Category Archives: Evolution

Randomness and evolution

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Here’s a simple experiment one can actually try. Take a bag of M&M’s, and without peeking reach in and grab one. Eat it. Then grab another and return it to the bag with another one, from a separate bag, of the same colour. Give it a shake. I guarantee (and if you tell me how big your bag is I’ll have a bet on how long it’ll take) that your bag will end up containing only one colour. Every time. I can’t tell you which colour it will be, but fixation will happen.
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Random Mutations: vjtorley

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vjtorley, at UD, writes a post entitled It’s time for scientists to come clean with the public about evolution and the origin of life that includes this:

Edward Frenkel, a professor of mathematics at the University of California, Berkeley, recently reviewed a book titled, Probably Approximately Correct: Nature’s Algorithms for Learning and Prospering in a Complex World (Basic Books, 2013) by computer scientist Leslie Valiant, in a report for the New York Times (Evolution, Speeded by Computation, September 30, 2013). The following excerpt conveys the gist of Dr. Valiant’s conclusions:

The evolution of species, as Darwin taught us, relies on natural selection. But Dr. Valiant argues that if all the mutations that drive evolution were simply random and equally distributed, it would proceed at an impossibly slow and inefficient pace.

Darwin’s theory “has the gaping gap that it can make no quantitative predictions as far as the number of generations needed for the evolution of a behavior of a certain complexity,” he writes. “We need to explain how evolution is possible at all, how we got from no life, or from very simple life, to life as complex as we find it on earth today. This is the BIG question.”

Dr. Valiant proposes that natural selection is supplemented by ecorithms, which enable organisms to learn and adapt more efficiently. Not all mutations are realized with equal probability; those that are more beneficial are more likely to occur. In other words, evolution is accelerated by computation.

The criticisms being made here of the Darwinian theory of evolution are pretty devastating: not only is it far too slow to generate life in all its diversity, but it’s also utterly incapable of making quantitative predictions about the time required for a structure of known complexity to evolve, by natural selection. And there’s no reason to believe that the “nearly neutral theory of evolution” espoused by biologists such as Professor Larry Moran would fare any better, in this regard.

 

Dr Torley is a scholar and a gentleman and someone for whom I have a great deal of personal respect. In fact I owe him more than one debt of personal kindness.  But that does not mean that I think his ideas are correct, and I submit he is profoundly wrong here in an extremely useful way.  Unusually, the passage he cites is very specific about the kind of randomness that cannot be the kind of randomness that would produce Darwinian evolution: equally distributed.

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A Statistics Question for Barry Arrington

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Re your post here:

  • If you came across a table on which was set 500 coins (no tossing involved) and all 500 coins displayed the “heads” side of the coin, how on earth would you test “chance” as a hypothesis to explain this particular configuration of coins on a table?

Even if the observer was not party to the information that there was “no tossing  involved”?

The reason I ask, is that you seem to have revealed an conceptual error that IMO bedevils much discussion about evolution as an explanation for the complexity of life.

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How Was Darwin Wrong? – Darwin’s Errors

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O.k. then, here’s your chance, TSZ folks. Have at it.

Darwin made errors, even Darwinian evolutionist Mike Elzinga agrees.

What are/were those errors/mistakes?

Perhaps the odd closet ‘Darwinist’ might even think to change their mind about calling them-self a ‘Darwinist’ as a result of answers provided in this thread…or it could be a rather short thread, with few admissions.

Context: Preprint for a Douglas Allchin paper in American Biology Teacher, 2009 (same Journal that published Theodosius Dobzhansky’s theistic evolution: “Nothing in Biology Makes Sense…” paper, 1973) Celebrating Darwin’s Error’s.

Title Changed: from “How Darwin Was Wrong” to “How Was Darwin Wrong?” – 06-12-2013

“The selective incompleteness of the fossil record”

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Denyse O’Leary quotes Steve Meyer’s question:

Why, he [Agassiz] asked, does the fossil record always happen to be incomplete at the nodes connecting major branches of Darwin’s tree of life, but rarely—in the parlance of modern paleontology—at the “terminal branches” representing the major already known groups of organisms?…

Was there any easy answer to Agassiz’s argument? If so, beyond his stated willingness to wait for future fossil discoveries, Darwin didn’t offer one.

and responds:

And no one else has either.

Oh, yes, they have, Denyse.  That’s what what punk eek was.  But it also falls readily out of any simulation – you see rapid diversification into a new niche at a node, and thus few exemplars, followed by an increasingly gradual approach to a static optimum, and thus lots of exemplars.  But I present an even more graphic response: when you chop down a tree, and saw it up into logs for your fire, what proportion of your logs include a node?

