List of All Laws of Nature

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jewish_scientist
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Re: List of All Laws of Nature

Postby jewish_scientist » Fri Apr 22, 2016 3:52 pm UTC

Spoiler:
aph wrote:
jewish_scientist wrote:Dear everyone who responded to my one word statement on anatomy,
I was writing a huge thing about Truth-Maker theory, falsification and cow on the Moon; however, it was getting too long and was impossible to understand, so I am just going to ask you a question. Can you prove the null hypothesis of one of these Laws of Anatomy? Remember that every law does not apply to every organism, so you cannot disprove Listing's Law with snails or flies.

My main objection to using particular facts about anatomy as equivalent to natural laws is that there is no limit to the number of them - they are very narrow and you can find every branching of every nerve fiber in every known species and call that fact a law - "nerve A branches off from nerve B carrying an identical signal".. We know the whole connectome of C. elegans, and we just call it a connectome.

I can make arbitrarily large amounts of laws of physics in the same way:
The amount of force exerted on a piece of lead is equal to the product of its mass and its acceleration.
The amount of force exerted on a piece of steel is equal to the product of its mass and its acceleration.
The amount of force exerted on a piece of copper is equal to the product of its mass and its acceleration.
The amount of force exerted on a piece of ice is equal to the product of its mass and its acceleration.
The amount of force exerted on a piece of glass is equal to the product of its mass and its acceleration.
The amount of force exerted on a piece of plastic is equal to the product of its mass and its acceleration.
The amount of force exerted on a piece of graphite is equal to the product of its mass and its acceleration.


Spoiler:
aph wrote:
Just because we do not understand everything about neurology right now does not mean that the things that we do understand are false.

And what DO we understand? A proof of understanding is prediction. The better the understanding, the more precise the predictions. There is a story (the theory), and there are the models (the equations). Neuroscience (not just neurology) has a huge number of different theories, and a large number of models that aren't that good at predicting (say, behavior of an organism or its nervous system).

I am fairly sure that predicting the behavior of an organism is the job of a behavioral biologist or a psychologist; neurologists have a very detailed understanding of how different stimuli, such are chemicals, affect the nervous system of different animals.


Spoiler:
aph wrote:
jewish_scientist wrote:Muscles do not actual contract during an isometric contraction, so Sherrington's Law does not apply.

From one of your links:
Isometric Contractions: Tension but no shortening of the muscle occurs.
Another one: Isometric strength is defined as the capacity to produce force or torque with a
voluntary isometric (muscle[s] maintain[s] a constant length) contraction.

So, there is different terminology used, some people call the whole system of muscle fibers and tendons - a muscle, while some only call just the muscle fibers 'muscle'. Muscle fibers contract during any contraction, but if it is isometric, then there is no contraction/shortening of the 'fibers+tendon system' and there is no reciprocal 'loosening' of the antagonist. I mean, just try flexing your muscles. Sherrington's law applies to some situations, but it doesn't hold at all times.

I went to all my sources and the few that do mention the word 'tendon' do not use it the way you said the do. Even your quotes do not use the word. Contraction on a microscopic level does not correspond to contraction on a macroscopic level. Sherrington's law says what happens when a muscle contracts; when muscles are not contracting it does not apply. Similarly, Newton's Third Law of Motion which says what happens when a force is exerted; when no forces are being exerted then Newton's Third Law of Motion does not apply.
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Re: List of All Laws of Nature

Postby aph » Fri Apr 22, 2016 6:59 pm UTC

jewish_scientist wrote:I can make arbitrarily large amounts of laws of physics in the same way:
The amount of force exerted on a piece of lead is equal to the product of its mass and its acceleration.
The amount of force exerted on a piece of steel is equal to the product of its mass and its acceleration.
The amount of force exerted on a piece of copper is equal to the product of its mass and its acceleration.
The amount of force exerted on a piece of ice is equal to the product of its mass and its acceleration.
The amount of force exerted on a piece of glass is equal to the product of its mass and its acceleration.
The amount of force exerted on a piece of plastic is equal to the product of its mass and its acceleration.
The amount of force exerted on a piece of graphite is equal to the product of its mass and its acceleration.[/spoiler]

Well.. exactly. Instead of making arbitrarily large amounts of laws of physics, we are trying to find general laws. That is why we should find general laws describing development of anatomical features, not laws describing each feature.
I am fairly sure that predicting the behavior of an organism is the job of a behavioral biologist or a psychologist; neurologists have a very detailed understanding of how different stimuli, such are chemicals, affect the nervous system of different animals.

Nice cartoon :D

jewish_scientist wrote:I went to all my sources and the few that do mention the word 'tendon' do not use it the way you said the do. Even your quotes do not use the word. Contraction on a microscopic level does not correspond to contraction on a macroscopic level. Sherrington's law says what happens when a muscle contracts; when muscles are not contracting it does not apply.

Spoiler:
What exactly is a 'muscle' is defined differently in motor control literature. For example, here the researchers use the term 'musculotendon complex', and make a difference between the contractive component (muscle fibers) and the elastic element (tendon) link. You can find more if you google the term 'muscle-tendon complex' or 'muscle-tendon unit'. During isometric movements, the whole muscle-tendon complex does not change in length, but the tendon elongates and the muscle (fibers) shorten to produce the tension.

Muscle fibers are contracting in both isotonic and isometric movements. That is not microscopic level, you can see and feel the bulging of muscles. Anyway, Sherrington's law was important for the discovery of spinal level connections between agonist and antagonist muscles (so - anatomical features), it doesn't describe accurately the forces of muscle contraction for skeletal muscles, nor the activation of muscles. I can only find it is used for ocular muscles that have direct agonist-antagonist pairs and it seems to be important for strabismus. Skeletal muscles in normal operation don't make clean isotonic or isometric movements, so length and tension change at the same time. Additionally, there are rarely direct agonist and antagonists pairs - usually, several muscles are synergistic for the movement of a single joint. Again, no use of Sherrington's law - it is not general and it doesn't work as a quantitative description of muscle activation. It has big historical importance.

