1039: "RuBisCO"

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cellocgw
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Re: 1039: "RuBisCO"

Postby cellocgw » Fri Apr 06, 2012 1:09 pm UTC

StClair wrote:
everycredit wrote:
Diadem wrote:Chemists? Really? What does RuBisCO have to do with chemistry? It's straight up biology.

Biology is just applied chemistry.

Chemistry is just applied physics.

This goes on for a while. Top down:
Philosophy -> math -> physics -> {chemistry, engineering} -> .... turtles.
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Re: 1039: "RuBisCO"

Postby Antior » Fri Apr 06, 2012 1:10 pm UTC

WillParry wrote:The way I understand it, is that there's an other flaw: it's really slow. It only catalyzes about three reactions per second. So to get any significant amount of product, a lot of the enzyme is needed. Rubisco was explained to me as being a leaky old steam machine.

Also, something to think about: every organic molecule in your body was orginally created by Rubisco!

Oh, and biology might be applied chemistry, but in my experience chemists are kind of scared by biochemical reactions. Doesn't really stand to reason they'd use it as a safeword.


Chemist reporting!

This is not true. In the real world, things are like this:
Within a few months of starting an university level chemistry study, the students naturally divide themselves in two camps.
On one side (let's call it A), there's the biochemists and organic chemists. They tend to use lots of little empirical rules and realize that a large part of their field is too complicated to understand with pure math, unless you have lots of time and a good supercomputer or distributed computing project running. The other side (B) makes fun of them because they are so INEXACT. B doesn't see how you can understand anything about anything without exact mathematical rules.

The other side (B) contains inorganic chemists and physical chemists. They tend to use formulas, math and 'hard' laws of nature to figure things out. Side A makes fun of THEM because they keep wasting their time playing with useless numbers, while they could've been doing experiments in the lab. A doesn't see how math can help you figure out things in a purely empirical science.

Of course, A uses math too, while B does laboratory experiments as well. If you analyse it, this division in camps doesn't make that much sense scientifically. It still happens. Probably a social thing. Similar to the differences between biologists and physicists, but a bit less clear.

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Re: 1039: "RuBisCO"

Postby javahead » Fri Apr 06, 2012 1:26 pm UTC


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Re: 1039: "RuBisCO"

Postby J Thomas » Fri Apr 06, 2012 2:03 pm UTC

pɔʞx wrote:
StClair wrote:
everycredit wrote:Biology is just applied chemistry.

Chemistry is just applied physics.

Almost there, almost there...
Wait for it...


Physics is just applied reductionism.
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Re: 1039: "RuBisCO"

Postby The Old Wolf » Fri Apr 06, 2012 2:20 pm UTC

I swear, if it weren't for Wikipedia I wouldn't get half of what Munro does. I suppose, however, I'm to be excused for today since I'm not expected to be into BDSM.
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Re: 1039: "RuBisCO"

Postby PaulBurnett » Fri Apr 06, 2012 2:27 pm UTC

"Dihydrogenmonoxide" is a good safeword, as it's not a "normal" word that one might accidentally utter.

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Re: 1039: "RuBisCO"

Postby Роберт » Fri Apr 06, 2012 2:46 pm UTC

Louis XIV wrote:I bet Randalph has been watching the Youtube channel "Crashcourse Biology". In the last-but-second episode, they talk a lot about RuBisCo.

See http://www.youtube.com/watch?v=sQK3Yr4Sc_k&list=UUX6b17PVsYBQ0ip5gyeme-Q&index=6&feature=plcp, min 9:13.

Who is Randalph?
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Re: 1039: "RuBisCO"

Postby keltor » Fri Apr 06, 2012 2:49 pm UTC

Interestingly, with 16years in the BDSM community, I have met 0 physical science people in the community. In fact I've probably met people from every other industry under the sun OTHER than physical science. Nursing, teaching and various computer fields far and away dominate the community, in my experience.

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Re: 1039: "RuBisCO"

Postby StClair » Fri Apr 06, 2012 3:01 pm UTC

kargoth wrote:So much *woosh* going on in this thread.

I'll break up the fun:
http://xkcd.com/435/

Got it in one.
(I thought of linking it myself, but we still had math to go...)

