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  Molecular biology (Message 276 to 285 of 465)  
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From: Patrick Elliott
Subject: Re: Molecular biology
Date: 14 Jan 2011 22:23:48
Message: <4d311344$1@news.povray.org>
On 1/14/2011 2:27 AM, Invisible wrote:
>>> 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.
>
> Yes, there is a cost. What I'm saying is that it's a very small cost.
>
>> 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.
>
> It's not like a computer, doing a linear scan of the entire genome
> looking for active genes. It doesn't work like that.
>
> As far as I know (and I'm not an expert on the subject), having extra
> inactive genes imposes very little penalty for transcription.
>
>> 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
>
> False.
>
> Unicellular organisms might not build colonies of differentiated cells,
> but that does *not* mean that all genes are switched on, all the time.
>
> There are organisms that can metabolise both aerobically and
> anaerobically. That's two different metabolic pathways, involving
> different sets of proteins. Many if not most organisms can utilise more
> then one food source. That's different sets of proteins. Many organisms
> have a life-cycle more complex them just "grow, divide, grow, divide".
> That requires different sets of proteins. Some cells even signal each
> other, and undergo limited differentiation under certain conditions.
> More sets of genes. Then there are genes only used in response to attack
> or damage. And so forth.
>
> Seriously. Few if any organisms go around with *all* their genes
> switched on all the time.
Well.. Ok, saying "all" may have been a bit inaccurate. What I meant is 
you don't generally see, with a few exceptions, entire sets of genes 
"off" all the time, once they have been used, such as developmental 
precursors, etc. In any case, you assumption of what the cost may be is 
precisely that, an assumption. My assumption is, based on the article I 
linked to, that the costs *must* be higher than you are assuming.

-- 
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: Patrick Elliott
Subject: Re: Molecular biology
Date: 14 Jan 2011 22:31:40
Message: <4d31151c$1@news.povray.org>
On 1/14/2011 10:17 AM, Darren New wrote:
> Warp wrote:
>> Darren New <dne### [at] sanrrcom> wrote:
>>> 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?
>>
>> I don't think you get it. What I said is that the claim "two groups of
>> animals have been speciated away from each other if they won't interbreed
>> because of instinctual preference" (rather than their genes being
>> incompatible) is an incorrect definition.
>>
>> You can't argue pro that definition with the argument "well, you can't
>> give a better definition". That argument coulud be used to defend
>> anything.
>
> I'm not arguing against it. I'm asking you what your definition is. You
> say "it's genetics", but that isn't enough. You're treating my question
> as if I'm saying "you're wrong." I'm happy to be shown you're right, but
> you haven't done that yet.
>
> *You* are the one asserting it's genetics and can't be just behavior.
> *You* are saying *I* am wrong. But you're not supporting that. You're
> just saying it louder.
>
The problem here is that, in the case of fruit flies, the "behavior" is 
genetic, but your counter example is not. Thus, it cannot represent 
either a valid counter example, nor an invalidation of Warp's claim. 
Show that the behavior of the fruit flies can be "trained", or otherwise 
altered, without changing the genetics, or introducing, say, the right 
pheromone on the female (which is just a short cut to altering *its* 
genetics).

-- 
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();
}

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3D Content, and 3D Software at DAZ3D!</A>


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From: Patrick Elliott
Subject: Re: Molecular biology
Date: 14 Jan 2011 22:48:44
Message: <4d31191c$1@news.povray.org>
On 1/14/2011 10:21 AM, Jim Henderson wrote:
> On Thu, 13 Jan 2011 21:49:42 -0700, Patrick Elliott wrote:
>
>> Well, the reason both sides make the argument is that its correct. If
>> you don't enforce absolute moral codes
>
> The world is shades of grey, not just black and white.
>
> Jim
I know this, you know this, they... often make the accusations like 
"moral relativism", which is *literally* the statement that, "You treat 
the world as shades of gray, but in *fact* its black and white!" If you 
deal with the world based on trying to comprehend why things work, you 
end up with a case of moral relativism, and uncertainty, where the 
answer cannot always be known, or even suspected, merely because you 
find the behavior questionable, but it fails to fit neatly into some 
preexisting box.

