Jonathan Bartlett’s “open-ended loop” argument

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In the “Evolving complex features” thread, TristanM asks:

I’m curious what the group’s thoughts are on Jonathan Bartlett’s (AKA “JohnnyB”) argument about open-loops in the AVIDA program?

I haven’t studied Jon’s argument yet, but I think some of you have. What did you think?

Why I Love AVIDA – Detecting Design in Digital Organisms

Thoughts on Parameterized vs. Open-Ended Evolution and the Production of Variability

Irreducible Complexity and Relative Irreducible Complexity: Foundations and Applications

Equivocation

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Just out of interest … this word gets bandied about a lot, mainly by evolution opponents hereabouts. They seem to use it when a word with multiple meanings is used. The accusation tends not to be withdrawn even when the intended meaning is unequivocally clarified – a bizarre situation where someone commits to a meaning and is still equivocating!

A typical definition is “The use of ambiguous language to conceal the truth or to avoid committing oneself”. There is a veiled hint of dishonesty – making an honest mistake with alternative definitions of a word is not strictly equivocation as defined there. That is, it is not merely ‘using ambiguous language’, still less ‘confusing two definitions of one word’, but purposefully being vague or misleading. But the use of the word rarely seems appropriate to me in the contexts in which it is used – generally, even the charge of ambiguity is unjustified, let alone nefarious motive. Numerous derails are provoked when one party says ‘you are equivocating’ and the other says ‘no I’m not’. I almost invariably find myself siding with (or being) the ‘no I’m not’ party (or, for self-referential funzies, “maybe I am, maybe I’m not”!).

Is this a quirk of American English (Americans forming the majority of opponents in these discussions)? Or is it a meme that has been unconsciously passed from one to another among the evolution-skeptical fraternity? Or something else?

Baby or Vat?

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Zachriel asks, at UD:

Here’s a simple thought-experiment. There’s a fire at an fertility clinic, and there is precious little time before the entire building is engulfed in flames. Down one hallway, there’s the soft purring sound of an incubator with a thousand frozen embryos; down the other hallway, the cries of a newborn baby. Which do you choose to save?

Usually, people answer “the baby” and the interesting debate then concerns why.

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Evolving complex features

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The Lenski et al 2003 paper, The evolutionary origin of complex features, is really worth reading.  Here’s the abstract:

A long-standing challenge to evolutionary theory has been whether it can explain the origin of complex organismal features. We examined this issue using digital organisms—computer programs that self-replicate, mutate, compete and evolve. Populations of digital organisms often evolved the ability to perform complex logic functions requiring the coordinated execution of many genomic instructions. Complex functions evolved by building on simpler functions that had evolved earlier, provided that these were also selectively favoured. However, no particular intermediate stage was essential for evolving complex functions. The first genotypes able to perform complex functions differed from their non-performing parents by only one or two mutations, but differed from the ancestor by many mutations that were also crucial to the new functions. In some cases, mutations that were deleterious when they appeared served as stepping-stones in the evolution of complex features. These findings show how complex functions can originate by random mutation and natural selection.

The thing about a computer instantiation of evolution like AVIDA is that you can check back every lineage and examine the fitness of all precursors.  Not only that, but you can choose your own environment, and how much selecting it does.  There are some really key findings:

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The Cosmological Argument

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I am currently working my way through the book A Natural History of Natural Theology: The Cognitive Science of Theology and Philosophy of Religion.

There is already a thread here dedicated to the book, but I decided to separate the thesis of the book from the actual natural theological arguments themselves. The evidence that the premises upon which these natural theological arguments rest are natural and intuitive are the subject of that thread.

In this thread I’d like to explore how the cosmological argument for the existence of God is presented in the book and provide a place where these cosmological arguments can be examined and criticized.

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Natural Selection and Adaptation

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Cornelius Hunter seems very confused.

