Antievolution.org - Antievolution.org Discussion Board -Topic::Biology @ Coastal Carolina & UNCW

Posted: Sep. 24 2008,14:21

Quote (Lou FCD @ Sep. 24 2008,20:01)

Midwife, it seems the only route to go, if one wants to understand the sentences.

Thanks for the enumeration, Henry. But what makes an s orbital different from a p orbital? Why is it different?

Is this what you were touching on, Steve? Shape? If so, why is the shape of one orbital different from the shape of another in the same orbital (or even in different orbitals, for that matter)? Why does the second shell have one s and three p orbitals? Why not two and two or all of one or the other, for instance?

And what makes a d or f orbital different from s or p orbitals?

Does the p stand for pi and the s for sigma, as in Louis' previous explanation, or is that a whole 'nuther thing?

I think I'd have to get all that before I could even begin to understand resonance and continue with his explanation.

Ahhhh this is where the good stuff comes in. S does not stand for sigma nor p for pi (although the terms sigma and pi ARE derived from s and p). Sigma and pi are molecular orbitals and s and p (and d and f) are atomic orbitals. Atomic orbitals combine to form molecular ones. Molecular orbitals are what we refer to when we talk about (covalent) bonds.

The explanation I gave above hops about a bit and doesn't explain its terms well, I promise I'll do a proper post where all will be revealed.

Resonance is sort of like an "emergent property" don't worry about it too much yet (although it becomes very important in organic chemistry and hence biology). In the phosphate example above, imagine that all those oxygens are identical, it doesn't matter to the molecule which oxygen forms the double bond so it can form with any of them. What we draw as phosphate PO₄^3- is a simplified picture of all those electronic movings around I mention. The reason I stuck the red labelled oxygen in there is so you could see that they were different, i.e. see the double bond moving.

This is a fascinating subject, the quantum mechanical picture of the atom IS complex but it is very useful when you understand it. It has those real world consequences that I hear so much about!

Louis

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Henry J

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Posted: Sep. 24 2008,14:23

Quote

It has those real world consequences that I hear so much about!

What, argument from consequences?

Henry J

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Posted: Sep. 24 2008,14:25

Quote

Sigma and pi are molecular orbitals and s and p (and d and f) are atomic orbitals.

Ah. I was wondering what the sigma and pi represented. Until now they were Greek to me. (ha ha.)

Henry

Louis

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Posted: Sep. 24 2008,14:27

Quote (Henry J @ Sep. 24 2008,20:25)

What, argument from consequences? ;)

Little known fact:

The quantum mechanical model of the atom is strongly correlated with teen pregnancy and reduction in church attendance.

It's true I tells ya.

Louis

Edited to get the right quote in. I'm off home, I've been here 12 hours already!

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Posted: Sep. 24 2008,15:24

ah, thank you sir, for the clarification.

The waters are suddenly a bit less murky.

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Linky“. ~ Steve Story, Legend

stevestory

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Posted: Sep. 24 2008,15:51

Quote (Lou FCD @ Sep. 24 2008,15:01)

Midwife, it seems the only route to go, if one wants to understand the sentences.

Thanks for the enumeration, Henry. But what makes an s orbital different from a p orbital? Why is it different?

Is this what you were touching on, Steve? Shape? If so, why is the shape of one orbital different from the shape of another in the same orbital (or even in different orbitals, for that matter)? Why does the second shell have one s and three p orbitals? Why not two and two or all of one or the other, for instance?

And what makes a d or f orbital different from s or p orbitals?

Does the p stand for pi and the s for sigma, as in Louis' previous explanation, or is that a whole 'nuther thing?

I think I'd have to get all that before I could even begin to understand resonance and continue with his explanation.

Somebody's exclusion rules say only one electron can be in a given quantum state. Since s is spherically symmetrical, you can only put two electrons in that state--one with spin up, one with spin down. the next electrons, in p, have an x y or z orientation, so you can fix 6 more there p_x spin up, p_x spin down, p_y spin up, p_y spin down, p_z spin up, p_z spin down, a sigma bond is like two dumbbells--two p bonds--with one side of the weights touching. a pi bond is like two dumbbells with both the weight parts touching, so there's more overlap, lower energy, and therefore stronger. The hybrids are some weirder shapes that result from mathematically mixing several bonds and there's also some more stuff about symmetry and anti-symmetry and I haven't thought about this stuff for about 4 years and so I've probably done more harm here than good and it won't make any sense without diagrams and factier facts than I can recall. Also, electrons can effect the energy states of other electrons by repulsing them and shielding the positive charge from the nucleus. Like Louis said, I would go get the wikipedia articles until he returns.

