1430: "Proteins"

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1430: "Proteins"

Postby yellow103 » Mon Oct 06, 2014 4:22 am UTC

Image

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

just adding quotes to the title - Angua

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Re: 1430: Proteins

Postby rhomboidal » Mon Oct 06, 2014 5:01 am UTC

I'd love to enter a PhD program in "biolorigami."

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Re: 1430: Proteins

Postby Envelope Generator » Mon Oct 06, 2014 6:25 am UTC

She could just ask the turtles.
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Re: 1430: Proteins

Postby Krutonium » Mon Oct 06, 2014 6:27 am UTC

Do you guys do all of your Folding@Home?

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Re: 1430: Proteins

Postby Eternal Density » Mon Oct 06, 2014 6:36 am UTC

Here's a harder problem: designing life from scratch. If you want an even harder challenge, design and simulate a new set of laws of physics and physical constants for a new universe which can support intelligent life of your own design.

If you want an easier challenge, try to pretend that the existance of our universe and the intelligent life within it was a total fluke. (I've heard a lot of people are pretty good at this.)

Edit: relevant google search: native folds in polypeptide chains 1
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Re: 1430: Proteins

Postby Krutonium » Mon Oct 06, 2014 6:39 am UTC

Eternal Density wrote:Here's a harder problem: designing life from scratch. If you want an even harder challenge, design and simulate a new set of laws of physics and physical constants for a new universe which can support intelligent life of your own design.


So basically a massively advanced game of Life - I wonder how hard it would be to create such a inverse in practice - How close can our universes be?

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Re: 1430: Proteins

Postby hetas » Mon Oct 06, 2014 6:53 am UTC

Well you can all try it at FoldIt.

I haven't checked out the site myself but recently saw a snippet of documentary mentioning the project. Basically the idea is to use puzzle games to crowdsource protein folding. The documentary said the've had some good results.

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Re: 1430: Proteins

Postby Wooloomooloo » Mon Oct 06, 2014 7:27 am UTC

Eternal Density wrote:If you want an easier challenge, try to pretend that the existance of our universe and the intelligent life within it was a total fluke. (I've heard a lot of people are pretty good at this.)

Yeah, those folks are clearly delusional. Those who say that given a high enough number of universes we were a statistical inevitability, on the other hand...

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Re: 1430: Proteins

Postby _P_ » Mon Oct 06, 2014 7:41 am UTC

Tangentially related, but check out some of Robert Lang's work (you'll have to find it on your own, can't post links yet). So far as origami goes, one of the most influential and accessible sources of information on the mathematics behind it, plus many very nicely folded cranes.

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Re: 1430: Proteins

Postby Eternal Density » Mon Oct 06, 2014 7:42 am UTC

Wooloomooloo wrote:
Eternal Density wrote:If you want an easier challenge, try to pretend that the existance of our universe and the intelligent life within it was a total fluke. (I've heard a lot of people are pretty good at this.)

Yeah, those folks are clearly delusional. Those who say that given a high enough number of universes we were a statistical inevitability, on the other hand...
Yes, proposing some sufficiently large number of other inobservable universes is clearly good science and solves every problem perfectly.
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Re: 1430: Proteins

Postby Ehsanit » Mon Oct 06, 2014 8:39 am UTC

And then, once I know the beautiful intricacy of each kind of protein, I'll incinerate, masticate, and bathe them in acid.
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Re: 1430: Proteins

Postby azule » Mon Oct 06, 2014 8:51 am UTC

I predict a heavy chance of ... religion. Good luck with this thread, y'all!
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Re: 1430: Proteins

Postby Garnasha » Mon Oct 06, 2014 10:08 am UTC

Eternal Density wrote:
Wooloomooloo wrote:
Eternal Density wrote:If you want an easier challenge, try to pretend that the existance of our universe and the intelligent life within it was a total fluke. (I've heard a lot of people are pretty good at this.)