 …This brings us back to the UC Berkeley “Understanding Evolution” website. It abuses science in its utterly unfounded claim that “natural selection can produce amazing adaptations.”

In fact natural selection, even at its best, does not “produce” anything. Natural selection does not and cannot influence the construction of any adaptations, amazing or not. If a mutation occurs which improves differential reproduction, then it propagates into future generations. Natural selection is simply the name given to that process. It selects for survival that which already exists. Natural selection has no role in the mutation event. It does not induce mutations, helpful or otherwise, to occur. According to evolutionary theory every single mutation, leading to every single species, is a random event with respect to need.

He has forgotten what “adaptation” means.  Of course he is correct that “Natural selection is simply the name given to [differential reproduction]”.  And that (as far as we know), “every single mutation …is a random event with respect to need”.

And “adaptation” is the name we give to variants that are preferentially reproduced. So while he would be correct to say that “natural selection” is NOT the name we give to “mutation” (duh); it IS the name we give to the very process that SELECTS those mutations that promote reproduction.  i.e. the process that produces adaptation.

Cornelius should spend more time at the Understanding Evolution website.

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Is Religious Belief Natural?

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Questions about the existence and attributes of God form the subject matter of natural theology, which seeks to gain knowledge of the divine by relying on reason and experience of the world. Arguments in natural theology rely largely on intuitions and inferences that seem natural to us, occurring spontaneously — at the sight of a beautiful landscape, perhaps, or in wonderment at the complexity of the cosmos — even to a non-philosopher.

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Moderation at TSZ, part 1

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Gathering my thoughts on moderation at TSZ, I found that I really have two OPs to write: one discussing the effects of rules and moderation at TSZ, and another exploring why the moderation — particularly the Guano-related stuff — has those effects. The second topic is by far the more interesting, but it’s the first topic that has the most practical import, so I’ll address it now.

In a nutshell: We’ve already experimented with different levels of moderation at TSZ, and the results are in. Less moderation works better.

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Cabbages and Kings: open thread

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Having taken a brief break from commenting and still taking a break from proactive moderating, I still find myself sucked into reading OP’s and comments. Not wanting to stir the hornet’s nest of currently active discussion and not having enough time to get up to speed on all the current issues where commenters are discussing deep issues of the day, I wondered about opening a thread titled something like “Suggestion Box” to get people’s thinking on any improvements Lizzie could consider that might ameliorate concerns over site policy, aims, aspirations etc. Continue reading →

Repetitive DNA and ENCODE

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[Here is something I just sent Casey Luskin and friends regarding the ENCODE 2015 conference. Some editorial changes to protect the guilty…]

One thing the ENCODE consortium drove home is that DNA acts like a Dynamic Random Access memory for methylation marks. That is to say, even though the DNA sequence isn’t changed, like computer RAM which isn’t physically removed, it’s electronic state can be modified. The repetitive DNA acts like physical hardware so even if the repetitive sequences aren’t changed, they can still act as memory storage devices for regulatory information. ENCODE collects huge amounts of data on methylation marks during various stages of the cell. This is like trying to take a few snapshots of a computer memory to figure out how Windows 8 works. The complexity of the task is beyond description.
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Abortion & Euthanasia: Why I’m All For Both

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Simply put, liberals/progressives are the ones who, IMO, are going to utilize these services the most. So, yeah, the fewer babies they get to raise, and the earlier we can stop them from voting, the better. On the conservative side we have the Duggars and highly religious people breeding like crazy and clinging to life for every breath they can take – which puts and keeps more conservatives in the voting pool longer.

So, as a pragmatic political matter, I say let ’em abort their young and kill themselves off to their heart’s content.

The Sugar Code and other -omics

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[Thank you to Elizabeth Liddle, the admins and the mods for hosting this discussion.]

I’ve long suspected the 3.1 to 3.5 gigabases of human DNA (which equates to roughly 750 to 875 megabytes) is woefully insufficient to create something as complex as a human being. The problem is there is only limited transgenerational epigenetic inheritance so it’s hard to assert large amounts of information are stored outside the DNA.