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Re: 1039: "RuBisCO"

Postby JustDoug » Fri Apr 06, 2012 3:20 pm UTC

radtea wrote:[
This. Kids today and their reductionism.

"Just" in ordinary English is a marker of falsehood or impossibility. "X is just Y" is what you say when you know damned well that "X is Y" is clearly and obviously false... so false it would make you sound like a moron to say it.

It follows from this that any question of the form "Can't you just do XYZ?" has the same answer: "No." [On the rare occasions when I've foregone self-employment for that weird alternative lifestyle known as "having a job" I've had to explain this to my boss so they stop asking me to "just" do stuff and restrict their requests to things that are actually possible.]


"In this particular case, 'Y' may be substitued for 'X'."

Just another qualifier, s'all.

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Re: 1039: "RuBisCO"

Postby keltor » Fri Apr 06, 2012 4:01 pm UTC

keltor wrote:Interestingly, with 16years in the BDSM community, I have met 0 physical science people in the community. In fact I've probably met people from every other industry under the sun OTHER than physical science. Nursing, teaching and various computer fields far and away dominate the community, in my experience.



In reply to my own comment. Most the of the Math people I know who are not in Academia can easily be lumped into "computer fields" even if they don't like it - I say this as a "Senior Mathematician" :D

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Re: 1039: "RuBisCO"

Postby TheKrikkitWars » Fri Apr 06, 2012 4:07 pm UTC

Antior wrote:
Spoiler:
Chemist reporting!

This is not true. In the real world, things are like this:
Within a few months of starting an university level chemistry study, the students naturally divide themselves in two camps.
On one side (let's call it A), there's the biochemists and organic chemists. They tend to use lots of little empirical rules and realize that a large part of their field is too complicated to understand with pure math, unless you have lots of time and a good supercomputer or distributed computing project running. The other side (B) makes fun of them because they are so INEXACT. B doesn't see how you can understand anything about anything without exact mathematical rules.

The other side (B) contains inorganic chemists and physical chemists. They tend to use formulas, math and 'hard' laws of nature to figure things out. Side A makes fun of THEM because they keep wasting their time playing with useless numbers, while they could've been doing experiments in the lab. A doesn't see how math can help you figure out things in a purely empirical science.


This is very true; you then get subdivisions in that too, A(i) are synthetic chemists, A(ii) are analytical & bio-chemists and A(iii) are computational chemists who got lost...

A(i) think they're better than the others because their discipline needs wide ranging knowlege, finesse, experience and a hearty tolerence to solvent inhalation.
A(ii) are meticulous, predictable, chemically perspicacious and believe the people from A(i) to be silly for working in a field where the success of any given research is uncertain at best...
A(iii) are terribly bright, but posess a certain intellectual masochism that makes them either terrbly dull or much too "interesting".
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Re: 1039: "RuBisCO"

Postby evac156 » Fri Apr 06, 2012 4:19 pm UTC

I was thinking of my field, software development, and what would be a good/bad safeword.

I think it would be funny to give someone a safeword of "if-then-else." Because if someone yells out, "IF! THEN! ELSE!" in the middle of a scene, I could simply reply, "Oh no, I make the rules here!"

Okay. We all know, "Unhandled exception!" would be the best and most obvious choice.

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Re: 1039: "RuBisCO"

Postby LqqkOutRigger » Fri Apr 06, 2012 4:36 pm UTC

Since "ase" usually indicates an enzyme, I'm surprised that someone would choose a catalyst to stop a scene...

Maybe an enzyme inhibitor would make more sense, such as: Diisopropylfluorophosphate ;)

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Re: 1039: "RuBisCO"

Postby Moonfish » Fri Apr 06, 2012 4:50 pm UTC

Use “Bananas”

Most people use “Bananas” because it’s easy to say even if you have something in your mouth.
As an engineer can you think of other optimal safe words?
  • Short
  • Not typical in erotic dialogue
  • Doesn’t require your tong to be free

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Re: 1039: "RuBisCO"

Postby Scars Unseen » Fri Apr 06, 2012 5:15 pm UTC

Moonfish wrote:Use “Bananas”

Most people use “Bananas” because it’s easy to say even if you have something in your mouth.
As an engineer can you think of other optimal safe words?
  • Short
  • Not typical in erotic dialogue
  • Doesn’t require your tong to be free


Not an engineer, but you could probably manage "hummus" in most circumstances.

