Darwin Unhinged: The Bugs in Evolution

I guess I got a little gung-ho there. The video turned out to be very interesting; I knew a little about infinities but  it went way beyond that. Thanks, Steve001, for sharing it.

The point being humans can intellectually conceive long time spans, but to intuitively know how long long can be is far beyond our ability and experience. It's difficult for anyone to know what living to 100 years of age feels like until you do it.

To me, that's like saying: "The process of monkeys typing randomly on keyboards is sufficient to produce a comprehensible story of any length, given enough time".

Assuming there is some sort of selection going on, I don't see why not.

The arguments raised in this thread, particularly around irreducible complexity and the bleakness of the protein landscape lead me to a tentative conclusion that's... not exactly affirmative.

Can you summarize what you think the compelling argument for IC is? We haven't even agreed on which definition to use. Nor has anyone dealt with the possibility of scaffolding.

There are many good papers on the protein landscape issue.

~~ Paul

Assuming there is some sort of selection going on, I don't see why not.

Can you summarize what you think the compelling argument for IC is? We haven't even agreed on which definition to use. Nor has anyone dealt with the possibility of scaffolding.

There are many good papers on the protein landscape issue.

~~ Paul

As for scaffolding, I don't pretend to know much about it in the biological sense but I've read the argument using the arch analogy. 

In this article, Casey Luskin describes the analogy and then claims that one problem is that there are no natural examples of such an arch being built in that manner. Here's the arch analogy described:

As early as the beginning of the 20th century, geneticist Herman Muller explained how biological systems that depend on the complex “interlocking” actions of many different components could come about by evolutionary processes: “Many of the characters and factors which, when new, were originally merely an asset finally became necessary because other necessary characters and factors had subsequently become changed so as to be dependent on the former” (Muller 1918, pp. 463-464). Thus, redundant complexity can eventually generate IC (under the weak interpretation). More recently, biochemist and molecular biologist A. G. Cairns-Smith proposed the analogy of “scaffolding” in the construction of an arch to explain the evolution of systems that are IC according to Behe (Cairns-Smith 1986; see also Orr 1997; Pennock 2000). A classical stone arch is IC in the weak sense, because the structure will collapse as soon as one removes either the keystone or one of the other stones. The support of scaffolding is necessary in building a stone arch, but once the arch is completed, the scaffolding can be safely removed. In a similar vein, a biochemical structure may have functioned as a scaffold in the evolution of an IC system before becoming dispensable and disappearing. That is, “Before the multitudinous components of present biochemistry could come to lean together they had to lean on something else” (Cairns-Smith 1986, p. 61).

Luskin comments:

This argument makes a valid point insofar that gradual evolution can remove parts in addition to adding them. However, I’ve heard this point made before, and in each case I’ve asked evolutionists to give me a biological analogue for the “arch” or scaffolding. It sounds nice in theory, but I have never been provided with a single specific real world example where this argument might actually have some relevance to the real world of biology.

So, in my google search on this issue, I came across several dismissive responses showing pictures of natural "arches" such as those created by weathering or sea erosion. They all seem to be missing the point from what I can see. Surely the point is that an architectural arch is a complex design created using specially shaped arch stones and the crucial keystone. The natural examples offered are nothing of the kind - they are pretty much just holes in the rock. Nothing complex about them at all.

Secondly, if you were to build an architectural arch including the correctly designed stones and use scaffolding to hold the structure in place until the keystone is in place, then surely you have an even more complex process with even more design involved?

As for scaffolding, I don't pretend to know much about it in the biological sense but I've read the argument using the arch analogy. 

In this article, Casey Luskin describes the analogy and then claims that one problem is that there are no natural examples of such an arch being built in that manner. Here's the arch analogy described:


Luskin comments:


So, in my google search on this issue, I came across several dismissive responses showing pictures of natural "arches" such as those created by weathering or sea erosion. They all seem to be missing the point from what I can see. Surely the point is that an architectural arch is a complex design created using specially shaped arch stones and the crucial keystone. The natural examples offered are nothing of the kind - they are pretty much just holes in the rock. Nothing complex about them at all.

