Planned Parenthood

Right now, for some bizarre reason (I have no idea how the topic relates to Intelligent Design), Uncommon Descent (“serving the Intelligent Design Community”) has an OP by Barry Arrington presented “without comment”, and consisting entirely of an image of Margaret Sanger, founder of Planned Parenthood, next to a sickening piece of racist text, which is attributed to her.

It turns out (h/t to various members here) that this quotation is widely attributed to Margaret Sanger on the web, usually to the Birth Control Review, April 1933, No such words are found in that journal – indeed, no article by Margaret Sanger appears in that journal that I can find. Another reference gives it as Birth Control Review, October 1926. Well, I can’t find it there either.

In other words, this calumny has been passed around the web, with faux “authoritative” citations, with nobody bothering to check the primary source, which is, in fact, easy to check.

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Hacking and access woes

Some folk might be having problems trying to login to the site.  I don’t know much about this, but here’s what I do know:

  • When I tried to login today, I received a response “WordPress administrator area access disabled temporarily due to widespread brute force attacks.”  As far as I know, you can neither login nor logout.  However, your current login will still expire (as did mine).
  • Here’s a report that is probably related: Brute Force Attacks Build WordPress Botnet.

In case you are wondering how I managed to post this – I was actually logged in with two different browsers.  My login with “firefox” (my preferred browser) has expired.  My login with “rekonq” has not yet expired.  I think it has another week to go.  So I am posting this from “rekonq”.

Knocking Out Evolution?

DennisJones at UncommonDescent has published an argument that Behe’s irreducible complexity has resisted all attempts at refutation.

…The only logic fallacy would be to draw a conclusion while resisting further examination. Such is not the case with irreducible complexity. The hypothesis has endured 17 years of laboratory research by molecular biologists, and the research continues to this very day.

An irreducibly complex system is one that
(a) the removal of a protein renders the molecular machine inoperable, and
(b) the biochemical structure has no stepwise evolutionary pathway.

Here’s how one would set up examination by using gene knockout, reverse engineering, study of homology, and genome sequencing:

I. To CONFIRM Irreducible Complexity:

Show:

1. The molecular machine fails to operate upon the removal of a protein.

AND,

2. The biochemical structure has no evolutionary precursor.

II. To FALSIFY Irreducible Complexity:

Show:

1. The molecular machine still functions upon loss of a protein.

OR,

2. The biochemical structure DOES have an evolutionary pathway

My (limited) understanding is that (1) will nearly always be confirmed.

The problem is confirming (2), the assertion that there is no evolutionary pathway.

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Searching for a search

Dembski seems to be back online again, with a couple of articles at ENV, one in response to a challenge by Joe Felsenstein for which we have a separate thread, and one billed as a “For Dummies” summary of his latest thinking, which I attempted to precis here. He is anxious to ensure that any critic of his theory is up to date with it, suggesting that he considers that his newest thinking is not rebutted by counter-arguments to his older work. He cites two papers (here and here) he has had published, co-authored with Robert Marks, and summarises the new approach thus:

So, what is the difference between the earlier work on conservation of information and the later? The earlier work on conservation of information focused on particular events that matched particular patterns (specifications) and that could be assigned probabilities below certain cutoffs. Conservation of information in this sense was logically equivalent to the design detection apparatus that I had first laid out in my book The Design Inference (Cambridge, 1998).

In the newer approach to conservation of information, the focus is not on drawing design inferences but on understanding search in general and how information facilitates successful search. The focus is therefore not so much on individual probabilities as on probability distributions and how they change as searches incorporate information. My universal probability bound of 1 in 10^150 (a perennial sticking point for Shallit and Felsenstein) therefore becomes irrelevant in the new form of conservation of information whereas in the earlier it was essential because there a certain probability threshold had to be attained before conservation of information could be said to apply. The new form is more powerful and conceptually elegant. Rather than lead to a design inference, it shows that accounting for the information required for successful search leads to a regress that only intensifies as one backtracks. It therefore suggests an ultimate source of information, which it can reasonably be argued is a designer. I explain all this in a nontechnical way in an article I posted at ENV a few months back titled “Conservation of Information Made Simple” (go here).