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Re: List of All Laws of Nature

Postby aph » Fri Apr 29, 2016 8:20 am UTC

Quizatzhaderac wrote:I'd guess APH is objecting to the implied "simply" before "causing". Mental illness is complex and any simple explanation is going to fall flat.

I don't know, it seems simplicity and complexity are features of theories, not of the phenomena they are describing. Like, geocentric epicycles are more complex then heliocentric ellipses. So it might turn out that any particular mental illness has a relatively simple explanation of causes or treatments, maybe not even in terms of neurobiology, but some abstract constructs such as 'inner conflict' or 'uncontrolled sexual urges' or whatever. Doesn't matter what the explanation is, if the treatments are working better then current best ones, or if they lead to prevention.

Quizatzhaderac wrote:I really see "chemical Imbalance" as more of the domain of pop-psych it's useful and less incorrect the other pop-pych explanations.

And we can't just not have pop-psych, it's just human nature to label and generalize and try to predict and influence others.


I'm not sure it is just pop psych, (sure, it is in that domain too), it is also in psychiatry. It is one of those things that looks very sciency, but has no more empirical backing then the ancient 'body humors' theory. When you hear that some drug is a 'serotonin reuptake inhibitor' and that serotonin levels are connected to symptoms of depression, it sounds a bit nicer than 'you have too much phlegm in your body and we need to cut you'. But then there are drugs that actually lower the levels of serotonin and still work as antidepressants, and you find out those first connections were made on rats and they apparently showed 'symptoms of depression' in their cages as judged by the researchers.

Some people also argue that the sciency look and feel make the 'chemical imbalance' theory a good vehicle for big pharma advertisements.

And just a disclaimer - the effectiveness of drugs has empirical support, the theories purported to explain why those effects happen do not have support.

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Re: List of All Laws of Nature

Postby Quizatzhaderac » Fri Apr 29, 2016 5:02 pm UTC

aph wrote:I don't know, it seems simplicity and complexity are features of theories, not of the phenomena they are describing. Like, geocentric epicycles are more complex then heliocentric ellipses.
As I see it, it's like developing a theories of why things move. Gravity moving the planets in a heliocentric solar system is a great theory, but it's going to fall flat in explaining sailing stones, because that's a different phenomena and you need either multiple theories to describe both phenomena or a more complicated unified theory.
I'm not sure it is just pop psych, (sure, it is in that domain too), it is also in psychiatry
Psychiatry is not a science, that's psychology (For that matter neither are clinical psychologists). Psychiatrists are very aware that with "chemical imbalances" they're just treating the symptoms rather than curing root causes. Psychiatrists/clinical psychologists have an enormously important part to play in pop-psychology as they need to explain these conditions to their patients.
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Re: List of All Laws of Nature

Postby aph » Sat Apr 30, 2016 7:02 am UTC

Quizatzhaderac wrote:Psychiatry is not a science, that's psychology (For that matter neither are clinical psychologists).

True, their primary job is treatment (just like neurology). They still do empirical test of the effectiveness of treatments and publish this in journals, as well as more theoretical work aiming to explain some or other disorder or treatment and propose a hypothetical mechanism. There is no clear line separating the three (neurology, psychiatry and clinical psychology), neurologists seem to be closer to biology, clin. psychologists to philosophy, and psychiatrists in between the two. General psychology is usually not dealing with disorders and illnesses.

That just goes to illustrate the main point - the disparate approaches to the study of brain and mind, the lack of proper general principles("laws of nature") and the pre-Galilean nature of the whole field of neuroscience.

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Re: List of All Laws of Nature

Postby Copper Bezel » Sat Apr 30, 2016 12:17 pm UTC

No, it illustrates that lumberjacks are probably not required to be the best botanists and that that's probably okay. Seriously, are you nearly finished with your PCT trolling?
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Re: List of All Laws of Nature

Postby aph » Sat Apr 30, 2016 1:45 pm UTC

:D
I'm not saying it is not OK that there is disparity in approaches. It should be with the current state of knowledge.
edit: For example, some issues are clearly in the neurology department, like epilepsy or parkinsons. For depression, ADHD/ADD, mania, some types of psychosis and similar, you can go to either of the three "head doctors". Schizophrenia is usually in the psychiatry department, but psychologists also take it on.

Also, this is unrelated to control theory. (found a couple of biologists/ethologists actually writing about PCT in the past few years and publishing so not done with that either, but collecting papers and online models and animations...).

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Re: List of All Laws of Nature

Postby Izawwlgood » Sun May 01, 2016 5:20 pm UTC

aph wrote:For example, some issues are clearly in the neurology department, like epilepsy or parkinsons. For depression, ADHD/ADD, mania, some types of psychosis and similar, you can go to either of the three "head doctors". Schizophrenia is usually in the psychiatry department, but psychologists also take it on.
Wow. You need to put down your theories and get up to speed on the research from... even up to the early 1990's would be a good starting point.
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Re: List of All Laws of Nature

Postby aph » Sun May 01, 2016 9:47 pm UTC

Oh, no linky linky? Last time you said the difference between neurology and neuroscience was a verbal quibble, and now you seem to be mixing research and clinical practice. Kinda doubt you even read what you quoted.

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Re: List of All Laws of Nature

Postby Izawwlgood » Sun May 01, 2016 10:52 pm UTC

Perhaps you were really leaning on that 'usually'. Perhaps you were wholly unaware of the... whole body of research that exists surrounding everything you wrote.
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Re: List of All Laws of Nature

Postby Angua » Mon May 02, 2016 9:20 am UTC

While the research into things that are classically 'psychiatry' get published in psychiatric journals, I know that neurologists do work on researching them, and as we get a better understanding of how best to treat these conditions, they may well merge into the domain of neurology. Currently the best treatments we have for things like suicide and schizophernia do revolve around the antidepressants and antipsychotics mixed with a lot of CBT, and it may well be that it stays that way, however if firm links like autoantibodies are the cause, then it will probably become more multi-disciplinary. Or things like DBS which are neurology at this time.

