Darwin Unhinged: The Bugs in Evolution

It's not just blundering. There's selection, too. We use evolutionary algorithms to solve problems.

https://en.wikipedia.org/wiki/Evolutionary_algorithm

Please stop saying it's random.

~~ Paul

Paul,

James Tour (and I) were discussing bio-genesis - at time before any life existed to be selected, or to pass on its genes!

In that context:

1)  The chemistry would be random.

2)  Selection of any sort could not happen.

3)  No chemicals produced by reactions would be purified, and as Tour said, that leads to an impossible build-up of side-products.

4)  No reactions could be catalysed by enzymes, because there would be no enzymes!

I wish his delivery had been a little easier on the ear, but other than that, there is nothing to fault. It says a lot that 'experts' are willing to invoke the concept of evolution even at a time when there were no organisms to be selected. However, who cares about logic, we are talking about dogma that is just as daft as the Trinity which is one and three at the same time!

David

I note that you keep making up examples: flagellum, rabbit fossil. Do you have any actual examples? I'm not sure how you could have one for irreducible complexity, since it ignores scaffolding. I'm not sure how you could have one for CSI, since it's never been calculated for any biological mechanism.

Concerning irreducible complexity.

"Scaffolding" is supposed to be one of the leading neo-Darwinistic explanations for irreducibly complex biological systems. A biochemical structure is supposed to have functioned as a sort of scaffold of initial additional ultimately unnecessary complexity in the evolution of an IC system before becoming dispensable and disappearing. Sort of a biological analog of the scaffolding needed to build an arch. It would be interesting to see some specific real world examples with complex biological mechanisms, where this argument might actually have some relevance to the real world of biology. I don't think there are any. Natural rock arches and parasites losing unnecessary body parts are not adequate. Another problem with this idea is that it actually adds to the necessary complexity of, and therefore the difficulty of unguided evolution in building, the original system. Scaffolding does nothing to change the fact that the basic function of an irreducibly complex system arises, by definition, only after all the core components of that system are in place. Given a functionally irreducibly complex system whose origin is to be explained by scaffolding, the challenge for the Darwinist is still to identify the sequence of gradual functional intermediaries leading to it.  

Exaptation (or co-option from a different use) is another standard orthodox explanation, but it also isn't adequate. The major problem with trying to explain an irreducibly complex system like the bacterial flagellum as a patchwork of co-opted preexisting components originally having different functions is that it requires multiple coordinated co-options. It's not just that one thing evolves for one function, and then, perhaps without any modification at all, gets used for some completely different function. The problem is that multiple protein parts from different functional systems all have to break free and then all have to coalesce to form a newly integrated system (as with an airplane formed by taking parts from a car, bicycle, motorboat, and train).

Even if all the parts (i.e., proteins) for a bacterial flagellum are in place within a cell but serving other functions (extremely unlikely in itself), there is no reason to think that those parts can come together spontaneously to form a tightly integrated system like the flagellum. The problem here is that parts performing functions in separate systems are unlikely to be adapted to each other so that they can work together coherently within a single system. Like a screw formed as part of one subsystem, and a nut formed as part of another subsystem that evolved independently of the first subsystem. It's extremely unlikely that the nut and screw will mechanically work together. This problem is of course much greater in the living cell.

These difficulties are compounded by the need for the simultaneous formation of the assembly system including the instructions for it.  

The overall problem with co-option can be summarized in the following. Each of the requirements 1-4 had to have been available simultaneously in the cell. The reader must judge how likely or unlikely this is.

1) All of the component parts must have been present at the same time and in roughly the same place, and all of them must have had other naturally-selectable, alternate useful functions. For the flagellum for example, there is no evidence whatsoever that this ever was the case, or that it ever even could have been the case.

2) The components would have to have been compatible with each other functionally. There is no evidence that this interface compatibility ever existed (between all those imaginary co-opted component parts), or that it even could have existed.

3) An assembly mechanism is required, and that mechanism must be complete in every detail, otherwise incomplete or improper assembly will result, and no naturally-selectable function will be produced. 

