1430: "Proteins"

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orthogon
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Re: 1430: Proteins

Postby orthogon » Mon Oct 06, 2014 5:45 pm UTC

addams wrote:
orthogon wrote:
Znirk wrote:
Garnasha wrote:Personally though, although I don't think it's a correct idea, I like the idea of a Grand Architect (that is, design once, add Big Band and leave alone)

The universe as a 1930s dance hall. What's not to like? :)
(sorry ...)

And Count Basie as the creator of the Universe... Which means we also know how it's going to end

Damn It!
I don't read music.

Why?
oh, Why, must I google?

Damn it!
Why don't I read Music??

I'm 99% sure you would know the Basie Ending if you heard it.
Check out this video...
Or this one ...
Really you need to hear a Big Band (ideally Basie's own band) playing it, but it might take me a while to find an example; who knows, I wouldn't be surprised if Basie never actually played it!

Edit: Here at 54:21, although the timing is different to the "classic" ending, with the penultimate note on "3" instead of pushed on the "and" of 2.
Last edited by orthogon on Mon Oct 06, 2014 6:17 pm UTC, edited 1 time in total.
xtifr wrote:... and orthogon merely sounds undecided.

Kit.
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Re: 1430: Proteins

Postby Kit. » Mon Oct 06, 2014 6:17 pm UTC

gmalivuk wrote:(For the record, there are on-topic threads to have such discussions, such as in SB, but I don't see why ED's trolling had to taint so much of this one.)

C-terminal tail is where phosphorylation happens. So, "tugging" it should be a quite common mechanism for affecting spatial configurations of proteins.

Here in this thread we have a small but nonzero chance that someone knowledgeable enough comes in and shows us how similarly-coded proteins are folded for different actions, and how differently-coded proteins are folded for the same action in different species (or not), thus making an additional illustration to the "Intelligent Designer" vs. "Blind Watchman" debate.

In SB... well, why such a person would even read SB?

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Re: 1430: Proteins

Postby Coyoty » Mon Oct 06, 2014 7:32 pm UTC

I may not matter to the universe, but the universe matters to me. As log as it matters to someone, it matters.

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Re: 1430: Proteins

Postby Flumble » Mon Oct 06, 2014 8:03 pm UTC

cellocgw wrote:...
"I write hardware" 40
Please no "in Soviet Russia" jokes

That's silly. Lots of researchers write hardware (in VHDL/Verilog) nowadays, why don't they mention it to the public? :o

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Re: 1430: Proteins

Postby Izawwlgood » Mon Oct 06, 2014 8:14 pm UTC

Kit. wrote:
gmalivuk wrote:(For the record, there are on-topic threads to have such discussions, such as in SB, but I don't see why ED's trolling had to taint so much of this one.)

C-terminal tail is where phosphorylation happens. So, "tugging" it should be a quite common mechanism for affecting spatial configurations of proteins.

Here in this thread we have a small but nonzero chance that someone knowledgeable enough comes in and shows us how similarly-coded proteins are folded for different actions, and how differently-coded proteins are folded for the same action in different species (or not), thus making an additional illustration to the "Intelligent Designer" vs. "Blind Watchman" debate.

In SB... well, why such a person would even read SB?

A ) I presume you don't mean 'C-terminal tail is where phophorylation happens' in all proteins, but either way, I want to disavow you/readers of that incorrect notion.

B ) Not what you're asking about, but the main aggregate forming protein in Alzheimers (AB) comes from a miscleaved receptor (APP) which can be cleaved in one of I think four ways. One of those cleavages is Bad News Bears.

C ) I assume you all are suggesting examples of analogous proteins, but the easiest and cheapest way to meet your request is to just point out any protein that has a different primary structure but maintains identical function. Which is... a lot of proteins.

Z ) Just... stahp. It is such a shame every time biology comes, someone wants to chime in with theology. Nothing about this comic really leads one to a discussion about Intelligent Design. Her comment in the fourth panel is to underline the complexity of foldIt, not to bring up synthetic life.
... with gigantic melancholies and gigantic mirth, to tread the jeweled thrones of the Earth under his sandalled feet.

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Re: 1430: Proteins

Postby DaveMcW » Mon Oct 06, 2014 8:50 pm UTC

Kit. wrote:Google:

"I write software that" - About 172,000 results
"I make software that" - About 27,400 results


172,000 programmers.
27,400 managers.

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Re: 1430: Proteins

Postby 5th Earth » Mon Oct 06, 2014 9:47 pm UTC

I think the comic overstates the difficulty a little. Since animals are assemblies of proteins, aren't they by definition more complicated than any of their constituent parts examined in isolation?
It seemed like a good idea at the time.

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Re: 1430: Proteins

Postby Mikeski » Mon Oct 06, 2014 10:25 pm UTC

DaveMcW wrote:
Kit. wrote:Google:

"I write software that" - About 172,000 results
"I make software that" - About 27,400 results


172,000 programmers.
27,400 managers.

That writes sense.

...seriously, though. From the hardware side of the fence, I could see software folks not saying "make software" because "make" is already a technical term for anyone who codes in a UNIX environment. And why overload an operator unnecessarily? :wink:

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Re: 1430: Proteins

Postby rmsgrey » Mon Oct 06, 2014 10:37 pm UTC

5th Earth wrote:I think the comic overstates the difficulty a little. Since animals are assemblies of proteins, aren't they by definition more complicated than any of their constituent parts examined in isolation?


Yes and no - it depends what level of granularity you're using, and, if you're prepared to accept statistical approximation rather than high precision, complex systems can be closely approximated by very simple ones. No-one worries about the individual quarks when they're studying protein folding, and, generally, when studying an animal, you only care about what the proteins are used for, not how they work.

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Re: 1430: Proteins

Postby Eternal Density » Mon Oct 06, 2014 11:46 pm UTC

Kit. wrote:
Eternal Density wrote:And I also see death and pain and suffering and hurt, and I think "This is bad. Something is wrong. The world contains both good and evil. Why is it like this and what can be done about it?"