This is all very neurosciency research into suicide and schizophrenia:
http://www.nature.com/news/brain-study- ... de-1.18870
http://www.sciencedirect.com/science/ar ... 3103002914
http://archpsyc.jamanetwork.com/article ... id=1558063
http://journals.cambridge.org/action/di ... 171300295X
http://www.journalofpsychiatricresearch ... 4/abstract
http://www.sciencedirect.com/science/ar ... 7X02000020
http://archpsyc.jamanetwork.com/article ... eid=207739
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Re: List of All Laws of Nature

Postby Izawwlgood » Mon May 02, 2016 10:33 pm UTC

To be a little less glib -

Pubmed search for 'schizophrenia fMRI' - 5703 hits

Pubmed search for 'schizophrenia neurotransmitter' - 25432 hits

Lets not pretend that schizophrenia is solely the realm of psychiatrists throwing around opinions-as-diagnoses willy-nilly, shall we? As usual, it's disrespectful to talk for scientists when you've little idea what it is they work on.
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Re: List of All Laws of Nature

Postby aph » Tue May 03, 2016 12:19 pm UTC

Angua wrote:While the research into things that are classically 'psychiatry' get published in psychiatric journals, I know that neurologists do work on researching them, and as we get a better understanding of how best to treat these conditions, they may well merge into the domain of neurology. Currently the best treatments we have for things like suicide and schizophernia do revolve around the antidepressants and antipsychotics mixed with a lot of CBT, and it may well be that it stays that way, however if firm links like autoantibodies are the cause, then it will probably become more multi-disciplinary.

There are lots of hypotheses floating around and being researched about the causes of schizophrenia (or suicide). Hopefully, new treatments will come from there. I'd bet more on luck and randomness and the sheer number of different drugs (and complementary therapy) being tested, then on a conceptual and causal understanding of the underlying processes.

It is terribly hard to do neurological research on mental disorders using today's tools. EEGs are imprecise, electrodes are invasive, fMRIs are known to find neural activity in dead fish, urine and blood test for levels of neurotransmitters are not representative of brain levels, PET scans have low temporal resolution... But technology is advancing quickly, so we'll see how that develops.

Izawwlgood wrote:Lets not pretend that schizophrenia is solely the realm of psychiatrists throwing around opinions-as-diagnoses willy-nilly, shall we? As usual, it's disrespectful to talk for scientists when you've little idea what it is they work on.

That is terribly disrespectful of psychiatrists. They do extensive empirical testing of their treatments and try to be as rigorous as possible with diagnoses. Or do you take neurology to be more 'scientific'? :D

I'm surprised you picked the 'schizophrenia is not yet treated by neurologists' as a point of dispute. Since, as you know, it is true that they are not treating it, and it is true they are doing research on it, and research and clinical practice are two different things.

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Re: List of All Laws of Nature

Postby aph » Tue May 03, 2016 1:05 pm UTC

As I've mentioned, there is a possible analogy between Galileo's telescopes and neuroscience's new imaging tools - with his telescope, he observed some very interesting phenomena like Saturn's rings, Jupiter's moons, Sun spots, Moon mountains and so on. Other astronomers also collected data about the Solar System and it didn't take much time for Newton to formulate a law describing very precisely what is happening with the planets and the moons at each point in time and space.

That is what we're waiting for in brain research (well, nervous system research, not all animals have 'brains'). First we need to observe in enough detail what is going on, then formulate the laws. It is too aggressive to say this is 'prescientific' or 'protoscience' (once again, sorry if anyone is offended) so I'll just say there is a possible analogy and we are also facing possible radical conceptual changes of the ways we are thinking about nervous systems. Just like there were changes in the concepts describing movements of Earth and other celestial bodies. I think that is very exciting and we should keep an open mind to different theories and just continually question our own assumptions of what is certain an known. Even the simplest nervous systems are much more complicated then the Solar System, so it might take some time.

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Re: List of All Laws of Nature

Postby Izawwlgood » Tue May 03, 2016 2:14 pm UTC

You are a fascinating mix of someone who is excited by science, unconvinced by science, doesn't understand science, and convinced you know a lot about science.

aph wrote:I think that is very exciting and we should keep an open mind to different theories and just continually question our own assumptions of what is certain an known. Even the simplest nervous systems are much more complicated then the Solar System, so it might take some time.
You frequently seem to state things along these lines - it's like a weird suggestion that things are too complicated to understand and that we know nothing, and it usually follows some bizarre assurance that either your theory is better, or that all the work that's been done and what we know is bunk because [reasons aph asserts despite not knowing much about the thing being discussed].
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Re: List of All Laws of Nature

Postby aph » Tue May 03, 2016 3:26 pm UTC

Yeah, Feynman used an interesting criterion of 'understanding a phenomenon' in science: if you can't build it, you don't understand it.

It was mentioned in the context of particular laws - if you can derive a law describing some specific phenomenon from more basic laws (you can build the specific law and not have to remember it), then you understand the phenomenon to a good measure. We can derive a lot about reflections of light from a speck of oil using quantum physics. Just like we can build satellites and send them to orbit and this demonstrates understanding of principles of gravity, some people in the Artificial Intelligence community (like Hawkins(fascinating talk, by the way) or more recently Hassabis) have used this to mean a similar thing - evidence of understanding the brain will be building an artificial one from first principles.

That is a sort of a heuristic way of judging how much a filed is advanced.

edit:
Apparently, Craig Venter wrote the sentence "What I cannot build, I don't understand" encoded in DNA to one of his synthetic cells.
Last edited by aph on Tue May 03, 2016 4:10 pm UTC, edited 1 time in total.

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Re: List of All Laws of Nature

Postby Izawwlgood » Tue May 03, 2016 4:01 pm UTC

Which is different from your handwavy statements insinuating we know nothing about the brain.

aph wrote:Yeah, Feynman used an interesting criterion of 'understanding a phenomenon' in science: if you can't build it, you don't understand it.
This isn't applicable to everything. Feynman was also, while a brilliant physicist and engineer, kind of a jackass who had a habit for opining heavily on things far outside his field of expertise. This is a terrible criteria towards understanding things in many (if not all!) biological systems. We can understand a great deal about a cell irrespective of our capacity to build one (from scratch?), and our ability to create synthetic organisms doesn't necessarily represent a step towards better understanding biological phenomena, or even an implicitly better tool for doing so. I'm sure creating a brain in a box will be cool and maybe even useful towards generating AI or snazzy computational stuff, but to claim we have almost no understanding of anything that happens above the neck because we haven't built a brain in a box is pretty ignorant.

