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Author Topic:   Disadvantageous Mutations: Figures
New Cat's Eye
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Message 61 of 93 (798925)
02-06-2017 3:08 PM
Reply to: Message 47 by CRR
02-01-2017 6:47 AM


Errr, no. It is quite obvious that the probability of landing on an edge is infinitesimal in the total result space.

That's what I'm saying. When you wrote:

quote:
A major problem is that functional proteins appear to be exceedingly rare in the space of all proteins. Axe estimated it to be about 1/10^77.

The probability of getting most of the proteins in "the space of all proteins" is also infinitesimal, so you have the wrong statistical estimate there. There is not equal weight on those improbable proteins forming so you can't include them like that in the estimate of the functional proteins forming. If you did, it would be just like including all the places where a coin could land on its edge in the calculation of the odds of it landing on heads or tails.

Rather the analogy would be that finding a functional proteins would correspond to a flipped coin landing on its edge.

Then something has to be wrong, because functional proteins do form. The problem is that proteins don't form from random pieces randomly coming together and joining mechanically. There's chemistry involved and some reactions are catalyzed and some are practically impossible. To calculate the odds of one particular protein forming out of the space of all proteins is not the right calculation to determine the chances of a particular protein forming.

In fact, some proteins could form inevitably.


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CRR
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Joined: 10-19-2016
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Message 62 of 93 (800754)
02-27-2017 2:50 PM
Reply to: Message 61 by New Cat's Eye
02-06-2017 3:08 PM


Functional proteins do form today in cells because they are specified and constructed by cellular machinery. Proteins don't form from random pieces randomly coming together and joining mechanically.

However novel functional proteins seem to be exceedingly rare. An attempt by Axe to quantify this was the point of his research. Even quite minor changes are beyond the reach of the mutation/selection mechanism.


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New Cat's Eye
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From: near St. Louis
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Message 63 of 93 (800760)
02-27-2017 5:25 PM
Reply to: Message 62 by CRR
02-27-2017 2:50 PM


Functional proteins do form today in cells because they are specified and constructed by cellular machinery.

Where by "machinery" you mean "chemicals doing chemistry"...

Proteins don't form from random pieces randomly coming together and joining mechanically.

That's what I said. But the calculation of a protein forming from the space of all proteins assumes they do randomly come together and join mechanically, so the calculation is the wrong one.

However novel functional proteins seem to be exceedingly rare.

And the same calculation done on the space of all coin landings shows us that coin flips landing on either the heads or tails side are exceedingly rare.

Even quite minor changes are beyond the reach of the mutation/selection mechanism.

The math is bad.


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CRR
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Posts: 532
From: Australia
Joined: 10-19-2016
Member Rating: 1.3


Message 64 of 93 (801290)
03-04-2017 9:56 PM
Reply to: Message 63 by New Cat's Eye
02-27-2017 5:25 PM


It's a lot more than "chemical doing chemistry". If that was all the frog in a blender experiment should work. Have a look at ATP synthaze for example. It is a nanotechnology machine powered by a flow of protons through a turbine.

The extreme rarity of functional proteins means that it is practically impossible to get from one functioning protein to another by incremental beneficial steps. Let alone explaining the appearance of the original protein.

And the same calculation done on the space of all coin landings shows us that coin flips landing on either the heads or tails side are exceedingly rare.

I assume you mean "neither the head or the tail".
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Dr Adequate
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Message 65 of 93 (801301)
03-04-2017 11:09 PM
Reply to: Message 64 by CRR
03-04-2017 9:56 PM


It's a lot more than "chemical doing chemistry".

Nope.

If that was all the frog in a blender experiment should work.

Your reference is obscure and your reasoning absent.

The extreme rarity of functional proteins means that it is practically impossible to get from one functioning protein to another by incremental beneficial steps.

Then it's strange how often it happens.

Let alone explaining the appearance of the original protein.