Secondly, if you were to build an architectural arch including the correctly designed stones and use scaffolding to hold the structure in place until the keystone is in place, then surely you have an even more complex process with even more design involved?

An architectural arch has a predetermined end point ‘in mind’ at the design stage. The process of evolution (in the mainstream view) has no end point in mind. Thus, examples of naturally occurring arches maybe more relevant than you credit?

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 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.

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

Not so fast. 
A new paper that undermines the mathematical foundations of neo-Darwinism has been published in the Springer peer-reviewed Journal of Mathematical Biology. The title is The Fundamental Theorem of Natural Selection With Mutations. 

The following is from an article on this. It necessarily gets rather technical.

From the paper (emphasis added):

"We have re-examined Fisher’s fundamental theorem of natural selection, focusing on the role of new mutations and consequent implications for real biological populations. Fisher’s primary thesis was that genetic variation and natural selection work together in a fundamental way that ensures that natural populations will always increase in fitness. Fisher considered his theorem to essentially be a mathematical proof of Darwinian evolution, and he likened it to a natural law. Our analysis shows that Fisher’s primary thesis (universal and continuous fitness increase) is not correct. This is because he did not include new mutations as part of his mathematical formulation, and because his informal corollary rested upon an assumption that is now known to be false.

We have shown that Fisher’s Theorem, as formally defined by Fisher himself, is actually antithetical to his general thesis. Apart from new mutations, Fisher’s Theorem simply optimizes pre-existing allelic fitness variance leading to stasis. Fisher realized he needed newly arising mutations for his theorem to support his thesis, but he did not incorporate mutations into his mathematical model. Fisher only accounted for new mutations using informal thought experiments. In order to analyze Fisher’s Theorem we found it necessary to define the informal mutational element of his work as Fisher’s Corollary, which was never actually proven. We show that while Fisher’s Theorem is true, his Corollary is false.

In this paper we have derived an improved mutation–selection model that builds upon the foundational model of Fisher, as well as on other post-Fisher models. We have proven a new theorem that is an extension of Fisher’s fundamental theorem of natural selection. This new theorem enables the incorporation of newly arising mutations into Fisher’s Theorem. We refer to this expanded theorem as “The fundamental theorem of natural selection with mutations”.

After we re-formulated Fisher’s model, allowing for dynamical analysis and permitting the incorporation of newly arising mutations, we subsequently did a series of dynamical simulations involving large but finite populations. We tested the following variables over time: (a) populations without new mutations; (b) populations with mutations that have a symmetrical distribution of fitness effects; and (c) populations with mutations that have a more realistic distribution of mutational effects (with most mutations being deleterious). Our simulations show that; (a) apart from new mutations, the population rapidly moves toward stasis; (b) with symmetrical mutations, the population undergoes rapid and continuous fitness increase; and (c) with a more realistic distribution of mutations the population often undergoes perpetual fitness decline."

Is this unfair to a historical figure? What about models developed after Fisher?

"In the light of Fisher’s work, and the problems associated with it, we also examined post-Fisher models of the mutation–selection process. In the case of infinite population models, what has commonly been observed is that populations routinely go to equilibrium or a limit set — such as a periodic orbit. They do not show perpetual increase or decline in fitness, but are restricted from either behavior because of the model structure (an infinite population with mutations only occurring between pre-existing genetic varieties). On a practical level, all biological populations are finite. In the case of finite population models, the focus has been upon measuring mutation accumulation, as affected by selection. Finite models clearly show that natural populations can either increase or decrease in fitness, depending on many variables. Not only do other finite mathematical population models show that fitness can decrease — they often show that only a narrow range of parameters can actually prevent fitness decline. This is consistent with very many numerical simulation experiments, numerous mutation accumulation experiments, and observations where biological systems have either a high mutation rate or a small population size. Even when large populations are modeled, very slightly deleterious mutations (VSDMs), can theoretically lead to continuous fitness decline."