Now, apply Feynmans cutesy quote to something like ecology or climate, or hilariously, anatomy and physiology, and tell me again how useful this criterion is for defining 'whether or not we understand a thing'.
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Re: List of All Laws of Nature

Postby aph » Tue May 03, 2016 6:07 pm UTC

(I edited the above post to include Venter)

Izawwlgood wrote: This is a terrible criteria towards understanding things in many (if not all!) biological systems. We can understand a great deal about a cell irrespective of our capacity to build one (from scratch?), and our ability to create synthetic organisms doesn't necessarily represent a step towards better understanding biological phenomena, or even an implicitly better tool for doing so.

There is certainly a wide space between understanding nothing and understanding enough to build an artificial system. Most of biology is somewhere on that spectrum today, over on the right. We know how to synthesize organic molecules (either purely chemically, or extracting them from modified organisms), we create DNA sequences at will. Building an artificial cell from scratch will definitely be a proof of excellent understanding of single cell organisms. Building an artificial heart or artificial kidneys is a similarly good criterion of showing an understanding of how they function.

There might be technical barriers - we might understand the process but not be able to build an artificial one for a lack of adequate materials or energy sources or sensors and actuators. In that case, building a simulation, which is just a mathematical model, will be good enough proof. There are artificial arms and legs today, even connected to the nervous system, but they are not as functional as 'naturally grown', so that is a nice indicator of where we need to go and how much we understand.
I'm sure creating a brain in a box will be cool and maybe even useful towards generating AI or snazzy computational stuff, but to claim we have almost no understanding of anything that happens above the neck because we haven't built a brain in a box is pretty ignorant.

We don't have to go above the neck. Spinal reflexes are still very confusing, computationally. Worms are on the brink of being explained, but still no cigar. All of that is in very early stages of research - mostly because it is hard to validate. That is the approach to neuroscience I'm interested in (I almost equate it with the term 'neuroscience', kinda like you do with 'neurobiology'), and hardly anything is understood, there are no first principles - even the Hodgkin-Huxley is disputed as irrelevant (not as incorrect!) if we assume rate coding or population coding.
Computational neuroscience is not just 'dealing with parts that do computation', it is a computational approach to the whole system, relations of quantities of neurotransmitters and firing rates and receptor activation and environmental changes. To make an analogy, the law of gravitation is a computational approach to movement of celestial and other bodies. It is not that some planets are doing computation, it is us who are doing the computing in trying to describe precisely what is happening.

Now, apply Feynmans cutesy quote to something like ecology or climate, or hilariously, anatomy and physiology, and tell me again how useful this criterion is for defining 'whether or not we understand a thing'.

I think some criterion like that (sure, maybe not literally 'build an artificial system') is really needed to keep us honest in talking about what we know and understand. 'Building a simulation' of the system is a good candidate.

Climate science is all about simulations and computational models - you turn the model on with certain parameters that fit history, and see what happens, and use it to predict possible future scenarios. Don't know were we are with computational physiology and anatomy.

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Re: List of All Laws of Nature

Postby Izawwlgood » Tue May 03, 2016 8:19 pm UTC

aph wrote:Apparently, Craig Venter wrote the sentence "What I cannot build, I don't understand" encoded in DNA to one of his synthetic cells.
This is extremely disingenuous of you - if you click on the link, you'll see that he's included 3 quotes in his 'watermarking' technology, and one of those quotes is the attributed Feynman quote. The other two are -

"TO LIVE, TO ERR, TO FALL, TO TRIUMPH, TO RECREATE LIFE OUT OF LIFE." - from James Joyce's A Portrait of the Artist as a Young Man.

and

"SEE THINGS NOT AS THEY ARE, BUT AS THEY MIGHT BE.”- a quote from the book, American Prometheus which discusses J. Robert Oppenheimer and the first atomic bomb.

So, clearly Venter has grabbed three quotes by inspirational people, and popped them into his watermarking tech in his synthetic organisms. Indeed, the Feynmann quote is apropos here, though hardly indicative of Venter believing it's impossible to understand something unless he built it.

aph wrote:We know how to synthesize organic molecules (either purely chemically, or extracting them from modified organisms)
Or by using molecular machinery derived from organisms.

aph wrote:we create DNA sequences at will
Again, by using modified organisms or molecular machinery derived from organisms.

aph wrote:Building an artificial heart or artificial kidneys is a similarly good criterion of showing an understanding of how they function.
I don't see why. One need not build a skyscraper to prove you can build a house, or more to the point, to prove you know how a hammer works. You're almost sounding alchemical in your claims here, truthfully - 'We must master complete control of the elements to understand how the proton works!'

aph wrote:Building an artificial cell from scratch will definitely be a proof of excellent understanding of single cell organisms.
Will it? We already have fantastic models/tools for understanding key biological phenomena. Synthetic organisms are another tool, but in many cases not superior to the ones we already have. For example, my thesis work involved using a fly model for understanding molecular events in neurodegenation. A synthetic organism wouldn't have been useful to me. The next lab over was studying actin - again, a synthetic organism isn't useful to them.

I'm not being pedantic - I'm trying to underline that you're making assertions based on an obviously incomplete understanding of the material you're opining on.

aph wrote:Worms are on the brink of being explained, but still no cigar.
The entire worm connectome is known. Yes, we cannot accurately model a molecularly accurate worm in a natural complex environment. That doesn't mean we can't 'explain' worms.

aph wrote:In that case, building a simulation, which is just a mathematical model, will be good enough proof.
Or we could... not... need to do that? Again, you're opining on something you don't seem to know much about.

aph wrote:I think some criterion like that (sure, maybe not literally 'build an artificial system') is really needed to keep us honest in talking about what we know and understand. 'Building a simulation' of the system is a good candidate.
And I, and indeed, most scientists working in the field, would disagree with you. We can say an awful lot about what we know without having to build it ourselves. One of the awesome things about biological systems is the tools we've developed to probe them, which lets us observe them, often in great detail, in real time, in vivo. There's a reason in vitro studies are in some cases limited. And you want to do this ex situ, or even in silico?

aph wrote:Climate science is all about simulations and computational models - you turn the model on with certain parameters that fit history, and see what happens, and use it to predict possible future scenarios. Don't know were we are with computational physiology and anatomy.
Right - notice, we aren't creating climate systems from scratch to study them. It's an observational field, and the computational models are aimed at best fit predictions.

