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Professor Smarmiarty
06-03-2010, 10:32 AM
Don't know if this trhead will be interesting to anyone, thought people might like to know. Would have been news thread but links too old.

So there's been a bit of a spat over evolution lately but unlike our normal spats ("Metabolic-systemists suck balls!") this one was played out in newspapers because a man named Fodor wrote a book called "What Darwin got wrong"- which I shall summarise:
Basically it seeks to show that natural selection cannot be the sole determiner of evolution/is meaningless in statement. The idea at the core is simple
A) Biological systems are so ridiculously interwoven and coeffect each other in such a myriad of ways that properties of organisms are basically interlinked.
B) Any selection for fitness cannot distinguish between properties that are interwoven
and thus
C) Selection for fitness is meaningless- selection for fitness won't lead to overall increases in fitness as while you select individual organisms that are fitter this won't increase fitness in a heritable way.

Now the main problem with this is that I made this very argument, while boozed, to a bunch of biologists to see if I could rankle them. People have made similar arguments in passing before, in the field I work (prebiotic chemistry where we deal with trying to make first cells) it is pretty much our biggest problem.

Various people have responded the most common undercurrent being that requiring natural selection to distinguish between which trait is actual the causal increase of fitness and whatever traits free-ride on that is a ridiculously harsh criteria that wouldn't be needed in many other fields. The problem is that in this response they greatly weaken their position by reinforcing the idea of natural selection as an explanatory force, not a predictory one- that natural selection can be used to explain wh things happen but can't predict them in future- a crucial scientific test. This is somewhat ignoring an important set of studies in the 80-90s on population analysis which tried to show that natural selection could be a predicitve force but if anything these may now have been torpedoed.
What people have been tying to do on the chemical side is precisely what Fodor wants- that is to understand why mechanisms are inherentely selected- to make a mathematical model but such things are limited to single cells.
Once you get larger than this, plasticitiy of organisms takes over. This is the key point that environments actually shape organisms as much as they select them- plasticity in gene structure and organism development lead to a breakdown of simple cause-effect relationships. This is where population studies take over but again they are limited by the free-rider/fitness creator problems. So basically we've got the same problems that emerged in the 50s, just people have managed to ignore them for a while till people write a book promoting public spats.S
Sources of these:

http://bostonreview.net/BR35.2/darwin_exchange.php

What is the point of this thread? Oh shit I don't know

Geminex
06-03-2010, 10:40 AM
Hey, sithdarth gets to make threads about quantum physics, you get to make threads about biology. I'm as tired as you are drunk right now, so lemme think on that. What does Fodor (sounds like the product of a middle-earth witness protection program) mean by point B? I don't get it, but that might be because it's past midnight. I'll get back to you tomorrow.

ThatPoorMessenger
06-03-2010, 10:44 AM
Don't know if this trhead will be interesting to anyoneI find it interesting. Also, Fodor made a rather...weak point at best with this, I would claim. After all, point b), which exists mainly to linked a) and c):
Any selection for fitness cannot distinguish between properties that are interwoven and thusis rather shaky logic.

Professor Smarmiarty
06-03-2010, 11:04 AM
Point B is that any thing that selects for a trait that corresponds to fitness will also select for any traits attached to that trait. Therefore it is really selecting for all the traits, not just the trait that causes increased fitness.
In this way the argument is that natural selection cannot actually select for fitness, it selects for traits that come packaged together- one or two of which cause increased fitness.
Therefore if you apply such a selection over multiple generations you won't necessary end up with an increase in fitness over time because of how these trait packages are passed on hereditarily.

I should point out the contrasting view- which is the current big thing in evolution- "evo-devo"- or evolutionary development- which is trying to mix in pure genetic evolutionary selection with how organisms- particularly brains develop in emybro/first stages of life.
Ther eis a particularly remarkable study on fruitflies which shows that genetically/molecular makeup fruit-flies are basically human- but somewhere a quirk of development drove them into a different path- this quirk is speculated to be related to something that happens during embryo growth/or first few years of life in environment, it reall can't be genetically related.
This has been called the Lego theory- in that life is built of lego blocks and minor quirks one way or other send them spiralling into different directions.
HOWEVER- this is a massive problem for us chemical biologists as we can't find a reason for the lego block theory, there are other- in some ways more efficient- blocks that could have developed, but we're not sure why.
One interesting stud that I actually consulted on involved taking pretty much every chemical reaction known to man, starting with a few simple molecules, then working outwards- reacting them in any reaction that could happen and studying the results. Remarkably energy profiles tended to lead towards biotically relevant molecules though we have no idea why and its something we are thinking about.