In fact, in reference to an example already included, even the ones that 
do, often turn out to have negative consequences only *because of* the 
conditions they where tried in. I would argue, for example, that the 
consequence for some girl playing naughty with her dog today might 
*maybe* be having the dog taken away, and jail time. A few hundred years 
ago they had the girl and dog burned to ash, and the ashes scattered, 
to, "prevent anyone even thinking of such a thing ever again". Its even 
a bit iffy as to whether or not something that can rip your throat out, 
if angered, can't "consent", which is the core argument for even 
requiring jail time, or removal of the animal.

But that is an example that "most" people still find objectionable 
enough to demand it remain illegal. There are thousands of others, from 
showing ankles, or marrying between "races" that we reject as invalid 
things to disdain now. Why? Because a) the arguments against them where 
invalid to start with, and based solely on either "ick", prejudice, 
tradition, or religion, and b) every single imagine consequence of them 
proved to be wrong. And.. While we get different hypothesis, based on 
completely different sets of imaginary threats, both from the far left 
and right, I would argue that, for the more "reality based" community in 
the middle, the far lefts kind of crazy is *way* less accepted than the 
right's. Why? Because the right's is religious, traditional, caters to 
existing prejudice, perceptions of "ick" already in place, etc., while 
the other side's is often foreign, if it is traditional some place, not 
common place, or flat pulled out of their asses yesterday, not out of 
someone else's 1,000 years ago or more.

This is why some crazy seems crazier than others, even when both are 
supported *only* by rhetoric, wild hypothesis about consequences, 
appeals to authority, and denial of contrary data and evidence.

In short, what you already believe is more likely to be true *seems* 
more true, even when supported by the same level of complete absence of 
actual facts, and even if confronted with those that directly imply that 
it is wrong, flawed, or too generalized, in some fundamental way.

-- 
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: 14 Jan 2011 22:55:10
Message: <4d311a9e$1@news.povray.org>
On 1/14/2011 10:27 AM, Jim Henderson wrote:
> On Thu, 13 Jan 2011 22:37:52 -0700, Patrick Elliott wrote:
>
>> Its this thinking, and the inadvertent support for it, which makes the
>> national day of prayer a problem. For them, it *does* endorse it, and
>> they quite clearly do not think that "endorsing" religion, even their
>> own, is a problem, only denying others their own (save, again, for any
>> conflicts in expression, in which case their own overrides the "wrong"
>> one).
>
> So if even one nutjob thinks that something the government does is an
> endorsement of religion, then it is?
>
Not just the nut jobs. The problem is, the Overton Window has shifted so 
badly, in some cases, to one side, than even the people that might 
otherwise *not* be classified as nuts accept that it *is* a sort of 
indirect endorsement, and that there isn't any real problem doing so. 
That the real nut jobs would turn around and declare 90% of Christians 
in the country as "false believers", and have stated as much in public 
forums, is either ignored as unlikely, waved off as not a real threat, 
or completely missed, by people who, never the less, if polled, would 
insist that the NDoP is OK, and so is posting the Ten Commandments on 
every building in the city.

When things get that far out of sync, "framing" things, so they are 
supposed to be universally good for everyone, only benefits the people 
that want to use that framing to shove the window even farther over.

-- 
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: Darren New
Subject: Re: Molecular biology
Date: 14 Jan 2011 23:43:17
Message: <4d3125e5$1@news.povray.org>
Patrick Elliott wrote:
> The problem here is that, in the case of fruit flies, the "behavior" is 
> genetic, but your counter example is not. 

What counter-example do you think I'm claiming?

 > Thus, it cannot represent
> either a valid counter example, nor an invalidation of Warp's claim. 

I'm not trying to invalidate Warp's claim. Nowhere did I say Warp was wrong 
in his claim. I just asked him how he defines "species" beyond "it's 
genetic". Because by *his* definition, two men are not of the same species.

> Show that the behavior of the fruit flies can be "trained", or otherwise 
> altered, without changing the genetics, 

Well, you take a homogenous group of fruit flies. You put them in a two 
different environments for a while. You bring them back together. Their 
behavior is changed. I don't know if the change is genetic or not. It would 
seem to me that fruit flies have very little behavior that isn't dictated 
genetically - it's not like you can train them to do tricks. I didn't see 
anything in the reference I gave that said the fruit flies were still 
genetically compatible. Warp seems to be asserting that the fruit flies are 
still genetically compatible, and it's just that they're not sufficiently 
friendly with the other group any more or something.