Arden Chatfield

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Posted: Sep. 24 2008,15:56

Quote (Lou FCD @ Sep. 21 2008,04:23)

Quote (keiths @ Sep. 21 2008,02:49)

Dig the dehydration sex. �But why does she get to have an orgasm while he doesn't?

Because I ran out of gas and the artistic editing ended prematurely.

XVIVO better look out. There's a new animator in town.

Whoa. Robert Marks is gonna be pissed.

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"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

Wesley R. Elsberry

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Posted: Sep. 24 2008,17:56

Quote (Arden Chatfield @ Sep. 24 2008,15:56)

Quote (Lou FCD @ Sep. 21 2008,04:23)

Quote (keiths @ Sep. 21 2008,02:49)

Dig the dehydration sex. But why does she get to have an orgasm while he doesn't?

Because I ran out of gas and the artistic editing ended prematurely.

XVIVO better look out. There's a new animator in town.

Whoa. Robert Marks is gonna be pissed.

Then what explains his behavior to this point?

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Posted: Sep. 24 2008,18:24

Quote (Lou FCD @ Sep. 24 2008,11:50)

Quote (Tracy P. Hamilton @ Sep. 24 2008,11:28)

Quote (Lou FCD @ Sep. 21 2008,00:21)

In order to digest cellulose, water and cellulase are needed. Animals don't make cellulase in their bodies, and so can't digest cellulose. Hearkening back to the termite lab, remember that termites subsist on a diet of wood. Wood is made of cellulose. How do they do that? They depend on little microorganisms to digest the cellulose for them.

Some animals do produce cellulase! �Termites are an example.

�

Quote

Scientific Correspondence

Nature 394, 330-331 (23 July 1998) | doi:10.1038/28527
A cellulase gene of termite origin

Hirofumi Watanabe1, Hiroaki Noda1, Gaku Tokuda2 and Nathan Lo3

The traditional view of cellulose digestion in animals is that they cannot produce their own cellulase, and so rely on gut microorganisms to hydrolyse cellulose. A classic example of this symbiosis is that between phylogenetically lower termites and the unicellular organisms (protists) that colonize their hindguts: cellulose fermented to acetate by the protists can be used as an energy source by the termite1. There is evidence for the production of endogenous cellulase components by termites and other wood-feeding insects2; however, an unambiguous origin for such enzymes1 has not been established, to our knowledge, until now. Here we describe the first insect cellulase-endoding gene to be identified, RsEG, which encodes an endo-beta-1,4-glucanase (EC 3.2.1.4) in the termite Reticulitermes speratus

See, Doc specifically talked about the microcritters producing the cellulase for the termites. I'll have to point him to that.

Thanks for your input here, by the way. I appreciate the assists.

The microcritters also produce cellulases! I merely pointed out that the animals were once not thought to do it.

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Posted: Sep. 24 2008,18:25

Quote (Henry J @ Sep. 24 2008,14:25)

Quote

Sigma and pi are molecular orbitals and s and p (and d and f) are atomic orbitals.

Ah. I was wondering what the sigma and pi represented. Until now they were Greek to me. (ha ha.)

Henry

You don't want to know about the capital letters S, P, D, F etc and Sigma, Pi, etc.

Trust me.

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"Following what I just wrote about fitness, you�re taking refuge in what we see in the world." �PaV

"The simple equation F = MA leads to the concept of four-dimensional space." GilDodgen

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Posted: Sep. 24 2008,18:31

Quote (Henry J @ Sep. 24 2008,11:04)

Quote (Tracy P. Hamilton @ Sep. 24 2008,09:19)

Quote (Lou FCD @ Sep. 20 2008,13:18)

4. Phospate Group

A Phosphate Group is a Phosphorus bonded with two negatively charged Oxygen atoms, one regular Oxygen atom, and double bonded with one Oxygen atom. It's molecular formula is PO42- or sometimes OPO32-, to separate the double bonded Oxygen.

