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From: scott
Subject: Re: Molecular biology
Date: 11 Jan 2011 05:06:30
Message: <4d2c2ba6@news.povray.org>
>> That's a terrible argument. "I couldn't imagine how something as complex
>> as predicting the future that way could have happened" is just as bad an
>> argument as "I couldn't imagine how hemoglobin came about."
>
> OK, well how about chaos theory? That puts hard bounds on what can and
> cannot be predicted. I should imagine that over the course of 4 billion
> years, one single stray photon would probably be enough to perturb the
> system sufficiently that it wildly diverges from your predictions.

Unless you run your prediction simulation on the same "hardware" as the 
real thing.

I can run some chaotic program on my PC and the results look pretty 
chaotic, yet I am then able to predict *exactly* the outcome if you run 
it again on your PC (assuming same CPU architecture etc).

I can then be the intelligent designer, playing about with the initial 
conditions until I find something that looks nice.  Then I can inform 
you the initial values and you get to see the nice outcome too.


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From: Invisible
Subject: Re: Molecular biology
Date: 11 Jan 2011 05:07:06
Message: <4d2c2bca$1@news.povray.org>
On 10/01/2011 06:05 PM, Darren New wrote:
> Invisible wrote:
>> The fundamental difference between ST and ID, of course, is that ST
>> has a realistic possibility of becoming testable some day soon. ID
>> does not.
>
> ID is testable. It just failed the tests. But it's certainly testable.

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.

Now, if ID supplied some actual details - who the designer was, why they 
went to all this trouble, when the designing happened, how the designer 
could do something that we cannot, etc. - then there would be some 
danger of finally nailing it to the floor.

Don't hold your breath...


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From: Invisible
Subject: Re: Molecular biology
Date: 11 Jan 2011 05:19:23
Message: <4d2c2eab$1@news.povray.org>
>> OK, well how about chaos theory? That puts hard bounds on what can and
>> cannot be predicted. I should imagine that over the course of 4 billion
>> years, one single stray photon would probably be enough to perturb the
>> system sufficiently that it wildly diverges from your predictions.
>
> Unless you run your prediction simulation on the same "hardware" as the
> real thing.
>
> I can run some chaotic program on my PC and the results look pretty
> chaotic, yet I am then able to predict *exactly* the outcome if you run
> it again on your PC (assuming same CPU architecture etc).
>
> I can then be the intelligent designer, playing about with the initial
> conditions until I find something that looks nice. Then I can inform you
> the initial values and you get to see the nice outcome too.

Computer systems are designed to be predictable.

The trouble with unpredictable systems such as the Earth's atmosphere is 
that arbitrarily tiny perturbations of the initial state yield huge 
divergences in the end result.

If I set my Earth up the same way as your Earth, but with a 10^-47 error 
in wind speed in one place, the weather patterns of my Earth will 
rapidly diverge from the weather patterns you got.

On top of all that, the Earth has been here for a few billion years. 
Where did the designer find the time (and space?) to rerun their 
simulation countless hundred trillion times to get it all to work out? 
The only really plausible explanation is a designer "outside" of the 
universe - the old "the universe is a computer simulation on somebody's 
desk" theory.

In short, to make the implausible ID theory work, you need to postulate 
even more radical theories such as the designer running the universe as 
a computer simulation...


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From: scott
Subject: Re: Molecular biology
Date: 11 Jan 2011 05:31:03
Message: <4d2c3167@news.povray.org>
> The trouble with unpredictable systems such as the Earth's atmosphere is
> that arbitrarily tiny perturbations of the initial state yield huge
> divergences in the end result.

Same if I have a 4GB chaotic simulation running on my machine, just one 
bit different in the initial conditions will yield 4GB of completely 
different data.  Yet it will be totally repeatable.

> If I set my Earth up the same way as your Earth, but with a 10^-47 error
> in wind speed in one place, the weather patterns of my Earth will
> rapidly diverge from the weather patterns you got.

Sure, but what if you set up your Earth with the *exact* same initial 
conditions?  I know there is randomness inherent at the quantum level, 
but maybe that's just because we haven't figured out yet what is driving 
those events, so they just *appear* random to us.

> On top of all that, the Earth has been here for a few billion years.
> Where did the designer find the time (and space?) to rerun their
> simulation countless hundred trillion times to get it all to work out?

Who knows what is going on outside of our universe, or before our 
universe was started?

> In short, to make the implausible ID theory work, you need to postulate
> even more radical theories such as the designer running the universe as
> a computer simulation...

So if you got a computer simulation running here on Earth, that somehow 
simulated molecular interactions etc, and then you started it off with 
the DNA of an ant or something, you would have an ant "alive" in your 
computer.  If you made the computer big enough that you can simulate 
more complex lifeforms, and then intelligent lifeforms, how would they 
ever figure out what was going on outside of their "world"?  Obviously 
the "world" and complexity of the simulation would have to be orders of 
magnitude smaller than our universe, but that simply means some "parent" 
universe of ours would just need to be bigger and more complex.


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From: Invisible
Subject: Re: Molecular biology
Date: 11 Jan 2011 05:36:50
Message: <4d2c32c2$1@news.povray.org>
On 11/01/2011 10:31 AM, scott wrote:
>> The trouble with unpredictable systems such as the Earth's atmosphere is
>> that arbitrarily tiny perturbations of the initial state yield huge
>> divergences in the end result.
>
> Same if I have a 4GB chaotic simulation running on my machine, just one
> bit different in the initial conditions will yield 4GB of completely
> different data. Yet it will be totally repeatable.

Only because it's data in a computer.

> Sure, but what if you set up your Earth with the *exact* same initial
> conditions?

In general, that's not physically possible.

It's like the fact that, according to the laws of physics, it is 
possible to UNscramble an egg. But have you tried it recently? It's 
quite hard.

> So if you got a computer simulation running here on Earth, that somehow
> simulated molecular interactions etc, and then you started it off with
> the DNA of an ant or something, you would have an ant "alive" in your
> computer. If you made the computer big enough that you can simulate more
> complex lifeforms, and then intelligent lifeforms, how would they ever
> figure out what was going on outside of their "world"? Obviously the
> "world" and complexity of the simulation would have to be orders of
> magnitude smaller than our universe, but that simply means some "parent"
> universe of ours would just need to be bigger and more complex.

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.


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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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