 

 

ID & Explanations

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Every camp in the ‘biological origins debate’ has its own explanation(s) as to where the complexity and diversity of life comes from. Some of these explanations would seem to be driven by prior commitments and ideologies (on both sides) and in some cases (notably from the DI and over at UD) they are part of a bigger assault on the opposing viewpoints perceived commitments themselves.

So what makes for a good explanation? Here’s a couple of resources I found interesting:

http://www.culturallogic.com/research-links/

http://philosophicaldisquisitions.blogspot.com/2009/12/explanations-gentle-introduction_28.html

http://philosophicaldisquisitions.blogspot.com/2010/05/what-good-is-explanation-part-1.html

http://philosophicaldisquisitions.blogspot.com/2010/06/what-good-is-explanation-part-2.html

Perhaps we could have a discussion on what makes for a good explanation and look at the various available explanations for biological origins in this framework?

[Multiple edits]

Junk DNA

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Well, I just got banned again at UD, over my response to this post of Barry’s:

In a prior post I took Dr. Liddle (sorry for the misspelled name) to task for this statement:

“Darwinian hypotheses make testable predictions and ID hypotheses (so far) don’t.”

I responded that this was not true and noted that:

For years Darwinists touted “junk DNA” as not just any evidence but powerful, practically irrefutable evidence for the Darwinian hypothesis. ID proponents disagreed and argued that the evidence would ultimately demonstrate function.

Not only did both hypotheses make testable predictions, the Darwinist prediction turned out to be false and the ID prediction turned out to be confirmed

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Reification of the tree metaphor

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A brief note to a regular reader.

The Darwinian “tree of life” is not an actual tree. It is a diagram of relationships. Therefore it can survive without having established its “roots”.

It could be granted that the origin of life was artificial, or even supernatural, and the theory of evolution would still be applicable within its domain.

This is not the first time the error in the essay challenge has been pointed out, but it costs us little to hope that a sincere individual, in no way guilty of peddling a religiopolitical agenda, would acknowledge the mistake.

The Limits of Evolutionism: ‘Things That Don’t Evolve’

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Just like the ideology of ‘naturalism’ claims that *everything* is ‘natural,’ the ideology of ‘evolutionism’ says that *everything* ‘evolves.’ As you have seen recently, I am questioning the ideology of evolutionism openly and directly here at TSZ.

As such, I have a simple challenge for people here:

What are examples of things that don’t ‘evolve?’

It’s a very basic and straightforward question. But it’s one that shows itself to be very difficult for people who are or consider themselves evolutionists to answer due to the ideological exaggeration of evolutionary theory (biological, cosmological, cultural or otherwise) into the belief that everything evolves, i.e. into ‘evolutionism.’ Those who are not ‘evolutionists’ (whether theists or atheists) usually find it easier to answer and thus to circumscribe the meaning of ‘evolution.’

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New body plans — a thought experiment

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Since there’s been some discussion on new body plans, here is my understanding of how they come about. Note that I am not a biologist. I’m sure someone will correct me if I am wrong. Most of this has to do with how branching processes work.

To explore how new body plans arise, we are going to travel back in time with my trusty time machine. I obviously don’t have a time machine, which is why this is only a thought experiment. As I travel back in time, I take along a passenger, whom I shall call “William”. We want to find out where the octopuses, with an obviously different body plan, arose.

We start our journey in the present, looking at a person — perhaps at William himself. Then we go back in time to look at the ancestors. Well go fast, or this would take for ever.

As we go back in time examining ancestors, we see earlier vertebrates, such as fish. We keep on going, and get to the early chordates. They had a neural bundle, but no vertebrae. We have to go further back to find the ancestors of the octopus. As we go back, we see ancestors without even a neural bundle. Eventually, we get back to the point where the ancestors of the octopus branched off.

At this point, we see two sibling organisms. One of those is an early ancestor of us, and the other is an early ancestor of the modern octopus.

I hand William a microscope, and ask him to examine both as closely as possible, and to describe the body plan that he can see in each. “What body plan” says William. “I don’t see any body plan.”

That’s where the phylum branching occurred. The body plans came later. The whole idea of “macro-evolution”, as that term is used by creationists and ID proponents, is just a complete misunderstanding.

Evolution trounces Intelligent Design with real data.

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Man has created many sophisticated modelling tools, all of which have different strengths and weaknesses. A good ‘solution’ or ‘description’ of a problem should not be overly complex (parsimony) and also have high descriptive power. Let’s look at how some of these cutting edge tools compare to Nutonian‘s symbolic regression / evolutionary computation product Eureqa:

from: http://blog.nutonian.com/bid/330675/How-does-Eureqa-Compare-to-Other-Machine-Learning-Methods#!

Looks like we get highly efficient yet incredibly accurate models. Huzzah! Don’t believe me? try it yourself. They “ran Eureqa on seven test-cases for which data is publically available, and compared performance to four standard machine learning methods. The implementations used were the WEKA codes, with settings optimized for best performance”. Weka is free and the Eureqa trial version is free.