If the universe was designed and made, right and wrong matter. Everything you do matters. Everything you say matters. Everything you think matters. Everything you love matters.

Actually, suffering is the main reason to doubt that what matters to me also matters to your imaginary person.
What matters to you, and why?
Garnasha wrote:In short, I object to any decisions made based on the existence of God if that existence is at all necessary to justify such decisions.

In other words, you want to live your life your own way and don't want anyone else telling you what's right and wrong, is that a fair assessment? You like having your own morality that you've decided works for you.
Garnasha wrote:By the way, while evolutionary ethics is not a system of ethics, it is an explanation why all systems of ethics have similar core rules without invoking a single entity imposing those core rules. Groups without those core rules can't cooperate as effectively and die out eventually. By now, it's most likely inherent to the human blueprint just like a preference for nourishing food and an aversion to pain are.
A problem with that line of thought is that the value of human life is dependant upon its usefulness to the group. If someone is not of use to the group, the most optimal or 'right' thing to do would be to kill that person.
rmsgrey wrote:
Eternal Density wrote:When I look at the world, I see people with personalities and think "these came from a greater person with greater personality". I see communication and think "this came from someone with greater communication". I see creativity and think "this came from someone with amazing creativity". I see beauty and think "this came from someone who values beauty".

And where did this greater person's greater personality come from? Is it turtles all the way up? Or do you reach a level where the existence of a personality doesn't require something to have created it?

There's something depressing about a worldview that insists that no human can create anything greater than themself.
While I see our attempts at creating something greater that ourselves as a colossal waste of time and resources. (The 'where it came from' thing I already discussed in an earlier post.)
Kit. wrote:This is a false dichotomy. Or at least I see nothing that would prevent an infinite being from creating infinite universes unobservable by men.
Sure, but why would an infinite being need to create infinite useless lifeless universes when he can just skip to creating the one that works? My point wasn't so much the dichotomy as "there's infinite *something* outside our universe, so why not an infinite being?" Or said another way "Everything in our universe has a cause, so something had to be uncaused, so why not an uncaused person to intentionally design our universe, rather that a whole lot of other equally uncaused universes?"

Garnasha wrote:Also, science doesn't judge, but it does tell you what will make people happier/safer and will reduce their suffering. Since it's easy to recognize such results as "good", science does in fact tell us what actions will result in good, and therefore can be considered good actions. Science also gives us tools to reach what we want, so yes, if someone wants to do evil, science can make that evil greater. It does not, however, excuse such evil, and if saying "you deliberately caused suffering" isn't a condemnation, I don't know what is.
Why is suffering evil? Why is happiness and safety good? If the earth and everything on it was destroyed (perhaps by one of the various What-If methods :P), then what's that to the rest of the universe? If we were all dead, there'd be no more human suffering. Sure, there'd be no more happiness either but how is human happiness a benefit to the universe at large?

CigarDoug wrote: I would argue that since God is NOT human, we have no moral basis to attach our own human morals to him
Also, since God is God, he has the right to attach his morals to us. Which is why a lot of people really don't like the idea of God.
orthogon wrote:: there is no correct plural of Lego because Lego is an uncountable noun.
Indeed.
Hmm, maybe I should have said "the fight over the word 'literally'" Just take this and scale it up to the universe.
Garnasha wrote:happiness in this life is real. Suffering in this life is real. Reality doesn't depend on eternity to be true, or have value. Nor does it depend on an outside observer. Nor does it depend on evolutionary ethics, those try to explain why we feel the way we do, not judge those feelings (evolutionary ethics isn't nor aspires to be a system of ethics).
Where did you get those ideas from?
You may think it's self evident, but many (such as some Bhuddists) would disagree.

As for Pascall's Wager, I'm not saying "You should agree with me because of the consequences if I'm right", I'm just saying that this is an important issue and it's in your best interest to be sure to investigate it carefully.