4) Finally, assembly instructions are required. Assembly must be timed and coordinated properly. And the assembly instructions must be complete in every detail, otherwise no function will result. As noted, the assembly mechanism and the instructions for it are as complicated as the mechanism being assembled, and are also IC.

What is needed is seamless Darwinian accounts that are both detailed and testable of how biological subsystems undergoing "scaffold" formation and removal and coevolution and co-option could gradually transform into irreducibly complex mechanisms, including the assembly mechanisms and instructions. It would be needed to show that it is, at the very least, plausible that a selective advantage could be acquired by the organism at each relatively simple step involving no more than a few mutations at a time (taking into account that more than two coordinated specific mutations at a time are exceedingly unlikely), and identify those steps and the mutations. This hasn't been done yet for the flagellum or any other functionally IC system that I know of.  

No such accounts are available or forthcoming. The scientific literature shows a complete absence of detailed, testable, step-by-step proposals for how scaffolding, coevolution and co-option could actually produce irreducibly complex biochemical systems. In place of such proposals, Darwinists simply blithely assert that these general concepts are so compelling that this is how the various functionally IC systems must have come about. I guess we are just supposed to take them at their word. 

If such accounts were available, critics of intelligent design would be citing them, and intelligent design would be refuted. Until that happens, such assertions are just statements of faith.

James Tour (and I) were discussing bio-genesis - at time before any life existed to be selected, or to pass on its genes!

    In that context:

    1)  The chemistry would be random.

Well, it's not random. It follows the laws of chemistry.

2)  Selection of any sort could not happen.

Some macromolecules are more stable than others. They are selected.

3)  No chemicals produced by reactions would be purified, and as Tour said, that leads to an impossible build-up of side-products.

It leads to side-products. You're going out on a long limb to say that this makes anything interesting impossible.

4)No reactions could be catalysed by enzymes, because there would be no enzymes!

There were no modern enzymes. But enzymes are just fancy catalysts. Some interesting articles:

https://www.ncbi.nlm.nih.gov/pubmed/773920

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3534232/

http://sandwalk.blogspot.com/2012/08/on-...etely.html

I wish his delivery had been a little easier on the ear, but other than that, there is nothing to fault. It says a lot that 'experts' are willing to invoke the concept of evolution even at a time when there were no organisms to be selected. However, who cares about logic, we are talking about dogma that is just as daft as the Trinity which is one and three at the same time!

How do you know there is nothing to fault? In order to know this, you have to know more evolutionary biology than he does. Anyway, why don't you quote something and let's see how adamant he really is.

I have no problem with Tour doubting the origin of life. As Moran says:

"We don't understand how life originated. Any scientist who is confident about their understanding of the origin of life is wrong. I strongly doubt that James Tour has ever met a scientist working on the origin of life who claims that he/she knows the answer."

~~ Paul

I could not delete this post.

Concerning irreducible complexity.

    "Scaffolding" is supposed to be one of the leading neo-Darwinistic explanations for irreducibly complex biological systems. A biochemical structure is supposed to have functioned as a sort of scaffold of initial additional ultimately unnecessary complexity in the evolution of an IC system before becoming dispensable and disappearing. Sort of a biological analog of the scaffolding needed to build an arch. It would be interesting to see some specific real world examples with complex biological mechanisms, where this argument might actually have some relevance to the real world of biology. I don't think there are any. Natural rock arches and parasites losing unnecessary body parts are not adequate. Another problem with this idea is that it actually adds to the necessary complexity of, and therefore the difficulty of unguided evolution in building, the original system. Scaffolding does nothing to change the fact that the basic function of an irreducibly complex system arises, by definition, only after all the core components of that system are in place. Given a functionally irreducibly complex system whose origin is to be explained by scaffolding, the challenge for the Darwinist is still to identify the sequence of gradual functional intermediaries leading to it.

This is all very nice, but aren't we getting ahead of ourselves? Can you name an irreducibly complex biological mechanism that we can focus on?

