Academics: Don’t you dare let the public know what we are talking about!

May 21, 2013

Physicist David Tyler who posts here notes over at Access Research Network that some professionals inb bioethics get angry when the public comes to hear about their discussions, for example around how and why killing infants after birth should be legal. Those who allow the public to know that their tax dollars are spent on this are “abusing academic freedom” in the view of some academics.

This question is relevant to our issues at Uncommon Descent. One characteristic of corruption in academic life is the desire to shut both intelligent lay people and the practitioners of other disciplines out of discussions that must concern them.

Bioethicists don’t think we should know how many of them endorse killing babies after birth, just as a prominent evolutionary biologist thinks that math doesn’t matter and a prominent cosmologist thinks there is no scientific method.

In other words, no matter what is going on, move right along folks, there’s nothing to see here, and the standards by which you might assess our results don’t apply in our elite little (usually) publicly funded group.

Nice work if they can get it. Tyler writes,

Academics adopting the secular materialist worldview will always find themselves demolishing traditional values. They have failed to develop any ethical principles based on secular materialist foundations and they end up as pragmatists, postmodernists or social constructivists. Their conclusions about infanticide are entirely predictable. What is controversial is not that they say such things, but that they are so hostile to philosophical theism appearing in the pages of their academic journals. This is the crunch issue for academic freedom that has yet to be recognised. (In re: After-birth abortion: why should the baby live?, Alberto Giubilini, Francesca Minerva, Journal of Medical Ethics, 2013; 39(5), 261-263 | doi:10.1136/medethics-2011-100411More.

See also: “What Darwin’s Enforcers Will Say About Darwin’s Doubt: A Prediction” for how this claim will likely be explicitly used to defend Darwinism from math and assorted other terrors.

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Darwin-doubting mathematician David Berlinski on why math IS really important

May 21, 2013

… contrary to what evolutionary theorist E. O. Wilson thinks.

Yes, you heard that right. It’s the guy who doubts Darwin who thinks math is important.

Discussing the recent discovery of the Higgs boson, Berlinski offers some thoughts that provide a partial response to E. O. Wilson’s notion that real biologists don’t need math:

Across the vast range of arguments offered, assessed, embraced, deferred, delayed or defeated, it is only within mathematics that arguments achieve the power to compel allegiance because they are seen to command assent. And it is only by means of mathematics that the powerful ideas of an alien discipline such as theoretical physics may step by step be returned to the ordinary human power to grasp things without mediation and so to grasp things at once.

In short, the reason that Darwinian biologists and evolutionary psychologists don’t need math is that most of what they are doing isn’t science (and the rest is likely wrong, but at least science).

Berlinski, an agnostic, is at his best when puncturing pretentious atheists. Here are some of his better known essays in that line, including the most recent, “The Ineffable Higgs”, about the celeb boson that never quite turned out to be the hoped-for God particle.

If you’d rather vid than read, here’s Berlinski in a recent vid:

Or here.

An insurrection against “journal impact factors” in science?

May 21, 2013

Yes, an “insurrection” and meant in all seriousness and supported by name journals.

Apparently, the original reason for creating the metric “journal impact factor”—average number of citations in a set period —was to determine what science journals cash-strapped academic libraries should order in the 1950s. Now, its influence is accused of distorting science:

The San Francisco declaration cites studies that outline known defects in the JIF, distortions that skew results within journals, that gloss over differences between fields, and that lump primary research articles in with much more easily cited review articles. Further, the JIF can be “gamed” by editors and authors, while the data used to compute the JIF “are neither transparent nor openly available to the public,” according to DORA.

Since the JIF is based on the mean of the citations to papers in a given journal, rather than the median, a handful of highly cited papers can drive the overall JIF, says Bernd Pulverer, Chief Editor of the EMBO Journal. “My favorite example is the first paper on the sequencing of the human genome. This paper, which has been cited just under 10,000 times to date, single handedly increased Nature’s JIF for a couple of years.”

Remember this stuff when someone tries to downplay an article that casts doubt on Darwinism (or similar flimflam) by claiming that the journal that published it has a low impact factor.

The critics can only have it both ways if they are truly Darwinists. But so many of them claim not to be “that kind of Darwinist any more” that they probably can’t make use of their “have it both ways” exemption so safely ( = the Darwin-doubting article doesn’t matter if a “low impact” journal published it, but they will spend publicly funded time persecuting the author anyway).