Garnasha wrote:Religion is too often an excuse to do horrible things, or a whip to coerce people to give up significant portions of their health, wealth or happiness.
I agree.
Garnasha wrote:It also severely hinders one's ability to form models of the world which let one make accurate predictions, either about what one will later observe or what the result of one's actions will be, and conversely, what actions would be necessary to achieve a desired result.
I'm not quite sure what you mean by 'religion' in this context, and I think it's important to be very clear in this statement. Are you just referring to belief that a deity exists? Or similarly that there's something supernatural, outside our observable universe and not bound by the laws of physics that we can test? Or do you mean something else?
I personally haven't observed any hindrance to the abilities that you've listed. My understanding of cause and effect and probability and action and reaction and how to model how the world will work seem to be as good as anyone else's. So I would have to disagree with your statement, if that's what you mean by it.
Not that your point isn't often valid, for instance among groups with capricious gods. (The Ancient Greeks took centuries to develop any sort of science because it was only the occasional philospher who claimed that every event had a natural cause. Thales, Parmenides, and Aristotle were all in different centuries.)
Garnasha wrote:People who try to refine our collective world-view to be better able to make such predictions are called scientists.
Yes.
Garnasha wrote:The idea that religion distorts such a functionally predictive (scientific) worldview is based on the fact that being a scientist negatively correlates with being religious, with a stronger negative correlation as one gets closer to the "top".
There is no such fact.
What metrics are you using for "being religious"? Number of deities? In that case I guess Christians aren't very religious on your scale, which I suppose does fit what you're saying after all.
Garnasha wrote:This scientific world-view has proven itself plenty of times: modern sanitation, chemistry, computers, GPS, antibiotics, structural engineering, agriculture, etc.;
The way you've put those sentences together makes it look like the obvious conclusion is "we only have all these things because of anti-religious people". That only follows if your false dichotomy was valid. But atheism is not a requirement for the formation and application of the scientific method. You're stealing science as an exclusive part of your worldview, but it's not. And really, if you started out with the base assumption "the universe is an accident with no intention behind it" then how do you get from there to "there must be laws which govern how the universe works and we should be able to discover them and use them to predict things"?
Garnasha wrote:the scientific world-view has caused enough good in the world (where good is the increase of happiness(distinct from pleasure) and the decrease of suffering) with no end in sight that by now, contributing to it can itself be considered a minor good,
First, saying "science has increased happiness, so contributing to science increases happiness" is a tautology. Second, by referring to "the scientific world-view" you're sneaking in the claim "we can only have nice things from science if we're unreligious" (where you haven't really clearly defined what you mean be religion) which history shows is quite bogus.
Garnasha wrote:and trying to keep others (children) away from it as if it were a competing religion a major evil.
You've switched back to using loaded moral language like "evil" rather than your previous definition. So what you really said is "keeping people away from science (which increases happiness) reduces happiness" which is again a tautology. And I guess you're making a claim that "religious people" see science as "a competing religion". Well you're the one who just said that there's a negative correletion between being a scientist and being religous. You're the one claiming that science and religion are opposed. Maybe it's not science that they're keeping children away from, maybe it's just your idea that science and religion are opposed that they're keeping them away from.
Garnasha wrote:We have no good evidence for or against the existence of hobbits
Many paleontoligists would disagree with you (though it's the usual thing of finding human remains and claiming they're a new species because finding humans is boring).
Garnasha wrote:Therefore, if science tells us that good is achieved through action A, but religion tells us good is achieved through action B, and those conflict, one should follow the course of action suggested by the world-view with the best track record for keeping its promises in a way we can confirm while we can still act on it, rather than a world-view without anything for it except "we can't conclusively prove it's wrong".
Who gets to decide what happiness is and who is human? Is the most important field of science that of accurately modelling future human happiness?
Can we accurately judge the potential happiness a person will cause before they are even born? A lot of people seem to think so. My grandmother's mother decided that having another baby would make her unhappy, so she attempted to prevent this reduction in happiness. She failed in her attempts at preventing what you would call 'evil', and my grandmother was born. Should we look back at history and judge how much happiness or suffering has eventuated as a result of that failure? Can we accurately model how much happiness and suffering would have eventuated if she'd succeeded? Can we then compare those numbers to evaluate whether her action was good or evil (causing a net positive or negative happines/suffering balance)? Or should we wait a few more generations?

The only way to know for sure would be to accurately simulate the entire probability space of future human happiness and suffering, find the one with the highest happiness quotient, and make sure that everyone does the right thing to cause that future to eventuate. Anything else would be 'evil' according to you.
Really, if good and evil are determined by the amount of resultant human happiness and suffering, then we have absolutely no clue whether our actions are good or evil. Our actions today may only affect a few people, but after years a lot more people will be affected, and we have no way to account for that.

If morals are purely scientific, then we'd better find a way of testing whether a fetus will become the next mass murderer. Or maybe not, maybe the world would be a happier place with all those people dead. How do we know?

Here's something interesting:
http://en.wikipedia.org/wiki/Happiness_ ... d_children
Gilberts writes that prospective parents know that raising children will be laborious, yet they believe it will make them very happy. In fact, studies show it does just the opposite, and that levels of parental happiness don't rise until kids leave for college ... Still, if happiness is thought of in terms of a broader life narrative, rather than just specific moments of teething, diaper changing and petty-cash culling, it's pretty clear that kids do add value ... married couples test happier, but it's unclear if that's because happy people marry ... "We are the product of our genes and our societies," says Gilbert. Traditions will trump the empirical evidence that money and kids won't make us happy.
Looks like everyone who has children is going against your suggested course of action.
Flumble wrote:That's silly. Lots of researchers write hardware (in VHDL/Verilog) nowadays, why don't they mention it to the public?
Vital HotDog Language?
(Sorry, that's an OTTer in-joke.)
Mikeski wrote: From the hardware side of the fence, I could see software folks not saying "make software" because "make" is already a technical term for anyone who codes in a UNIX environment. And why overload an operator unnecessarily?
I don't make software, because I'm programming in python and javascript :P
Izawwlgood wrote:Z ) Just... stahp. It is such a shame every time biology comes, someone wants to chime in with theology.
...oops.
Carl Wieland was in town for the weekend so...
*scrolls up and sees how long and rambling this post is*
*cringes*
Meh, I wasted half my morning writing it so I might as well post it.

-Definitely Not Summer Glau

[edit] So this went up today. A couple days late, but oh well. http://creation.com/on-theorigin-of-universes
Last edited by Eternal Density on Thu Oct 09, 2014 9:22 am UTC, edited 1 time in total.
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Re: 1430: Proteins

Postby gmalivuk » Tue Oct 07, 2014 12:31 am UTC

Great. Can we take that closing to mean you're now done posting your long-winded ramblings in this thread about science and philosophy that have nothing to do with the comic?
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Re: 1430: Proteins

Postby Rombobjörn » Tue Oct 07, 2014 12:33 am UTC

Farabor wrote:Anyone up to explaining the alt text to those of us who are biology and/or origami impaired?

I think I can do better than this.

The two ends of the long chain of amino acids that a protein is made of are called the N-terminus and the C-terminus. The N-terminus is built first and the C-terminus last. I guess that's why the C-terminus is also called the C-terminal tail.

Proteins aren't rigid objects. They have a shape, but the shape is flexible. Electrical forces from nearby molecules cause the atoms in the protein to move around a bit. This causes other atoms in the protein to move, which in turn affects yet other atoms, so that the whole protein changes its shape a little. A protein's function is very dependent on its shape, so these shape changes can make a protein much more or much less active. Enzymes (which are proteins) are often sensitive to the presence of one or several specific molecules, called activators and inhibitors, which bind to specific sites on the enzyme and cause the active site elsewhere on the enzyme to change and become more active or less active. The active site is the part of the enzyme that carries out the enzyme's function of converting a certain other molecule. The molecule that gets converted is called the substrate. Thus the concentrations of activators and inhibitors control how fast the substrate gets converted. Another more permanent way of activating or inhibiting an enzyme is to attach an additional group of atoms so that it becomes a part of the protein molecule. The group may for example be a phosphate group. Attaching a phosphate group is called "phosphorylation", which Kit mentioned. By becoming a part of the protein the phosphate group is held in place, so its effect becomes more permanent than that of an ordinary activator or inhibitor.