Yeah, those folks are clearly delusional. Those who say that given a high enough number of universes we were a statistical inevitability, on the other hand...
Yes, proposing some sufficiently large number of other inobservable universes is clearly good science and solves every problem perfectly.
Then again, it's no worse than supposing some sentient being designing the laws of physics and then either creating the Big Bang and guiding history to cause us, or creating a world with us in it and then planting fake evidence to the contrary. That, 1. Just shifts the problem to "what caused that being to exist?" and 2. Adds the additional problem "what are the chances of such a being deciding to create us?"

The answer, so far, as far as I'm concerned, is that we just don't know, probably can't know. We can guess, though, and we certainly can recognize outdated man-made theories for what they are. If something exists, nobody knows anything about it, and probably nobody can know anything about it. Except that it has either 1. no power over us or 2. no interest in us or 3. acts predictably enough to build a science called "physics" around its behaviour, since for all practical purposes it doesn't seem to be there. "Observations" by one person which can't be correlated by anyone who is interested don't count, since man's ability to fool himself is a matter of record, and religious experiences tend to have mild "symptoms" compared to psychoses or similar breakdowns of brain function. So yeah, can't know, but no reason at all to go thinking something must've created us.

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) keeping an eye on us and making sure if someone poses a question to the universe by running an experiment which should yield the answer, such an answer actually exists. In other words, making up the more obscure laws of physics as we discover them. Also, those laws must match all observations thus far. Right now, all the weirdness in quantum theory, as well as relativity needing a "dark matter/energy" patch would be evidence of him having painted himself into a corner, likely with some earlier contradiction, which he's hoping like buggery we won't figure out. Ooh, maybe it's a game, he gets a flawed (as in, having contradictory rules) universe to patch, we get to live in it, we win if we can figure out the fundamental flaw despite all his patches?


Foldit was sort of fun, but it's really hard to bend stuff in the direction you want if your interface is a 2D plane with one point of interaction (mouse pointer). I'm not sure how to fix that. Maybe a pair of power gloves? They kinda tanked first time they were tried... 25 years ago, with a clunky keyboard/controller thing stuck to them. Since then, technology has come a long way, and it should be possible to now make a glove which tracks position and bend/flex/rotation of every joint (wrist as one and three per finger, thumb included), and properly processes all that information.

However, plenty of people seem able to work with it, so maybe I'm just stupid/clumsy.

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Re: 1430: Proteins

Postby Farabor » Mon Oct 06, 2014 10:43 am UTC

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

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Re: 1430: Proteins

Postby Eternal Density » Mon Oct 06, 2014 11:16 am UTC

azule wrote:I predict a heavy chance of ... religion. Good luck with this thread, y'all!
Indeed. I decided to be the one to kick it off for a change :D
Garnasha wrote:Then again, it's no worse than supposing some sentient being designing the laws of physics and then either creating the Big Bang and guiding history to cause us, or creating a world with us in it and then planting fake evidence to the contrary. That, 1. Just shifts the problem to "what caused that being to exist?" and 2. Adds the additional problem "what are the chances of such a being deciding to create us?"

While I'd quibble with the 'fake evidence to the contrary' thing, I think it's more productive to approch this from a different angle for a change.

On the one hand, you have some cosmic accident or fluke, or an infinite number of universes and by virtue of the ability to observe we're in the one we're able to exist in, or perhaps there's an infinite chain of universes or something like that. In essence, our origin involves infinite(or thereabouts :P) time/space/mass/something in other unobservable universes.

On the other hand, you have an infinite being: a person, possessing logic and reason and creativity and the ability to communicate. I'd say that this being is 'eternal': outside of time, having no beginning or end, and came up with the whole concept of 'time' and 'beginnings' and 'cause and effect' and 'creating stuff'. That concept (of an eternal being) is kinda hard to understand and explain for us temporal beings, but 'other universes' or Hawking's idea of the universe beginning "in just about every way imaginable (and maybe some that aren't)" is really no better. (Besides, you can't use math and physics to explain the origin of math and physics.)

