Evolving complex features

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:

Continue reading

Natural Selection and Adaptation

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.

Continue reading

ID and AGW

Can someone familiar with the thinking at Uncommon Descent explain why there is such opposition to the idea of Anthropogenic Global Warming?  There’s this today, following several long commentaries by VJ Torley on the pope’s encyclical, mostly negative. I don’t get the connection. Is it general distrust of science? Or of the “Academy”?  Or is there something about the idea that we may be provoking a major extinction event that is antithetical to ID?  Or is it, possibly, that the evidence for major extinction events in the past is explains the various “explosions” that are adduced as evidence, if not for ID, then against “Darwinism”?

Continue reading


Apologies to anyone who tried to post an OP or send a PM over night and couldn’t.  Permissions are restored.

I was trying to set up a means for the admins to confer together on site rather than singly by PM  or by email, as a result, set the cat among the pigeon (skua among the penguins?) by first of all making a “password protected” page for the admins, new comments to which appeared in the “new comments” list, arousing great alarm, and in any case turned out to be visible from the dashboard.  So I tried another WP option which was to make it a “private” page, but people could still see it from the dashboard.  So I switched off that.  But then people couldn’r post OPs or receive PMs.  So I’ve restored it again.  We will keep the “private” admin page, but for those curious about it, you will find you can access its comments via the dashboard.   Which is fine by me – it wasn’t like we wanted to plot anything anyway, just have a means of conferring about stuff (security issues, strategies, plug-ins, rules etc) between our selves.  So this seems a good solution.  Nobody need get paranoid because they can always check the record, but it won’t be a prominent feature of the site.

Bad Materialism

In various threads there have been various discussions about what materialism is, and isn’t, and various definitions have been proposed and cited.  In this thread I want to ask a different question, addressed specifically to those who regard “materialism” as a bad thing.  William, for instance, has said that “materialism” was “disproven” in the 18th century, yet laments

the spread of an 18th century myth in our public school system and in our culture at large.

So here is my question: if you are against something called “materialism” and see it as a bad thing (for whatever reason), what is your definition of the “materialism” you are against?


n a piece posted on the Discovery Institute website, responding to bad publicity surrounding the Wedge Document , the author or authors write:

Far from attacking science (as has been claimed), we are instead challenging scientific materialism –  the simplistic philosophy or world-view that claims that all of reality can be reduced to, or derived from, matter and energy alone. We believe that this is a defense of sound science.

So there we have a one definition of “scientific” materialism: “the world-view that claims that all of reality can be reduced to, or derived from, matter and energy alone”.

Continue reading

Alzheimer’s and Evolution

I have to say, while the UD “newsdesk” is terrible source for comment on scientific news, the links themselves are often interesting.  Today, the UD “newsdesk” reports on a pretty interesting study, reported in Nature, here, and a preprint of which seems to be open access here

It’s been apparent for a while from Genome-Wide Association Studies (GWAS) that “risk” alleles for various mental disorders, despite being statistically significant, have extremely small effect sizes.  In other words, while the studies show that many mental disorders are indeed associated with specific alleles (and we already know that many are highly heritable, including schizophrenia, ADHD and Alzheimer’s), there aren’t just a few rogue alleles of large effect (well, there are, but they are far rarer than these disorders), but instead, a whole cocktail of alleles with very slightly raised Odds Ratios for certain disorders (and some are shared between multiple disorders).  This means that the vast majority of people carrying these “risk alleles” are perfectly fine. That would help explain why they have not been weeded out by selection.

Continue reading


…in the beginning, God was no size at all. Because there was no Space. And no age at all, because there was no Time.

God just was.

And perhaps, because she was lonely, God grew.

And when God grew, Time and Space exploded into being.

Stuff at colossal temperatures shot outwards, clumping into clouds of burning
gas and splashes of red hot liquid. Suddenly God was everywhere, because there was everywhere to be.

And God called Time and Space her Universe.

Continue reading

Thinking about Free Will

A few years ago, there was an article in New Scientist by Dan Jones,entitled, Grand delusions: Why we’re determined to be free.  It began:

IT IS the year 2500. Physicists have long had a Grand Unified Theory of Everything and neuroscientists now know precisely how the hardware of the brain runs the software of the mind and dictates behaviour. Lately, reports have begun to emerge that computer engineers at the Institute for Advanced Behavioural Prediction have built a quantum supercomputer that draws on these advances to predict the future, including what people will do and when. Trusted sources say that IABP researchers have secretly run thousands of predictions about citizens’ behaviour – and they have never been wrong.