 

As far as I can see from his For Dummies version, as well as from his two published articles, he has reformulated his argument for ID thus:

Patterns that are unlikely to be found by a random search may be found by an informed search, but in that case, the information represented by the low probability of finding such a pattern by random search is now transferred to the low probability of finding the informed search strategy.  Therefore, while a given search strategy may well be able to find a pattern unlikely to be found by a random search, the kind of search strategy that can find it itself commensurably improbable i.e. unlikely to be found by random search.

Therefore, even if we can explain organisms by the existence of a fitness landscape with many smooth ramps to high fitness heights, we have are left with the even greater problem of explaining how such a fitness landscape came into being from random processes, and must infer Design.

I’d be grateful if a Dembski advocate could check that I have this right, remotely if you like, but better still, come here and correct me in person!

But if I’m right, and Dembski has changed his argument from saying that organisms must be designed because they cannot be found by blind search to saying that they can be found by evolution, but evolution itself cannot be found by blind search, then I ask those who are currently persuaded by this argument to consider the critique below.

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Dembski challenges Felsenstein

at ENV to get up to date on the Law of Conservation of Information:

So, what is the difference between the earlier work on conservation of information and the later? The earlier work on conservation of information focused on particular events that matched particular patterns (specifications) and that could be assigned probabilities below certain cutoffs. Conservation of information in this sense was logically equivalent to the design detection apparatus that I had first laid out in my book The Design Inference (Cambridge, 1998).

In the newer approach to conservation of information, the focus is not on drawing design inferences but on understanding search in general and how information facilitates successful search. The focus is therefore not so much on individual probabilities as on probability distributions and how they change as searches incorporate information. My universal probability bound of 1 in 10^150 (a perennial sticking point for Shallit and Felsenstein) therefore becomes irrelevant in the new form of conservation of information whereas in the earlier it was essential because there a certain probability threshold had to be attained before conservation of information could be said to apply. The new form is more powerful and conceptually elegant. Rather than lead to a design inference, it shows that accounting for the information required for successful search leads to a regress that only intensifies as one backtracks. It therefore suggests an ultimate source of information, which it can reasonably be argued is a designer. I explain all this in a nontechnical way in an article I posted at ENV a few months back titled “Conservation of Information Made Simple” (go here).

So what’s the take-home lesson? It is this: Stephen Meyer’s grasp of conservation of information is up to date. His 2009 book Signature in the Cell devoted several chapters to the research by Marks and me on conservation of information, which in 2009 had been accepted for publication in the technical journals but had yet to be actually published. Consequently, we can expect Meyer’s 2013 book Darwin’s Doubt to show full cognizance of the conservation of information as it exists currently. By contrast, Felsenstein betrays a thoroughgoing ignorance of this literature.

It seems to me that Dembski has still entirely missed the point of Felsenstein’s (and others’) critique of his “Law of Conservation of Information”.  But perhaps it’s worth tackling Dembski’s newer formulations here?  The Dembski-Marks published papers, or perhaps the For Dummies article at ENV he links to above.

(Link to previous discussion of Dembsi’s Specification paper here, now re-un-stickied)

What is ID?

Stephen B, at UD, says:

Since ID does not, at least for now, hypothesize an “intelligent mind,” …

To which I can only respond – WTF?

Seriously, can any ID proponent explain what Stephen means here, and whether they agree with it?

From the UD resources section:

ID Defined

The theory of intelligent design (ID) holds that certain features of the universe and of living things are best explained by an intelligent cause rather than an undirected process such as natural selection. ID is thus a scientific disagreement with the core claim of evolutionary theory that the apparent design of living systems is an illusion.

In a broader sense, Intelligent Design is simply the science of design detection — how to recognize patterns arranged by an intelligent cause for a purpose. Design detection is used in a number of scientific fields, including anthropology, forensic sciences that seek to explain the cause of events such as a death or fire, cryptanalysis and the search for extraterrestrial intelligence (SETI). An inference that certain biological information may be the product of an intelligent cause can be tested or evaluated in the same manner as scientists daily test for design in other sciences.

ID is controversial because of the implications of its evidence, rather than the significant weight of its evidence. ID proponents believe science should be conducted objectively, without regard to the implications of its findings. This is particularly necessary in origins science because of its historical (and thus very subjective) nature, and because it is a science that unavoidably impacts religion.

Positive evidence of design in living systems consists of the semantic, meaningful or functional nature of biological information, the lack of any known law that can explain the sequence of symbols that carry the “messages,” and statistical and experimental evidence that tends to rule out chance as a plausible explanation. Other evidence challenges the adequacy of natural or material causes to explain both the origin and diversity of life.