Now, we live in a world that has logic and reason and rationality and people and personalities and imagination and intelligence and creativity [citation needed]. And outside our universe there's either a whole lot of dead universes completely lacking all these things, or there's God with an unlimited amount of these things who intentionally put them into a world.

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 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.

If the universe is just the lucky one amount countless others, in which the conditions happened to be right and we won the biochemical lottering and happen to exist against all odds, and one day it'll all collapse again, and nothing beyond this temporary universe cares, then billions of people having enough food to eat has about as much significant as whether they have the correct plural of LEGO®. People can talk about 'evolutionary ethics' and such all they like but the universe(s) really don't care in the slightest.

Garnasha wrote: If something exists, nobody knows anything about it, and probably nobody can know anything about it. Except that it has either 1. no power over us or 2. no interest in us or 3. acts predictably enough to build a science called "physics" around its behaviour, since for all practical purposes it doesn't seem to be there.
That's a pretty big claim. How thoroughly have you checked? This is something that you seriously don't want to get wrong. If you're right, nothing matters, but if you're wrong, everything matters.
Farabor wrote:Anyone up to explaining the alt text to those of us who are biology and/or origami impaired?
Well, there's a protein called Tobacco Etch Virus nuclear inclusion a endopeptidase, which consists of two β-barrels and a flexible C-terminal tail, like this. Covalent catalysis is performed with an Asp-His-Cys triad, split between the two barrels (Asp on β1 and His and Cys on β2). The substrate is held as a β-sheet, forming an antiparallel interaction with the cleft between the barrels and a parallel interaction with the C-terminal tail. The enzyme therefore forms a binding tunnel around the substrate and side chain interactions control specificity.

I have no idea what that means, but see here for how to make an origami bird which flaps its wings when you pull its tail.
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Re: 1430: Proteins

Postby cellocgw » Mon Oct 06, 2014 11:26 am UTC

Making fancy origami figures is hard enough -- I've seen some of the spectacular figures here and there -- but proteins turn out to be pretty good at folding themselves into fractal spheres. That's just plain awesomeness.
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Re: 1430: Proteins

Postby iGEM Team Heidelberg » Mon Oct 06, 2014 11:34 am UTC

In addition to FoldIt there are some other open science projects focusing on protein folding. Like Folding@home and iGEM@home. They use a distributed computing approach where the hard work protein folding is distributed to volunteers who register their home PC's and the folding is done when computer is idle.


Disclaimer: We created iGEM@home

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Re: 1430: Proteins

Postby _P_ » Mon Oct 06, 2014 11:54 am UTC

Eternal Density wrote:That's a pretty big claim. How thoroughly have you checked? This is something that you seriously don't want to get wrong. If you're right, nothing matters, but if you're wrong, everything matters.


What's 'matters'? Why is it good that things 'matter'? Is it something you came up with yourself, or did someone tell you about it? If the latter, where did they find out?
Serious questions here.

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Re: 1430: Proteins

Postby CigarDoug » Mon Oct 06, 2014 12:35 pm UTC

_P_ wrote:
Eternal Density wrote:That's a pretty big claim. How thoroughly have you checked? This is something that you seriously don't want to get wrong. If you're right, nothing matters, but if you're wrong, everything matters.


What's 'matters'? Why is it good that things 'matter'? Is it something you came up with yourself, or did someone tell you about it? If the latter, where did they find out?
Serious questions here.

If nothing matters, there is no moral framework. Kill people, break things, ruin lives, it matters not.

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.

Humans, then, are not simple animals because we have a far more complex moral code which we can abandon at will. We kill a lot of things to gain no value from it other than sport, or let most of the animal go to waste. Or, we can kill something to eat it, use it's body for raw materials, and waste little. Arguably, finding other sources for raw materials so we don't have to kill the animal is better, from a moral sense.

We kill a person (or used to) when that person was a threat to the community, because they killed for no good reason. We as a society made the moral decision to preserve the society by removing the threat.