Yeah. I think your understanding of experimentation is super flawed.
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Re: List of All Laws of Nature

Postby gmalivuk » Tue May 03, 2016 9:43 pm UTC

aph wrote:In that case, building a simulation, which is just a mathematical model, will be good enough proof.
How good does the simulation need to be?

Keep in mind that, despite having known about Newtonian gravitation for centuries, we still can't perfectly simulate the behavior of three or more mutually gravitating bodies.
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Re: List of All Laws of Nature

Postby jewish_scientist » Wed May 04, 2016 12:14 pm UTC

gmalivuk wrote:
aph wrote:Keep in mind that, despite having known about Newtonian gravitation for centuries, we still can't perfectly simulate the behavior of three or more mutually gravitating bodies.


I thought that we could model 3 bodies in orbit, they just always ended up crashing into each other at some point.
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Re: List of All Laws of Nature

Postby gmalivuk » Wed May 04, 2016 12:46 pm UTC

Which is therefore obviously not an accurate model.
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Re: List of All Laws of Nature

Postby jewish_scientist » Wed May 04, 2016 12:53 pm UTC

The solar system has more than 3 bodies in it, so we do not know if a 3 bodied system is destined to crash together or not. I know that the effect of most bodies in the system is very small on any 3 given bodies. However, maybe those really small forces contribute enough to stop awesome fireworks displays the collisions; or the solar system is unstable and the fireworks collisions have not happened yet.
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Re: List of All Laws of Nature

Postby aph » Wed May 04, 2016 12:57 pm UTC

Izawwlgood wrote:So, clearly Venter has grabbed three quotes by inspirational people, and popped them into his watermarking tech in his synthetic organisms. Indeed, the Feynmann quote is apropos here, though hardly indicative of Venter believing it's impossible to understand something unless he built it.

It's a cute quote, it's often used, people find it inspiring. Like Sagans 'extraordinary claims require extraordinary evidence'. If someone claims to *fully* understand life, he better show up with abiogenesis.

The fact that we can create genetically modified organisms is an indicator of just how much of genetics and cellular machinery we really understand. We still need to figure out some parts, but we obviously know a huge deal. It is a good heuristic, you don't need to understand how it is done in order to see that experts really do understand a lot.
aph wrote:Building an artificial heart or artificial kidneys is a similarly good criterion of showing an understanding of how they function.
I don't see why. One need not build a skyscraper to prove you can build a house, or more to the point, to prove you know how a hammer works. You're almost sounding alchemical in your claims here, truthfully - 'We must master complete control of the elements to understand how the proton works!'

When we figured out how the atom works, we made nuclear bombs and power plants. I mean, it is sort-of alchemical the way uranium transmutes to plutonium, isn't it?
So, the question is, why don't we have a fully functioning artificial heart or artificial kidneys, and what is missing from our understanding so that we could build them - they would certainly be very, very useful. It is not that we don't know nothing about the heart, we know a whole lot, but the artificial heart will be an extraordinary piece of evidence of extraordinary understanding.
aph wrote:Building an artificial cell from scratch will definitely be a proof of excellent understanding of single cell organisms.
Will it? We already have fantastic models/tools for understanding key biological phenomena. Synthetic organisms are another tool, but in many cases not superior to the ones we already have. For example, my thesis work involved using a fly model for understanding molecular events in neurodegenation. A synthetic organism wouldn't have been useful to me. The next lab over was studying actin - again, a synthetic organism isn't useful to them.

Genetically modified strains of flies are used all around for experimentation, they may not be "synthetic life forms" in the way Venter bacteria are (will be), but they are in a very real sense artificial, and by all means, not the only tool available.
aph wrote:Worms are on the brink of being explained, but still no cigar.
The entire worm connectome is known. Yes, we cannot accurately model a molecularly accurate worm in a natural complex environment. That doesn't mean we can't 'explain' worms.

We cannot fully explain the functioning of its nervous system, that is what we're ultimately interested in. There is no need for simulating molecular interactions, that may be way too much detail, unless we are specifically interested in molecular interactions. But really, it is not yet exactly clear what level of detail should be modeled in order to reproduce worm behavior, some recent models already do reproduce chemotaxis and klinotaxis if the worm is represented as a 'point'. Some simulate just a small number of sensory and motor neurons and partially reproduce behavior. We are definitely closing in on it, both from 'bottom up' and 'top down'.

aph wrote:I think some criterion like that (sure, maybe not literally 'build an artificial system') is really needed to keep us honest in talking about what we know and understand. 'Building a simulation' of the system is a good candidate.
And I, and indeed, most scientists working in the field, would disagree with you. We can say an awful lot about what we know without having to build it ourselves. One of the awesome things about biological systems is the tools we've developed to probe them, which lets us observe them, often in great detail, in real time, in vivo. There's a reason in vitro studies are in some cases limited. And you want to do this ex situ, or even in silico?

Oh, mosdef, in silico life will be an extremely useful tool. The only thing stopping us from making that tool is the fact we don't yet understand how to make it. Computer simulations are from the time they were first used in designing the nuclear bomb, referred to as "computational experiments" (often with the quote marks). They are cheaper than real experiments, you can do a whole lot of them in short time, and they evolve in precision and accuracy of prediction along with real experiments.

Right - notice, we aren't creating climate systems from scratch to study them. It's an observational field, and the computational models are aimed at best fit predictions.

That is the weakness of the field - if there were ways of validating the models in experiments (building climate systems from scratch), and not just waiting years and decades to see how they predicted the climate, that would go a long way in improving the models and our understanding of the climate.