What possible intelligent causative agency would not have a mind? Does “mindless intelligent cause” mean anything coherent?  Apart from, possibly, evolutionary processes? (which could be said, conceivably, to be intelligent but mindless…)

 

Kairosfocus’ complaints about this site

Meta, but possibly necessary:  Kairosfocus, at UD, has a long, and, to my mind, very odd, piece that refers to this blog, called: FOR RECORD: I object — a “tour of shame” concerning well-poisoning strawman tactics joined to denial of abuse of design theory proponents at TSZ

Most of the piece I find frankly incomprehensible, but it includes the accusation that I am “enabling evil” here at TSZ:

And, they particularly need to recognise what going along with or making excuses for activists indulging in evil is: enabling.

This brings us to a live case, one implicating a commenter at TSZ, and unfortunately, the blog owner.

apparently because I did not suppress some comment made by OMagain, in response (as it were, given weirdness of the megaphone communication channel between the here and UD) to a comment by Kairosfocus at UD.  Now I don’t, as I say, understand the link KF seems to make between mainstream science and fascist regimes, and like OM, I find it odd that KF on the one hand rightly, in my view, warns of the dangers of suppressing dissent, and on the other, wants me to suppress points of view that dissent from his (or, at least, dissent from what KF feels is a misrepresentation of his point of view).  But I want to reiterate my own principles here: I will not ban any dissenting view here unless it advocates illegal activities (and possibly not even then – civil disobedience is often ethically justified), nor any member unless they post content that compromises the integrity of people’s computers (including links to porn or malware).  This is precisely because I think that suppressing dissent can lead to great evil, although I would point out that turning down an article for publication is not “suppressing” that view, as KF implies with his reference to Granville Sewell’s rejected manuscript on the Second Law of Thermodynamics (far from it – it’s probably had at least as much currency on the web as it would have done if published in print, and I myself have posted links to it, and invited Granville to discuss it here).. Furthermore, I think discussing dissenting views in as civil a manner as is possible to mortals, can lead to great good.

But KF goes on:

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Reductionism Redux

As I’ve mentioned, I’m a great fan of Denis Noble, and recommend his book, the Music of Life, but you can get the content pretty well in total in this video of a lecture:

Principle of Systems Biology illustrated using the Virtual Heart

and there’s other material on his site.

So I was interested to see Ann Gauger making a very similar set of points in this piece: Life, Purpose, Mind: Where the Machine Metaphor Fails.

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Open House Party

Sorry I’ve been away for a while, and especially sorry about the  hack!  From the rapidly repopulating user list, it looks as though most regulars have signed back on, and it’s good to see new faces too.

So this thread is for general chit chat – introduce yourself, make yourself at home, have a beer.

Mine’s one of these:

Wolfram’s “A New Kind of Science”

I’ve just started reading it, and was going to post a thread, when I noticed that Phinehas also brought it up at UD, so as I kind of encouragement for him to stick around here for a bit, I thought I’d start one now:)

I’ve only read the first chapter so far (I bought the hardback, but you can read it online here), and I’m finding it fascinating.  I’m not sure how “new” it is, but it certainly extends what I thought I knew about fractals and non-linear systems and cellular automata to uncharted regions.  I was particularly interested to find that some aperiodic patterns are reversable, and some not – in other words, for some patterns, a unique generating rule can be inferred, but for others not.  At least I think that’s the implication.

Has anyone else read it?

“Natural Selection’s [too limited] Reach”

I hadn’t realised that the Biologic Instute had a diary/blog.

February’s article is by Ann Gauger, although it consists largely of quotations from Douglas Axe, and is called Natural Selection’s Reach.

What continues to astonish me about ID proponents is just how ignorant they are of evolutionary theory.  Ann Gauger starts by setting out to address a reader’s query:

A reader wrote us recently to ask why natural selection can’t extract enough information from the fitness landscape to explain complex features.

Well, obviously I dispute the premise of the question, but assuming that the reader and Gauger share the view that natural selection’s “reach” is too limited to “explain complex features”, let’s see how Gauger explains her stance.  She starts by rightly saying that:

It all depends on what you think the fitness landscape looks like

and then lets Axe go on to explain further.  Unfortunately, Axe appears to think it looks like this:

with complex features situated on the high distant peaks, and natural selection only able to move a step at a time, and only upwards.