We have the capacity to live with nature, or to disregard it and soil our own nests so we make it unliveable for ourselves and the animals. We can allow any sort of behavior that is destructive to the self and the community, or we can demand a moral code which makes life tolerable for those around us and preserves the species. I wouldn't want to live in a society that had no moral code it followed. Mad Max might be a fun movie, but would you really want to live in that world for long?

If there is something higher than us (which I absolutely believe there is), it calls on us to live by a moral code. If we are the top of the food chain in the universe, and nothing matters, and there is no life beyond this one, then there is no good reason not to get as much as you can and screw everybody else. Enjoy your brief, short, life with no moral restrictions whatsoever. I submit that even atheists believe in a moral code, although they would argue man imposes it on himself. They don't want to live in Mad Max world, either.

I don't think most people came up with this idea on their own, most of us seem to share it, even if we learned it from others. But I submit most rational people would agree with the results being a good thing to shoot for. "Do unto others as you would have them do unto you" is common across all religions in the world. It's the best moral code I can think of, even if you don't want to believe in my God.
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Re: 1430: Proteins

Postby Garnasha » Mon Oct 06, 2014 12:43 pm UTC

Eternal Density wrote:
Garnasha wrote: If something exists, nobody knows anything about it, and probably nobody can know anything about it. Except that it has either 1. no power over us or 2. no interest in us or 3. acts predictably enough to build a science called "physics" around its behaviour, since for all practical purposes it doesn't seem to be there.
That's a pretty big claim. How thoroughly have you checked? This is something that you seriously don't want to get wrong. If you're right, nothing matters, but if you're wrong, everything matters.
That's Pascal's Wager, or very close to it. To which one answer is the Church of Last Thurday. I thought xkcd itself did a similar refutation of Pascal's Wager, something about proposing, then and there, an even more vindictive god who made Hell look like a walk in the park and dumps everyone from any religion or worldview other than the one with him at the top. Then going on to say something like "unless of course you exclude patently ridiculous theories from your estimation what the best course of action is". However, I can't find it anymore. Anyone?

Either way, even if I'm wrong, that doesn't make you right, whatever you believe. No part of Pascal's Wager tells us which religion knows the truth, except that it's safest to believe in the biggest asshole (see vindictive god above). It does so happen that few religions seem to believe in a god as powerful and disagreeable as the Judeo-Christian one, so there's a point for them, though I'm not sure if they should be proud of that. Also, I might just be under-informed about the assholery of other, less dominant supernaturals.

Either way, if I'm right, it still matters a lot. Nihilism is for theists who lost their concept of God and lack the philosophical strength to fill the hole. Human 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). 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. 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. People who try to refine our collective world-view to be better able to make such predictions are called scientists. 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".

This scientific world-view has proven itself plenty of times: modern sanitation, chemistry, computers, GPS, antibiotics, structural engineering, agriculture, etc.; 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, and trying to keep others (children) away from it as if it were a competing religion a major evil.

Actually, this boils down to a different argument: We have no good evidence for or against the existence of hobbits (or djinn, or other supernatural beings, either of limited or infinite power). However, we do have good evidence for the efficacy of science, and we hopefully agree on a baseline form of "natural good" (happiness and non-suffering, esp. for others). Generally, "religious good" is rewarded by promises of such "natural good", possibly in the afterlife, and "natural evil" in this life is excused similarly. We have no evidence for or against the validity of these promises. On the other hand, we can clearly see the natural good and evil in this world, and science tells us how to influence the prevalence of either, with good credentials. 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". The magnitude of the promises made does not affect their reliability, and if I promise you a billion dollars I don't have, that's no better than if I promise you a million I don't have. Going with action B here is at the least gullible, but more likely plain evil, and religion is evil for causing it.

tl;dr: Religion has zero evidence for or against, but science has plenty of evidence for, which makes that the new baseline, and religion falls short.