ThatPoorMessenger
06-03-2010, 11:13 AM
One interesting stud that I actually consulted on involved taking pretty much every chemical reaction known to man, starting with a few simple molecules, then working outwards- reacting them in any reaction that could happen and studying the results. Remarkably energy profiles tended to lead towards biotically relevant molecules though we have no idea why and its something we are thinking about. Lets see, about 110 elements on the current periodic table (can't remeber the exact figure and we're not even including variants such as different forms of Fe), say 110P3 (and even then, nothing is made of just 3 elements), you're looking at forming 1294920 different compounds and you've not even hit different methods of reaction. Would take a loooong time.
In this way the argument is that natural selection cannot actually select for fitness, it selects for traits that come packaged together- one or two of which cause increased fitness.On the other hand, although the difference in say, the average length of a species neck affects a lot of other traits, the trait itself is chosen independantly and other develop from it's own occurence.

Also, while we're talking about evolution (and by extension, Darwin), a little side fact is that he was part of a club that endevored to eat one of every species on Earth.

Magic_Marker
06-03-2010, 11:36 AM
WALL OF WORDS

I'm about to mangle your explaination in an attempt to see if I've got it. I understand things best through abstraction and metaphore so forgive the implications of intelligence in natural selection, and the over simplification of a complex issue, what I want to know is if I have the CORE of it down.

So, if I'm understanding right, Point B is a little like if Natural Selection worked like a Class Based RPG. It can make choices but with those choices come a packaged deal. Like, if you want to cast spells in D&D you have to be a mage and mages can't wear armor. The selected trait (spells) is packaged with the rest (having to use simple weapons, wearing robes etc.) The problem with this theory is how the packages came to be. Why is it that trait A can't be had with Traits B-F? In an RPG you say that Gygax designed it that way, but that doesn't work in Science.

An attempt to solve it is the Lego theory which is more like a point buy based RPG. Traits and stats are bought up individually. This explains why oragnisism are similiar in the embryo stage because that's like a blank slate where traits are then 'selected' like a two players putting states in STR. Sure they start out remarkably similar when the two players start applying points but at a certain point you know that these two embryos/character sheets are going to be very, very different after they are done. The problem with this theory is that certain points going into a certain build would have been much better than others and it is not understood why these 'lego peices' weren't chosen.

This has been: Mangling Science with Magic Marker.

Professor Smarmiarty
06-03-2010, 12:40 PM
Lets see, about 110 elements on the current periodic table (can't remeber the exact figure and we're not even including variants such as different forms of Fe), say 110P3 (and even then, nothing is made of just 3 elements), you're looking at forming 1294920 different compounds and you've not even hit different methods of reaction. Would take a loooong time.
There are only really 4 revelant elements H, N, C, O and postulated simple reactions and there are only about 30 prebiotic components that have been really speculated. With simple filters it only took about a year or so.

On the other hand, although the difference in say, the average length of a species neck affects a lot of other traits, the trait itself is chosen independantly and other develop from it's own occurence.
That is not really how biology works. Like at all. Pretty much every thing in your body does a whole shit load of different things because of how intertied everything is. It would be very rare for say a gene to code for longer neck, it would code for a longer neck and shit loads of other things which depend upon how the organism develops. So while you cna pass on the long neck gene it doesn't mean your dchildren will have long necks which is a problem for heritable advantage.

Also, while we're talking about evolution (and by extension, Darwin), a little side fact is that he was part of a club that endevored to eat one of every species on Earth.
More importantly Origin of species was equally as much a political as a scientific text, he loaded it with political analogy.


I'm about to mangle your explaination in an attempt to see if I've got it. I understand things best through abstraction and metaphore so forgive the implications of intelligence in natural selection, and the over simplification of a complex issue, what I want to know is if I have the CORE of it down.

So, if I'm understanding right, Point B is a little like if Natural Selection worked like a Class Based RPG. It can make choices but with those choices come a packaged deal. Like, if you want to cast spells in D&D you have to be a mage and mages can't wear armor. The selected trait (spells) is packaged with the rest (having to use simple weapons, wearing robes etc.) The problem with this theory is how the packages came to be. Why is it that trait A can't be had with Traits B-F? In an RPG you say that Gygax designed it that way, but that doesn't work in Science.
Two things
Firstly- you've actually hit upon a different point which is also quite interesting but I didn't mention, which is that we generally see lots of traits which only come with each other and we can't figure out why- there is generally one trait that gives you an advantage (casting spells) but the other trait is detrimental, a free-rider (no armour) and there is no reason why they are directly related and the disadvantageous trait should have been got rid of.
Secondly- the main thrust of Fodor is more like this- how do oyu determine what is a wizard- is it spell casting ability or not wearing armour, these two things are always seen together. A human could determine the difference between the two but a blind force could not.
Now let's say you wanted to breed a super wizard. Humans would determine their magical ability and breed together the strongest. Nature could do this or it could equally select for who wears the least armour- these properties are inseperable.