I'm simply asking Warp to tell me what test he would use to find out if two 
individuals are the same species. You can't just say "it's genetic." Yes, we 
understand that, but the details are what we're arguing about.

-- 
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: 15 Jan 2011 00:13:47
Message: <4d312d0b$1@news.povray.org>
Patrick Elliott wrote:
> nor an invalidation of Warp's claim. 

Or, to put it another way, it seems very odd to say "No, your definition is 
wrong", and when I ask "Well, what's the right definition, then?" for the 
other party to go on the defensive. I find it's very rare for someone to 
claim that the definition of a scientific word is wrong without actually 
being able to specify what they think the definition is.

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


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From: Jim Henderson
Subject: Re: Molecular biology
Date: 15 Jan 2011 15:27:07
Message: <4d32031b$1@news.povray.org>
On Fri, 14 Jan 2011 22:50:20 +0000, Stephen wrote:

> On 14/01/2011 10:16 PM, Jim Henderson wrote:
>> Yes, I particularly liked "Hit me with your Battle Hymn", but they all
>> were outstanding.:-)   It's rare for that game not to be good, unless
>> Jeremy's involved.;-)
>>
>>
> Oh! No! Jeremy's great.

s/great/grate - fixed that for you. ;-)  (Seriously, though, he's very 
funny because he knows he can't sing and has fun with it - and that *is* 
funny.)

>> It's funny that you mention Beethoven's 5th, because we've started
>> listening to ISIRTA again as well, and as you know, that's a regular
>> feature of that show.
> 
> No I didn't. I listened to ISIRTA live when it was broadcast. And that
> was a long time ago.

:-D  I've listened to them all once already, we're on our second go-
around with ISIRTA.  Haven't yet got to them singing the Angus Prune 
song, it's just instrumental at this point.

>> Which episode was "Where Did you Get That Hat" to "Dambuster's March"? 
>> I probably have it already (I've got what I*think*  is a complete
>> collection of all the shows, but I've been wrong before<G>).
>>
> S5 E2 Series 5 Episode 2
> I've got a lot that were recorded and uploaded on The Goons Depository.
> If you have any missing I may have them. Unfortunatly the sound quality
> is a bit iffy on some of them.

That may be where I found the recordings myself, or where they originated 
from.  radioarchive.cc is a good resource as well.  Do you know the 
broadcast date on that one?

> s01e04 had Tim, Graeme, Bill Oddie and John Clease

Always a good combination, esp. since Bill and John were in ISIRTA as 
well.

> Do you know Radio Archive? It is a good source.
> http://radioarchive.cc/index.php

LOL, I hadn't seen this part of the message when I wrote the above 
reference to that site. :-)

Jim


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From: Stephen
Subject: Re: Molecular biology
Date: 15 Jan 2011 16:29:24
Message: <4d3211b4$1@news.povray.org>
On 15/01/2011 8:27 PM, Jim Henderson wrote:

> :-D  I've listened to them all once already, we're on our second go-
> around with ISIRTA.  Haven't yet got to them singing the Angus Prune
> song, it's just instrumental at this point.
>

To be honest, I find ISIRTA dated now and I’ve never been a fan of John 
Cleese.

>>> Which episode was "Where Did you Get That Hat" to "Dambuster's March"?
>>> I probably have it already (I've got what I*think*  is a complete
>>> collection of all the shows, but I've been wrong before<G>).
>>>
>> S5 E2 Series 5 Episode 2
>> I've got a lot that were recorded and uploaded on The Goons Depository.
>> If you have any missing I may have them. Unfortunatly the sound quality
>> is a bit iffy on some of them.
>
> That may be where I found the recordings myself, or where they originated
> from.  radioarchive.cc is a good resource as well.  Do you know the
> broadcast date on that one?
>

Yes.

>> s01e04 had Tim, Graeme, Bill Oddie and John Clease
>
> Always a good combination, esp. since Bill and John were in ISIRTA as
> well.
>

Have you sceen "do not adjust your set" or "At lat the 1948 show"?