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Re: 1430: Proteins

Postby orthogon » Mon Oct 06, 2014 12:56 pm UTC

Eternal Density wrote:[...]then billions of people having enough food to eat has about as much significan[ce] as whether they have the correct plural of LEGO®.

Quite so: i.e. a profound and fundamental significance, worthy of fighting wars over ;-) Anyway, this is a trick question: there is no correct plural of Lego because Lego is an uncountable noun.
xtifr wrote:... and orthogon merely sounds undecided.

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Re: 1430: Proteins

Postby Znirk » Mon Oct 06, 2014 1:04 pm UTC

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 ...)

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Re: 1430: Proteins

Postby CigarDoug » Mon Oct 06, 2014 1:09 pm UTC

Garnasha wrote:tl;dr: Religion has zero evidence for or against, but science has plenty of evidence for, which makes that the new baseline, and religion falls short.

I don't dispute that man's brain has allowed him to create marvelous things, which make life tolerable, pleasurable, and longer-lasting. But where does science encourage man to act in a moral fashion? Science has also given us the technology to kill large numbers of human, animals, and plants with very little effort. Science has given us numerous chemical combinations that can ruin drinking supplies and kill people who come in contact with it. Thus, we must be responsible with our new toys, although we often are not. Science allows us to create new hearts, limbs, and other body parts over here to replace the ones we destroyed in the war over there. Science allows us to create cures for various diseases and viruses while creating even more deadly ones. We sure do run the gamut.

Science, and intelligence, in and of itself, is not enough. Where does morality come from? Would we survive for long if we had no moral code whatsoever? When talking about religion, some people get too wrapped up in why God does what he does and how he will treat those who don't follow him. I would argue that since God is NOT human, we have no moral basis to attach our own human morals to him. But all of this is basically academic, since we can't actually determine what God is and what he wants, we only have faith to go on.

But all religions are fairly consistent in the rules they give us to live our lives: "Be excellent to each other", to quote two famous philosophers. You can resent the idea that there is something out there more powerful than you, who will judge you by their own standard and you don't have much say in the matter. But the more important question is, are you making things better for the people around you? If you choose to follow the moral code that most of us claim is given to us by God, would it really be that horrible for you to try? If everyone followed the Golden Rule, and we are right, we make life better for everyone here on Earth, AND we go to Heaven. If we are wrong, we make life better for everyone here on Earth, and we are worm-food anyway. So, what's the down side?
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Re: 1430: Proteins

Postby Garnasha » Mon Oct 06, 2014 1:29 pm UTC

CigarDoug wrote:<post before my previous>
As you correctly nuanced yourself, not all atheists (or even most, or even a significant minority) become Ayn Rand. There's someone I wish had never become literate. Ideological toxin.

Also, I find it insulting to be told my morality must be imposed on me outside my knowledge by a higher being. Evolution gave me the capacity for moral judgement, my education instilled in me a moral framework, and by my choice I live by it. I am accountable to myself and to my fellow man (or woman, the man(kind) and man(male) homonym is an annoying accident of linguistics), not to a supernatural parent substitute who punishes me for being bad.

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.

Ps. Being accountable to oneself also takes away the "but God told me to" justification when one does evil in the eyes of man, which might keep one from feeling justified in committing said evil in the first place, which might in turn prevent such evil.

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Re: 1430: Proteins

Postby Garnasha » Mon Oct 06, 2014 1:44 pm UTC

CigarDoug wrote:<post ending in worm-food>
I have nothing about following those parts of a religious morality which can stand on their own merits, including the Golden Rule and "be excellent to each other". I do object to "you shall keep such-and-so day holy" and "if any man lies with another man as one lies with a woman, he must be stoned" unless that is an instruction to smoke pot (and even then, that can't be healthy in the long term). I also object to drawing any other conclusions from the speculated existence of any kind of God if such conclusions lead to any behaviour which is not completely harmless in the eyes of science.

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.

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.

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Re: 1430: Proteins

Postby orthogon » Mon Oct 06, 2014 1:47 pm UTC

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
xtifr wrote:... and orthogon merely sounds undecided.