The final blow comes wrapped in compliments:

"Fisher was unquestionably one of the greatest mathematicians of the twentieth century. His fundamental theorem of natural selection was an enormous step forward, in that for the first time he linked natural selection with Mendelian genetics, which paved the way for the development of the field of population genetics. However, Fisher’s theorem was incomplete in that it did not allow for the incorporation of new mutations. In addition, Fisher’s corollary was seriously flawed in that it assumed that mutations have a net fitness effect that is essentially neutral. Our re-formulation of Fisher’s Theorem has effectively completed and corrected the theorem, such that it can now reflect biological reality."

What they mean to say is stated most bluntly earlier in the article:

"Because the premise underlying Fisher’s corollary is now recognized to be entirely wrong, Fisher’s corollary is falsified. Consequently, Fisher’s belief that he had developed a mathematical proof that fitness must always increase is also falsified."

That’s the “biological reality.” Fisher’s work is generally understood to mean that natural selection leads to increased fitness. While this is true taken by itself, mutation and other factors can and do reduce the average fitness of a population. According to Basener and Sanford, at real levels of mutation, Fisher’s original theorem, understood to be a mathematical proof that Darwinian evolution is inevitable, is overthrown.

As for scaffolding, I don't pretend to know much about it in the biological sense but I've read the argument using the arch analogy.

I don't know of any specific example of scaffolding in the evolution of a gene. I'm not sure it's the sort of thing we could detect, if the ancestor genes are no longer around. I'll see what I can find.

~~ Paul

An architectural arch has a predetermined end point ‘in mind’ at the design stage. The process of evolution (in the mainstream view) has no end point in mind. Thus, examples of naturally occurring arches maybe more relevant than you credit?

Sorry but I think you are still missing the point. Correct me if I'm wrong but the original analogy was to show that something like an architectural arch, which would fall down without those stones in place, required scaffolding to hold it up until the keystone was in place. Then the scaffolding could be discarded. How does the analogy work with simple erosion wearing a hole in the rock? Surely there is no complexity therefore no analogy?

That’s the “biological reality.” Fisher’s work is generally understood to mean that natural selection leads to increased fitness. While this is true taken by itself, mutation and other factors can and do reduce the average fitness of a population. According to Basener and Sanford, at real levels of mutation, Fisher’s original theorem, understood to be a mathematical proof that Darwinian evolution is inevitable, is overthrown.

I'm not sure what the issue is here, though I haven't read the paper in detail. Minsky's theorem says nothing about fitness. Biologists have understood for a while that certain fitness measures of a population can decrease with time.

From the paper:

"In this paper we have derived an improved mutation–selection model that builds upon the foundational model of Fisher, as well as on other post-Fisher models. We have proven a new theorem that is an extension of Fisher’s fundamental theorem of natural selection. This new theorem enables the incorporation of newly arising mutations into Fisher’s Theorem. We refer to this expanded theorem as “The fundamental theorem of natural selection with mutations”.
...
Our re-formulation of Fisher’s Theorem has effectively completed and corrected the theorem, such that it can now reflect biological reality."

~~ Paul

Sorry but I think you are still missing the point. Correct me if I'm wrong but the original analogy was to show that something like an architectural arch, which would fall down without those stones in place, required scaffolding to hold it up until the keystone was in place. Then the scaffolding could be discarded. How does the analogy work with simple erosion wearing a hole in the rock? Surely there is no complexity therefore no analogy?

Does ‘how’ we arrive at an arch determine its complexity? All I’m seeing is a loaded definition of what complexity is.

Does ‘how’ we arrive at an arch determine its complexity? 

Yes.