Some people have tried to explain this with reference to the activity of an invisible wizard who lives in the sky, but of course that just raises the question of what processes could produce an invisible sky-wizard.


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NosyNed
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Message 66 of 93 (801314)
03-05-2017 1:02 AM
Reply to: Message 64 by CRR
03-04-2017 9:56 PM


coins
I assume you mean "neither the head or the tail".

No, I am pretty sure that isn't what he means. He means that a head result or a tail result are only 2 out of many, many other results. Taking that space of possible results and using the wrong method of calculating the odds produces a result saying a head (or a tail) is going to be very unlikely.


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CRR
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Posts: 532
From: Australia
Joined: 10-19-2016
Member Rating: 1.3


Message 67 of 93 (801388)
03-05-2017 4:56 PM
Reply to: Message 65 by Dr Adequate
03-04-2017 11:09 PM


If that was all the frog in a blender experiment should work.

Your reference is obscure and your reasoning absent.

Put a frog in a blender and blend well. All the chemicals are there so the chemical reactions should continue if it's just chemicals doing chemistry. https://www.youtube.com/watch?v=_Ea2d09r18o

The extreme rarity of functional proteins means that it is practically impossible to get from one functioning protein to another by incremental beneficial steps.

Then it's strange how often it happens.

Then you should have no problem giving 5 observed examples.


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RAZD
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Posts: 18855
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.6


Message 68 of 93 (801393)
03-05-2017 5:16 PM
Reply to: Message 67 by CRR
03-05-2017 4:56 PM


Put a frog in a blender and blend well. All the chemicals are there so the chemical reactions should continue if it's just chemicals doing chemistry. ...

They do. It just doesn't look like a frog anymore, because those structures have been disrupted.

Mostly you will have the bacteria continue to thrive and the tissue remnants will be consumed by rot.

Enjoy


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Dr Adequate
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Posts: 15948
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Message 69 of 93 (801403)
03-05-2017 9:38 PM
Reply to: Message 67 by CRR
03-05-2017 4:56 PM


Put a frog in a blender and blend well. All the chemicals are there so the chemical reactions should continue if it's just chemicals doing chemistry.

If you mash up any chemical system you'll change the outcome of the chemical process. 'Cos of, you know, breaking the test-tubes and stuff.

Smash it to pieces, it won't work any more than the frog does.

Then you should have no problem giving 5 observed examples.

http://www.gate.net/~rwms/EvoMutations.html


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AZPaul3
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Posts: 3428
From: Phoenix
Joined: 11-06-2006


(1)
Message 70 of 93 (801431)
03-06-2017 7:35 AM
Reply to: Message 67 by CRR
03-05-2017 4:56 PM


Put a frog in a blender and blend well. All the chemicals are there so the chemical reactions should continue if it's just chemicals doing chemistry.

Oh, how asinine.

When we say "just chemicals doing chemistry" ignorant people try to twist this into "all chemistry is every chemistry" as your blended frog example attempts to smear.

No. We mean that when the components and the environment are right the specific chemistry happens without the need of some inexplicable invisible magic.

When hydrogen gas and oxygen gas mix under a condition of thermodynamic excess ... poof!... chemistry happens. Water is formed. No magic sky daddy with his magic dick in the apparatus is necessary.

Chemicals doing chemistry. Making water the non-magic way.

In your frog example you have disrupted the chemical environment to the point it can no longer do its frog thing. You have only a non-differentiated mush that not even your imagined magic sky daddy could form back into a frog. Go ahead. Leave it on your kitchen counter. Let's see how long it takes for your magic man to put it back together.

Edited by AZPaul3, : No reason given.



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New Cat's Eye
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Posts: 11665
From: near St. Louis
Joined: 01-27-2005
Member Rating: 2.5


(1)
Message 71 of 93 (801447)
03-06-2017 10:28 AM
Reply to: Message 64 by CRR
03-04-2017 9:56 PM


And the same calculation done on the space of all coin landings shows us that coin flips landing on either the heads or tails side are exceedingly rare.