This unspecified protein, which is probably an enzyme and may or may not be the endopeptidase that Eternal Density mentioned, has a part that is called the "binding tunnel". It's called "binding" because it binds a certain other molecule. It probably contains the enzyme's active site. (In that endopeptidase it does.) The protein is arranged such that when something "tugs" the C-terminal tail, perhaps by phosphorylation, then the shape of the binding tunnel changes. The tunnel may for example close ("squeeze") so that there isn't room for the substrate, which would prevent the enzyme from working (that is, inhibit it). The title text compares this shape change to that of an origami animal that moves in some way when one tugs its tail.

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Re: 1430: Proteins

Postby Pfhorrest » Tue Oct 07, 2014 12:36 am UTC

Eternal Density wrote:Why is suffering evil? Why is happiness and safety good?

Even presuming that an intelligent creator of the universe and humanity existed and wanted or even commanded us to do or not do certain things, why would that make those things good or evil? (Note that if the answer is "he will reward/punish you", your position collapses to the same hedonistic one you're questioning.)
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Re: 1430: Proteins

Postby helo darqness » Tue Oct 07, 2014 2:46 am UTC

You guys should see this. It's free on Netflix.

Image

It's about the scientific, mathematical, biological and practical applications for origami. It does touch an the artistic aspect of it too, but origami is everywhere, from how to get an airbag in a steering wheel to folding antennas on satellites.

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Re: 1430: Proteins

Postby addams » Tue Oct 07, 2014 3:58 am UTC

yellow103 wrote:Image

Alt: "Check it out--when I tug the C-terminal tail, the binding tunnel squeezes!"

To me, This is one of the all time Greats!
It all makes perfect sense. It's funny.

Once upon a time, not so long ago, Human beings, not much different from you and me, figured out Protein Production.

Then they told me.
I believed them.

I looked away, when I looked back the Poor, Poor University Students had to know
all three part of a ribosome and what kind of a charge holds it together.

Stop Science!
And; Stop it Now!

Think of the Children.
Life is, just, an exchange of electrons; It is up to us to give it meaning.

We are all in The Gutter.
Some of us see The Gutter.
Some of us see The Stars.
by mr. Oscar Wilde.

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Those that do not Know; Don't tell them.
They do terrible things to people that Tell Them.

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Re: 1430: Proteins

Postby orthogon » Tue Oct 07, 2014 8:48 am UTC

gmalivuk wrote:Great. Can we take that closing to mean you're now done posting your long-winded ramblings in this thread about science and philosophy that have nothing to do with the comic?

Yeah, let's get back to talking about Big Band Jazz!
OK, sorry, I mean proteins. I propose a vote of thanks to Rombobjörn for that explanation.
xtifr wrote:... and orthogon merely sounds undecided.

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Re: 1430: Proteins

Postby JustDoug » Tue Oct 07, 2014 9:42 am UTC

CigarDoug wrote:Animals have either no moral code or a much better and complete moral code than us: They eat to survive; they don't kill something except to eat it or to defend themselves and their young; they don't spoil their own nests; they exist in harmony with the rest of nature.


I'll leave the balance already addressed by others, but this... You obviously have not heard about wars between troops of chimps and their pile-on murders of outsiders, or what happens to the cubs in a pride of lions when a new male(s) install(s) himself/themselves, often after killing the previous one and many other familair behaviorial quirks that we human all know and love so much. As for not killing something for fun... Heck, watch a domestic cat or troop of bored babboons (or chimps again; they have a rep for being particularly viciously murderous at times).

You'll find that people in the know about animal behvior don't buy that nature film morality or 'Inherent naural nobility of nature' at all, and know that critters can often be just as mean, cruel and vicious as us. The animals just don't boast about it afterwards. Anything resembling animals having a morality is something imposed by us humans anthropomorphaziing them and about as real as the Tooth Fairy

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Re: 1430: Proteins

Postby addams » Tue Oct 07, 2014 10:18 am UTC

Yep. What you wrote.

Except; Animals, the bastards, boast about it afterwards.
Have you never heard a Coyote bark?
Life is, just, an exchange of electrons; It is up to us to give it meaning.

We are all in The Gutter.
Some of us see The Gutter.
Some of us see The Stars.
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Those that do not Know; Don't tell them.
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Re: 1430: Proteins

Postby cellocgw » Tue Oct 07, 2014 12:13 pm UTC

addams wrote:Yep. What you wrote.

Except; Animals, the bastards, boast about it afterwards.
Have you never heard a Coyote bark?


Dunno, but I've seen tree1 bark in the forest and if there's there's no coyote nearby to see it, is it really there? :oops:



[1] Treeish!
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Re: 1430: Proteins

Postby Kit. » Tue Oct 07, 2014 1:08 pm UTC

Eternal Density wrote:What matters to you, and why?

The neural wiring of my brain is what determines things that matter to me. In particular, ventral tegmental area (VTA), a group of neurons in midbrain, with its system of neural links to and from other areas of the brain, is currently believed to be most closely associated with goal-setting in animals.

These neural links are long, which means that they cannot grow in response to the current "goal-setting" stimuli, and need to be pre-wired, i.e. their wiring needs to be pre-encoded in the animal's DNA. The exact molecular mechanisms of how axons find their path where to grow (axon guidance) are understood well enough to be not a mystery anymore. In particular, they involve different receptor proteins, which change the direction of the axon's growth cone depending on how their tails (or any sensitive parts protruding on the extra-cellular side of the growth cone's cell membrane) are tugged by the chemistry of the local environment that the growth cone just reached.