Not only is there no scientific method, but biology does not need math – says prominent evolutionary biologist

May 21, 2013

Okay, so cosmic Darwinism’s Lee Smolin doesn’t think there is a scientific method, and now it turns out the founder of sociobiology (father of evolutionary psychology), E.O. Wilson, doesn’t think that math matters much to science:

During my decades of teaching biology at Harvard, I watched sadly as bright undergraduates turned away from the possibility of a scientific career, fearing that, without strong math skills, they would fail.

Yes but—and this is said in charity—maybe those students would fail. The way a surgeon with poor hand co-ordination or a medications nurse who is no good with decimal fractions might just plain fail. We can blame anyone we want, but how seriously we take it maybe depends on how much we think is at stake. A bacterial culture or your best friend?

Wilson argues,

This mistaken assumption has deprived science of an immeasurable amount of sorely needed talent. It has created a hemorrhage of brain power we need to stanch.

Hmmm. It’s not clear if his career is any indicator.

His sociobiology (accused of racism—in all fairness, maybe quite wrongly) gave way to evolutionary psychology, as in the Bedrock school of human psychology. All any math-challenged psych major had to do was come up with an apparently plausible thesis about how paleo man supposedly behaved in order to explain the world around us today —like shopping, voting, or tipping at restaurants.Gosh, if math had done nothing at all except chase all these people off the scene, it would definitely be worth its chalk.

Wilson goes on:

Fortunately, exceptional mathematical fluency is required in only a few disciplines, such as particle physics, astrophysics and information theory. Far more important throughout the rest of science is the ability to form concepts, during which the researcher conjures images and processes by intuition.

So, evolutionary psychologists, come right on in!

There are rules, of course. You can say that “People who consider themselves liberals or atheists tend to have higher IQs than those who are more religious or conservative,” but you must not say that women of one ethnic group are perceived as more attractive than others.

If Wilson is right, current evolution theory has nothing to do with basic concepts like math. The popular TV talk shows will give you a much better idea of what you need to know.

A corrective to some remarks regarding first principles of reason, showing that such first principles are just that . . .

May 20, 2013

It seems I need to headline a corrective footnote on basic reasoning, from an ongoing exchange in a current discussion thread:

________

>> I decided to take a look around via Google.

It was saddening but unsurprising to see the party-spirited objections to first principles of reason coming from the circle of objector sites. Inadvertently, they show the very reason why there is a serious problem of want of basic rationality in our civilisation in general, but in particular among those strongly influenced by avant garde, ideologically popular secularist, evolutionary materialist progressivism and that species of ultra-modernity that likes to call itself post modernism.

A few points:

1 –> The first steps in reasoning do start with our common sense status as potentially reasonable creatures in our world. And in that context, the first step of reasoning is to recognise distinctions.

2 –> Those distinctions exist as realities before we recognise them and make accurate statements — i.e. true ones — about them.

A bright red ball on a table
in a wider, distinct world:
{ A | NOT_A}

3 –> The bright red ball on the table, NR, is there whether or not you accept that reality. Long before Boole et al came along, or for that matter Aristotle et al.

4 –> And if our ball is bright cherry-red because it just came out of a furnace, if you have any common good sense you had better adapt to the reality instead of expecting that reality to reflect your whims and fancies, talking points or whatever.

5 –> Once that reality of distinction is there, NR, the rest follows is IMMEDIATELY, instantly present. That is the ball is distinct, it is diverse from what is not the ball (including the tongs and leather gloves, safety goggles etc) and there is no conflation or confusion of the two.

6 –> Perceptions, descriptions, symbols, reasonings etc reflect and recognise that reality, such as the symbol: { A | NOT-A }. This act of distinction is the first step of thought and indeed of language and communication. And yes, that reality is prior to taking sides in design debates. Thank God for the small mercy that many recognise these things whatever side of issues they fall on. But, for many years now it has been a pattern to see design objectors following down the usual ideological lines and almost predictably swallowing ultimately absurd objections to first foundational principles of reasoning.

7 –> Notwithstanding, all reasoned thought, all symbolic expression thereof, all speech, all writing immediately and implicitly, inescapably uses it. Such is truly foundational. We cannot but build on it, and to try is to immediately land in patent self referential absurdity. As has so often happened in and around UD.

8 –> To be direct, again . . . it is so hard to break through avant garde programming and fashionable views: once an object is distinct, the identity cluster obtains as reality. And our symbolic representation will inevitably use such and states such.