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Re: 1430: Proteins

Postby PolakoVoador » Mon Oct 06, 2014 1:50 pm UTC

cellocgw wrote:Making fancy origami figures is hard enough -- I've seen some of the spectacular figures here and there -- but proteins turn out to be pretty good at folding themselves into fractal spheres. That's just plain awesomeness.


Wait, what?

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Re: 1430: Proteins

Postby Xeio » Mon Oct 06, 2014 1:57 pm UTC

CigarDoug wrote:Science, and intelligence, in and of itself, is not enough. Where does morality come from? Would we survive for long if we had no moral code whatsoever? When talking about religion, some people get too wrapped up in why God does what he does and how he will treat those who don't follow him. I would argue that since God is NOT human, we have no moral basis to attach our own human morals to him. But all of this is basically academic, since we can't actually determine what God is and what he wants, we only have faith to go on.
Well, if we don't mind breaking a lot of ethical rules and kidnapping people, we could bottle up a bunch of psychopaths in their own society and see what happens.

I mean, "god" or whomever seems to have forgotten to give them the same morals the rest of us seem to have. Or... you know, we could look at what's different in their brains and find a naturalistic reasoning for the way humans (and other animals!) tend to behave.

Probably easier to blame it on a god. Science is too much work.

CigarDoug wrote:So, what's the down side?
Depends on the religion. Some of them are pretty shitty to other people (nonbelievers/other religions). For example, harmful attitudes regarding sex and contraceptives. Some (Jehovah Witnesses, and I'm sure others) are exclusionary to the extreme of disowning family members for being non-believers. Some that advocate for violence (luckily mainly confined to extremists).
Last edited by Xeio on Mon Oct 06, 2014 2:45 pm UTC, edited 1 time in total.

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Re: 1430: Proteins

Postby Garnasha » Mon Oct 06, 2014 2:09 pm UTC

Xeio wrote:<post>
Thank you. Can you take over from here? I just spent my monthly allotment of time arguing religion. I should go back to arguing science. Or rather, being amazed by its beauty. If God does exist, he's a physicist. Or a mathematician, quotespace hasn't decided yet. Not a biologist though, too many ugly bits there alongside the beautiful stuff.

So... What's this I'm hearing about fractal self-folding proteins? What's the minimum scale, what's the maximum? Could anyone link an example?

*Edit: double post*
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
Whoops, only now realized my typo. Yeah, actually, a Big Band sounds like a good start. Preceded by someone counting "1, 2, 1, 2, 3, 4". Ask the Listening Monks for more.

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Re: 1430: Proteins

Postby Kit. » Mon Oct 06, 2014 2:20 pm UTC

Eternal Density wrote:On the one hand, you have some cosmic accident or fluke, or an infinite number of universes and by virtue of the ability to observe we're in the one we're able to exist in, or perhaps there's an infinite chain of universes or something like that. In essence, our origin involves infinite(or thereabouts :P) time/space/mass/something in other unobservable universes.

On the other hand, you have an infinite being:

This is a false dichotomy. Or at least I see nothing that would prevent an infinite being from creating infinite universes unobservable by men.

Eternal Density wrote:Now, we live in a world that has logic and reason and rationality and people and personalities and imagination and intelligence and creativity [citation needed]. And outside our universe there's either a whole lot of dead universes completely lacking all these things, or there's God with an unlimited amount of these things who intentionally put them into a world.

Nah. We live in a world where our logic and reason and intelligence and creativity makes us slightly better at propagating our genes compared to other beings of similar mass around us.

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".

The question is: can you prove that it's not just your delusion?

Because evolutionary psychologists can prove their evolutionary sources of your wonders, or at least they claim so.

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.

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Re: 1430: Proteins

Postby addams » Mon Oct 06, 2014 2:20 pm UTC

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??
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Some of us see The Gutter.
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Re: 1430: Proteins

Postby Heimhenge » Mon Oct 06, 2014 4:04 pm UTC

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?

