The Cambrian Explosion

[Believe]

Bad ass! Finally an answer!!!! Or at least the best answer I've heard so far....

http://io9.com/5903330/toxic-oceans...explosion-in-biodiversity-earth-has-ever-seen

 

[Aqueous Id]

Enjoyed reading your cite. I am impressed by the idea that to rid themselves of excess minerals, they began building shells and bones. That's a great idea. I immediately thought of the oyster secreting pearl - it's such a waste. My latest info on this had to do with the Great Oxygenation Event, which threatened the photosynthesizing cyanobacteria, and the iron oxide that resulted had some similar effects on evolution.

(You might want to change the thread title to "Cambrian Explosion" or something like that so people who are interested will know what the subject is).

 

[Hercules Rockefeller]

Mod note: thread title changed to "Cambrian Explosion". Original title text transferred to opening post.

 

[tantalus]

Interesting. There are actually alot of theories. Still, consider the below...

The ‘new animal phylogeny’ reveals that many of
the groups known to biomineralize sit among close relatives
that do not, and it favours an interpretation of convergent or
parallel evolution for biomineralization in animals. In addition,
the fossil record of the earliest mineralized skeletons

presents a rapid proliferation of biomineralization across a
range of animal phyla with fossil representatives of many
modern biomineralizing phyla. A synthesis of molecular, developmental,
phylogenetic and fossil evidence demonstrates
the convergent or parallel evolution of biomineralization in
animals at the phylum level. The fossil record of the Cambrian
explosion not only provides vital evidence for the evolution
of animal mineralized tissues but also suggests a mechanism
for its rapid and synchronous convergent origin.

and more or less the same again from the same paper

Recent evidence from
molecular studies supports this interpretation of multiple
origins rather than a single origin of the animal skeleton
and further suggests that the developmental and molecular
architecture may have evolved prior to the divergence
of the metazoan phyla, providing a possible mechanism
for synchronous multiple origins of biomineralization
through exaptation of existing genes.

http://palaeo.gly.bris.ac.uk/donoghue/PDFs/2011/Murdock_Donoghue_2011.pdf

I had thought that a single evolutionary step regarding calcium secretion and shell formation etc was resopnsible for most biomineralisation that appeared suddenly with the cambrian explosion. When I mean suddenly, I still expected millions of years to be available for subsequent rapid divergence. This paper indicates not, and the nature of the proposed mechanism fits with the one mentioned in the OP. Ofcourse I am sure there are still other credible mechanisms that fit that profile.

 

[wellwisher]

One thing that is always left out of discussions of evolution is the global impact of the cellular water. Water is more than an inert solvent but participates in all aspects of life. There is no replacement for the utility of water.

If you look at CaPO4 or calcium phosphate, both of these ions are considered kosmotropic and will create order within the structure of water/organics compared to pure water. Ironically, this ordering means expression at the DNA becomes less random; due to added kosmotropic order.

What this suggests is rather than the previous trial and error, with respect to genetic diversity, with most trials subjective to failure, the CaPO4 mineralization added order to the DNA. This meant less randomness. The result were fewer random duds and more winners (ordered).

There logic behind this analysis has to do with the hydrogen bonding within water and the pressure differential between two stable hydrogen bonding states of water. The more stable hydrogen bonded state of water has covalent character. To get proper covalent orbital overlap, the hydrogen and oxygen at the hydrogen bond need to expand,slightly. This hydrogen bonding state is way water expands when it freezes. This is a water anomaly. The other stable hydrogen bonding state is polar and this type of hydrogen bond gets stronger as distance decreases. This hydrogen bonding state contracts and defines higher entropy. In the water, at any time, we have both expanded and contracted water shapes, both are stable. These define water have been labelled as pressure pixels.

The impact of the kosmotropes like CaPO4, is to make more expanded water since this creates more order in water. This excess expansion puts the squeeze on all the organics in the cell, so they have to compact more efficiently. With an exoskeleton the pressure is maintained. Later on, this external order/pressure plate is removed for an internal skeleton, changing the position of the order induction, so it is closer to the nervous system which now becomes more ordered.