Further, the question arises how is this non-DNA information stored since it’s not easy to localize, in fact, if there is a large amount of information outside the DNA, it is in a form that is NOT localizable, but distributed and so deeply redundant that it provides the ability to self-heal and self-correct for injury and error. If so, in a sense, damage and changes to this information bearing system is not very heritable since bad variation in the non-DNA information source can get repaired and reset, otherwise the organism just dies. In that sense the organism is fundamentally immutable as a form, suggestive of a created kind rather than something that can evolve in the macro-evolutionary sense.
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Bad Dogs and Defective Triangles

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Is a dog with three legs a bad dog? Is a triangle with two sides still a triangle or is it a defective triangle? Perhaps if we just expand the definition of triangle a bit we can have square triangles.

There is a point of view that holds that to define something we must say something definitive about it and that to say that we are expanding or changing a definition makes no sense if we don’t know what it is that is being changed.

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Same Sex Science

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It is often asserted that modern science had it’s roots in Christian culture and could in fact only have gotten started given such a milieu.

…the flowering of modern science depended upon the Judeo-Christian worldview of the existence of a real physical contingent universe, created and held in being by an omnipotent personal God, with man having the capabilities of rationality and creativity, and thus being capable of investigating it.

– The Soul of Science: Christian Faith and Natural Philosophy

An award-winning philosopher uncovers the Christian foundations of modern science. Renowned historian and philosopher of science Stanley Jaki boldly illumines one of the best-kept secrets of science history — the vital role theology has historically played in fruitful scientific development.

Beginning with an overview of failed attempts at a sustained science by the ancient cultures of Greece, China, India, and the early Muslim empire, Jaki shows that belief in Christ — a belief absent in all these cultures — secured for science its only viable birth starting in the High Middle Ages.

– The Savior of Science

In Pearcey’s latest book Finding Truth: 5 Principles for Unmasking Atheism, Secularism, and Other God Substitutes she goes beyond these perhaps less controversial claims.

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Gay marriage and cakes: Not the post you expect.

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The case of a christian cake making couple refusing to make a wedding cake for lesbian couple in Oregon has made the news recently:

http://www.huffingtonpost.com/2015/07/02/sweet-cakes-by-melissa-fined-same-sex-wedding_n_7718540.html

That’s the HuffPo’s account, a publication that I find to be quite a crappy rag, made worse by endorsement of all things Chopra and Woo. There is much celebration of the ruling in some liberal circles, and I’m going to put a few general thoughts here before I continue:

  • There are anti-discrimination laws in Oregon.
  • The cake makers violated those laws.
  • The couple should have a nice cake.
  • Don’t pick a career that will conflict with your religious views (faith healing MD, Amish Arline Pilot, etc)

That being said, $135k damages for not getting a fucking cake?? And against a small business of people who don’t have the same religious views as me but seem pretty decent otherwise. Sure they could learn a little tolerance and empathy, but couldn’t we all? Speaking of which, here is a list of the ‘physical harm’ caused by not receiving the cake. (quick side note, I’m sure that friction with non-accepting factions of society is terrible and persistent and I wish it didn’t happen, but this is about NOT GETTING A CAKE):

“Mental Rape”? “Loss of appetite” and ‘Weight gain”? 88 symptoms in total. Have a read.

I think liberals need not hold up these folks as champions of equality. I’m calling bullshit on the monetary damages and the symptoms as well.

I wish the lesbian couple had forgiven the christian cake-makers, instead showing them their shared humanity and the positive values they can hold. Instead we fan the flames of the culture war and give the religious right something legitimate to gripe about; I can see no way that the damages are legitimate or that the ruling is in any way proportionate / fair. Legals scholars (we have a coupe I think) – please correct me if I have misunderstood any of this.