As the wiring plan is encoded in DNA, it is influenced by such factors as random combinatorial and mutational disturbances, genetic drift and natural selection. Which makes my innate goal-setting mechanism a good but imprecise indicator of what a locally optimal goal-setting plan would be for human genes surviving in human's (pre-historical) ecological niche.

But it also means that my innate goal-setting plan is unlikely to be exactly the same as your innate goal-setting plan (even if you were the same sex as me). Although there is a vast set of goals that we would have in common.

Eternal Density wrote:
Garnasha wrote:In short, I object to any decisions made based on the existence of God if that existence is at all necessary to justify such decisions.

In other words, you want to live your life your own way and don't want anyone else telling you what's right and wrong, is that a fair assessment?

No, it doesn't follow.

Eternal Density wrote:A problem with that line of thought is that the value of human life is dependant upon its usefulness to the group. If someone is not of use to the group, the most optimal or 'right' thing to do would be to kill that person.

No, because evolution doesn't care what is "the most optimal" thing to do. Neither it cares about ultimate logicality. It just selects those slightly-more-optimal goals human genes have found (and doesn't select all those slightly-or-even-vastly-more-optimal goals human genes have missed), even if such goals are not logical.

Eternal Density wrote:Sure, but why would an infinite being need to create infinite useless lifeless universes when he can just skip to creating the one that works?

Why would an infinite being need to agree with you on what works?

Eternal Density wrote:Or said another way "Everything in our universe has a cause,

Wrong.

Causality is just a quirk in our brains' pre-wiring that made us more fitting on average by allowing us to faster detect immediate dangers and to develop simple tools. There is no notion of causality in the physics of our world since at least Newton's.

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Re: 1430: Proteins

Postby Garnasha » Tue Oct 07, 2014 3:20 pm UTC

Eternal Density wrote:huge wall of text
Please, repost this in a separate thread and invite everyone discussing it here to discuss it there (final post here or PM all participants). I'm already sorry for rising to the bait in this thread. Actually, could a moderator please perform some kind of thread split?

As for proteins: Does anyone know if there's any projects similar to FoldIt around, or do they have a monopoly on folding games?

Btw. Anyone who has not yet played FoldIt: I eventually got tired of it because it felt too clunky, but it is really a great game to familiarize yourself with the details of how proteins fold, and when I followed a course on molecular biology, it offered a huge amount of intuition on the subject.

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Re: 1430: Proteins

Postby Mokele » Tue Oct 07, 2014 4:35 pm UTC

CigarDoug wrote:Animals have either no moral code or a much better and complete moral code than us: They eat to survive; they don't kill something except to eat it or to defend themselves and their young; they don't spoil their own nests; they exist in harmony with the rest of nature.


I've personally seen two small crocodilians (less than 1 kg each) kill and *shred* over 20 lbs of (unfortunately very expensive) koi fish in a single night. They got fed plenty in their home cage (which we didn't know they could escape from), but they still hopped the barrier and basically killed everything in sight.

This is also the same taxonomic group for whom a major predator of young individuals is adult individuals. Much as I love them, they're not exactly beacons of enlightenment.
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Re: 1430: Proteins

Postby orthogon » Tue Oct 07, 2014 4:37 pm UTC

Meanwhile, Basie plays his eponymous ending more conventionally here at 3:12, although the unaccompanied flute solo/cadenza makes it harder to hear how it fits with the underlying beats (the flute part is in time though, keep tapping your foot through it and you'll hear it). There's an almost perfect example here at 4:32, except it's a false ending. The search for a truly platonic example goes on...
xtifr wrote:... and orthogon merely sounds undecided.

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Re: 1430: Proteins

Postby gmalivuk » Tue Oct 07, 2014 4:54 pm UTC

JustDoug wrote:
CigarDoug wrote:Animals have either no moral code or a much better and complete moral code than us: They eat to survive; they don't kill something except to eat it or to defend themselves and their young; they don't spoil their own nests; they exist in harmony with the rest of nature.


I'll leave the balance already addressed by others, but this... You obviously have not heard about wars between troops of chimps and their pile-on murders of outsiders, or what happens to the cubs in a pride of lions when a new male(s) install(s) himself/themselves, often after killing the previous one and many other familair behaviorial quirks that we human all know and love so much. As for not killing something for fun... Heck, watch a domestic cat or troop of bored babboons (or chimps again; they have a rep for being particularly viciously murderous at times).

You'll find that people in the know about animal behvior don't buy that nature film morality or 'Inherent naural nobility of nature' at all, and know that critters can often be just as mean, cruel and vicious as us. The animals just don't boast about it afterwards. Anything resembling animals having a morality is something imposed by us humans anthropomorphaziing them and about as real as the Tooth Fairy

We only call nature "harmonious" because we don't care as much about animals dying horribly at the hands and teeth and claws of other animals as we do when people are involved.

By the numbers, human beings are some of the most peaceful animals on the planet. No other primate species could live in close proximity to as many others of its own kind with as *little* violence as we have in most cities.
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Re: 1430: Proteins

Postby Izawwlgood » Tue Oct 07, 2014 5:11 pm UTC

And 'harmoniously living with nature' in 'simpler times' really just means 'high infant mortality rates and dying to infection when you cut yourself while preparing food' and 'not sleeping soundly at night because the wolves are circling'.
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Re: 1430: Proteins

Postby Tyndmyr » Tue Oct 07, 2014 5:59 pm UTC

Mokele wrote:
CigarDoug wrote:Animals have either no moral code or a much better and complete moral code than us: They eat to survive; they don't kill something except to eat it or to defend themselves and their young; they don't spoil their own nests; they exist in harmony with the rest of nature.


I've personally seen two small crocodilians (less than 1 kg each) kill and *shred* over 20 lbs of (unfortunately very expensive) koi fish in a single night. They got fed plenty in their home cage (which we didn't know they could escape from), but they still hopped the barrier and basically killed everything in sight.