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Optimus reponds to Kantian Naturalist

Like kairosfocus, I thought this was an excellent defence of ID, and deserves a response from those of us who can no longer post at UD (a little additional formatting applied by me):

KN

It’s central to the ideological glue that holds together “the ID movement” that the following are all conflated:Darwin’s theories; neo-Darwinism; modern evolutionary theory; Epicurean materialistic metaphysics; Enlightenment-inspired secularism. (Maybe I’m missing one or two pieces of the puzzle.) In my judgment, a mind incapable of making the requisite distinctions hardly deserves to be taken seriously.

I think your analysis of the driving force behind ID is way off base. That’s not to say that persons who advocate ID (including myself) aren’t sometimes guilty of sloppy use of language, nor am I making the claim that the modern synthetic theory of evolution is synonymous with materialism or secularism. Having made that acknowledgement, though, it is demonstrably true that

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Douglas Axe

has an interview on youtube (well, I assume it’s an interview – only his responses are shown).  Here’s a transcript, with some commentary by me, and no doubt other comments will be forthcoming 🙂

In Darwins’ day we knew very little about cellular chemistry, for one thing, we knew very little about  metabolism, about how cells go about making the chemicals that they need to make the big, the big parts of living cells.  We now understand that in some detail, we also understand about the proteins that do the chemistry of life. These are called enzymes.  We understand how large these enzymes are.  We understand that they are encoded by genes, and we understand how that encoding takes place, that’s called the genetic code.  So, really, you put all that together, we now understand something about digitally encoded information, in cells, encoded in the genome, we understand why it’s there, to code proteins, and how the proteins function to do the chemistry of life.  And we also have the ability to measure, to some degree, how much information is there.

All true, and clearly stated.  No issue from me there.

If you put all that together, we know see something that looks very much like human designs where we use digitally encoded information to accomplish things

Well, maybe.  A little.  One huge difference is that biological “designs” are self-reproducing organisms, and so far human designs are resolutely non-self-reproducing.  In fact, the obvious answer to the alien who finds a watch on a heath, and wonders if it was designed or not, is: “well, does it reproduce?”  If yes, it is probably biological.  If no, it’s probably designed by a person. But I’ll grant Axe his digitality – yes, nucleotides are discrete, and yes, their sequence is determines results in the cell products that go to make cells into reproducing organisms (and reproducing cells within organisms, of course.)

But after this excellent, clearly well informed and well-articulated start, he then adds a comment of mind-boggling ignorance:

and we know that it’s impossible to get information on that scale through a chance process that Darwinism employed.

What?

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Reductionism

Mona_Lisa,_by_Leonardo_da_Vinci,_from_C2RMF_retouched

It’s what many scientists are accused of by those who condemn science as “evolutionary materialism” and “evolutionary materialism” with “atheism”.

But what is “reductionism” supposed to mean?  Evolution News and Views has an article up today (h/t to bornagain77 at UD) that is a critique of an article on “neuroaesthetics” in PLOS biology.

The EnV article begins:

Evolutionary materialists must believe, at some level, that the experience of beauty can be reduced to actions of neurons in the brain

(my emphasis)

Well, I guess I’m an “evolutionary materialist”, and I’m also a neuroscientist.  But I was also trained in the arts, and spent most of my life as a musician.  Do I think that “the experience of beauty can be reduced to actions of neurons in the brain”?

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Some Help for IDists: Benford’s Law

Guys, as your scientific output is lacking at the moment, allow me to point you towards Benford’s law: http://en.wikipedia.org/wiki/Benford’s_law

Benford’s law, also called the first-digit law, refers to the frequency distribution of digits in many (but not all) real-life sources of data. In this distribution, the number 1 occurs as the first digit about 30% of the time, while larger numbers occur in that position less frequently: 9 as the first digit less than 5% of the time. This distribution of first digits is the same as the widths of gridlines on a logarithmic scale. Benford’s law also concerns the expected distribution for digits beyond the first, which approach a uniform distribution.

 

TSZ team: Can we build this into a statistically testable (Null hypothesis?) ID Hypothesis?