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Re: List of All Laws of Nature

Postby Izawwlgood » Wed May 04, 2016 1:46 pm UTC

aph wrote: If someone claims to *fully* understand life, he better show up with abiogenesis.
And yet, you're the only person around her talking about *fully* understanding anything. Honestly, I think you have a difficult time with nuance - you continually talk about how little we know, and frame it as an issue based on the fact that we cannot *fully* create and 100% accurately model a thing in a Matrix like simulation.

aph wrote:The fact that we can create genetically modified organisms is an indicator of just how much of genetics and cellular machinery we really understand. We still need to figure out some parts, but we obviously know a huge deal. It is a good heuristic, you don't need to understand how it is done in order to see that experts really do understand a lot.
I think it really depends on the level of detail you want. We can build a skyscraper, but I don't think that means we fully understand the atom. We can cobble together Frankencells, but I don't think that means we fully understand the entire proteome. We can simulate bacterial colony growth, but I don't think that means we fully understand intracellular communication or dynamics.

And I think these glaringly obvious points would be more evident to you if you were more familiar with the fields.

aph wrote:The fact that we can create genetically modified organisms is an indicator of just how much of genetics and cellular machinery we really understand. We still need to figure out some parts, but we obviously know a huge deal. It is a good heuristic, you don't need to understand how it is done in order to see that experts really do understand a lot.
See, this is a funny statement to me - I think there is an enormous amount we don't have a clue about pertaining to genetics and cellular machinery, and that we can build a Frankencell doesn't actually tell us much about those things. There are better existing tools for studying them, and indeed, we use them.

aph wrote:When we figured out how the atom works, we made nuclear bombs and power plants. I mean, it is sort-of alchemical the way uranium transmutes to plutonium, isn't it?
Not really, I'd say - A ) I don't think we've really 'figured out' the atom yet, to the level of detail you're wanting, and B ) it's somewhat akin to claiming we understand forest ecology because we set a forest fire.


aph wrote:So, the question is, why don't we have a fully functioning artificial heart or artificial kidneys, and what is missing from our understanding so that we could build them - they would certainly be very, very useful. It is not that we don't know nothing about the heart, we know a whole lot, but the artificial heart will be an extraordinary piece of evidence of extraordinary understanding.
I'd say because we don't know enough presently about the molecular mechanisms underpinning development, namely, the interplay between the entire system in vivo, secondly, because of ethics involving stem cell research, and thirdly, because our bioreactor technology is still somewhat infantile.

A reminder to you - bioreactor technology will be useful for generating organs from scratch, but not implicitly towards understanding how those organs function. I'm sure there are SOME things we can learn from synthesized organs, but I wouldn't say that our understanding of said organs is inherently incomplete BECAUSE we haven't yet fully generated one from scratch.

aph wrote:Genetically modified strains of flies are used all around for experimentation, they may not be "synthetic life forms" in the way Venter bacteria are (will be), but they are in a very real sense artificial, and by all means, not the only tool available.
Believe me, I am well aware of how modified Drosophila are. They are as synthetic, say, as dog breeds are, and I didn't say they were the ONLY tool available, I said they were the best for the questions I was asking. If you came to me with a Frankencell and said 'behold, I have a fully synthetic neuron', I'd have said neat and gone back to my own research.

aph wrote:We cannot fully explain the functioning of its nervous system, that is what we're ultimately interested in. There is no need for simulating molecular interactions, that may be way too much detail, unless we are specifically interested in molecular interactions. But really, it is not yet exactly clear what level of detail should be modeled in order to reproduce worm behavior, some recent models already do reproduce chemotaxis and klinotaxis if the worm is represented as a 'point'. Some simulate just a small number of sensory and motor neurons and partially reproduce behavior. We are definitely closing in on it, both from 'bottom up' and 'top down'.
You really don't understand the field of neurobiology.

This may come as a shock to you, but a nervous system is not a system of wires. It's a complex system of highly interactive and sensitive cells, and this may be the most surprising thing to you, but these cells are sometimes called 'professional secretory cells'. What do you think neurons secrete and sense? Spoiler alert - molecular signals.

You're again making a lot of claims about what is un/known, and what we SHOULD know, and it's highly indicative that you simply are unfamiliar with the work that's going on in the field and are favoring your pet theories/opinions.

aph wrote:Oh, mosdef, in silico life will be an extremely useful tool. The only thing stopping us from making that tool is the fact we don't yet understand how to make it. Computer simulations are from the time they were first used in designing the nuclear bomb, referred to as "computational experiments" (often with the quote marks). They are cheaper than real experiments, you can do a whole lot of them in short time, and they evolve in precision and accuracy of prediction along with real experiments.
My point was that they're useful MODELS or EXPERIMENTS, they're not NECESSARY lynch pins in our understanding of a thing.

aph wrote:That is the weakness of the field - if there were ways of validating the models in experiments (building climate systems from scratch), and not just waiting years and decades to see how they predicted the climate, that would go a long way in improving the models and our understanding of the climate.
This is also demonstrative of a system that involves physical scales and durations that complicate research. We can, for example, observe a great deal about stars to learn about them, and we do not need to create a star in a lab in order to 'fully understand' stars.
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Re: List of All Laws of Nature

Postby aph » Wed May 04, 2016 1:47 pm UTC

gmalivuk wrote:
aph wrote:In that case, building a simulation, which is just a mathematical model, will be good enough proof.
How good does the simulation need to be?

Keep in mind that, despite having known about Newtonian gravitation for centuries, we still can't perfectly simulate the behavior of three or more mutually gravitating bodies.

How good? Well, good enough to be useful in some practical sense, in predicting how changes in some relevant variable X will affect changes in variable Y.

The 3-body problem is somewhat of a special case, we do have pretty accurate multi-body simulations. There is no perfection, there is always some amount of error, but the solar system model is accurate in predicting eclipses within thousands of years, based on fitting historical mentions of eclipses link.