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Re: 1039: "RuBisCO"

Postby pootle » Fri Apr 06, 2012 5:29 pm UTC

Scars Unseen wrote:
Moonfish wrote:Use “Bananas”

Most people use “Bananas” because it’s easy to say even if you have something in your mouth.
As an engineer can you think of other optimal safe words?
  • Short
  • Not typical in erotic dialogue
  • Doesn’t require your tong to be free


I can vocalise most words whatever is happening to my tong...
but click constants are good if your mouth is full

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Re: 1039: "RuBisCO"

Postby bob » Fri Apr 06, 2012 6:08 pm UTC

most of the chemists i know (and i'm a chemist myself) tend to prefer trivial names or abbreviations to (complex and time consuming) systematic names... who would speak of "sodium dodecyl sulfate polyacrylamide gel electrophoresis", "incredible natural-abundance double-quantum transfer experiment", "1,3-Dimethyltetrahydropyrimidin-2(1H)-one", "attenuated total reflectance fourier transform infrared spectroscopy" or "Ribulose-1,5-bisphosphatecarboxylaseoxygenase", if one could say "sds-page", "inadequate", "dmpu", "aft-ftir" or "rubisco"... (of course, every abbreviation must be explained at the end of your thesis...).

btw, the most interesting abbreviation i've come across is "CuNT" ... for "Copper Nano Tubes"

@moonfish: "honolulu" might work as well

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Re: 1039: "RuBisCO"

Postby rcox1 » Fri Apr 06, 2012 6:18 pm UTC

WillParry wrote:
ahammel wrote:
Diadem wrote:
ijuin wrote:http://en.wikipedia.org/wiki/Rubisco

For those who care, RuBisCO is the most abundant protein in most plants, as it is a key enzyme in photosynthesis.

It's actually the most abundant protein in the world.

The reason for that is that it is fundamentally flawed. That O at the end of the name shouldn't be there. Rubisco facilitates the first step of carbon fixation. It binds atmospheric CO2 so that plants can use it in their photosynthesis. Hence the "carboxylase" part of the name. However it also binds to 02, sending the entire photosynthesis cycle hurling off a cliff. Plants compensate for this by making ridiculous amounts of rubisco, so they'll always have enough.

How does that work? Surely, given constant oxygen, more RuBisCO just means more photorespiration? I can't say I've ever heard of increased RuBisCO expression as an anti-photorespiration measure.


The way I understand it, is that there's an other flaw: it's really slow. It only catalyzes about three reactions per second. So to get any significant amount of product, a lot of the enzyme is needed. Rubisco was explained to me as being a leaky old steam machine.

Also, something to think about: every organic molecule in your body was orginally created by Rubisco!

Oh, and biology might be applied chemistry, but in my experience chemists are kind of scared by biochemical reactions. Doesn't really stand to reason they'd use it as a safeword.


It my experience anyone crazy enough to do practical organic chemistry have a death wish. Leaving the relatively safety of physics and inorganic chemistry is insane. I would not doubt anything.

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Re: 1039: "RuBisCO"

Postby fukdiomam » Fri Apr 06, 2012 6:22 pm UTC

We get it Randall, you're into bdsm.

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Re: 1039: "RuBisCO"

Postby vilidice » Fri Apr 06, 2012 6:42 pm UTC

"FLÜGGÅƎNK∂€ČHIŒβØL∫ÊN"

if you use germanic cues it's, kind of, sort of, close to:

Fluug-awaenk-deuro-chhi-osh-yul-sehn

∂ and ∫ don'thave a great deal of pronunciation cues to draw on (being partial derivative and integral symbols) so I used "d" and s from my (very) limited experience. (I also don't have a huge command of the phonetic alphabet, or expect terribly many others to, so I tried to get as close as possible without it) in this case the ae should be pronounced with a long "A", and "yu" as a long "U".

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Re: 1039: "RuBisCO"

Postby Whitekiboko » Fri Apr 06, 2012 7:05 pm UTC

My initial reaction was "It must suck to be a german chemist."

Роберт wrote:Who is Randalph?


A cartoonist who died. But he hadn't made enough socially awkward people laugh and was sent back.