Exaptation (or co-option from a different use) is another standard orthodox explanation, but it also isn't adequate. The major problem with trying to explain an irreducibly complex system like the bacterial flagellum as a patchwork of co-opted preexisting components originally having different functions is that it requires multiple coordinated co-options. It's not just that one thing evolves for one function, and then, perhaps without any modification at all, gets used for some completely different function. The problem is that multiple protein parts from different functional systems all have to break free and then all have to coalesce to form a newly integrated system (as with an airplane formed by taking parts from a car, bicycle, motorboat, and train).

The flagellum is not IC. Again, can we pick something that is?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1943423/

I won't worry about the rest of your post until we have picked an IC mechanism. But I will come back to it.

Also, could we decide on which definition of IC we're using? For example, is an IC mechanism one which, when reduced, does not maintain its original function or does not have any function? Here are four definitions:

http://www.asa3.org/ASA/education/origins/ic-cr.htm

"Demonstration that a system is irreducibly complex is not a proof that there is absolutely no gradual route to its production. Although an irreducibly complex system can't be produced directly, one can't definitively rule out the possibility of an indirect, circuitous route."
---Behe, 1996

~~ Paul

Well, it's not random. It follows the laws of chemistry.

Some macromolecules are more stable than others. They are selected.

Great - welcome to the planet of polythene - goodbye RNA! Part of the problem is that stable molecules are by definition less reactive! 

It leads to side-products. You're going out on a long limb to say that this makes anything interesting impossible.

Well I have thought that for a long time - and said it in conversations with you. Molecules are not organisms, if a reaction ends up with zillions of different molecules being created, nothing is going to pull out the odd 'useful' molecule from the mess. I don't know if you have ever done any laboratory organic chemistry - I have done a little, years ago - but exactly as Tour says, a major part of the process is extracting the one desired products and cleaning it up, usually at every step.

There were no modern enzymes. But enzymes are just fancy catalysts. Some interesting articles:

https://www.ncbi.nlm.nih.gov/pubmed/773920

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3534232/

http://sandwalk.blogspot.com/2012/08/on-...etely.html

I'll take a look at those, however this quote doesn't bode well: "In this paper we speculate on the origin and early evolution of transition element enzymes."

You would need to really flesh out what you mean by evolution in the pre-life context, if you want to persuade me.
[Image: sidney-harris-cartoon-a-miracle-occurs-h...=300&h=364]

How do you know there is nothing to fault? In order to know this, you have to know more evolutionary biology than he does. Anyway, why don't you quote something and let's see how adamant he really is.

I have no problem with Tour doubting the origin of life. As Moran says:

"We don't understand how life originated. Any scientist who is confident about their understanding of the origin of life is wrong. I strongly doubt that James Tour has ever met a scientist working on the origin of life who claims that he/she knows the answer."

The problem with that, is that saying "we don't know the answer yet", can simply be a way of postponing indefinitely the conclusion that natural processes would not produce life from non-life.

There was great optimism after the Urey Millar experiment that the origin of life might be a relatively simple problem, This was partly because far less of the actual complexity of living cells had been realised back then. Since that time, there has been an exponential decay in that optimism, but very little of that ever gets passed on to the general public - lest they begin to wonder if life really did start by accident. James Tour's biggest 'sin' is perhaps, that he spelled out the size of the problem to a larger audience.

His video points out the sheer improbability that random (I note your objection but randomness doesn't have to mean all probabilities are equal) chemistry will produce anything useful because of its complexity. Yes, if you had a gadget that could pull out a handful of molecules from the resultant sludge, based on some deliberate intention to create something (which would itself imply intelligence) things might be different. Indeed, J. Scott Turner, points out that the opposite is really true - before life - before cells - diffusion processes would tend to dissipate any tiny concentrations of 'useful' molecules that did develop.