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Re: List of All Laws of Nature

Postby aph » Wed May 04, 2016 2:10 pm UTC

Izawwlgood wrote:
aph wrote: If someone claims to *fully* understand life, he better show up with abiogenesis.
And yet, you're the only person around her talking about *fully* understanding anything. Honestly, I think you have a difficult time with nuance - you continually talk about how little we know, and frame it as an issue based on the fact that we cannot *fully* create and 100% accurately model a thing in a Matrix like simulation.

No, the claim is we don't understand even the very basic principles of information transfer in the nervous systems, and the proof of that claim is that we don't have an accurate model (not necessarily precise) of how signaling between neurons (including electrical and chemical signals) produces the behavior of a very small animal whose whole connectome is known.

Similarly, we don't understand how the simplest neural circuits in humans, those for spinal-level motor control, produce movements; and the proof of that is the lack of such models or artificial system doing the same thing. It is not at all about the level of detail, it is about the 'laws of nature', that this topic is about, the first principles that describe the interaction between the environment and the organism.

edit:
Now, granted, information transfer is not the only important or interesting thing in neuroscience, not to mention neurobiology or neurology, but it does have potential to advance the study of all the other interesting parts, since 'information' is really just a different way of talking about quantitative modeling of nervous systems.

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Re: List of All Laws of Nature

Postby gmalivuk » Wed May 04, 2016 2:16 pm UTC

jewish_scientist wrote:The solar system has more than 3 bodies in it, so we do not know if a 3 bodied system is destined to crash together or not. I know that the effect of most bodies in the system is very small on any 3 given bodies. However, maybe those really small forces contribute enough to stop awesome fireworks displays the collisions; or the solar system is unstable and the fireworks collisions have not happened yet.
We know that our computed solutions are inexact, from a purely mathematical perspective. It doesn't matter that the real solar system has more bodies or that we haven't observed it for an infinite amount of time.

We *know* that a simulation using Newton's laws doesn't give the same results as a reality using Newton's laws.

(Also, the inexactitude is for all numbers greater than 2. You don't get out of the problem by adding more objects.)
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Re: List of All Laws of Nature

Postby Izawwlgood » Wed May 04, 2016 3:08 pm UTC

aph wrote:No, the claim is we don't understand even the very basic principles of information transfer in the nervous systems
That's an even more moronic claim than the one I thought you were making. Again, depending on what level of detail you want to look, you are demonstrably and factually wrong in this statement.

aph wrote:and the proof of that claim is that we don't have an accurate model (not necessarily precise) of how signaling between neurons (including electrical and chemical signals) produces the behavior of a very small animal whose whole connectome is known.
You've actually just indicated two entirely separate things. The capacity to accurately model signaling between neurons, in terms of electrochemical signaling, is something we are quite good at and have some brilliant models for. Mapping the worm connectome was done both with ephys and molecular experimentation. Now, creating an accurate replicate of said connectome is another matter, and is NOT necessary for our understanding of it.
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Re: List of All Laws of Nature

Postby aph » Wed May 04, 2016 3:29 pm UTC

Izawwlgood wrote:
aph wrote:No, the claim is we don't understand even the very basic principles of information transfer in the nervous systems
That's an even more moronic claim than the one I thought you were making. Again, depending on what level of detail you want to look, you are demonstrably and factually wrong in this statement.

Your proof that we understand how information transfer results in behavior is a link to the wiki about neurotransmitters? I'll just agree I'm a moron for wasting my time discussing with you.

There is plenty of people that don't share your opinion and see the information transfer/flow between the organism and the environment in production of behavior as one of the most important unsolved problems in neuroscience. Maybe you're just not that into those sorts of things, or interpret their claims somehow differently then I do, I don't care to find out.

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Re: List of All Laws of Nature

Postby Soupspoon » Wed May 04, 2016 3:49 pm UTC

aph wrote:but the solar system model is accurate in predicting eclipses within thousands of years
Minor pedantry... It'd best be described as being sufficiently accurate over thousands of years (the larger the timescale, the better we are running the simulation in the long-term), whilst also having those future predictions accurate to within seconds, minutes or whatever (the smaller the timescale, the better we are at extracting that last ounce of precision of an otherwise known event).

:D

(Now, this leads to me wondering when we.'give up' in making a prediction. i.e. how far in the future is the first solar eclipse (say) where the current error-bars, never mind actual "unknown unknowns" of an orbit-shifting variety/etc, make it indefinite whether it will be an eclipse, or not? Presumably a pole-scraping penumbra where it is uncertain whether an arctic/antarctic explorer needs to stand on a step-ladder or not for their instrumentation to detect the slightest of slight bites taken out of the Sun by an extremity of the Moon. May be subject to what we've built/sunk at the relevent pole, or constructed ourselves on the given limb of the Moon's 'horizon zone', even, but that's part of the unknown unknowns bit, really.)

1 If you prefer to zero in on whether it'll be full (somewhere) or merely partial, or the Moon might only give an annular eclipse at the distance and offset it lies upon at the time, feel free. Umbral/penumbral uncertainties are as good as penumbral/nothing ones, in this little idle pondering of mine. :P

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Re: List of All Laws of Nature

Postby PAstrychef » Wed May 04, 2016 4:20 pm UTC

aph wrote:
Izawwlgood wrote:
aph wrote:No, the claim is we don't understand even the very basic principles of information transfer in the nervous systems
That's an even more moronic claim than the one I thought you were making. Again, depending on what level of detail you want to look, you are demonstrably and factually wrong in this statement.

Your proof that we understand how information transfer results in behavior is a link to the wiki about neurotransmitters? I'll just agree I'm a moron for wasting my time discussing with you.

There is (sic) plenty of people that don't share your opinion and see the information transfer/flow between the organism and the environment in production of behavior as one of the most important unsolved problems in neuroscience. Maybe you're just not that into those sorts of things, or interpret their claims somehow differently then I do, I don't care to find out.

Bolded by me. People have cut you all kinds of slack in this discussion. If you don't care to find out about the actual science of neurotransmission and how well it can be modeled, then I suggest you find a place more agreeable to spout nonsense in.
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Re: List of All Laws of Nature

Postby gmalivuk » Wed May 04, 2016 4:27 pm UTC

PAstrychef wrote:People have cut you all kinds of slack in this discussion. If you don't care to find out about the actual science of neurotransmission and how well it can be modeled, then I suggest you find a place more agreeable to spout nonsense in.
Quoted for mod voice.
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Re: List of All Laws of Nature

Postby aph » Wed May 04, 2016 4:34 pm UTC

@Soupspoon, thanks!