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Re: 1039: "RuBisCO"

Postby TheKrikkitWars » Fri Apr 06, 2012 7:19 pm UTC

rcox1 wrote:
WillParry wrote:Oh, and biology might be applied chemistry, but in my experience chemists are kind of scared by biochemical reactions. Doesn't really stand to reason they'd use it as a safeword.


It my experience anyone crazy enough to do practical organic chemistry have a death wish. Leaving the relatively safety of physics and inorganic chemistry is insane. I would not doubt anything.


[Puts hand up] :D

I wouldn't say that chemists are scared of biochemical reactions so much as they have limited relevance and require different techniques; as such it's seen to be best left to the specialists (biochemists and biochemical engineers)... This said, more and more attention is being given to what we can learn by looking at the mechanisms of biosynthetic reactions, especially in the natural products relm.
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Re: 1039: "RuBisCO"

Postby harperska » Fri Apr 06, 2012 7:41 pm UTC

vilidice wrote:"FLÜGGÅƎNK∂€ČHIŒβØL∫ÊN"

if you use germanic cues it's, kind of, sort of, close to:

Fluug-awaenk-deuro-chhi-osh-yul-sehn

∂ and ∫ don'thave a great deal of pronunciation cues to draw on (being partial derivative and integral symbols) so I used "d" and s from my (very) limited experience. (I also don't have a huge command of the phonetic alphabet, or expect terribly many others to, so I tried to get as close as possible without it) in this case the ae should be pronounced with a long "A", and "yu" as a long "U".



Fluug-owaenk-deuro-chhi-oss-yul-sehn
or
Fluug-owaenk-deuro-chhi-ob-yul-sehn

depending on whether 'β' is supposed to be a greek beta or a german eszett.

The letter Å is of swedish origin, where it is pronounced "oh"

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Re: 1039: "RuBisCO"

Postby Antior » Fri Apr 06, 2012 7:42 pm UTC

vilidice wrote:"FLÜGGÅƎNK∂€ČHIŒβØL∫ÊN"

if you use germanic cues it's, kind of, sort of, close to:

Fluug-awaenk-deuro-chhi-osh-yul-sehn

∂ and ∫ don'thave a great deal of pronunciation cues to draw on (being partial derivative and integral symbols) so I used "d" and s from my (very) limited experience. (I also don't have a huge command of the phonetic alphabet, or expect terribly many others to, so I tried to get as close as possible without it) in this case the ae should be pronounced with a long "A", and "yu" as a long "U".


IMO the partial derivative symbol looks more similar to the Old English and Icelandic letter ð which is the English th-sound.

Whitekiboko wrote:My initial reaction was "It must suck to be a german chemist."

Until about half a century ago, nearly all chemical literature was in German. If you were bad at German, you wouldn't become a good chemist. It must have been a terrible time for science. At least Latin used to be classy... Obviously, scientific literature is mostly in English now, even the still very important German journal 'Angewandte Chemie' has an English International Edition. However, here in Holland, lots of high school science classrooms still have this ancient-looking German "Periodensystem der Elemente" on the wall.

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Re: 1039: "RuBisCO"

Postby Whizbang » Fri Apr 06, 2012 7:58 pm UTC

Do any other non-chemists/biologists/physicists just read the first couple of syllables and the tag “saurus” on the end?

“Ribulosaurus”

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Re: 1039: "RuBisCO"

Postby bob » Fri Apr 06, 2012 8:01 pm UTC

Whitekiboko wrote:My initial reaction was "It must suck to be a german chemist."


Why that?

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Re: 1039: "RuBisCO"

Postby DannyboyO1 » Fri Apr 06, 2012 8:14 pm UTC

This entire subject confuses the hell out of me. The purpose of a safeword is to swiftly indicate that things aren't right in a circumstance where cries of pain are to be expected. It should be easy to remember and unlike anything that would come up in the course of roleplay...

So... why doesn't everyone use "safeword" as their safeword?
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Re: 1039: "RuBisCO"

Postby Persona » Fri Apr 06, 2012 8:17 pm UTC

All you guys, aren't any of you wondering about why megan and cueball would overhear someone's safe word while sitting and reading? Is someone doing BDSM in the library? Or is the porn they're watching on an off-screen TV so boring that they resort to reading and reddit? And if so, why is there chemist porn anyways? These questions need answers!