Here is where the lecture ended. Although I asked in a later lecture about the odd bondings here that seem to break the rules that we earlier set forth, Doc basically said, "It's complicated, and you don't need to know that for this class, though you'll learn about it in a Chemistry class if you take one." Ok, fair enough.

Chemical education discourages the use of the double bond in phosphate, and in sulfate groups as well. �As you noticed, it violates the octet rule, and does so unnecessarily! �There are some molecules where we chemists violate the rule out of necessity, such as having five atoms bonded to P, which requires 5 bonds.

The double bonds in phosphate and sulfate are historical, hence the biologists still use it a lot because that is how they learned it. �:O

So is the proper way to do it to put a - sign on three of the O's and a + sign on the P?

YES. Don't listen to the old fogey Louis.

What Louis says is correct, though.

Chemists have this resonance idea, but the question is which is more important: a structure that obeys the octet rule but has +1 on P and -1 on each O, or a structure that disobeys the octet rule and has charge 0 on P, and 0 on one O. Is having a positive charge on P so bad, and having negative on O so bad? Answer: no. Louis finds it offensive, apparently. :p

I wonder if Louis would draw BF3 with a double bond or not, and whether there is any pi bonding in it (his justification for drawing P=O in phosphate).

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"Following what I just wrote about fitness, you�re taking refuge in what we see in the world." �PaV

"The simple equation F = MA leads to the concept of four-dimensional space." GilDodgen

"We have no brain, I don't, for thinking." Robert Byers

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Posted: Sep. 24 2008,18:33

Quote (Henry J @ Sep. 24 2008,14:12)

The details would get into quantum mechanics that's over my head. But roughly, each type of orbital has a characteristic shape that and a minimum size. The 1st shell is simply too small to hold a p, d, or f, and the 2nd is too small for d or f, and the 3rd is too small for f.

Actually, it is a math thing. The jellium model of the nucleus has "orbitals", where 1p, 1d functions etc are possible.

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"Following what I just wrote about fitness, you�re taking refuge in what we see in the world." �PaV

"The simple equation F = MA leads to the concept of four-dimensional space." GilDodgen

"We have no brain, I don't, for thinking." Robert Byers

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Posted: Sep. 24 2008,18:34

Quote (Henry J @ Sep. 24 2008,14:23)

Quote

It has those real world consequences that I hear so much about!

What, argument from consequences? ;)

It keeps me employed, for example. :)

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"Following what I just wrote about fitness, you�re taking refuge in what we see in the world." �PaV

"The simple equation F = MA leads to the concept of four-dimensional space." GilDodgen

"We have no brain, I don't, for thinking." Robert Byers

Texas Teach

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Posted: Sep. 24 2008,18:38

Quote (Lou FCD @ Sep. 24 2008,14:01)

Midwife, it seems the only route to go, if one wants to understand the sentences.

Thanks for the enumeration, Henry. But what makes an s orbital different from a p orbital? Why is it different?

Is this what you were touching on, Steve? Shape? If so, why is the shape of one orbital different from the shape of another in the same orbital (or even in different orbitals, for that matter)? Why does the second shell have one s and three p orbitals? Why not two and two or all of one or the other, for instance?

And what makes a d or f orbital different from s or p orbitals?

Does the p stand for pi and the s for sigma, as in Louis' previous explanation, or is that a whole 'nuther thing?

I think I'd have to get all that before I could even begin to understand resonance and continue with his explanation.

Lou, it's all based on energy. �Lower energy is more stable. �The shapes can be derived from looking at the energy values of electrons in each orbital and the fact that electrons have wave-like properties and are subject to things like interference.

(My brain hurts from trying to reach back to everything I used to know but haven't thought about in years since I don't get to teach it in HS. �Thanks, Louis, for the refresher.)

edited to have only one conjugation of a verb in any given sentence.

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midwifetoad

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Posted: Sep. 24 2008,19:02

Quote

Somebody's exclusion rules say only one electron can be in a given quantum state.

That's probably Pauli's exclusion principle which states, if I remember correctly, that Pauli and a successful experiment cannot exist at the same time and place.