The cell is a crowded place with molecule touching molecule. There is not a lot of room for free movement. For example, statistical mechanics predicts an average protein folded shape. Yet observation shows that the shape will have a probability of 1.0 and therefore is not under statistical mechanics. The reason is the crowded nature of the cellular water and affects like aqueous pressure and surface tension, which puts the squeeze on randomness in favor of order. The fold of the enzyme is forced to stay at attention since water is not an inert material.

 

[origin]

There logic behind this analysis has to do with the hydrogen bonding within water and the pressure differential between two stable hydrogen bonding states of water.

What are you talking about? Are you just making stuff up again?

The more stable hydrogen bonded state of water has covalent character. To get proper covalent orbital overlap, the hydrogen and oxygen at the hydrogen bond need to expand,slightly. This hydrogen bonding state is way water expands when it freezes.

A water molecule is an oxygen atom and 2 hydrogen atoms that have covalent bonds. It is not the more stable bonded state it is the only bonded state. Water expands when it freezes because it forms hexagonal crystals that have a lot of open area.

This is a water anomaly. The other stable hydrogen bonding state is polar and this type of hydrogen bond gets stronger as distance decreases.

The hydrogen bonding has nothing to do with the individual water molecules which have covalent bonds. The polar nature of the water molecules is what leads to the hydrogen bonding. The 2 hydrgen atoms are only separated by ~104 degress, so the molecule looks a bit like Mickey Mouse ears. The 2 hydrogen atoms are essentially 2 positive protons offset on the molecule giving it a slightly postive end and a slightly negative end.

The slightly postive end of the water molecule where the hydrogens atoms are is attracted to the slightly negative side of the water molecule opposite to the hydrogen atoms.

This hydrogen bonding state contracts and defines higher entropy.

Oh goody, you got to throw in entropy!

In the water, at any time, we have both expanded and contracted water shapes, both are stable. These define water have been labelled as pressure pixels.

WTF? Why do you just make stuff up present it like you have a clue?

 

[wellwisher]

Origin, you don't know what you are talking about. If you wish to learn about water, and not just set up smoke, here is a useful link:

http://www.lsbu.ac.uk/water/index2.html

From that link, below is a relative energy curve for the two hydrogen bonding states of water; polar (a) and partial covalent (b). Water can self ionize to form the phenomena called pH. This requires breaking and reforming strong O-H covalent bonds. The partial covalent nature of the hydrogen bond has the orbital already aligned so the jump is easy.

Relative to the pressure pixel, water exists as icosahedral clusters composed of 280 molecules of water. Based on the ratio of the two hydrogen bonding states, these water clusters moves between expanded and collapsed structures. This cluster is the basic unit of a water pressure pixel. This is show below: You will notice, if we go from left to right or expanded to collapsed we get an entropy increase, an enthalpy increase and a volume decrease. This is important if an energy balance is important. If perpetual motion is fine, we can skip it.

If we return to a cell, the inside of a cell is a very crowded place. It is not organics molecules in empty space. Picture going to a concert near the stage where everyone is standing and pushing to get closer. It is tight and movement is restricted. Water is the usher. You need volume changes and pressure changes, via the pressure pixels to tighten or loosen the crowding so things can move or change.

Relative to CaPO4 and its kosmotropic nature:

Large singly charged ions, with low charge density (for example, SCN-, H2PO4-, HSO4-, HCO3-, I-, Cl-, NO3-, NH4+, Cs+, K+, (NH2)3C+ (guanidinium) and (CH3)4N+ (tetramethylammonium) ions; exhibiting weaker interactions with water than water with itself and thus interfering little in the hydrogen bonding of the surrounding water), are chaotropes whereas small or multiply-charged ions, with high charge density, are kosmotropes (for example, SO42-, HPO42-, Mg2+, Ca2+, Li+, Na+, H+, OH- and HPO42-, exhibiting stronger interactions with water molecules than water with itself and therefore capable of breaking water-water hydrogen bonds).b Kosmotropes remain hydrated near the water surface, while the chaotropes lose their hydration sheath

