Science!! Fucking magnets, how do they work?

Picasso_sl said:

Why can't chemistry be consistent?

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To put it in simplest terms, similar shapes fill the same hole, and target similar locations. A good example is the way mutations occur during replication.

These are your 5 base pairs (Uracil replaces Thymine in RNA)



As DNA is being rebuilt by the various enzymes responsible for guiding each new base pair into proper position along the template strand during replication, the chemicals don't have a conscious ability to select from, for instance, adenine instead of guanine. Most of the time they'll get it correct, but lots of times they get it wrong. Other enzymes then have to come in and correct those errors by excising the incorrect base pairs and then rebuilding news ones. This process, as well, is imperfect. This is how mutations come about, primarily, and is pretty much the entire basis of why natural selection works. As these mutations are formed and then passed on to off spring, some increase survival and some decrease survival. Many lead to fetal inviability.

As long as purely chemicals are doing the job, without some sort of device that we've designed to examine and determine if the molecule being selected for is the exact proper one, there will probably always be some error built into the system.

That's why its good that the primary amino acids for life can also be formed from several different combinations of base pairings.

Glycine, for instance, can be formed by alleles made up of combinations of GGU, GGC, GGA, or GGG. Phnylalanine can be made up of UUU or UUC. Remember, again, that Uracil is replaced by Thymine in the DNA. So those would be GGT, GGC, GGA, GGG, and TTT, TTC respectively on the actual DNA strand.

The CRISPR-Cas9 system utilizes specially designed cocktails of enzymes to attempt to cut the DNA at a precise location, and insert new genes into that location, before "resealing" the DNA strand. These cocktails of enzymes are the same enzymes we see performing these operations in nature, mostly synthesized, and therefore suffer from the same imprecision.

For instance, when the Chinese researchers were modifying embryos using this technique, one of the biggest flaws was the failure rate, and the head scientist at the time was talking about how he would basically have to go back to the drawing board and redesign the cocktails of enzymes used to target the locations he wanted to insert these genes into, because the failure rate was so high.

pharmakos_sl said:

would it even be possible to create a nanomachine small enough to manipulate codons?

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Single atom transistors already exist, so in the future probably.

pharmakos_sl said:

you know, it has always kind of baffled me that when it comes to the origin of life, the prevailing scientific theory seems to be "molecules just sort of spontaneously started self-replicating"... and when asked why that happened, the two main responses are "it was random" or "thats just the way the universe is."

its one of the only scientific theories where many scientists seem to be pretty content to just say "yeah thats just the way it is."

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I'm gonna try to explain this to you.

First of all, the word "random" is really bad to use here. I would much prefer the word "inevitable" when discussing the origins of life in the universe, and I'll get to why that is here in a bit. First, some groundwork.

The origins of life, as far as we can tell, is founded in the semi unique chemistry of the carbon atom. Atoms have varying numbers of electrons surrounding them. Carbon has four. Lower order elements follow a rule called the octet rule. The octet rule essentially states that for a lower order atom to achieve its lowest energetic state, it requires 8 valence electrons, which are the electrons which fill its outer shell. Because carbon has 4 valence electrons, it desires to share up to 4 more valence shell electrons with other atoms, in order to reach energetic stability. This all ties into thermodynamics and entropy, which drives this process. Carbon tends to share electrons with lower order elements near it on the periodic table, such as Nitrogen, Oxygen, Hydrogen, Boron, Sulfur, Chlorine, other Carbon atoms, so forth and so on. If you know even a middle school amount of chemistry, you're probably beginning to notice that a lot of these elements are the core elements that make up pretty much all organic molecules that are involved in life processes. Of course, the very word "Organic" implies a predominately Carbon heavy molecule in the first place, as organic chemistry IS the chemistry of the Carbon atom.

