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From: andrel
Subject: Re: Molecular biology
Date: 13 Jan 2011 15:58:21
Message: <4D2F6777.7050506@gmail.com>
On 12-1-2011 18:01, scott wrote:
>>>>> 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?
>>
>> Look up "Bell's Inequality." It has recently (in the last couple of
>> years) gone on from there to prove that the problem is not non-local
>> interactions.
>
> But does that really prove that there is nothing else controlling what
> we are measuring? If you liken our universe to a computer simulation,
> then outside of the simulation none of the limitations inside the
> simulation necessarily apply.

The technical term for that is a 'hidden variable theory'; the variable 
has a value except we don't know it. Bell has shown that if the universe 
can be described by a hidden variable theory some measurable quantities 
have different values than if the variable has no value until measured. 
Alain Aspect has shown that nature is incompatible with a hidden 
variable theory. So Darren is right, and you, Einstein, Podolsky, and 
Rosen are proven wrong. Nothing to be ashamed of, I'd say.


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From: andrel
Subject: Re: Molecular biology
Date: 13 Jan 2011 16:30:20
Message: <4D2F6EF6.6060603@gmail.com>
On 13-1-2011 12:45, Warp wrote:
> Invisible<voi### [at] devnull>  wrote:
>> On 12/01/2011 04:12 PM, Warp wrote:
>>> Invisible<voi### [at] devnull>   wrote:
>>>> 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.
>>>
>>>     I don't think that is what defines a species. It's about genetics.
>
>> How about this: There are two species of grasshopper that never
>> interbreed. The females of species A ignore the songs of males of
>> species B. However, if you mute the male and play back a recording of a
>> male of species A, the two will mate, and produce viable offspring. It's
>> just that this only ever happens in the lab.
>
>    The definition of species is related to genetics, not to behavior.

No that is a choice and one that not everybody agrees on. It might be in 
your biology book but that does not prove much.

>> Similarly, there are probably classes of birds where you could do the
>> same thing by putting coloured visors over the bird's eyes, or moths
>> where you could mask one chemical pheromone with another. Are these
>> separate species?
>
>    It's about genetics, not about behavior.
>
>> You can apparently mate a lion with a tiger, producing either a "liger"
>> or a "tiglon". (Go look them up.) But this never happens in the wild (as
>> far as we know).

Given that their habitats do not overlap...

> Are these separate species?
>
>    The offspring must be fertile. Ligers and tigons aren't.

That too is a choice that not everybody agrees on. It is still often 
used as a definition, read the origin of species for many examples where 
this does not make sense. Among other things offspring of two 'species' 
that are more viable than the pure breeds.

No definition of species exists that is not violated in some 'species'. 
I think it may be hard to find a biologist in this field that would 
supply you with something more than: 'in most cases this will match you 
intuitive concept'. I can live with that. People whose mental health 
depend on the assumption that there is a clear definition of 'species' 
may freely ignore the evidence.


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From: andrel
Subject: Re: Molecular biology
Date: 13 Jan 2011 16:36:52
Message: <4D2F707E.9040204@gmail.com>
On 13-1-2011 13:00, Warp wrote:
> Darren New<dne### [at] sanrrcom>  wrote:
>> Surprisingly enough, it really is trivial.
>
>> http://en.wikipedia.org/wiki/Speciation#Artificial_speciation
>
>    It talks about preference, not about capability. Just because some man will
> not mate with fat women doesn't make the man a different species.
>
It talks about both: 'Diane Dodd was also able to show how reproductive 
isolation can develop from mating preferences' see also the discussion 
on speciation genes somewhat lower on the page.


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From: Warp
Subject: Re: Molecular biology
Date: 13 Jan 2011 17:09:17
Message: <4d2f780d@news.povray.org>
Jim Henderson <nos### [at] nospamcom> wrote:
> On Thu, 13 Jan 2011 15:03:01 -0500, Warp wrote:

> >> Like I sorta said earlier, talking with you is often like talking to a
> >> brick wall.  It's all black-and-white to you, isn't it?
> > 
> >   I understand that reply to mean that no, your so-called "atheism day"
> > is not official, mandated by your congress. That's my point. There's a
> > definite bias.

> Um, no, my comment was nothing more than a comment on your obstinance.  
> It should not be taken as an answer to your question, nor should this be.

> It's a shame that I have to *explain* that something that isn't an answer 
> to your question *isn't an answer to your question*.

  And it's a shame I have to point out when I'm being sarcastic since you
don't seem to get it.

-- 
                                                          - Warp


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From: Jim Henderson
Subject: Re: Molecular biology
Date: 13 Jan 2011 18:02:25
Message: <4d2f8481$1@news.povray.org>
On Thu, 13 Jan 2011 17:09:17 -0500, Warp wrote:

>   And it's a shame I have to point out when I'm being sarcastic since
>   you
> don't seem to get it.

That's what sarcasm tags are for - it's very difficult in a written-only 
medium to pick up on those cues.

Jim


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From: Jim Henderson
Subject: Re: Molecular biology
Date: 13 Jan 2011 18:02:37
Message: <4d2f848d$1@news.povray.org>
On Thu, 13 Jan 2011 20:52:18 +0000, Stephen wrote:

> On 13/01/2011 8:38 PM, Jim Henderson wrote: ...
>>
>> Jim
> 
> Mornington Crescent! :-P

It's about time! :-)

Jim


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From: Darren New
Subject: Re: Molecular biology
Date: 13 Jan 2011 18:09:11
Message: <4d2f8617$1@news.povray.org>
Warp wrote:
>   The offspring must be fertile. Ligers and tigons aren't.