Suddenly, deep philosophical questions are making headlines as commentators sound the death knell for free will. On the face of it, the consequences of proving all our actions are predetermined look bleak. Psychological experiments have shown that undermining people’s sense of free will leads them to behave more dishonestly, more selfishly and more aggressively. But perhaps there is no need to panic. Some philosophers have found that our sense of free will is less threatened by determinism than the commentators suppose – so even faced with incontrovertible evidence that behaviour is predetermined, we still see ourselves as free and responsible for our own actions. Nothing will change.

Who is correct? Will the public buy this reassuring message? Or will the manifest truth of determinism kill off belief in free will, taking down notions of moral culpability and punishment with it? Will nihilism, moral disintegration and anarchy follow?

I composed a response, which I ended up not sending, but sent to Daniel Dennett instead, from whom I received a very nice reply, in which he attached a relevant article he’d recently written, Some Observations on the Psychology of Thinking About Free Will.  Here is the draft of my own response to New Scientist:

Continue reading

The Wedge

The Wedge Document, which appeared on the internet in 1999, is a curious thing.  I don’t want to discuss is merits and demerits in this post, but what it says about fear: on the one side of the wedge, the fear that motivated its writing, and on the other side, the fear of those who felt targetted by it.

Because even though the document itself has ceased to have force, the mutual distrust remains.

Continue reading

Poof! The ID energy question

ID proponents often portray ID critics as “materialists”, and recently someone asked whether a force was “material”.  Well, if a force isn’t “material” then there are no “materialists”.  So yes, is the answer to that question.  A force that can move matter is a material force.  A force that can’t move matter isn’t a force at all.

And this matters for the Intelligent Design argument, because when we infer that an object has been intelligently designed, we are also inferring that it was fabricated according to that design. And to fabricate an object, or modify it, the fabricator has to accelerate matter, i.e. give its parts some kinetic energy it did not otherwise possess, by applying a force.

Continue reading

The Inadequacy of ALL scientific models.

Kairosfocus discusses this comment of mine at UD:

Elizabeth: That’s not what “undermines the case for design” William.What undermines the “case for design” chiefly, is that there isn’t a case for a designer.

If current models are inadequate (and actually all models are), and indeed we do not yet have good OoL models, that does not in itself make a case for design.It merely makes a case for “our current models are inadequate”.

Even if it could be shown that some oberved feature has no possible evolutionary pathway, that wouldn’t make the case for design.What might would be some evidence of a design process, or fabrication process, or some observable force that moved, say, strands of DNA into novel positions contrary to known laws of physics and chemistry.

And it would be interesting.

I’m not going to discuss things at UD until Barry makes it clear that he will not retrospectively delete, wholesale, posts by posters he subsequently decides to ban. It makes discussion pointless.  In any case, comments are closed on that thread.

But I will respond to one thing in Kairosfocus’ post here:

Continue reading

ID in E-prime

I’d like to start a thread about the proposition that features of the universe indicate that a designer designed and created it for a purpose.

We have had many such discussions on this blog previously, but I propose that in this thread we abide by a new rule: we will conduct the discussion solely in the form of English called E-prime:

E-Prime (short for English-Prime, sometimes denoted É or E′), a prescriptive version of the English language, excludes all forms of the verb to be. E-Prime does not allow the conjugations of to bebe, am, is, are, was, were, been, being—the archaic forms of to be (e.g. art, wast, wert), or the contractions of to be—’m, ‘s, ‘re (e.g. I’m, he’s, she’s, they’re).

Continue reading

The Rules of the TSZ Game

As we have some newcomers, and some new-oldcomers (including me!) I thought I’d just draw everyone’s attention to the Rules of the Game at TSZ.  They are written here and updated from time to time, but I have also pasted them below.  We do try not to be heavy-handed with them, and to be as equitable as is humanly possible, but we will make judgements that you disagree with, possibly with good reason.  The good news is that you can discuss these in Moderation Issues, and that, with the exception of a very narrow and specific range of material, posts will only be moved, not deleted.  Moving a post because it contravenes a rule does NOT imply ANY kind of moral judgment on the post.  A post can be morally justified yet contravene the rules, and can be morally indefensible yet remain within it.  The rules are entirely orthogonal to morality, and when we ask you to “assume all other posters are posting in good faith” we do not require that you believe it, any more than the assumption of innocence until proven guilty requires belief in a person’s innocence.That is why I call them “Game rules”.  They are simply the rules of the discussion game as played here at TSZ.  We also have the Sandbox for off-topic scrapping that is getting in the way of discussion, or even off-topic chat about fun stuff.

