Darwin Unhinged: The Bugs in Evolution

Ah, okay, so we aren't talking about the flagellum as it stands, but about a "conserved core" of proteins. I'm happy to stipulate that if you remove all the proteins that aren't absolutely necessary, you will indeed end up with a subset that are necessary for motility. This would be true of all existing mechanisms, natural or human-designed. Water is irreducibly complex, as long as we are talking about original function.

This explicitly admits to the problem of IC. It's not just any additional necessary (including accessory or interfacing) parts of the cellular apparatus we are talking about, it's the core components of the flagellar machine. Are you claiming that any of the core components (filament, hook, and basal body/stator/rotor assembly) can be removed without the flagellum losing its propulsive function?  

Actually, it does refute the IC of actual flagella.

 
Please explain how the paper you posted (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1943423/, title The Protein Network of Bacterial Motility) refutes the irreducible complexity of the bacterial flagellum. Here I refer to the original definition of IC in Darwin's Black Box, which concentrates on single, coherent systems. I don't see how the paper has much to do with IC. If anything the extra proteins that affect mobility show the problem is worse than just needing the core proteins (like needing equipment to manufacture gasoline so that an outboard motor can work). The large number of different gene deletions having reduced or no motility has nothing to do with the irreducible complexity of the basic flagellar mechanism. This IC was demonstrated by Scott Minnich's gene knockout experiments. Most of these 159 gene deletion strains described in the paper probably interfered with motility by interfering with or deleting other interfacing components of the cell, rather than by directly disrupting or deleting the core components of the flagellum.

You'll notice that Behe's original definition is not the one used today.

I'm not aware of of anything in print by Michael Behe in which he formally substitutes in an actual book or paper a new operational definition of IC replacing the one in Darwin's Black Box (other than some theorizing about problems of the need for multiple unselected mutations, in The Edge of Evolution). The core of the different versions remains the observation that there are certain biological machines where the removal of any part causes the mechanism to stop functioning. It's mere quibbling to argue over whether there could be some other functionality (and therefore selectability) with one or more parts removed. Behe conceded in Darwin's Black Box that there is no strictly logical barrier; it is ultimately one of plausibility or probability.

Videos from Nour foundation:

Is Intelligence the Inevitable Outcome of Evolution?
Simon Conway Morris, Ian Tattersall & Melanie Chang discuss the evolution of human intelligence and whether it is the natural consequence of evolutionary forces.

Are the Forces Driving Evolution Truly Random?
Ian Tattersall and Simon Conway Morris talk about "random" events and cause and effect in evolution.

Above are excerpts from a longer discussion:
The Story of Life: Critical Insights from Evolutionary Biology

This explicitly admits to the problem of IC. It's not just any additional necessary (including accessory or interfacing) parts of the cellular apparatus we are talking about, it's the core components of the flagellar machine. Are you claiming that any of the core components (filament, hook, and basal body/stator/rotor assembly) can be removed without the flagellum losing its propulsive function? 

No, but the "original function" requirement is no longer part of the definition of IC. And even if it were, it ignores the possibility of scaffolding. That requirement was eliminated because it renders everything IC, including things no one believes were designed.

Please explain how the paper you posted (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1943423/, title The Protein Network of Bacterial Motility) refutes the irreducible complexity of the bacterial flagellum. Here I refer to the original definition of IC in Darwin's Black Box, which concentrates on single, coherent systems. I don't see how the paper has much to do with IC. If anything the extra proteins that affect mobility show the problem is worse than just needing the core proteins (like needing equipment to manufacture gasoline so that an outboard motor can work). The large number of different gene deletions having reduced or no motility has nothing to do with the irreducible complexity of the basic flagellar mechanism. This IC was demonstrated by Scott Minnich's gene knockout experiments. Most of these 159 gene deletion strains described in the paper probably interfered with motility by interfering with or deleting other interfacing components of the cell, rather than by directly disrupting or deleting the core components of the flagellum.