Enjoy the full post here

Unfortunately I think Hod’s interpretation of NFL isn’t quite there, though. 😉

Is there an ‘Intelligent Design’ Community of Philosophers? A Response to Neil Rickert’s Hypothesis

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Here is what started this conversation:

“At risk of being a bit off-topic, let me add that there is a far larger “intelligent design” community. I am talking about philosophy, particularly academic philosophy. Philosophers, as a group, tend to look at things from what I consider a[n] intelligent design perspective. That perhaps comes from Plato. Perhaps it is a natural way of thinking. To be clear, that particular intelligent design community is honest and largely non-political, unlike the religious version. And yes, there are “fine tuning” ideas coming from that community.” – Neil Rickert (http://theskepticalzone.com/wp/?p=2926&cpage=2#comment-27860)

I asked him:

“could you elaborate on this: “Philosophers, as a group, tend to look at things from what I consider a[n] intelligent design perspective”? … which philosophers, specifically who … which you suggest display a “natural way of thinking” about ‘intelligent design’?”

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A Question for those that doubt Common Descent

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Recent posts by Sal remind me that there are some intelligent educated people who doubt Common Descent.  What I don’t understand what they think the alternative is. Put simply I take Common Descent as the position that :

* At one time there was only very simple unicellular life on earth (this is not a debate about how that unicellular life originated)

* Complex life forms (eukaryotes) are created by slight modifications from other life forms (which are their parents). We have never observed them being created any other way!

* All complex life forms are the descended from a very small number of simple life forms – quite possibly just one.

The alternatives I can imagine are:

* Complex life descended many different times from simple life forms – so e.g. mammals descended from a different simple life form from fish. This flies in the face of the fossil record and the hierarchical nature of complex life but I can sort of understand it.

* Complex life from time to time gives birth to wholly different species – massively implausible.

* Complex life is created anew by some process never imagined or observed – even more implausible but presumably what Young Earth creationists believe.

But maybe there is another option?

If Sal or someone could explain I would be interested.

The Blind Watchbreaker would dispose of lunches even if they were free — mootness of anti-NFL arguments

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[cross posted at UD: The Blind Watchbreaker would dispose of lunches even if they were free — mootness of anti-NFL arguments]

Our colleague Elizabeth Liddle has described the process of human design as trial and error, tinkering and iteration. Like Dawkins, she has argued nature (like human designers) is able to construct biological designs via trial and error, tinkering and iteration. However, when nature is properly compared and contrasted with the way humans go about creating designs, it is apparent Dawkins’ claim of a blind watchmaker is false.

I refer to Elizabeth’s description because she articulated some aspects of the blind watchmaker hypothesis better than Dawkins, but in so doing actually helped highlight why Dawkins’ blind watchmaker is refuted by the evidence.

[this is a follow up post to Selection falsely called a mechanism when it should be called an outcome]
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Is ‘Darwinism’ Science or Ideology or Both or Neither?

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Recently, Neil Rickert wrote to me:

“To me, the technical distinction between “Darwinian” and “Darwinism” is that “Darwinian” is a adjective while “Darwinism” is a noun.

Please start a separate thread to help clear this up.”

Similarly, this post was added recently at UD and has generated some feedback from TSZers who dialogue there:

“Everyone now knows that Darwinism, adn [sic] its parent materialism, are ridiculous, but for some people they are the only possible position. Those people would abandon the follies in an instant if they could just come up with a reliably non-theistic alternative. Meantime, the public face of Darwinism is dominated by anti-religious fanatics and self-condemned trolls. That is a key reason we can dispense with any notion that Darwinism is some kind of a science. A real science offers few attractions for such types.” – Denyse O’Leary

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“Darwin’s Delusion” Concise Version

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LONG WINDED VERSION AT UD:
Darwin’s Delusion vs. Death of the Fittest

CONCISE VERSION AT TSZ
From Kimura and Mayurama’s paper The Mutational Load (eqn 1.4), Nachman and Crowell’s paper Esitmate of the Mutation Rate per Nucleotide in Humans (last paragraph), Eyre-Walker and Keightley’s paper High Genomic Deleterious Mutation rates in Homonids (2nd paragraph) we see that by using the Poisson distribution, it can be deduced that the probability P(0,U) of a child not getting a novel mutation is reasonably approximated as:

where 0 corresponds to the “no mutation” outcome, and U is the mutation rate expressed in mutations per individual per generation.

If the rate of slightly dysfunctional or slightly deleterious mutations is 6 per individual per generation (i.e. U=6), the above result suggests each generation is less “fit” than its parents’ generation since there is a 99.75% probability each offspring is slightly defective. Thus, “death of the fittest” could be a better description of how evolution works in the wild for species with relatively low reproductive rates such as humans.