This is also the same taxonomic group for whom a major predator of young individuals is adult individuals. Much as I love them, they're not exactly beacons of enlightenment.


Yeah, anyone who believes animals only kill to survive is...wildly inexperienced in the ways of animals. Hell, plenty of them kill purely for entertainment, or will kill their own.

So, pretty much just like humans, then.

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Re: 1430: Proteins

Postby Morgan Wick » Tue Oct 07, 2014 6:31 pm UTC

Eternal Density wrote:
Garnasha wrote:In short, I object to any decisions made based on the existence of God if that existence is at all necessary to justify such decisions.

In other words, you want to live your life your own way and don't want anyone else telling you what's right and wrong, is that a fair assessment? You like having your own morality that you've decided works for you.

I don't have a problem with someone telling me what's right or wrong, so long as they can explain to me why it's right or wrong. Unfortunately, a lot of Christians take the inscrutability of their God as a point of pride.
Garnasha wrote:By the way, while evolutionary ethics is not a system of ethics, it is an explanation why all systems of ethics have similar core rules without invoking a single entity imposing those core rules. Groups without those core rules can't cooperate as effectively and die out eventually. By now, it's most likely inherent to the human blueprint just like a preference for nourishing food and an aversion to pain are.
A problem with that line of thought is that the value of human life is dependant upon its usefulness to the group. If someone is not of use to the group, the most optimal or 'right' thing to do would be to kill that person.

The problem then is that the group is not always the best judge of what is best for itself. Would it be right if someone did something incredibly important to the group but out of anyone's notice, and got killed because his perceived value to the group was nil? Killing someone is irreversible, so it is generally safer not to kill someone than to kill them just in case they might have some value at a later point (which could be as simple as drawing from their knowledge), unless they have irreversibly lost all their value (i.e. they're irreversibly brain-dead). Despite this, it is worth noting that many cultures in history precisely did kill people who had outlived their perceived usefulness (indeed, it could be argued that suicide is a result of people perceiving their own usefulness to the group to be nil), that many tenets of our morality do hold that some people are more valuable than others (e.g. "women and children first"), and that letting people who might not even be brain-dead but just have a terminal disease die is becoming an increasingly popular option, possibly even as the "moral" thing to do not merely for the group but even for the person themselves.
Garnasha wrote:Also, science doesn't judge, but it does tell you what will make people happier/safer and will reduce their suffering. Since it's easy to recognize such results as "good", science does in fact tell us what actions will result in good, and therefore can be considered good actions. Science also gives us tools to reach what we want, so yes, if someone wants to do evil, science can make that evil greater. It does not, however, excuse such evil, and if saying "you deliberately caused suffering" isn't a condemnation, I don't know what is.
Why is suffering evil? Why is happiness and safety good? If the earth and everything on it was destroyed (perhaps by one of the various What-If methods :P), then what's that to the rest of the universe? If we were all dead, there'd be no more human suffering. Sure, there'd be no more happiness either but how is human happiness a benefit to the universe at large?

What value does the universe at large have to us if we're not in it?

CigarDoug wrote: I would argue that since God is NOT human, we have no moral basis to attach our own human morals to him
Also, since God is God, he has the right to attach his morals to us. Which is why a lot of people really don't like the idea of God.

The question is, how do you know that God's morals are what people say they are? Especially when people can disagree on what the same God's morals are.
Garnasha wrote:Therefore, if science tells us that good is achieved through action A, but religion tells us good is achieved through action B, and those conflict, one should follow the course of action suggested by the world-view with the best track record for keeping its promises in a way we can confirm while we can still act on it, rather than a world-view without anything for it except "we can't conclusively prove it's wrong".
Who gets to decide what happiness is and who is human? Is the most important field of science that of accurately modelling future human happiness?
Can we accurately judge the potential happiness a person will cause before they are even born? A lot of people seem to think so. My grandmother's mother decided that having another baby would make her unhappy, so she attempted to prevent this reduction in happiness. She failed in her attempts at preventing what you would call 'evil', and my grandmother was born. Should we look back at history and judge how much happiness or suffering has eventuated as a result of that failure? Can we accurately model how much happiness and suffering would have eventuated if she'd succeeded? Can we then compare those numbers to evaluate whether her action was good or evil (causing a net positive or negative happines/suffering balance)? Or should we wait a few more generations?

The only way to know for sure would be to accurately simulate the entire probability space of future human happiness and suffering, find the one with the highest happiness quotient, and make sure that everyone does the right thing to cause that future to eventuate. Anything else would be 'evil' according to you.

We can be reasonably sure that the one with the highest happiness quotient will not involve forcing people to bring it about, making the entire notion a contradiction in terms.
If morals are purely scientific, then we'd better find a way of testing whether a fetus will become the next mass murderer.
Unless science determines that upbringing is a major or the only factor in producing the next mass murderer. If so, it would be immoral not to raise said fetus to avoid the fate of becoming a mass murderer, assuming he's already been conceived. (Not to abort him: you have no way of knowing whether or not the traits that would have made him a mass murderer could have been turned towards an avenue that's productive to society, such as becoming a [INSERT OCCUPATION YOU WANT TO MAKE THIS A JOKE AT THE EXPENSE OF HERE].
Or maybe not, maybe the world would be a happier place with all those people dead.
You mean, if his name was Dexter Morgan?

Here's something interesting:
http://en.wikipedia.org/wiki/Happiness_ ... d_children
Gilberts writes that prospective parents know that raising children will be laborious, yet they believe it will make them very happy. In fact, studies show it does just the opposite, and that levels of parental happiness don't rise until kids leave for college ... Still, if happiness is thought of in terms of a broader life narrative, rather than just specific moments of teething, diaper changing and petty-cash culling, it's pretty clear that kids do add value ... married couples test happier, but it's unclear if that's because happy people marry ... "We are the product of our genes and our societies," says Gilbert. Traditions will trump the empirical evidence that money and kids won't make us happy.
Looks like everyone who has children is going against your suggested course of action.

