scott <sco### [at] scottcom> wrote:
> Is it a requirement of life to have frozen water around?  Couldn't life 
> start on a planet where there were areas that never froze (or at least 
> didn't freeze for long enough for life develop sufficiently)?

  I don't know. There are tons and tons of things that allowed life to
form of Earth, and changing even one of them would have made it a lot
more difficult, if not impossible. (Christians will say that the Earth
is like that because God created it like that. Scientists will simply
point out the anthropic principle: Earth was not created for us. We are
on earth because of all the countless random planets on the Universe Earth
happened to be optimal for the formation of life, so it did.)

  It might be that if the weather system on Earth (over periods of millions
of years) was such that water never froze at large portions of it, it might
be hostile for life for other reasons. Perhaps a changing climate is somehow
necessary for life. As said, I don't know.

-- 
                                                          - Warp


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