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Re: 1039: "RuBisCO"

Postby da Doctah » Fri Apr 06, 2012 8:23 pm UTC

FarmerJoe wrote: "FLÜGGÅƎNK∂€ČHIŒβØL∫ÊN"

I have no clue how to pronounce that.


Neither do I, but there's a "buy two get one free" sale on it at IKEA.

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Re: 1039: "RuBisCO"

Postby Tyrannosaur » Fri Apr 06, 2012 8:25 pm UTC

J Thomas wrote:
pɔʞx wrote:
StClair wrote:
everycredit wrote:Biology is just applied chemistry.

Chemistry is just applied physics.

Almost there, almost there...
Wait for it...


Physics is just applied reductionism.


Reductionism is just applied recuctionism.

Reductionism.
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Re: 1039: "RuBisCO"

Postby CanadianNomad » Fri Apr 06, 2012 8:40 pm UTC

I think we need to explore the other side of this: How can we verify someone's public key signature in the heat of the moment...

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Re: 1039: "RuBisCO"

Postby dan_dassow » Fri Apr 06, 2012 8:54 pm UTC

Kyreles wrote:
StClair wrote:
everycredit wrote:Biology is just applied chemistry.

Chemistry is just applied physics.


Physics is just applied math.


Math is just applied magic. :wink:

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Re: 1039: "RuBisCO"

Postby Pfhorrest » Fri Apr 06, 2012 9:06 pm UTC

mric wrote:Indeed, you could also argue that the inability of chemistry to describe biological processes with the appropriate natural types of biological explanations combined with the reality of multiple realisability ensure that any epistemic reduction to chemistry is necessarily disjunctive. Though that isn't, in my view, a knockout blow for reductionism, it does point out the false assumption behind the word 'just'.

Multiple realizability doesn't refute reductionism.

Software is multiply realizable on different hardware, but whenever some software is doing something, there is nothing more happening than some hardware doing something. Software is not ontologically separate from hardware, it is not a separate thing beyond the hardware; it is an abstraction of certain functions the hardware can perform. That different hardware can perform those same functions doesn't change that fact.

Likewise, when something biological is happening, there is nothing more happening than something chemical happening. Biology is not ontologically separate from chemistry, there is no vital force or anything beyond the chemical processes which make up a biological process. But biological processes are abstractions of certain functions of chemical processes; multiple chemical processes can perform the function of a given biological process. That doesn't mean anything more than chemistry is going on whenever biology is going on.

Likewise chemistry to physics a step below, and psychology to biology a step above (that's really just back to software/hardware again).

Physics, on the other hand, does not reduce to math, because there is something ontologically different between a mathematical model and a physical system that fits that model; namely, the physical system exists, where as the mathematical model only describes something that might exist.

I might accept a reduction of math to philosophy, though philosophy is also dependent in many ways on math (in the form of logic); either way, the two are up on the same level outside the reductionist chain down to physics, as they are second-order disciplines used to determine things about the things discussed in the disciplines in that chain. "Art" in a certain sense (critical aesthetic judgement) is out on that second-level tier as well.

radtea wrote:"Just" in ordinary English is a marker of falsehood or impossibility. "X is just Y" is what you say when you know damned well that "X is Y" is clearly and obviously false... so false it would make you sound like a moron to say it.

It follows from this that any question of the form "Can't you just do XYZ?" has the same answer: "No." [On the rare occasions when I've foregone self-employment for that weird alternative lifestyle known as "having a job" I've had to explain this to my boss so they stop asking me to "just" do stuff and restrict their requests to things that are actually possible.]

No, "just" means "no more than".

"Psychology is no more than biology".
"Biology is no more than chemistry."
"Chemistry is no more than physics."

But physics is not just math -- that is to say, it is more than math. Simple negation.
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Re: 1039: "RuBisCO"

Postby Gauteamus » Sat Apr 07, 2012 12:14 am UTC

cellocgw wrote:This goes on for a while. Top down:
Philosophy -> math -> physics -> {chemistry, engineering} -> .... turtles.