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Posted: Sep. 24 2008,19:34

Quote (Tracy P. Hamilton @ Sep. 24 2008,09:19)

� �

Quote (Lou FCD @ Sep. 20 2008,13:18)

4. Phospate Group

A Phosphate Group is a Phosphorus bonded with two negatively charged Oxygen atoms, one regular Oxygen atom, and double bonded with one Oxygen atom. It's molecular formula is PO₄^2- or sometimes OPO₃^2-, to separate the double bonded Oxygen.

Here is where the lecture ended. Although I asked in a later lecture about the odd bondings here that seem to break the rules that we earlier set forth, Doc basically said, "It's complicated, and you don't need to know that for this class, though you'll learn about it in a Chemistry class if you take one." Ok, fair enough.

Chemical education discourages the use of the double bond in phosphate, and in sulfate groups as well. �As you noticed, it violates the octet rule, and does so unnecessarily! �There are some molecules where we chemists violate the rule out of necessity, such as having five atoms bonded to P, which requires 5 bonds.

The double bonds in phosphate and sulfate are historical, hence the biologists still use it a lot because that is how they learned it. �

Well my issue here is actually not just that there is an extra bond there with the one Oxygen.

On top of that Phosphorus in particular only has three unpaired valence electrons to begin with, so should only be able to form 3 bonds (according to the rules), not even four, let alone five.

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Linky“. ~ Steve Story, Legend

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Posted: Sep. 24 2008,19:38

Quote (stevestory @ Sep. 24 2008,16:51)

Quote (Lou FCD @ Sep. 24 2008,15:01)

Midwife, it seems the only route to go, if one wants to understand the sentences.

Thanks for the enumeration, Henry. But what makes an s orbital different from a p orbital? Why is it different?

Is this what you were touching on, Steve? Shape? If so, why is the shape of one orbital different from the shape of another in the same orbital (or even in different orbitals, for that matter)? Why does the second shell have one s and three p orbitals? Why not two and two or all of one or the other, for instance?

And what makes a d or f orbital different from s or p orbitals?

Does the p stand for pi and the s for sigma, as in Louis' previous explanation, or is that a whole 'nuther thing?

I think I'd have to get all that before I could even begin to understand resonance and continue with his explanation.

Somebody's exclusion rules say only one electron can be in a given quantum state. Since s is spherically symmetrical, you can only put two electrons in that state--one with spin up, one with spin down. the next electrons, in p, have an x y or z orientation, so you can fix 6 more there px spin up, px spin down, py spin up, py spin down, pz spin up, pz spin down, a sigma bond is like two dumbbells--two p bonds--with one side of the weights touching. a pi bond is like two dumbbells with both the weight parts touching, so there's more overlap, lower energy, and therefore stronger. The hybrids are some weirder shapes that result from mathematically mixing several bonds and there's also some more stuff about symmetry and anti-symmetry and I haven't thought about this stuff for about 4 years and so I've probably done more harm here than good and it won't make any sense without diagrams and factier facts than I can recall. Also, electrons can effect the energy states of other electrons by repulsing them and shielding the positive charge from the nucleus. Like Louis said, I would go get the wikipedia articles until he returns.

Ok, by "spin", are we talking about a physical spin, a rotation of the electron about a given spatial axis? Or is "spin" something more esoteric?

If the former, is that spacial axis relative to the nucleus, or is it more absolute, or neither?

Edited by Lou FCD on Sep. 24 2008,20:51

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“Why do creationists have such a hard time with commas?

Linky“. ~ Steve Story, Legend

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Posted: Sep. 24 2008,19:39

Quote (Tracy P. Hamilton @ Sep. 24 2008,19:24)

The microcritters also produce cellulases! �I merely pointed out that the animals were once not thought to do it.

Gotcha, thanks for the clarification.

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Posted: Sep. 24 2008,19:39

Quote (Wesley R. Elsberry @ Sep. 24 2008,18:56)

Then what explains his behavior to this point?

lol. I have some thoughts about that, none of which are terribly kind.

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Posted: Sep. 24 2008,19:49

Quote (Texas Teach @ Sep. 24 2008,19:38)

Quote (Lou FCD @ Sep. 24 2008,14:01)

Midwife, it seems the only route to go, if one wants to understand the sentences.

Thanks for the enumeration, Henry. But what makes an s orbital different from a p orbital? Why is it different?