Now here's where things get interesting, because those Carbon atoms tend to form really long chains of molecular polymers. The polymers are formed of amino acids, which have been found to form spontaneously in nature all over the place. That probe that landed on that comet not too long ago even found basic amino acid polymers ON THE COMET. Long polymers of amino acids have another name, and that name is PROTEINS. Proteins form complex configurations as a result of the atomic bonding forces found within them, that's why they look like little clumps of elements all bound up with one another. Example


When you start taking biology classes at the university level, if your professor is any good, he'll point out that protein's changing shape is what drives pretty much all of life's processes in some form or another. So, in nature, when these complex protein polymers form and then interact with one another, it should come as no surprise that....things....happen. Biological things. And this process becomes more complex as more of these molecules exist and interact, especially in bodies of water being supplied energy in the form of heat from the Sun and thermal vents. We've even found clays that occur in nature that help drive the polymerization (formation of these compound polymers) from lower order amino acids, much in the same way that our RNA transcribes and translates DNA alleles into amino acids and then polymerizes these into functional proteins in our own bodies.

Now, here where the inevitability of things comes in, and I'm going to use an analogy to make this more easily understood. Say you have a lottery that runs for several billion years, and you get to play numbers to win that lottery billions of times per second, every second. And say that the numbers you need to win that lottery aren't just one set of numbers, but a near infinite set of possible combination of numbers will allow you to win that lottery. Would you call your eventually winning that lottery random chance, or an inevitable conclusion?

Because that's what we have with self replication. The reason we don't know the exact self replicating molecule that first brought about life on this planet is because it could be ANY of a near infinite number of possible amino acid polymer combinations that began the process, so its basically "Pick your favorite one". But scientists most definitely aren't taking the position "Well that's just how it is" in terms of like, throwing up their hands in disgust and having no answer to the WHY of how that is. That's more of a Creationist sort of misrepresentation of the science, actually. "You can't explain exactly how life forms, so your argument is it just is that way". No, the laws of entropy and the chemistry of the carbon atom very strongly indicate WHY life forms spontaneously (rather than randomly) in the universe.

There are also a lot of theories about the way that living material organizes and retains and distributes energy that point to the inevitability of living organisms as a way to better harness the energy from the Sun and elsewhere that contribute to the concept of life being an inevitable outcome of the general rules of organic chemistry.

Here's an article on Jeremy England, an MIT physicist, who is making the case for 'the origin and subsequent evolution of life follow from the fundamental laws of nature and "should be as unsurprising as rocks rolling downhill."'

A New Thermodynamics Theory of the Origin of Life | Quanta Magazine

ZyyzYzzy_sl said:

My question is would nanomacmhines really be better than manipulating and customizing proteins and other molecules that have had a few billion years of refinement behind them?

I can see the use of nanomachines to drive certain chemical modifications such as very specific site methylation of DNA. But there is also the problem of how would you make these machines "non-immunognic" if they are used in humans ir animals?

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When I used the word nanomachines, I was really thinking something with the capacity to judge them based on shit like mass spec known weights and shit. It was more conjectural, like, "We would have to design something that could go in, analyze and recognize the particular molecules we're seeking". They would probably have to be specifically engineered for these purposes, and would probably have to have some way to access large databases of known molecules. Clearly, at this time, such technology is beyond us, and the tools nature has already given us would be far superior to anything we could engineer at this moment.

Next step, nano-machines refolding prions all proper like... Make it so!

pharmakos_sl said:

you could have skipped most of that, hodj (i'm a chemist).

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Wasn't aware, good to know.

uh, no, it definitely should be surprising. lifeless matter given enough time will eventually turn into complex life forms like human beings?

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That's not at all what I said. Complex intelligence was the result of many different evolutionary steps that may or may not occur in any particular environment.

lifeless matter given enough time will eventually turn into complex life forms like human beings?

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You're going to first have to abandon this idea that there is some magic divide between LIVING and NON LIVING. There really isn't, in terms of biochemistry and chemistry, which you should know. Molecules are molecules. They function according to the same general rules. And you have shifted the argument from the emergence of life in general to complex life forms like human beings. I can explain the general evolutionary trajectory, and all the interesting and peculiar changes that led to, specifically, human beings, and those events are fairly random and special in terms of the evolutionary pressures applied to the mammalian line that resulted in the differentiation into anthropoids and eventually humans, but that wasn't the discussion we were having. The discussion we were having related explicitly only to the formation of life in general in the universe.

it doesn't matter how you slice it up -- the origin of life is INCREDIBLY bizarre.