An attempt to solve it is the Lego theory which is more like a point buy based RPG. Traits and stats are bought up individually. This explains why oragnisism are similiar in the embryo stage because that's like a blank slate where traits are then 'selected' like a two players putting states in STR. Sure they start out remarkably similar when the two players start applying points but at a certain point you know that these two embryos/character sheets are going to be very, very different after they are done. The problem with this theory is that certain points going into a certain build would have been much better than others and it is not understood why these 'lego peices' weren't chosen.
That's pretty accurate.
How I would run it is stats blocks are your DNA, every character has very similar stats/DNA, they all start out the same. Your classes are your development- slight changes in class selection lead to wild variations in final species.
The problem is that we are not sure why stat blocks are structure d like they are- averages of 10. It would be more efficient if everyone developed into all 18s or maybe developed into min-maxers with 18's and 6's but species all tend to average 10s in stats and we don't know why.

I hope that makes some sense, if it makes less sense I'll try again and actually think about what I'm typing instead of aimlessly.

ThatPoorMessenger
06-03-2010, 12:55 PM
There are only really 4 revelant elements H, N, C, O and postulated simple reactions and there are only about 30 prebiotic components that have been really speculated. With simple filters it only took about a year or so.True, however, you're still looking at a lot of possible experiements. Rediculous numbers like I originally stated are merely a fraction.

That is not really how biology works. Like at all. Pretty much every thing in your body does a whole shit load of different things because of how intertied everything is. It would be very rare for say a gene to code for longer neck, it would code for a longer neck and shit loads of other things which depend upon how the organism develops. So while you cna pass on the long neck gene it doesn't mean your dchildren will have long necks which is a problem for heritable advantage.Yes, I did explain it very badly, I was rushing a bit but I would still argue it is much more likely traits within a species develop more independantly than I believe Fodor was implying (unless I misunderstood him).

Nique
06-03-2010, 01:44 PM
Perhaps you've simplified this as much as you are able but it's still pretty steeped in terms that are not accessible to me because, well, I barely passed highschool chemistry. But I'm very interested in understanding what exactly this is all about. Basically what I'm gathering is;

1) 'We thought evolution worked this way, because the system/ field of study we are using to measure/examine it gave us results that made sense (Natural selection).

2) 'Now some guy is speculating that it works that way (Not-natural selection but... random craziness?)'

3)???

4) Profit(?)

I guess it sort of sounds like the apparent disparity between Newtonian Physics and Quantum mechanics? Like that we are aware that there is a kink in the current method of understanding? Again though; Me. Bad with science. I may be completely missing the mark.

Professor Smarmiarty
06-03-2010, 02:36 PM
True, however, you're still looking at a lot of possible experiements. Rediculous numbers like I originally stated are merely a fraction.
That is why computers are AWESOME!

Yes, I did explain it very badly, I was rushing a bit but I would still argue it is much more likely traits within a species develop more independantly than I believe Fodor was implying (unless I misunderstood him).
Yeah and most biologists would agree with you. The problem is proving it.

As for Nique, I'll come bac kand explain it properly after taking a rest, I drunk off my tits right now. I also whore out my own research (how do we go from nothing to DNA) if people are interested which has also exploded in debate recentely as people thought it was pretty much solved in the 50s before realising- oh wait, no it wasn't.

ThatPoorMessenger
06-03-2010, 02:39 PM
That is why computers are AWESOME!Damnit. *adds 70years to age* All these kids these days with their computers, medical students never touched a patient, blarg. :rolleyes: Still, I don't know why that option escaped me

Professor Smarmiarty
06-03-2010, 05:50 PM
Like half my experiments are run on computers these days. That's what most people in this field do cause it allows large scale analysis.

ThatPoorMessenger
06-03-2010, 05:54 PM
Like half my experiments are run on computers these days. That's what most people in this field do cause it allows large scale analysis.It is (despite my previous joke), a wonderful method of scientific practise. Although I'm damned amazed to see anyone who can successfully program such a thing.

Professor Smarmiarty
06-03-2010, 06:06 PM
Half of my drunken posts come as I drink away frustration at trying to get my cod e to work and I get like 99% of it prewritten.

ThatPoorMessenger
06-03-2010, 06:15 PM
Half of my drunken posts come as I drink away frustration at trying to get my cod e to work and I get like 99% of it prewritten.
As I said, I'm in awe when someone can do it, because it's that damnedably hard.

Classy Hand
06-09-2010, 03:28 PM
I find it interesting. Also, Fodor made a rather...weak point at best with this, I would claim.

Well what do you expect when a TRAVEL writer (http://my-photo-blog.com/wp-content/uploads/2007/04/Fodors-Costa-Rica-blog.jpg)starts thinking he can be an evolutionary biologist!

shiney
06-09-2010, 04:18 PM
Biological memory? Comparing DNA/etc to computational structures, perhaps everything averages out because the "max memory" the molecular structure can hold is 10, and instead of us being actually average 10s across the board, we've more or less maxed out our biological potential inasmuch as our cellular structures are able to define and retain?