Is this what you were touching on, Steve? Shape? If so, why is the shape of one orbital different from the shape of another in the same orbital (or even in different orbitals, for that matter)? Why does the second shell have one s and three p orbitals? Why not two and two or all of one or the other, for instance?

And what makes a d or f orbital different from s or p orbitals?

Does the p stand for pi and the s for sigma, as in Louis' previous explanation, or is that a whole 'nuther thing?

I think I'd have to get all that before I could even begin to understand resonance and continue with his explanation.

Lou, it's all based on energy. �

(forgive the multiple comments, I'm trying to keep each conversation here separate in my head.)

Quote (Texas Teach @ Sep. 24 2008,19:38)

Lower energy is more stable. �

OK, got that.

Quote (Texas Teach @ Sep. 24 2008,19:38)

The shapes can be derived from looking at the energy values of electrons in each orbital

In what way? How does the energy value affect the shape? When you say energy value, are you referring to the potential energy derived from distance from the nucleus, or something else?

Quote (Texas Teach @ Sep. 24 2008,19:38)

and the fact that electrons have wave-like properties and are subject to things like interference.

Which properties are relevant here? How does it work?

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Linky“. ~ Steve Story, Legend

Henry J

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Posted: Sep. 24 2008,19:56

Quote (Lou FCD @ Sep. 24 2008,18:34)

Just wondering, but is the dash on the right side of the rightmost O atom supposed to be a minus sign? Cause it looks like a bond in search of another atom.

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Posted: Sep. 24 2008,20:01

Quote (Henry J @ Sep. 24 2008,20:56)

Quote (Lou FCD @ Sep. 24 2008,18:34)

Just wondering, but is the dash on the right side of the rightmost O atom supposed to be a minus sign? Cause it looks like a bond in search of another atom.

Actually, it is a bond in search of another atom, as we were pulling it out of context to isolate it and discuss it as a functional group as part of a larger molecule.

The dash remains to remind me that there's more to the molecule than this part.

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Posted: Sep. 24 2008,20:33

Quote (Lou FCD @ Sep. 24 2008,19:34)

�

Quote (Tracy P. Hamilton @ Sep. 24 2008,09:19)

� � � �

Chemical education discourages the use of the double bond in phosphate, and in sulfate groups as well. �As you noticed, it violates the octet rule, and does so unnecessarily! �There are some molecules where we chemists violate the rule out of necessity, such as having five atoms bonded to P, which requires 5 bonds.

The double bonds in phosphate and sulfate are historical, hence the biologists still use it a lot because that is how they learned it. �

Well my issue here is actually not just that there is an extra bond there with the one Oxygen.

On top of that Phosphorus in particular only has three unpaired valence electrons to begin with, so should only be able to form 3 bonds (according to the rules), not even four, let alone five.

There is that also. �Usually, a bond is formed when one electron comes from one atom, and the second from the other. �Therefore carbon has four bonds and no lone pairs usually. �Phosphorus usually has 3 bonds and one lone pair. �However, if electronegative atoms are also involved (especially fluorine, all of the electrons can be used for a bond. �PF5 can be made, PH5 is rather dubious (oh how some chemists would love to make something like that). �All seven valence electrons of iodine can be used to make IF7.

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"Following what I just wrote about fitness, you�re taking refuge in what we see in the world." �PaV

"The simple equation F = MA leads to the concept of four-dimensional space." GilDodgen

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Posted: Sep. 24 2008,20:39

Quote (Lou FCD @ Sep. 24 2008,19:38)

Ok, by "spin", are we talking about a physical spin, a rotation of the electron about a given spatial axis? Or is "spin" something more esoteric?

If the former, is that spacial axis relative to the nucleus, or is it more absolute, or neither?

Yes. �

Seriously the electron has no size, so no axis to spin around. The value of its spin angular momentum cannot be changed, to do so would mean it is not an electron.

If the electrons spin was an integer by the way, there is no Pauli exclusion principle, all electrons could be in the lowest orbital (like 1s^6 for carbon) and there would be no chemistry.