The original definition isn't interesting anymore. Here are the three definitions in order of appearance:

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

The one that Behe currently uses involves unselected "steps."

    I'm not aware of of anything in print by Michael Behe in which he formally substitutes in an actual book or paper a new operational definition of IC replacing the one in Darwin's Black Box (other than some theorizing about problems of the need for multiple unselected mutations, in The Edge of Evolution). The core of the different versions remains the observation that there are certain biological machines where the removal of any part causes the mechanism to stop functioning. It's mere quibbling to argue over whether there could be some other functionality (and therefore selectability) with one or more parts removed. Behe conceded in Darwin's Black Box that there is no strictly logical barrier; it is ultimately one of plausibility or probability.

Mere quibbling? In other words, you reject all the subtleties?

http://www.ideacenter.org/contentmgr/sho...php/id/840

~~ Paul

In the Montanez et al. paper:

"1. The perceptron structure. The perceptron structure is predisposed to generating strings of ones sprinkled by zeros or strings of zeros sprinkled by ones. Since the binding site target is mostly zeros with a few ones, there is a greater predisposition to generate the target than if it were, for example, a set of ones and zeros produced by the flipping of a fair coin."

I have no idea what he's trying to say here. The entire chromosome is initialized randomly.

"In the search for the binding sites, the target sequences are fixed at the beginning of the search. "

No, they aren't.

~~ Paul

[Laird]

"1. The perceptron structure. The perceptron structure is predisposed to generating strings of ones sprinkled by zeros or strings of zeros sprinkled by ones. Since the binding site target is mostly zeros with a few ones, there is a greater predisposition to generate the target than if it were, for example, a set of ones and zeros produced by the flipping of a fair coin."

I have no idea what he's trying to say here. The entire chromosome is initialized randomly.

This claim seems to be based on the idea that a "bias" is subtracted from a (potential) site's weight prior to comparing that site's weight with the threshold weight (thus predisposing it to not making the threshold, thus predisposing the process to evaluate fewer sites as binding than non-binding, which is one of the requirements for ultimate success). I see no evidence of such a bias parameter in either your code or the interface of the program though, but perhaps it was present in an earlier version of the program?

"In the search for the binding sites, the target sequences are fixed at the beginning of the search. "

No, they aren't.

I think what they're referring to here is the effect of line 115 in Simulator.java:

Code:

   determineBindingSites();

[Laird]

This claim seems to be based on the idea that a "bias" is subtracted from a (potential) site's weight prior to comparing that site's weight with the threshold weight (thus predisposing it to not making the threshold, thus predisposing the process to evaluate fewer sites as binding than non-binding, which is one of the requirements for ultimate success). I see no evidence of such a bias parameter in either your code or the interface of the program though, but perhaps it was present in an earlier version of the program?

Actually I think I misinterpreted what they mean by bias: I think what they mean by "bias" is the threshold weight. They put it in terms of subtracting the "bias" (threshold weight) from the (potential) site's weight, and then checking whether the result is positive. I'm not sure I understand their argument after all, but if you want to examine it yourself, it's between pages 3 and 4 of their paper.

If consciousness is an epiphenomenon, then how is it that we are talking about it?

I think people who believe it's an epiphenomenon haven't worked out the ramifications.

~~ Paul

Hi Paul,

I had a question about this, so I started a new thread under "Consciousness" for anyone who may be able to help me.

http://psiencequest.net/forums/thread-co...phenomenon

Linda

This claim seems to be based on the idea that a "bias" is subtracted from a (potential) site's weight prior to comparing that site's weight with the threshold weight (thus predisposing it to not making the threshold, thus predisposing the process to evaluate fewer sites as binding than non-binding, which is one of the requirements for ultimate success). I see no evidence of such a bias parameter in either your code or the interface of the program though, but perhaps it was present in an earlier version of the program?

I don't think so. I don't remember implementing and then removing any such parameter, though it has been a long time.

I'll check out their argument in the paper.