David

Great - welcome to the planet of polythene - goodbye RNA! Part of the problem is that stable molecules are by definition less reactive! 
Well I have thought that for a long time - and said it in conversations with you. Molecules are not organisms, if a reaction ends up with zillions of different molecules being created, nothing is going to pull out the odd 'useful' molecule from the mess. I don't know if you have ever done any laboratory organic chemistry - I have done a little, years ago - but exactly as Tour says, a major part of the process is extracting the one desired products and cleaning it up, usually at every step.
I'll take a look at those, however this quote doesn't bode well: "In this paper we speculate on the origin and early evolution of transition element enzymes."

You would need to really flesh out what you mean by evolution in the pre-life context, if you want to persuade me.
[Image: sidney-harris-cartoon-a-miracle-occurs-h...=300&h=364]

The problem with that, is that saying "we don't know the answer yet", can simply be a way of postponing indefinitely the conclusion that natural processes would not produce life from non-life.

There was great optimism after the Urey Millar experiment that the origin of life might be a relatively simple problem, This was partly because far less of the actual complexity of living cells had been realised back then. Since that time, there has been an exponential decay in that optimism, but very little of that ever gets passed on to the general public - lest they begin to wonder if life really did start by accident. James Tour's biggest 'sin' is perhaps, that he spelled out the size of the problem to a larger audience.

His video points out the sheer improbability that random (I note your objection but randomness doesn't have to mean all probabilities are equal) chemistry will produce anything useful because of its complexity. Yes, if you had a gadget that could pull out a handful of molecules from the resultant sludge, based on some deliberate intention to create something (which would itself imply intelligence) things might be different. Indeed, J. Scott Turner, points out that the opposite is really true - before life - before cells - diffusion processes would tend to dissipate any tiny concentrations of 'useful' molecules that did develop.

David

So a MAL would consciously concentrate useful molecules? Is that what you are saying?

I have to say, for one who is beamoaning the lack of a detailed mechanism from Paul (despite his links) you (and others) are very cagey over those details.

So a MAL would consciously concentrate useful molecules? Is that what you are saying?

I have to say, for one who is beamoaning the lack of a detailed mechanism from Paul (despite his links) you (and others) are very cagey over those details.

A considerable bit of misdirection. Let's argue the weaknesses of my opponents position while ignoring weaknesses of my own.

So a MAL would consciously concentrate useful molecules? Is that what you are saying?

I have to say, for one who is beamoaning the lack of a detailed mechanism from Paul (despite his links) you (and others) are very cagey over those details.

It is quite 'interesting' that with a straight face they are willing to propose a creature whose like has never been seen - one whose interests are wholly aligned with ours, with both all-encompassing and sub-microscopic vision and reach, and with exquisite presentience - but find the idea of pre-life isolation of chemical processes too ridiculous to conceive.

https://www.quantamagazine.org/in-warm-g...-20160317/
https://www.nature.com/articles/317792a0

"Then a miracle occurs" indeed.

Linda

The problem with that, is that saying "we don't know the answer yet", can simply be a way of postponing indefinitely the conclusion that natural processes would not produce life from non-life.

So you have this same objection to all unanswered questions in science, right?

There was great optimism after the Urey Millar experiment that the origin of life might be a relatively simple problem, This was partly because far less of the actual complexity of living cells had been realised back then. Since that time, there has been an exponential decay in that optimism, but very little of that ever gets passed on to the general public - lest they begin to wonder if life really did start by accident. James Tour's biggest 'sin' is perhaps, that he spelled out the size of the problem to a larger audience.

I think you're being too pessimistic.

https://en.wikipedia.org/wiki/Miller%E2%...ed_studies

His video points out the sheer improbability that random (I note your objection but randomness doesn't have to mean all probabilities are equal) chemistry will produce anything useful because of its complexity.

It's not just (nonuniform) randomness.

Yes, if you had a gadget that could pull out a handful of molecules from the resultant sludge, based on some deliberate intention to create something (which would itself imply intelligence) things might be different. Indeed, J. Scott Turner, points out that the opposite is really true - before life - before cells - diffusion processes would tend to dissipate any tiny concentrations of 'useful' molecules that did develop.

So we agree that there probably had to be some sort of proto-membrane.

~~ Paul