You got it wrong there, the dependencies are actually:
biology -> chemistry -> physics -> math -> turtles -> turtles -> turtles -> turtles -> all the way down

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Re: 1039: "RuBisCO"

Postby iChef » Sat Apr 07, 2012 1:43 am UTC

FarmerJoe wrote: "FLÜGGÅƎNK∂€ČHIŒβØL∫ÊN"

I have no clue how to pronounce that.


I believe it's pronounced "driving enjoyment".
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Re: 1039: "RuBisCO"

Postby mgbeach » Sat Apr 07, 2012 1:48 am UTC

Physics is just applied Omnipotence

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Re: 1039: "RuBisCO"

Postby J Thomas » Sat Apr 07, 2012 2:25 am UTC

Pfhorrest wrote:
mric wrote:Indeed, you could also argue that the inability of chemistry to describe biological processes with the appropriate natural types of biological explanations combined with the reality of multiple realisability ensure that any epistemic reduction to chemistry is necessarily disjunctive. Though that isn't, in my view, a knockout blow for reductionism, it does point out the false assumption behind the word 'just'.

Multiple realizability doesn't refute reductionism.

Software is multiply realizable on different hardware, but whenever some software is doing something, there is nothing more happening than some hardware doing something. Software is not ontologically separate from hardware, it is not a separate thing beyond the hardware; it is an abstraction of certain functions the hardware can perform. That different hardware can perform those same functions doesn't change that fact.


If you can analyze your software in terms of abstract gates, and then it turns out you can create physical gates using electricity in transistors or water in pipes or air in ducts etc, I wouldn't think that the electricity or water or air are primary to the software. You can throw away all the details that aren't important for gates to work. (Of course one will be faster or smaller or cheaper than another, etc. And that's vitally important to engineers who want to solve real problems.)

Likewise, when something biological is happening, there is nothing more happening than something chemical happening. Biology is not ontologically separate from chemistry, there is no vital force or anything beyond the chemical processes which make up a biological process. But biological processes are abstractions of certain functions of chemical processes; multiple chemical processes can perform the function of a given biological process. That doesn't mean anything more than chemistry is going on whenever biology is going on.

Likewise chemistry to physics a step below, and psychology to biology a step above (that's really just back to software/hardware again).

Physics, on the other hand, does not reduce to math, because there is something ontologically different between a mathematical model and a physical system that fits that model; namely, the physical system exists, where as the mathematical model only describes something that might exist.


Thank you! You have provided a perfect example showing why I say physics is nothing but reductionism.

I think your claim is eminently defensible, if we are careful with our definitions. All we need is for physics to be the study of everything that can or can't happen in the real world plus everything that can or can't happen in hypothetical alternate universes, and then all the sciences are branches of physics. Along with chess, political science, business management, and poetry.

Physics, on the other hand, does not reduce to math, because there is something ontologically different between a mathematical model and a physical system that fits that model; namely, the physical system exists, where as the mathematical model only describes something that might exist.


You make a strong case that physics reduces to philosophy. Arguing that the physical system exists is a philosophical claim which might deserve very careful study.
The Law of Fives is true. I see it everywhere I look for it.

jokershigh
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Re: 1039: "RuBisCO"

Postby jokershigh » Sat Apr 07, 2012 3:09 am UTC

A Biologist's safe word is actually "TAG"

Rotherian
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Re: 1039: "RuBisCO"

Postby Rotherian » Sat Apr 07, 2012 3:11 am UTC

Pfhorrest wrote:
Likewise, when something biological is happening, there is nothing more happening than something chemical happening. Biology is not ontologically separate from chemistry, there is no vital force or anything beyond the chemical processes which make up a biological process. But biological processes are abstractions of certain functions of chemical processes; multiple chemical processes can perform the function of a given biological process. That doesn't mean anything more than chemistry is going on whenever biology is going on.



I agree with most of what you said (in the part that I snipped out). However, the part I quoted seems to indicate that you are implying that if one took all the chemical components which make up a living adult Homo sapiens and combined them in the proper proportions and locations, that one could produce a living Homo sapiens without needing to go through the messy process of procreation via fertilization and gestation.

I could be wrong, but even were one to combine those chemicals in exactly the right manner, the closest to the above outcome one would be capable of creating is a human corpse. (Which would be great, provided the organs were usable, but it still wouldn't be a living Homo sapiens.)
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