Continue reading

A rather topical Jesus and Mo today

Although I have to say, the adage that “you can’t reason a man out of beliefs he hasn’t reasoned himself into” always struck me as a load of cobblers.  Growing up is, to me, a process of discovering that what you always believed was true ain’t necessarily so.  But I’m sure it gets harder as you get older.

The Bowels of Christ

Barry Arrington writes:

For years I have been bemused by the website called The Skeptical Zone.  Every few months I go over there and peruse the posts.  And I think to myself, if they are so skeptical, why does practically everything they say line up with the received dogmas and conventional wisdom of the early 21st century Western intelligentsia?

Do they not know what the word “skeptical” means?  Are they going for ironical?

But in a flash of insight today, I finally figured it out.  The key is in the quote from Cromwell at the top of their homepage that serves as the motto for the site:

I beseech you, in the bowels of Christ, think it possible that you may be mistaken.

All of this time I mistakenly thought that they were using the aphorism the way Cromwell intended as in “We should bear in mind that each of us is fallible; it follows that each of us should always allow for the possibility that even his most intensely-held beliefs might possibly be mistaken.”

Yes, Barry, that is precisely what I intended it to mean.

No, that is not it.  It all becomes clear when you realize that they mean their motto quite literally and when they think of it they think of it this way:

I beseech you, in the bowels of Christ, think it possible that YOU may be mistaken.


The YOU refers to all those who read the words,  including the owner of the blog.

There you have it.  They are skeptical all right.  They are skeptical of everyone’s views but their own, which they hold with a breathtakingly dogmatic tenacity.  It all makes sense to me now

Well, we all tend to think that people who seem unable to see our point of view are holding that view “with a breathtaking dogmatic tenacity”.  After all, if we thought we were wrong, we’d change our minds, wouldn’t we?  It’s intrinsic to the nature of disagreement that we think the other guy is wrong, and greater the clarity with which we think we are seeing the truth, the more dogmatically tenacious the other guy seems to be for not seeing it.  Which simply goes to show that one [wo]man’s obvious is another [wo]man’s nonsense.

So: Just to remind everyone: No, the motto is neither ironical,  nor addressed to a subset of the world.  It is addressed to everyone, unironically, including me.  And of course Barry, should he come over, which I hope he will. Please regard it as the Primary Rule of this site.

Thanks 🙂

Edited to, I hope, avoid copyright violation.

Good UD post

Good guest post at Uncommon Descent by Aurelio Smith,


For those who prefer to comment here, this is your thread!

For me, the argument by Ewert Dembski and Marks reminds me of poor old Zeno and his paradox.  They’ve over-thought the problem and come to a conclusion that appears mathematically valid, but actually makes no sense.  Trying to figure out just the manner in which it makes no sense isn’t that easy, though I don’t think we need to invent the equivalent of differential calculus to solve it in this case.  I think it’s a simple case of picking the wrong model.  Evolution is not a search for anything, and information is not the same as [im]probability, whether you take log2 of it or not.  Which means that you don’t need to add Active Information to an Evolutionary Search in order to find a Target, because there’s no Target, no search, and the Active Information is simply the increased probability of solving a problem if you have some sort of feedback for each attempt, and partial solutions are moderately similar to better ones.


Darwin was wrong!!!!!

Stop the presses!

Seriously, are the ID proponents at UD ever going to wonder why Gould and Eldredge remained persuaded that common descent occurred, and that “punctuated equibrium”, although contrary the uniformly incremental pattern that Darwin envisaged, was nonetheless consistent with Darwin’s proposed adaptive mechanism of heritable variation in reproductive success?

Because Darwin was indeed wrong about uniform change.  Unlike us, he didn’t have computers with which to model the predicted output of his mechanism. Indeed he didn’t even know what the vector of heritability was.  We do.  Here’s a sample output from Eureqa, a program that uses Darwin’s proposed mechanism to “evolve” equations to fit data:

Continue reading