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"Following what I just wrote about fitness, you�re taking refuge in what we see in the world." �PaV

"The simple equation F = MA leads to the concept of four-dimensional space." GilDodgen

"We have no brain, I don't, for thinking." Robert Byers

stevestory

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Posted: Sep. 24 2008,20:49

Quote (Tracy P. Hamilton @ Sep. 24 2008,21:39)

The value of its spin angular momentum cannot be changed, to do so would mean it is not an electron.

But it can be flipped, right, between pos and neg 1/2?

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Posted: Sep. 24 2008,20:51

Quote (Tracy P. Hamilton @ Sep. 24 2008,21:33)

There is that also. �Usually, a bond is formed when one electron comes from one atom, and the second from the other. �Therefore carbon has four bonds and no lone pairs usually. �Phosphorus usually has 3 bonds and one lone pair. �However, if electronegative atoms are also involved (especially fluorine, all of the electrons can be used for a bond. �PF5 can be made, PH5 is rather dubious (oh how some chemists would love to make something like that). �All seven valence electrons of iodine can be used to make IF7.

Holy crap! People, Listen! Rules exist for a reason!

WHAT IS THE POINT OF MAKING ALL THESE RULES IF JERKS LIKE IODINE AND FLORINE ARE JUST GOING TO GO AROUND BREAKING THEM WILLY NILLY??????

Seriously, if we're just going to go let Iodine use all seven of its valence electrons to form bonds, what's next? Why stop there? Why not just let Iodine use all frickin' 53? Hell, why not just skip the electrons altogether? Let's just have a great big element orgy, and let the protons and the neutrons have some fun! Hey look! Its H₉₇C₃Uno₆₉HeK₂₂!

Geez, the moral fabric of society is at stake here folks!!! Next thing y'know, you'll be combining Xe and R, and gay people will be getting married!

WAKE UP AMERICA!

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Linky“. ~ Steve Story, Legend

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Posted: Sep. 24 2008,20:56

Quote (Tracy P. Hamilton @ Sep. 24 2008,21:39)

Quote (Lou FCD @ Sep. 24 2008,19:38)

Ok, by "spin", are we talking about a physical spin, a rotation of the electron about a given spatial axis? Or is "spin" something more esoteric?

If the former, is that spacial axis relative to the nucleus, or is it more absolute, or neither?

Yes. �:p

Seriously the electron has no size, so no axis to spin around. �The value of its spin angular momentum cannot be changed, to do so would mean it is not an electron.

If the electrons spin was an integer by the way, there is no Pauli exclusion principle, all electrons could be in the lowest orbital (like 1s^6 for carbon) and there would be no chemistry.

Wait. "No size" like in 0? It has mass, so wouldn't it then be a little black hole, infinite density, etc?

The rest of that is crazy talk, over my head still.

First you say "yes" then you say "no" and then you're talking about angular momentum in reference to an object you just asserted has no size, so I'm really confused now.

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“Why do creationists have such a hard time with commas?

Linky“. ~ Steve Story, Legend

Texas Teach

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Posted: Sep. 24 2008,21:21

Quote (Lou FCD @ Sep. 24 2008,19:49)

� �

Quote (Texas Teach @ Sep. 24 2008,19:38)

The shapes can be derived from looking at the energy values of electrons in each orbital

In what way? How does the energy value affect the shape? When you say energy value, are you referring to the potential energy derived from distance from the nucleus, or something else?

Potential energy, yes. �I had a mathematician explain this to me once. �It was a beautiful, clear explanation. I experienced an epiphany that day....I can't for the life of me recall the details. �

�Anyway, the shape is partly determined by potential energy due to the electrostatic charge between the electron and the nucleus, the charges of the electrons wrt each other, and the fact that the electrons' energies are only stable for certain values.

�

Quote (Lou FCD @ Sep. 24 2008,19:49)

��

Quote (Texas Teach @ Sep. 24 2008,19:38)

and the fact that electrons have wave-like properties and are subject to things like interference.

Which properties are relevant here? How does it work?

Ok, now you caught me forgetting physical chemistry I learned before I fled grad school for the friendlier environs of teaching in public school. �(Really!

�I fear I'd only confuse you and embarrass me. �Perhaps Louis, Tracy, or Henry (or someone else) can help?

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"Creationists think everything Genesis says is true. I don't even think Phil Collins is a good drummer." --J. Carr

"I suspect that the English grammar books where you live are outdated" --G. Gaulin

Henry J

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