And there's an awful lot of people that have decided they don't want to have children. On the other hand, if you adhere to the Dawkinsite Selfish Gene theory, you owe it to your genes to have children.

We're wired to have a lot of sex and produce substantially more children than the replacement level would warrant, partly because for much of human history a lot of those kids would die. Part of the reason religious people don't like contraception, I suspect, is because they see it as human interference in God's plan. When you have sex, it is because God wants you to produce a child, and interfering in that process - or performing it in a context they don't approve of having kids in, i.e. outside of marriage - is a sin. A scientific person, on the other hand, sees people having lots of casual sex as people following their instincts and contraception as a way to avoid having the multitudes of children those instincts are intended* to produce but that are no longer necessary or desirable, and sees the efforts of religious people to deny those people their freely willed pursuit of pleasure - which may not be happiness but is a form of happiness - or to force them to endure the unhappiness of having unwanted children and possibly an unwanted marriage as immoral.

(*No, I'm not using "intended" to imply the existence of some sort of intelligent designer who "intends" anything. I'm anthropomorphizing nature and evolution to make a point intelligible in English to a species prone to anthropomorphize everything.)

Relevant. Also relevant. Also also relevant.

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Re: 1430: Proteins

Postby EvanED » Tue Oct 07, 2014 7:23 pm UTC

Someone may someday find a harder one.

Hah, at least it's decidable. Try working on problems that are provably impossible to solve completely correctly and where even approximations are usually pretty poor (at best) or computationally infeasible. :-)

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Re: 1430: Proteins

Postby Izawwlgood » Tue Oct 07, 2014 7:24 pm UTC

EvanED wrote:
Someone may someday find a harder one.

Hah, at least it's decidable. Try working on problems that are provably impossible to solve completely correctly and where even approximations are usually pretty poor (at best) or computationally infeasible. :-)
This is exactly what protein folding was 20 years ago :)
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Re: 1430: Proteins

Postby EvanED » Tue Oct 07, 2014 7:36 pm UTC

Izawwlgood wrote:
EvanED wrote:
Someone may someday find a harder one.

Hah, at least it's decidable. Try working on problems that are provably impossible to solve completely correctly and where even approximations are usually pretty poor (at best) or computationally infeasible. :-)
This is exactly what protein folding was 20 years ago :)
Undecidable? Possibly, but I'd be surprised...

(Or maybe it's some stochastic process in reality, so in some sense the usual decidable/undecidable division doesn't make much sense)

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Re: 1430: Proteins

Postby Kit. » Tue Oct 07, 2014 8:17 pm UTC

Morgan Wick wrote:On the other hand, if you adhere to the Dawkinsite Selfish Gene theory, you owe it to your genes to have children.

Only if you want to make a cult out of it.

Your genes care no more about you having children than white color cares about a polar bear having white fur.
Last edited by Kit. on Tue Oct 07, 2014 10:30 pm UTC, edited 1 time in total.

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Re: 1430: Proteins

Postby Izawwlgood » Tue Oct 07, 2014 8:42 pm UTC

EvanED wrote:
Izawwlgood wrote:
EvanED wrote:
Someone may someday find a harder one.

Hah, at least it's decidable. Try working on problems that are provably impossible to solve completely correctly and where even approximations are usually pretty poor (at best) or computationally infeasible. :-)
This is exactly what protein folding was 20 years ago :)
Undecidable? Possibly, but I'd be surprised...

(Or maybe it's some stochastic process in reality, so in some sense the usual decidable/undecidable division doesn't make much sense)
Yeah, fair, I was focusing more on the 'poor approximations' and 'computationally infeasible' part.
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Re: 1430: Proteins

Postby ThemePark » Tue Oct 07, 2014 11:29 pm UTC

Heimhenge wrote:
Randall wrote: I make software that predicts how proteins will fold. [emphasis mine]

Since Randall's obviously done a lot of programming, I found that choice of word curious. I know a lot of programmers, and I've heard most say they "write" software, some say they "code" software, some say they "create" software, a few say they "compose" software ... but I swear I've rarely (if ever) heard a programmer say they "make" software. Maybe the company they work for "makes" software, or maybe that's what a non-programmer CEO might say.

Do any of the programmers on this forum ever say they "make" software? Maybe this is just a new turn of jargon?

Mikeski has already pointed the existence of the make software, used to compile your code into a piece of software, as I was about to. But mostly we don't work on something alone but as a part of a team, thus we only have a small part in a piece of software. And we only code, we don't necessarily write the GUI or the text or anything else, hence why we say write or code. But when you say make or create as in Randall's case, it means that he makes the software from start to finish all by himself, GUI, code, database, texts and all that.
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Re: 1430: Proteins

Postby PinkShinyRose » Wed Oct 08, 2014 10:15 pm UTC

EvanED wrote:
Izawwlgood wrote:
EvanED wrote:
Someone may someday find a harder one.

Hah, at least it's decidable. Try working on problems that are provably impossible to solve completely correctly and where even approximations are usually pretty poor (at best) or computationally infeasible. :-)
This is exactly what protein folding was 20 years ago :)
Undecidable? Possibly, but I'd be surprised...

(Or maybe it's some stochastic process in reality, so in some sense the usual decidable/undecidable division doesn't make much sense)

As far as biologists are concerned it's most probably stochastic (the molecular interactions in a cell are sufficiently complex for that). For physicists it may still effectively be stochastic as these interactions may depend on quantum collapse, I don't know enough about quantum physics to make a decent guess at this though.
ThemePark wrote:But when you say make or create as in Randall's case, it means that he makes the software from start to finish all by himself, GUI, code, database, texts and all that.

Can you use libraries in this case? If yes, isn't this how lots of tiny but really useful/fun programs start out until the initial creator gets bored? I'm thinking of dwarf fortress, minecraft, anki and liero.

