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From: Darren New
Subject: Re: Molecular biology
Date: 10 Jan 2011 17:12:11
Message: <4d2b843b@news.povray.org>
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.

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


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From: Invisible
Subject: Re: Molecular biology
Date: 11 Jan 2011 04:35:39
Message: <4d2c246b$1@news.povray.org>
On 10/01/2011 06:22 PM, Darren New wrote:
> Invisible wrote:
>> You seriously expect me to believe
>
> 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. So 
you'd have to predict solar activity too. (Not to mention random stray 
comets colliding with Earth.)

On top of that, the effect of living organisms themselves is 
significant. So in order to work out what what types of organisms you 
need to design, you need to know what environments will be available, 
which *depends on* what types of organisms you design.

Seriously, you don't need to be a chaos theory expert to see that all of 
this is wildly impossible. (Not forgetting that the original premis is 
already impossible because the number of species wildly exceeds the 
information content of the first genomes.)



Now, Behe put forth the idea of "irreducible complexity". The idea being 
that a system is irreducibly complex if removing any single component of 
it breaks the system. Such systems, Behe asserted, cannot evolve.

Of course, that's a bit like buying a car, removing the engine 
management system, observing that the car no longer works, and arguing 
that the car cannot have been invented before computer technology became 
available. Which, obviously, is absurd.

Then again, that's not *quite* the same, since the designs of artificial 
devices can make sudden jumps. Evolution, in general, can't do that.

Dawkins showed that irreducibly complex systems can in fact evolve. For 
example, suppose protein A exists, and does something useful. Now 
suppose that a protein B comes along, which makes protein A slightly 
more efficient. Assuming whatever A does is beneficial, doing it better 
is obviously something that natural selection would favour.

What happens next is that A and B co-evolve. Any change in B which 
enhances its effect on A would tend to be favoured. Any change in A 
which enhances the effect of B on it would also tend to be favoured. 
Fast-forward a few million generations and I wouldn't be at all 
surprised if we now have a situation where A doesn't even *work* any 
more without B.

In other words, the system has become irreducibly complex. And of 
course, there's no particular reason why a protein C can't join the 
party at some point along the smooth continuous route to irreducible 
complexity. And then we would have 3 interrelated proteins that only 
function in combination with each other.

Behe also chose an unfortunate example of an irreducibly complex system: 
a cellular motor. He pointed out that it's a complex of 9 proteins, and 
removing any one of them breaks the motor, so therefore it could not 
have evolved. Except that somebody recently discovered a parasite that 
uses just 2 of these proteins to make holes in the cell walls of its 
host. So those 2 proteins on their own do something useful. They don't 
make a motor, but they /are/ useful (for something slightly different).


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From: Invisible
Subject: Re: Molecular biology
Date: 11 Jan 2011 04:41:13
Message: <4d2c25b9$1@news.povray.org>
On 10/01/2011 05:03 PM, Warp wrote:

>    The theory of evolution != the theory of life's origins.
>
>    The theory of evolution says nothing about how life first came into
> existence on Earth. That would be abiogenesis.

Quite. And while the theory of evolution is universally accepted, 
abiogenesis is essentially still at the stage of "well, we've got some 
ideas, but basically nobody /really/ knows".

>    Basically the only thing that the theory of evolution postulates is that
> the genes of large populations change over time (something even the most
> hardcore young-earth creationists don't deny) and that some changes get
> preserved while others disappear due to natural selection (again, something
> the creationists don't deny). That's about it.

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.

That's about as much as evolution itself actually says about the origin 
of life; that life didn't originate as twenty billion species, but as 
just one. (Actually, it was probably a handful of species; it's just 
that only one of them left descendants. As far as we know.)


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From: Invisible
Subject: Re: Molecular biology
Date: 11 Jan 2011 04:54:59
Message: <4d2c28f3$1@news.povray.org>
On 10/01/2011 06:32 PM, Darren New wrote:
> Invisible wrote:
>> Actually I think you'll find it's that all tetrapods are descendants
>> of a single fish ancestor, which just happened to have 5 digits. By
>> now it would be far too difficult to change it.
>
> Sure. But we grew lungs, and new digestive systems, and homeostasis,

Just about every living organism has homeostasis. I presume you mean 
*temperature* homeostasis?

> scales and skin and fur and feathers, wings and hooves and talons, but
> we still all have five fingers, including the animals whose fingers are
> in a stiff and unbending mitten of cartilage. Look at the vast range of
> shapes out there, and tell me that it makes sense that none of them got
> rid of the pinky finger, or put on another bone somewhere.

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

Well, horses and similar have finger/toe bones fused together. But then, 
actually the anatomy of a horse leg is quite interesting. A human arm 
has two straight bits, a wrist and then a bunch of fingers. In a horse, 
the first straight bit is actually inside the body, the second straight 
bit is the top of the visible leg, and the remaining bones of the leg 
are actually what would be knuckle and finger bones in a human. Weird.

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...)

> No, that's the point. From what I read, you'd only have to change one
> gene. Except it's a gene in the middle of *another* sequence as well,
> which regulates development of the reproductive system.

Well, if that's the case, I haven't read about it myself. I would 
suggest though that something like this would require changing many, 
many genes, all at the same time, which is why it doesn't happen.

(Oh, you can probably make it happen by changing one of the cellular 
differentiation genes, which tell cells "where they are". But that would 
probably break stuff all over the place. Indeed, these genes tend to be 
extremely highly conserved.)


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From: Invisible
Subject: Re: Molecular biology
Date: 11 Jan 2011 04:56:34
Message: <4d2c2952$1@news.povray.org>
On 10/01/2011 06:32 PM, Darren New wrote:

> It's entirely possible to teach adults. :-)

You haven't met my work colleges...


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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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