How often do they have to be fertile for it to count. If 10% of the 
offspring are viable, is that enough? 1%?

Also, there are some tree species[*] C that's a cross between species A and 
species B. It won't fruit except in the presence of A or B. I.e., the 
offspring are fertile with their parents, but not with each other. Does that 
count?

And, has been mentioned, men are not the same species as other men, so it's 
difficult to understand exactly how to apply this definition to individuals.


[*] I thought it was tangelos, but wikipedia doesn't mention that on their page.

-- 
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: 13 Jan 2011 18:11:03
Message: <4d2f8687$1@news.povray.org>
Warp wrote:
>   It's just that defining "species" in terms of behavior is ludicrous.

Well, give a definition that shows two men are the same species, that a 
bacteria's descendants are the same species, and that these two populations 
of fruit flies are the same species.  What exactly has to be in the genetics?

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


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From: Patrick Elliott
Subject: Re: Molecular biology
Date: 13 Jan 2011 23:17:22
Message: <4d2fce52$1@news.povray.org>
On 1/13/2011 2:49 AM, Invisible wrote:
>>> The distinction you're looking for is between eukaryotes and
>>> non-eukaryotes.
>>>
>> Uh, yeah. Couldn't think of the proper term though. But, the rest is
>> correct. If you don't have excess resources to waste on messing with
>> extra baggage, you don't live long if you have it. If you do have the
>> "power plants", you can afford to waste more space in the genome on
>> things that don't work, duplicate results, etc.
>
>>> I'm not sure I actually agree with this assessment.
>>>
>> http://scienceblogs.com/pharyngula/2010/12/how_to_afford_a_big_sloppy_gen.php
>>
>>
>> As to the cite for prokaryotes not having as many copy errors, I think
>> it would be more accurate to say, "They don't *preserve* as many." If
>> they did, they would have way more junk DNA, which is precisely what
>> they can't afford to have laying around in the first place. The actual
>> number of such errors that happen is likely the same, but, when it comes
>> to costs, if you can't afford them, you don't see those copied chunks
>> sticking around long.
>
> I think we need to distinguish between DNA that isn't used for anything,
> and DNA which actually produces proteins, but they don't do anything
> really useful.
>
> Just having a sequence in your genome doesn't really cost that much.
> Synthesizing it into a protein is much more expensive.
>
> It wouldn't surprise me if non-eukaryotes have fewer genes turned on,
> and possibly smaller genomes, but I doubt that they have radically
> "cleaner" genomes.
You are forgetting that you *still* have to copy all that extra stuff, 
when ever you divide the cell, so there is still a cost to synthesize 
all the copies, before the cell splits to form new cells. Also, its not 
a simple case of, "just ignore the stuff I don't use", something has to 
run through the pattern, decide what needs to be unfolded, or folded, 
jump past any stuff that is folded into an unusable state, etc.

And, most of the code, unlike in multi-celled organisms, is going to be 
"on". There is no reason to turn parts off, except for mitosis, and the 
like, if you are not differentiating the cells, which requires shutting 
off the parts you don't need running at all. Something that has a mess 
of extra code is going to have a lot of stuff the maneuver around to get 
anything done, and those that don't, are not likely to have a lot of 
inactive code, which isn't doing synthesis, more or less massively 
parallel, constantly.

-- 
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: 13 Jan 2011 23:39:36
Message: <4d2fd388@news.povray.org>
On 1/13/2011 5:00 AM, Warp wrote:
> Darren New<dne### [at] sanrrcom>  wrote:
>> Surprisingly enough, it really is trivial.
>
>> http://en.wikipedia.org/wiki/Speciation#Artificial_speciation
>
>    It talks about preference, not about capability. Just because some man will
> not mate with fat women doesn't make the man a different species.
>
But, by the same token, just because a species has developed to "prefer" 
their own species, doesn't mean its 100% impossible for an impregnation 
to happen, it just isn't too common. The question then is, are the rest 
of the genes compatible at all. The answer is, "Depends". For common 
things, like insulin, the genome doesn't much care, as long as its 
"close enough". Basically, you have these barriers:

1. Pheromone response.
2. Reproductive compatibility (fusion will happen).
3. Number of chromosomes, though a difference of 1-2 may *not* be a big 
deal, as long as there are parallels, or the two available fill in any gaps.
4. Immune response - does the host mother's immune system see the cell 
as a problem?
5. Hormonal issues - the wrong levels "may" effect development, if far 
enough off.

Most of these are not likely to be surmountable by species in nature, 
short of a lot of very unusual mutations all coinciding. In principle, 
we could take steps to eliminate most of them, but no one is likely to 
do that (at least not in legit labs, in first, or probably even second, 
world countries). However, that the odds of a pure chance combination of 
factors resulting in a combination working being low doesn't mean 
"impossible". That is the problem. Of course, one big difference also 
comes down to the fact that "preference" in this case is *not* the same 
thing at all. For a fruit fly, preference means, short of outside 
intervention, its almost 100% certain they will never mate with a 
different species. The more complex the organism, the greater the odds 
it will "override" that preference, by self choice. Which is why you 
don't see, say, birds trying to mate spiders, but its not unheard of for 
dogs to try to mate with sheep, etc., or apes to mate with everything 
from frogs, to anything else that can't get away, mostly purely to "got 
off", which most simpler species don't do at all either. But, at that 
level of complexity, the number of barriers in place to prevent cross 
over is *very* high, even if they develop some truly odd preferences.

-- 
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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