@PAstrychef & gmalivuk, That is an interesting interpretation of the bold. No further comment. :D

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Re: List of All Laws of Nature

Postby jewish_scientist » Fri May 06, 2016 2:04 pm UTC

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Re: List of All Laws of Nature

Postby Izawwlgood » Fri May 06, 2016 3:32 pm UTC

So, out of curiosity, would you consider the pKa of amino acids a 'law'?

What about the coding paradigm of DNA? Of course, a different system may use a different code, though, maybe not!
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Re: List of All Laws of Nature

Postby jewish_scientist » Fri May 06, 2016 6:46 pm UTC



I would say no and I understand if someone else said yes. The reason is that those are the properties of an object. If there were a pattern to how these properties correlate (e.g. as the mass of a amino acid increases, so does the pKa value) then I would consider the formal statement expressing that pattern a law; I do not know of any such pattern nor do I see one on that table.

On the other hand, I have said multiple times that laws must be in the form "If A then B". Let A equals a set arrangement of a set number of atoms and let B equals the pKa value of those atoms as a whole. The statement "If A then B" is true with these definitions, so someone could argue that means this statement is a law.

What about the coding paradigm of DNA? Of course, a different system may use a different code, though, maybe not!


I have a book at home that mentions bacteria that do not use the same genetic code as other organism. To be clear, they use the same DNA base pairs and they use the same amino acids to create proteins; what is different is that one codon can correspond to different amino acids depending on what organism is building the protein. When I first learned this, I thought my head would EXPLODE! That is just SO COOL AND AWESOME! If you do not understand why I feel that way, nothing I write here explain.
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Re: List of All Laws of Nature

Postby Izawwlgood » Fri May 06, 2016 7:06 pm UTC

jewish_scientist wrote:The reason is that those are the properties of an object.
Wouldn't you say that 'properties of an object' could be a way of describing what, say, Coulombs Law is describing?

jewish_scientist wrote:If there were a pattern to how these properties correlate (e.g. as the mass of a amino acid increases, so does the pKa value) then I would consider the formal statement expressing that pattern a law; I do not know of any such pattern nor do I see one on that table.
The pKa is a function of the amino acid - changing the amino acid changes the pKa. I bet if you used, say, different isotopes of the atoms in each amino acid, you'd get slightly different pKa, but all that's really doing is adding another variable to the observed pKa. pKa is just measuring the acidity, which is, I would say (iirc) a chemical constant.

jewish_scientist wrote:I have a book at home that mentions bacteria that do not use the same genetic code as other organism. To be clear, they use the same DNA base pairs and they use the same amino acids to create proteins; what is different is that one codon can correspond to different amino acids depending on what organism is building the protein. When I first learned this, I thought my head would EXPLODE! That is just SO COOL AND AWESOME! If you do not understand why I feel that way, nothing I write here explain.
I may be wrong, but I think you're referring to how some bacteria use different tRNAs to call for amino acids from a given codon? I wouldn't be TOTALLY surprised if there are lifeforms that literally use a different genetic language, say, GGX to call for Alanine instead of Glycine, but I'd definitely be a little surprised.
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Re: List of All Laws of Nature

Postby jewish_scientist » Tue May 10, 2016 1:28 pm UTC

Izawwlgood wrote:
jewish_scientist wrote:The reason is that those are the properties of an object.
Wouldn't you say that 'properties of an object' could be a way of describing what, say, Coulombs Law is describing?

Coulombs Law takes two properties and states that there is a relationship between them. I did not see any relationship between the pKa values and another property, therefor I would not consider it a law.

jewish_scientist wrote:
If there were a pattern to how these properties correlate (e.g. as the mass of a amino acid increases, so does the pKa value) then I would consider the formal statement expressing that pattern a law; I do not know of any such pattern nor do I see one on that table.
The pKa is a function of the amino acid - changing the amino acid changes the pKa. I bet if you used, say, different isotopes of the atoms in each amino acid, you'd get slightly different pKa, but all that's really doing is adding another variable to the observed pKa. pKa is just measuring the acidity, which is, I would say (iirc) a chemical constant.

This is the counterargument that amino acids pKa values are a law. It is very good and hard to argue against. Formally, it is true; however, if we started listing everything that is formally a law things would become very redundant. I would say that a more general form of this idea may be considered a law informally because it would include this law in it. For example:

The Constant pKa Law = Identical molecules have identical pKa values.

jewish_scientist wrote:I have a book at home that mentions bacteria that do not use the same genetic code as other organism. To be clear, they use the same DNA base pairs and they use the same amino acids to create proteins; what is different is that one codon can correspond to different amino acids depending on what organism is building the protein. When I first learned this, I thought my head would EXPLODE! That is just SO COOL AND AWESOME! If you do not understand why I feel that way, nothing I write here explain.
I may be wrong, but I think you're referring to how some bacteria use different tRNAs to call for amino acids from a given codon? I wouldn't be TOTALLY surprised if there are lifeforms that literally use a different genetic language, say, GGX to call for Alanine instead of Glycine, but I'd definitely be a little surprised.

A DNA codon always corresponds to a single tRNA, which always corresponds to a single amino acid; therefor a DNA codon corresponds to a single amino acid because of the transitive property. I will look up exactly what my book said and post it here later. I think that most of the organisms that use alternative DNA codes are obscure bacteria and archaea. The book was discussing the definition of life and used this as proof that life cannot be defined as all organisms that have a common ancestor. I suppose we can all agree that this law is true:

The Constant Codon Law = Every ribosome in every organism of a given species interpretes tRNA identically.
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Re: List of All Laws of Nature

Postby BlackSails » Wed May 11, 2016 3:47 am UTC

jewish_scientist wrote:
The Constant Codon Law = Every ribosome in every organism of a given species interpretes tRNA identically.


Selenocystine?


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