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No, its not. The advancement to self awareness, however, may be considered bizarre. We have examples of other highly intelligent life forms here on Earth, but the physiological make up of our species in particular, with the capacity for language and tool making, as well as what we consider to be an extreme intelligence, all in combination in one species, is pretty special.

how about a reductio ad absurdium. i could say that since this cosmic lottery has been running for billions of years and there are billions of planets and yada yada yada, then somewhere on one of those planets at some point in time an exact copy of me has gotten a blowjob from an exact copy of Kim Kardashian.

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This isn't a reductio ad absurdum, going back to the discussion on the nature of existence and the possibility of multiple universes, this is actually almost certainly probable.

You're getting very mushy with your arguments here. Either your position, as originally stated, and which I was addressing, is "The emergence of ANY LIFE WHATSOEVER IN THE UNIVERSE is strange" or your position, as you've now changed it to, is that "The emergence of intelligent life is strange". Which one is it? Because you quote me quoting the MIT physicist explicitly saying only that the emergence of LIFE is an inevitability, and it is. Not the emergence of intelligent life.

My explanation was in regards to the emergence of life in general. Not the emergence of intelligent life. And it had nothing to do with infinite multiverses, or infinite possibilities. In fact I was very specific in pointing out that it was NEAR INFINITE, not INFINITE.

hodj_sl said:

Now, here where the inevitability of things comes in, and I'm going to use an analogy to make this more easily understood. Say you have a lottery that runs for several billion years, and you get to play numbers to win that lottery billions of times per second, every second. And say that the numbers you need to win that lottery aren't just one set of numbers,but a near infinite set of possible combination of numbers will allow you to win that lottery.Would you call your eventually winning that lottery random chance, or an inevitable conclusion?

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Speaking of Douglas Adams quotes, there's a parable in his last, post humously published, Hitchhiker's book called the parable of the puddle

"This is rather as if you imagine a puddle waking up one morning and thinking, 'This is an interesting world I find myself in - an interesting hole I find myself in - fits me rather neatly, doesn't it? In fact it fits me staggeringly well, must have been made to have me in it!' This is such a powerful idea that as the sun rises in the sky and the air heats up and as, gradually, the puddle gets smaller and smaller, frantically hanging on to the notion that everything's going to be alright, because this world was meant to have him in it, was built to have him in it; so the moment he disappears catches him rather by surprise. I think this may be something we need to be on the watch out for."

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The idea that life must be special is puddle thinking. The universe wasn't made for us, or any life form. Life simply is an inevitable conclusion of the laws of entropy applied to carbon chemistry.

pharmakos_sl said:

ah, i suppose we'll just have to disagree on our definitions of bizarre. i did read the article you linked. perhaps i should read literature from England himself, but it still seems to me that there are a lot of holes in the theory.

sunlight + water + hydrocarbons (with a nitrogen here and there) + time = life? just, wow.

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I mean the development of any particular species is very rare and special. Think about this statistically. The chance for ME in particular to win the mega millions lottery twice in, say, two years? The odds of that are astronomically low.

But the chance for ANYONE in general to win the mega millions lottery twice in, say, two years? Much higher, though maybe not "astronomically high".

Statistics is about framework, more often than not. What are we considering here? The possibility that SOMEWHERE at SOME POINT in BILLIONS OF YEARS a complex protein polymer will develop the ability to self replicate, and that errors in that process will lead to gradual advances in that form to more complex forms? Or the possibility that HUMANS IN SPECIFIC will develop AT THE EXACT TIME THEY DID?

The two are different statistical frameworks, and lead to very different conclusions.

Humans wouldn't have evolved as we are today were it not for some very specific, generally random, events, such as extreme climate variation over the period of tens of thousands of years in the region of the Great Rift Valley in Africa, during the time when our ancestors were forced to choose between life in the trees, or life on the ground, and then followed by successful invention of tool making and control of fire for cooking and so forth and so on. Not to mention the demise of all the dinosaurs who were the dominant life forms on this planet at the time when our earliest ancestors were no bigger than modern day squirrels, leading to a vast plethora of new species differentiation events as the remaining mammals and other species spread out to conquer the new open environments left behind in the dinosaurs' wake. Yes, all those events were very particular, and special and rare. Rare enough that only a handful of species that we know of were able to take advantage of them, and our species is the only one of them left alive today.

Picasso_sl said:

Oh I was asking dumar

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