This one piqued my interest:

“Frequency of first significant digit of physical constants plotted against Benford’s law” – Wikipedia

Barry Arrington Part II: questions from Phinehas

A very nice post by Barry at UD struck me as worth reposting here (as I can’t post there), inspired by Neil Rickert:

Phinehas asks Neil Rickert a fascinating question about the supposed direction of evolution.  Neil says he will address it in a separate thread, and I started this one for that purpose.  The rest of the post is Phenehas’ question to Neil:

@Neil I also appreciate the professional tone. I am a skeptic regarding what evolution can actually accomplish. In keeping with your demonstrated patience, I’d be grateful if you would give serious consideration to something that keeps tripping me up. I’ve often thought of natural selection as the heuristic to random mutations’ exhaustive search.

A path-finding algorithm can be aided in finding a path from point A to point B by using distance to B as a heuristic to narrow the search space. Without a heuristic, you are left to blind chance. It is said that evolution has no purpose or goal, so there is no point B. It is also claimed that evolution isn’t simply the result of blind chance, so a heuristic would seem to be required. Somehow, natural selection is supposed to address both of these concerns. Nature selects for fitness, we are told, so somehow we have a heuristic even without a point B.

But what is fitness? How does it work as a heuristic? How is it defined? Evidently, it is all about reproductive success. But how does one measure reproductive success? This is where things get fuzzy for me. Surely evolution is a story about the rise of more and more complex organisms. Isn’t this how the tree of life is laid out? Surely it is the complexity of highly developed organisms that evolution seeks to explain. Surely Mt. Improbable has man near its peak and bacteria near its base. But by what metric is man more successful at reproducing than bacteria? If I am a sponge somewhere between the two extremes, how is a step toward bacteria any less of a point B for me than a step toward man? Why should the fitness heuristic prefer a step upward in complexity toward man in any way whatsoever over a step downward in complexity toward bacteria?

It seems that, under the more obvious metrics for calculating reproductive success, bacteria are hard to beat. Even more, a rise in complexity, if anything, would appear to lead to less reproductive success and not more. So how can natural selection be any sort of heuristic for helping us climb Mt Improbable’s complexity when every simpler organism at the base of the mountain is at least as fit in passing on its genes as the more complex organisms near it’s peak? And without this heuristic, how are we not back to a blind, exhaustive search?

 

Excellent questions.

Is The Skeptical Zone Skeptical?

Barry Arrington pays us the somewhat dubious compliment of posting an article on the subject of The Skeptical Zone. I’d like to respond to it here (as I cannot respond to it there, although in contrast, Barry is welcome to come here if he would like to make a counter-point).

Barry writes:

For those of you who do not know, some months ago Elizabeth Liddle started the website known as The Skeptical Zone (TSZ). The site has a sort of symbiotic relationship with UD, because many, if not most, of the posts there key off our posts here.

Not only does TSZ have a name that invokes a skeptical turn of mind, it also has a motto apparently intended to bolster that attitude: “I beseech you, in the bowels of Christ, think it possible that you may be mistaken.” The motto is taken from Oliver Cromwell’s August 5, 1650 letter to the synod of the Church of Scotland urging them to break their alliance with royalist forces.

Now with a name and a motto like that, one might think the site is home to iconoclastic non-conformists bent on disrupting the status quo.

Well, up to a point, Lord Copper. Being “skeptical” doesn’t necessarily mean “disrupting the status quo”. It means, well, being skeptical – being prepared to doubt claims, to demand supporting evidence, to accept conclusions provisionally, and, above all, being prepared to hold one’s own assumptions up to scrutiny.  But be that as it may…

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Evolution disproven — by Hardy and Weinberg?

Over at Uncommon Descent, “niwrad” has argued that the equations of theoretical population genetics show that evolution is unlikely.  niwrad says that the equations of theoretical population genetics

consist basically in two main equations: the Hardy-Weinberg law and the Price equation.

Furthermore niwrad says that

The Hardy-Weinberg law mathematically describes how a population is in equilibrium both for the frequency of alleles and for the frequency of genotypes. Indeed because this law is a fundamental principle of genetic equilibrium, it doesn’t support Darwinism, which means exactly the contrary, the breaking of equilibrium toward the increase of organization and the creation of entirely new organisms.

I just finished teaching my course in theoretical population genetics (with lots of equations, but actually not the Price Equation, as it happens). And I can say that the statement about the Hardy-Weinberg law shows niwrad to be mixed up about the import of Hardy-Weinberg proportions. Let me explain …
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