The CaPO4 by being kosmotropic favors the expanded pressure pixel. This adds a bunch of giant body builders into the concept crowd near the stage. The crowd gets very tight and things need to rearrange and compact or else potential energy will increase as the girls start to scream, I can't breath. The enzymes lose their quantum mechanical wobble, turn and fold with 100% certainty to make room. Now she can breath. During the cambrian explosion organics have to shift.

 

[origin]

Origin, you don't know what you are talking about. If you wish to learn about water, and not just set up smoke, here is a useful link:

http://www.lsbu.ac.uk/water/index2.html

Nice link

From that link, below is a relative energy curve for the two hydrogen bonding states of water; polar (a) and partial covalent (b).

That is strange that your source does not say (b) is a partial covalent bond, it simply states that (b) is a hydrogen bond.

Water can self ionize to form the phenomena called pH.

The ionization of water is not called pH. The pH is the measure of the negative log of the hydronium ion concentration.

This requires breaking and reforming strong O-H covalent bonds. The partial covalent nature of the hydrogen bond has the orbital already aligned so the jump is easy.

Actually it takes quite a bit of energy to significantly ionize water. Pure water has very few hydronium and hydroxyl ions, the drivers for the breaking of the bond are acids and bases which result in a very exothermic reaction due to the high energy in the covalent H-O-H bonds.

Relative to the pressure pixel, water exists as icosahedral clusters composed of 280 molecules of water. Based on the ratio of the two hydrogen bonding states, these water clusters moves between expanded and collapsed structures. This cluster is the basic unit of a water pressure pixel. This is show below: You will notice, if we go from left to right or expanded to collapsed we get an entropy increase, an enthalpy increase and a volume decrease. This is important if an energy balance is important.

You are making rather large assumptions and stating untested hypothesis as facts.

If perpetual motion is fine, we can skip it.

I have no idea what that is suppose to mean.

If we return to a cell, the inside of a cell is a very crowded place. It is not organics molecules in empty space. Picture going to a concert near the stage where everyone is standing and pushing to get closer. It is tight and movement is restricted. Water is the usher. You need volume changes and pressure changes, via the pressure pixels to tighten or loosen the crowding so things can move or change.

Bull. This is your guess again. The water pressure in the cell will be influenced by several things the least of which is the arrangememt of any clumping. Do you have any information of water pixels besides a paper written in 1997?

The CaPO4 by being kosmotropic favors the expanded pressure pixel.

How about some evidence of this.

This adds a bunch of giant body builders into the concept crowd near the stage. The crowd gets very tight and things need to rearrange and compact or else potential energy will increase as the girls start to scream, I can't breath. The enzymes lose their quantum mechanical wobble, turn and fold with 100% certainty to make room. Now she can breath. During the cambrian explosion organics have to shift.

This is what caused the Cambrian explosion? The stuff you come up with.:shrug:

 

[Believe]

Mod note: thread title changed to "Cambrian Explosion". Original title text transferred to opening post.

Thanks! It was late and I was tired and excited when I wrote it so the title was a little off.

 

[wellwisher]

I have a question for the staff. When proof is being offered, at what level of expertise do you gear the proof? Do you try to prove it to the experts, to those whom you assume know more than the basics, or do you gear it to layman, like Origin, who might first require a lot of basic chemical background before he can understand anything?

In physics forums, some of the more advanced members post complicated mathematical proof. This level of analysis does not offer proof to the layman, even if it is entirely true and proven. The layman may need them to first do some basic algebra and then build other background before what is routine for the experts, appears to be proven.

Maybe the staff can set standards. We all have an area of expertise where we have a feel new analysis, and we also have areas of ignorance where everything is new and therefore unproven to us. To whom do we gear the proof and does this apply to all?