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Re: 1430: Proteins

Postby addams » Thu Oct 09, 2014 5:08 am UTC

Kit. wrote:
Morgan Wick wrote:On the other hand, if you adhere to the Dawkinsite Selfish Gene theory, you owe it to your genes to have children.

Only if you want to make a cult out of it.

Your genes care no more about you having children than white color cares about a polar bear having white fur.

That's true.
That's very hard for people to understand.

It is so elegantly said.
I'd like you to explain it, more.
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Re: 1430: Proteins

Postby Eternal Density » Thu Oct 09, 2014 9:30 am UTC

PinkShinyRose wrote:Can you use libraries in this case? If yes, isn't this how lots of tiny but really useful/fun programs start out until the initial creator gets bored? I'm thinking of dwarf fortress, minecraft, anki and liero.
(Emphasis added.)
What are you talking about? Dwarf Fortress is still in active development by the original creator!

ETA actually, a much better example would be Sandcastle Builder.
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Re: 1430: Proteins

Postby addams » Fri Oct 10, 2014 3:48 pm UTC

orthogon wrote:
addams wrote:
orthogon wrote:
Znirk wrote:
Garnasha wrote:Personally though, although I don't think it's a correct idea, I like the idea of a Grand Architect (that is, design once, add Big Band and leave alone)

The universe as a 1930s dance hall. What's not to like? :)
(sorry ...)

And Count Basie as the creator of the Universe... Which means we also know how it's going to end


Addams.

I'm 99% sure you would know the Basie Ending if you heard it.
Check out this video...
Or this one ...
Really you need to hear a Big Band (ideally Basie's own band) playing it, but it might take me a while to find an example; who knows, I wouldn't be surprised if Basie never actually played it!

Edit: Here at 54:21, although the timing is different to the "classic" ending, with the penultimate note on "3" instead of pushed on the "and" of 2.

So nice.
Thank you, for the links.
I get it, now.

That's a weird way to end The Universe.
The Whimper was weird, too.
Dr. Barnett ended it in Bells.

As long as it has an End, I'm good.
The human mind needs a Beginning, a Middle and an End.

Now! Back to the Comic.
Comic! Not, Cosmic!
Rombobjörn wrote:
Farabor wrote:Anyone up to explaining the alt text to those of us who are biology and/or origami impaired?

I think I can do better than this.

The two ends of the long chain of amino acids that a protein is made of are called the N-terminus and the C-terminus. The N-terminus is built first and the C-terminus last. I guess that's why the C-terminus is also called the C-terminal tail.

Proteins aren't rigid objects. They have a shape, but the shape is flexible. Electrical forces from nearby molecules cause the atoms in the protein to move around a bit. This causes other atoms in the protein to move, which in turn affects yet other atoms, so that the whole protein changes its shape a little. A protein's function is very dependent on its shape, so these shape changes can make a protein much more or much less active. Enzymes (which are proteins) are often sensitive to the presence of one or several specific molecules, called activators and inhibitors, which bind to specific sites on the enzyme and cause the active site elsewhere on the enzyme to change and become more active or less active. The active site is the part of the enzyme that carries out the enzyme's function of converting a certain other molecule. The molecule that gets converted is called the substrate. Thus the concentrations of activators and inhibitors control how fast the substrate gets converted. Another more permanent way of activating or inhibiting an enzyme is to attach an additional group of atoms so that it becomes a part of the protein molecule. The group may for example be a phosphate group. Attaching a phosphate group is called "phosphorylation", which Kit mentioned. By becoming a part of the protein the phosphate group is held in place, so its effect becomes more permanent than that of an ordinary activator or inhibitor.

This unspecified protein, which is probably an enzyme and may or may not be the endopeptidase that Eternal Density mentioned, has a part that is called the "binding tunnel". It's called "binding" because it binds a certain other molecule. It probably contains the enzyme's active site. (In that endopeptidase it does.) The protein is arranged such that when something "tugs" the C-terminal tail, perhaps by phosphorylation, then the shape of the binding tunnel changes. The tunnel may for example close ("squeeze") so that there isn't room for the substrate, which would prevent the enzyme from working (that is, inhibit it). The title text compares this shape change to that of an origami animal that moves in some way when one tugs its tail.

Beautiful and simply written.
It's funny. Right?

On several levels, it's funny.
I teeter on the edge of a Weird Godwin.

Who has the author been hanging out with?

He is a programer.
He has a background in Physics.

How did he learn about Proteins?
Language that uses the words terminal, tunnel and enzymes in this way......?

Who has the authors ear and imagination?
Sometimes 'Small things are Not for Small minds.'
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Some of us see The Gutter.
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Re: 1430: Proteins

Postby gmalivuk » Fri Oct 10, 2014 9:18 pm UTC

orthogon wrote:Meanwhile, Basie plays his eponymous ending more conventionally here at 3:12, although the unaccompanied flute solo/cadenza makes it harder to hear how it fits with the underlying beats (the flute part is in time though, keep tapping your foot through it and you'll hear it). There's an almost perfect example here at 4:32, except it's a false ending. The search for a truly platonic example goes on...

You know you can add times to youtube links, right? Just stick #t=3m10s at the end of the url, for example.

here at 3:12

here at 4:32
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Re: 1430: "Proteins"

Postby orthogon » Fri Oct 10, 2014 9:41 pm UTC

No, I... Wow. That rocks.
xtifr wrote:... and orthogon merely sounds undecided.

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Re: 1430: "Proteins"

Postby addams » Sat Oct 11, 2014 3:41 pm UTC

Really?
Testing the System with an unrelated U-Tube.
http://www.youtube.com/watch?v=cd2jXsmSaKc#t=1m11sec

It Works!
maybe.
Life is, just, an exchange of electrons; It is up to us to give it meaning.

We are all in The Gutter.
Some of us see The Gutter.
Some of us see The Stars.
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Those that want to Know; Know.
Those that do not Know; Don't tell them.
They do terrible things to people that Tell Them.


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