>> Do you know Radio Archive? It is a good source.
>> http://radioarchive.cc/index.php
>
> LOL, I hadn't seen this part of the message when I wrote the above
> reference to that site. :-)
>

Just to make sure you read to the end :-P

1976-03-13 - s05e02 - Politicians Ball

:-D

-- 
Regards
     Stephen


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From: Patrick Elliott
Subject: Re: Molecular biology
Date: 15 Jan 2011 21:46:43
Message: <4d325c13$1@news.povray.org>
On 1/14/2011 9:43 PM, Darren New wrote:
> Patrick Elliott wrote:
>> The problem here is that, in the case of fruit flies, the "behavior"
>> is genetic, but your counter example is not.
>
> What counter-example do you think I'm claiming?
>
>  > Thus, it cannot represent
>> either a valid counter example, nor an invalidation of Warp's claim.
>
> I'm not trying to invalidate Warp's claim. Nowhere did I say Warp was
> wrong in his claim. I just asked him how he defines "species" beyond
> "it's genetic". Because by *his* definition, two men are not of the same
> species.
>
>> Show that the behavior of the fruit flies can be "trained", or
>> otherwise altered, without changing the genetics,
>
> Well, you take a homogenous group of fruit flies. You put them in a two
> different environments for a while. You bring them back together. Their
> behavior is changed. I don't know if the change is genetic or not. It
> would seem to me that fruit flies have very little behavior that isn't
> dictated genetically - it's not like you can train them to do tricks. I
> didn't see anything in the reference I gave that said the fruit flies
> were still genetically compatible. Warp seems to be asserting that the
> fruit flies are still genetically compatible, and it's just that they're
> not sufficiently friendly with the other group any more or something.
>
> I'm simply asking Warp to tell me what test he would use to find out if
> two individuals are the same species. You can't just say "it's genetic."
> Yes, we understand that, but the details are what we're arguing about.
>
The distinction here would be, "Its genetic, but the genetics involve 
purely 'behavior', not development." Obviously, the combination of 
genetics from two individuals is a "developmental" issue, such that you 
could have compatibility on that level, but not in the behavior level. 
You could have the opposite (not terribly uncommon, despite the ick 
factor) where the developmental aspects are 100% incompatible, but 
behavior, for some reason, is driven wrong. For simpler species, which 
could be a tiny flaw in a pheromone receptor, which suddenly "reacted" 
to the wrong species. For complex ones, it can be a result of plasticity 
in the behavior, resulting in what amount to false associations with the 
target species. In either case, the "genetics" on the developmental 
level simply won't allow it to work.

That behavior "can be" driven by genetics is not the key factor. It is 
*if* the genetic driven characteristics actually result in changes 
either behaviorally, or developmentally, which prevent cross breeding. 
The fruit fly case is unusual, in that the deviation is purely, for now, 
in the behavioral aspects, but it wouldn't take too many tweaks in the 
rest of the genome, once trading of such changes no longer take place, 
to make it *both* behavioral and developmental.

Its still "genetics driven", either way. Its just more.. reversible, of 
other factors in the developmental process itself do not yet derail 
cross breeding. I would argue things like Ligers and the like, do not 
qualify the two species as "same", since the result can't produce more 
of its own, or of either of its parent species. The developmental code 
has changed sufficiently that even if the behavior can be overcome, the 
other aspects *cannot*. But, there was certainly, at some stage, a point 
where this wasn't true, or where it was only true for a larger 
percentage of offspring than it was successful.

-- 
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: 15 Jan 2011 21:48:54
Message: <4d325c96$1@news.povray.org>
On 1/14/2011 10:13 PM, Darren New wrote:
> Patrick Elliott wrote:
>> nor an invalidation of Warp's claim.
>
> Or, to put it another way, it seems very odd to say "No, your definition
> is wrong", and when I ask "Well, what's the right definition, then?" for
> the other party to go on the defensive. I find it's very rare for
> someone to claim that the definition of a scientific word is wrong
> without actually being able to specify what they think the definition is.
>
Scientific terms, like biology, get messy, when they skirt the edges of 
what they *do* define, especially *in* biology. In this case, the 
definition can get fuzzy, since some might argue that producing "any" 
offspring, sterile or not, makes for the same species. Others that this 
isn't any where near sufficient.

-- 
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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