I dunno, I am so far in over my head but it was an idea that appealed to me.

Osterbaum
06-09-2010, 05:47 PM
The thing about DNA though is, that it has the capacity to change and adapt. So I don't see any species hitting in any evolutionary walls at any point from part of their genome.

Professor Smarmiarty
06-10-2010, 03:58 PM
Real quick post (from Karl-Marx stadt, huzzah!)- Brains are complicated as shit, most of neuron connections/brain growth happens post birth- have read paper on this and they reckon that brain plasticity is high enough to allow far more growth and before that limit is hit you would run into problems powering that brain- it become energetically bad.

shiney
06-10-2010, 04:29 PM
So we may actually be limited not by DNA constraints, but by biological powering / sustenance constraints? We perform at our max possible limit due to not being able to adequately fund our body's need for more power or something?

We should hook SMB up to an electrical generator and see what happens to him. Or digitize his brain pattern.

Professor Smarmiarty
06-11-2010, 05:58 PM
So we may actually be limited not by DNA constraints, but by biological powering / sustenance constraints? We perform at our max possible limit due to not being able to adequately fund our body's need for more power or something?
.

Pretty much. The brain could make far more connections/increase processing speed than it does but there is no way to power that, it would be very energy hungry and you wouldn't be able to feed it.
One of the big questions is why we developed the quite large brains that we did before they were useful- we developed them in times of relative abundance when there was no need for large brain power to make tools and such like and they required additional nourishment. When the climate got colder and food got worse having large brains helped distinguish humans from related species with lower brain power but we're not sure why they developed them in the first place.

There is actually a hardlimit to our brains ability to process information (people have caluclated what they think it is but can't remember right now) but before we get there we would need some kind of super food.

Azisien
06-11-2010, 11:34 PM
Probably not even food that is the limit. I think taking North America by example we have no problem finding calories. The processing time for the food is probably what holds us back.

This can only be solved by nanites. Some kind of nanite will solve this, hopefully before a different kind of nanite destroys the Earth.

Professor Smarmiarty
06-14-2010, 12:16 PM
Azi: Well yeah that's why we had a super food which is all energy all the time! But our biology probably can't handle that.

Special holiday edition of Learn with SMB while he waits for the train and reading some evo-devo papers:
Assuming you've done your background reading like good students you will know there are 35 basic body plans that all animals follow.
Now there are certain genes which are conserved[I] between different types of animals- which means they serve the same role in multiple animals. For example Hox genes which dictate the body plan of some creatures-ie how things get organised from head to tail. They have been found in many types of creature. Basically the physical order of the Hox genes along the chromosone map to the reality of the creature- head genes are first, tail genes last. Now two creatures that both have Hox genes are fruit flies and chickens. Prepare for some crazy shit.
So some guys took fruit flies and turned off the genes which develop the head- these flies die as embryos. If you add in the correct "head" genes at the right time of development the flies are saved. But you don't have to add in fly head genes- you can add in chicken ones and the flies develop fine. Flies and chickens have completely different heads but somehow the machinery is similar enough that you can just swap head genes. Crazy shitttttttttttttttt.

Krylo
06-14-2010, 12:29 PM
Do they develop with tiny little chicken heads?

Edit: Could we do this with their legs and get tiny little drumsticks?

Edit to the Edit: Could we add a gene to produce hot sauce and make genetically engineered tiny little buffalo wings (drummies, whatever)?

Amake
06-14-2010, 12:34 PM
I recall some experiment where they swapped fruit fly chromosomes in the same fruit flies and got legs instead of eyes and disgusting things like that. Those things are the closest to Lego Genetics in the real world.

I wonder how they ended up with six chromosomes or whatever it is. Something to do with their super short life cycle maybe? They've evolved over probably billions of generations and become completely streamlined on a genetic level?

Azisien
06-14-2010, 12:37 PM
So some guys took fruit flies and turned off the genes which develop the head- these flies die as embryos. If you add in the correct "head" genes at the right time of development the flies are saved. But you don't have to add in fly head genes- you can add in chicken ones and the flies develop fine. Flies and chickens have completely different heads but somehow the machinery is similar enough that you can just swap head genes. Crazy shitttttttttttttttt.

It's crazy cool but really not that crazy when you consider from a fitness perspective how important it is for an organism to successfully, you know, develop a body. Super highly conserved genes ftw! But like you said genes are like a vague framework, for the flies especially their development is pretty much all perfectly timed hormone interactions. If we could finely tune hormone concentrations and timing in the fly we could probably make it turn into an ant. Maybe a chicken too but that would require more funding than the lab could get.