Sometimes trying to prove things to a disruptive student is not in the best interest of the rest of the class. That student might be seeking attention and not insight. The rest get ripped off.

 

[origin]

Geeze quit whining. If you don't want to answer my questions don't answer them. If your stuff is self-evidently right then all of your 'students' will get it.

This is so freaking funny. As anyone who has had the misfortune of reading anything I wrote knows, I cannot spell for crap. I intially misspelled whining as whinning so I when I put whinning into google to check it. The first thing that comes up is the Urban Dictionary with:

A word used by chemical engineers when referring to "quasi techs" during an impotent internet tirade

Apparently all Chemical Engineers took 'Spelin 101'!

 

[Aqueous Id]

Maybe the staff can set standards.

Isn't one of the standards to stay on topic:

"We're proposing a triggering mechanism for the Cambrian explosion. Our hypothesis is that biomineralization evolved as a biogeochemical response to an increased influx of continental weathering products during the last stages in the formation of the Great Unconformity."

http://io9.com/5903330/toxic-oceans-created-the-greatest-explosion-in-biodiversity-earth-has-ever-seen

You did an about face and went off into some personal opinions about how life evolved.

Sometimes trying to prove things to a disruptive student is not in the best interest of the rest of the class. That student might be seeking attention and not insight. The rest get ripped off.

From what you are teaching, the student's notes are something like this:

-impact of the cellular water.
-order within water/organics
-expression at DNA less random
-CaPO4 added order to the DNA.
-fewer random duds and more winners (ordered).
-hydrogen bonding contracts
-defines higher entropy
-expanded and contracted water shapes
-both are stable
-water pressure pixels.
-kosmotropes make more expanded water
-expansion puts squeeze on cell organics
-have to compact more efficiently.
-exoskeleton - pressure is maintained.
-external order/pressure plate
-removed for internal skeleton
-changing the position of order induction
-closer to nervous system
-becomes more ordered.
-cell is a crowded place
-molecule touching molecule.
-not a lot of room for free movement.
-statistical mechanics predicts average protein folded shape
-observation shows that the shape will have a probability of 1.0
-reason is the crowded nature of the cellular water
-aqueous pressure and surface tension
-puts squeeze on randomness in favor of order.
-fold of enzyme forced to stay at attention

You're complaining about a standard of proof? I'll give you one. Give us the links to the expert material that supports your claims.

As for transport inside the cytoplasm:

The motion of macromolecules within cells is normally random, occurring through Brownian motion that causes the molecules to diffuse through the cellular cytoplasm, which has viscosity similar to that of water.

...measurements show that the fluorescent molecules move about 15 times more slowly inside the cell than they do in a test tube...

The hydrodynamic interactions create cooperative motion between the molecules," Skolnick explained. "We see long-lived correlations between the molecules, independent of size, in space and time. This suggests that these correlated motions may be extremely important in the dynamics of molecules."

http://www.gatech.edu/newsroom/release.html?nid=62095

Even if you could address macromolecule transport at this level, you still leave your "students" wondering what this has to do with the ocean alkalinity increase at the Great Unconformity and the rise of biomineralization, leading to the Cambrian Explosion:

Here we use new stratigraphic and geochemical data to show that early Palaeozoic marine sediments deposited approximately 540–480 Myr ago record both an expansion in the area of shallow epicontinental seas and anomalous patterns of chemical sedimentation that are indicative of increased oceanic alkalinity and enhanced chemical weathering of continental crust. These geochemical conditions were caused by a protracted period of widespread continental denudation during the Neoproterozoic followed by extensive physical reworking of soil, regolith and basement rock during the first continental-scale marine transgression of the Phanerozoic. The resultant globally occurring stratigraphic surface, which in most regions separates continental crystalline basement rock from much younger Cambrian shallow marine sedimentary deposits, is known as the Great Unconformity. Although Darwin and others have interpreted this widespread hiatus in sedimentation on the continents as a failure of the geologic record, this palaeogeomorphic surface represents a unique physical environmental boundary condition that affected seawater chemistry during a time of profound expansion of shallow marine habitats. Thus, the formation of the Great Unconformity may have been an environmental trigger for the evolution of biomineralization and the ‘Cambrian explosion’ of ecologic and taxonomic diversity following the Neoproterozoic emergence of animals.