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Re: 1430: Proteins

Postby Kit. » Mon Oct 06, 2014 4:21 pm UTC

Google:

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

"I write software that predicts" - 2 results
"I make software that predicts" - 2 results (both at explainxkcd)

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Re: 1430: Proteins

Postby rmsgrey » Mon Oct 06, 2014 5:08 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.


Animals exist in harmony in much the same way as the US and USSR existed in harmony 1950-1980.

The very air we breathe is the result of an early lifeform coming up with an ultimate weapon and using it to exterminate nearly all other life.

The main reason animals don't kill frivolously is that they don't have the time or the energy to do so - give a cat shelter and a secure food supply so it never needs to kill anything ever again, and it'll still go out hunting...

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.

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Re: 1430: Proteins

Postby armandoalvarez » Mon Oct 06, 2014 5:11 pm UTC

Going back to the topic at hand, should I be doing some form of "Folding at Home," and if so, which program should I do?

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Re: 1430: Proteins

Postby cellocgw » Mon Oct 06, 2014 5:14 pm UTC

Kit. wrote:Google:

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

"I write software that predicts" - 2 results
"I make software that predicts" - 2 results (both at explainxkcd)


In that vein,
"I break software" 71
"I fix software" 56
or....
"I make hardware" 241 000
"I write hardware" 40
Please no "in Soviet Russia" jokes
Last edited by cellocgw on Mon Oct 06, 2014 5:15 pm UTC, edited 1 time in total.
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Re: 1430: Proteins

Postby Rombobjörn » Mon Oct 06, 2014 5:15 pm UTC

CigarDoug wrote:But where does science encourage man to act in a moral fashion?

Science doesn't tell you how to live your life, but it can experimentally explore why people act the way they do, for example to find an answer to the question:

CigarDoug wrote:Where does morality come from?

Scientists have arranged games about money, where the test subjects could choose to maximize their own reward, to cooperate for mutual gain, or to sabotage both their own and the other party's reward. They found that most people would punish those who were selfish even if that also meant that they earned less themselves. Apparently many humans have a strong drive to punish what they find to be unjust behaviour.

Similar experiments on monkeys with tasty fruits for rewards have given similar results. Monkeys also seem to have an instinct for justice, so apparently this instinct evolved long before humans evolved.

CigarDoug wrote:Would we survive for long if we had no moral code whatsoever?

Exactly. Primates who had this instinct were better survivors than those who lacked it. Evolution by natural selection.

CigarDoug wrote:But all religions are fairly consistent in the rules they give us to live our lives: "Be excellent to each other", to quote two famous philosophers.

And that's a big clue right there: Religions aren't at all consistent regarding what mythical beings they expect people to believe in, but they are fairly consistent regarding moral rules. Could it be because the mythical beings are fantasies with no basis in reality, while the moral actually exists in the form of human instincts?

So there. :P

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Re: 1430: Proteins

Postby Rombobjörn » Mon Oct 06, 2014 5:22 pm UTC

rmsgrey wrote:The very air we breathe is the result of an early lifeform coming up with an ultimate weapon and using it to exterminate nearly all other life.

Not really. They came up with a new energy source that allowed them to grow and reproduce faster. This new energy source produced some highly toxic waste, but they got rid of that by dumping it in the ocean. It was pollution, not war.

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Re: 1430: Proteins

Postby Rombobjörn » Mon Oct 06, 2014 5:27 pm UTC

cellocgw wrote:In that vein,
"I break software" 71
"I fix software" 56
or....
"I make hardware" 241 000
"I write hardware" 40
Please no "in Soviet Russia" jokes

No "in Soviet Russia". OK.

In 1984 you controlled your software. In 2014 your software controls you.

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Re: 1430: Proteins

Postby gmalivuk » Mon Oct 06, 2014 5:31 pm UTC

It's amazing how much more on-topic this discussion becomes if you ignore everything by or about Eternal Destiny and CigarDoug...

(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.)
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