I assume you mean "neither the head or the tail".

No, I meant what I wrote.

Heads and tails are 2 out of a nearly infinite number of places that a coin flip can land, if you are included all the places along the edge. So, using that in your calculation of the odds of it landing on heads or tails will get you an almost impossible chance of it.

Similiarly, that's why using the calculation in the space of "all possible proteins" is also erroneaous, for the reasons I've prevoiusly explained.

It's a lot more than "chemical doing chemistry".

Like what? Do you have an example?

All biology can be boiled down to complex chemistry, just like all chemistry can be boiled down to complex physics.

There are no exceptions that I am aware of. You?

If that was all the frog in a blender experiment should work.

Wrong. It takes more than just setting the ingredients in the oven to get bread, but the bread is not made of more than the ingredients.

It is a nanotechnology machine powered by a flow of protons through a turbine.

That's still chemicals doing chemistry.

The extreme rarity of functional proteins means that it is practically impossible to get from one functioning protein to another by incremental beneficial steps. Let alone explaining the appearance of the original protein.

That is based on bad math though, so it isn't true.

Added by edit:

From Message 67:

Put a frog in a blender and blend well. All the chemicals are there so the chemical reactions should continue if it's just chemicals doing chemistry.

No, this is completely wrong. Not all chemical reactions are the same. For example, some of them require catalysis while some of them are spontaneous.

The incredibly complex chemical system know as "a frog" cannot be created by simply setting all of the ingredients next to each other.

Salt water, on the other hand, yes - just mix them.

Edited by New Cat's Eye, : see Added by Edit


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RAZD
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Posts: 18855
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.6


Message 72 of 93 (801448)
03-06-2017 10:56 AM
Reply to: Message 71 by New Cat's Eye
03-06-2017 10:28 AM


Heads and tails are 2 out of a nearly infinite number of places that a coin flip can land, if you are included all the places along the edge. So, using that in your calculation of the odds of it landing on heads or tails will get you an almost impossible chance of it.

To say nothing of all the possibilities of landing on a surface that is not flat ... say at a 45° angle ... where do you arbitrarily draw the line?

And like chemical reactions some positions have more likelihood than others.

Enjoy


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
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to share.


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ringo
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Message 73 of 93 (801449)
03-06-2017 10:57 AM
Reply to: Message 67 by CRR
03-05-2017 4:56 PM


CRR writes:

Put a frog in a blender and blend well. All the chemicals are there so the chemical reactions should continue if it's just chemicals doing chemistry.


Yup. Just a different set of reactions. If you mix A and B you're going to get a different reaction than if you mix B and C but it's still just chemistry. No magic wand required.
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caffeine
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Message 74 of 93 (801478)
03-06-2017 2:32 PM
Reply to: Message 63 by New Cat's Eye
02-27-2017 5:25 PM


That's what I said. But the calculation of a protein forming from the space of all proteins assumes they do randomly come together and join mechanically, so the calculation is the wrong one.

That does not appear to be the calculation that Axe was doing. What he did* was take a specific protein (not the naturally occuring sequence, but one intentionally selected to be sensitive to mutation) and then subjected it to random mutation to see how many possible changes led to a functional protein (his conclusion - few). He then extrapolated from this that the probability of any protein performing a specific function was as low as 1 in 10^77.

Note that the probability of finding a protein which performs a specific function is of course a very different calculation than the probability of finding a protein with a function.

*with the caveat that this is what I understand he did - I am a little out of my depth.


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New Cat's Eye
Member
Posts: 11665
From: near St. Louis
Joined: 01-27-2005
Member Rating: 2.5


Message 75 of 93 (801488)
03-06-2017 3:05 PM
Reply to: Message 74 by caffeine
03-06-2017 2:32 PM


That does not appear to be the calculation that Axe was doing.

Got a link to the paper?


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