http://www.nature.com/nature/journal/v484/n7394/full/nature10969.html

And your point is . . . ? :shrug:

 

[wellwisher]

Thus, the formation of the Great Unconformity may have been an environmental trigger for the evolution of biomineralization and the ‘Cambrian explosion’ of ecologic and taxonomic diversity following the Neoproterozoic emergence of animals.

I was explaining how this may have occurred, so this opinion had legs to stand on. Just showing that there was a time period overlap does not explain cause and effect. I was alive when the space shuttle flew but had little to do with it. Cause and effect requires more than that.

The point I was making is the cellular water is not inert. Things added to the water impact the activity within the water. Changes in water activity impact how organics act. Now we get a possible sequence of cause and affect. The use of Ca+ to make shells and bones has an impact on the water and therefore will haver an impact on the organics within life.

One thing I would like to add is statistical mechanics predicted that protein folds should define average shapes. Yet they form very specific shapes with probability equal to 1.0. The statistical assumption for life does not apply, but can lead to false conclusions.

The reason the statistical assumption did not work out as predicted is biology ignores the impact of the water.

 

[Believe]

I was explaining how this may have occurred, so this opinion had legs to stand on. Just showing that there was a time period overlap does not explain cause and effect. I was alive when the space shuttle flew but had little to do with it. Cause and effect requires more than that.

The point I was making is the cellular water is not inert. Things added to the water impact the activity within the water. Changes in water activity impact how organics act. Now we get a possible sequence of cause and affect. The use of Ca+ to make shells and bones has an impact on the water and therefore will haver an impact on the organics within life.

One thing I would like to add is statistical mechanics predicted that protein folds should define average shapes. Yet they form very specific shapes with probability equal to 1.0. The statistical assumption for life does not apply, but can lead to false conclusions.

The reason the statistical assumption did not work out as predicted is biology ignores the impact of the water.

You water argument has nothing to do with the article. The article asserts that the extra minerals in the water were poisoning the creatures at that time and to stop this from happening they build bones and shells to get rid of the extra minerals. This has nothing to do with the way water behaves changing.

 

[Aqueous Id]

One thing I would like to add is statistical mechanics predicted that protein folds should define average shapes.

Statistical mechanics has no jurisdiction over a protein's shape. That is decided in the court of the nuclear DNA. Your argument is the same thing as saying that statistical mechanics produces randomized DNA which is obviously false. Your premise is therefore false. Figure out how ribosomes build a protein by assembling amino acids according to the codon triplets delivered to the ribosome by the messenger RNA. Then you will begin to understand why your idea is nonsensical.

Yet they form very specific shapes with probability equal to 1.0.

No, the proteins don't form anything. They are the result. DNA does the forming, via mRNA, ribosomes and free amino acids in the cytoplasm. It's a system, which you fail to recognize. There is no stochastic process in this, so your "probability=1.0" idea is incorrect. DNA is deterministic. Randomization comes into play when anomalies occur, most notably, mutations. This is yet another reason why it is absurd to assume "p=1.0". Again, since you are talking about protein shapes, they are dictated by the DNA that codes them, nothing more. Ignoring this only leads to false conclusions.

The statistical assumption for life does not apply, but can lead to false conclusions.

I have shown how and why your confusion between deterministic and stochastic processes leads to your false conclusions. I have also shown that your reasoning ignores the actual method of protein synthesis, and is therefore leading you to false conclusions.

The reason the statistical assumption did not work out as predicted is biology ignores the impact of the water.

False for the reasons given above, and absurdly cynical - both for ignoring the biological system of protein synthesis, and for disparaging the very science you fail to understand.

 

[Gravage]

Cool.