I think what they're referring to here is the effect of line 115 in Simulator.java:

        determineBindingSites();

Yes, the positions of the binding sites are predetermined. But their initial sequences are random.

The simulation could be modified to make the pressures even more abstract, but the point was to show that certain predicted amounts of information evolved.

The arguments about this center around what it means for information in the environment to transmute into information in the genome. Clearly there have to be environmental pressures to make anything interesting happen. Any pressure is, in some sense, "rigging" the simulation. But that's the way it works in nature, too.

~~ Paul

[Laird]

The arguments about this center around what it means for information in the environment to transmute into information in the genome. Clearly there have to be environmental pressures to make anything interesting happen. Any pressure is, in some sense, "rigging" the simulation. But that's the way it works in nature, too.

I don't doubt that in certain contexts, a process in which a population is subjected to random mutation after which the fittest amongst the population by some fitness criteria are selected can result in a... well, fitter... population, and, by some reasonable definition, an increase in information (in the population and/or its members). For example, in a Numerical Methods class at university, we were taught about and required to implement a genetic algorithm the purpose of which was to find a relatively optimal ("fit") solution to a numerical problem, and the algorithm worked just fine - one might say that its result was "informative".

I do think the critics of the "ev" program have a point in that (in my words, not theirs) that which is "fittest" is decided in advance, and that the program is merely being guided - by design - to that preconceived outcome, but that's not really what concerns me, because I take your point that (again, in my words, not yours) under the neo-Darwinian model, even in nature where there is no explicitly preconceived outcome, there might be seen to be implicit outcomes given the (admittedly loose) fitness criteria in play (based around capacity for reproduction, including both surviving for long enough to do so as well as attracting a mate).

The real question for me is whether this process is sufficient to explain the (information in the) life on this planet, given the many objections to its sufficiency that have been raised in this thread... and I won't even try to rehash them, but I do here express my appreciation to those who have raised them. Again, this has been a fascinating thread and I'm sure it will continue to be.

I don't doubt that in certain contexts, a process in which a population is subjected to random mutation after which the fittest amongst the population by some fitness criteria are selected can result in a... well, fitter... population, and, by some reasonable definition, an increase in information (in the population and/or its members). For example, in a Numerical Methods class at university, we were taught about and required to implement a genetic algorithm the purpose of which was to find a relatively optimal ("fit") solution to a numerical problem, and the algorithm worked just fine - one might say that its result was "informative".

Indeed. And we don't even need evidence that such a thing will work. From Marvin Minsky:

"The Process of Evolution is the following abstract idea:

There is a population of things that reproduce, at different rates in different environments. Those rates depend, statistically, on a collection of inheritable traits. Those traits are subject to occasional mutations, some of which are then inherited.

Then one can deduce, from logic alone, without any need for evidence, that:

THEOREM: Each population will tend to increase the proportion of traits that have higher reproduction rates in its current environment."

I do think the critics of the "ev" program have a point in that (in my words, not theirs) that which is "fittest" is decided in advance, and that the program is merely being guided - by design - to that preconceived outcome, but that's not really what concerns me, because I take your point that (again, in my words, not yours) under the neo-Darwinian model, even in nature where there is no explicitly preconceived outcome, there might be seen to be implicit outcomes given the (admittedly loose) fitness criteria in play (based around capacity for reproduction, including both surviving for long enough to do so as well as attracting a mate).

I might go so far as to say that some outcomes are preconceived, where "preconceived" is defined as a collection of pressures that result from the pre-existing environment. Of course, I'm misusing "preconceived" a bit, since we usually think only of intelligent beings as conceiving things.

The real question for me is whether this process is sufficient to explain the (information in the) life on this planet, given the many objections to its sufficiency that have been raised  in this thread... and I won't even try to rehash them, but I do here express my appreciation to those who have raised them. Again, this has been a fascinating thread and I'm sure it will continue to be.

I think the process is sufficient to explain any level of complexity, given enough time. So the question is: Has there been enough time?

~~ Paul