9 –> Similarly, the matter is prior to the theory or frame of classic propositional logic. And yes one may play all sorts of games with symbol systems, even try to reject such principles. But lo, the very symbols in use are distinct things that depend on our recognition: { A | NOT-A } etc. In short, there is a little matter of having a more foundational use of the identity cluster, even when one pretends to have a system that upends it.

10 –> This is the context of my remarks in and linked onward from the UD WACs on how Quantum physics reflects these principles, it does not violate them. Contrary to a set of popular talking points.

11 –> Likewise, EL, you should recognise that we are dealing with realities we can accurately and commonly recognise. Verbal games about objects being prior to axioms cut no ice when you make mistakes with red hot iron balls on tables. And debates over whether or no we are objects cut no ice when that pain from your burnt hand hits your consciousness of pain, intense pain occasioned by folly.

12 –> I therefore suggest a modest proposal. Lay aside the polarisation, the avant garde programming and party line, the dismissive sense of superiority over those IDiots etc, the snide talking points and reflect a bit on the matters pointed out here on. >>

________

I trust this will help set some matters straight in the teeth of some talking points out there. Discussion can continue at the linked thread. END

Is the Intelligent Designer an interventionist? A reply to Felsenstein and Liddle

May 20, 2013

In a recent post over at Panda’s Thumb, entitled, Does CSI enable us to detect Design? A reply to William Dembski (7 April 2013), Professor Joe Felsenstein takes issue with the claim made by Professor William Dembski and Dr. Bob Marks II that Darwin’s theory of evolution by natural selection, far from solving the problem of where the complex information found in the cells of living organisms originally came from, merely pushes it further back. The thrust of Dembski and Marks’ argument is that even if we grant (for argument’s sake) that Darwinian evolution is fully capable of generating the life-forms we find on Earth today, we haven’t explained the origin of biological complexity. For it turns out that Darwinian evolution could only work in a world that had very special properties, allowing evolution to work in the first place. In a 2006 paper (The Conservation of Information: Measuring the Cost of Successful Search (version 1.1, 6 May 2006), later published in IEEE Transactions on Systems, Man and Cybernetics A, Systems & Humans, 5(5) (September 2009): 1051-1061), Professor Dembski argues that worlds like that are very rare, as they require Nature to possess certain specific properties, which we can easily imagine that Nature might have lacked. These special properties that Nature would need to possess in order for Darwinian evolution to work can themselves be viewed as a kind of information. Thus we get an information regress: Darwinian evolution has to assume the existence of information in the properties of Nature herself, in order to explain where the complex information in living creatures came from. However, this begs the question of where Nature got its information from. Only if we posit a Designing Intelligence which chose to make this universe out of a vast range of possible alternatives can we resolve the problem satisfactorily, argues Dembski. For intelligence is the only thing that is capable of creating information from scratch. In the end, we are led to posit “an ultimate intelligence that creates all information and yet is created by none,” as Dembski puts it in his 2006 paper.

Professor Felsenstein is dubious of Dembski and Marks’ claim that Darwinian evolution could only work in a very special kind of universe, but his chief objection is that “Dembski and Marks have not provided any new argument that shows that a Designer intervenes after the population starts to evolve.” As I’ll argue below, Intelligent Design advocate Professor Michael Behe discussed this objection several years ago, and responded to it in his book, The Edge of Evolution. Interestingly, ID critic Dr. Elizabeth Liddle puts forward her own model of how Intelligent Design might work without the need for intervention, in a recent post over at The Skeptical Zone, entitled, Is Darwinism a better explanation of life than Intelligent Design? (14 May 2013). Her proposal bears some resemblance to Behe’s, and what both have in common is that they allow the Designer to make a very large number of selections from among possible worlds that He/She could have created [Liddle's Designer is of the feminine sex], but without having to make any interventions. Neither proposal is restricted to front-loading; both proposals explicitly allow the Designer of Nature to make selections that alter the course of evolution long after the first appearance of life on Earth. What’s more, both proposals envisage that these selections should be scientifically detectable, making design inferences legitimate.

Before we address Behe’s and Liddle’s speculative hypotheses regarding the Intelligent Designer’s M.O., or modus operandi, let’s review Dembski and Marks’ Law of the Conservation of Information, and how it points to a Designer of Nature. Dembski explains the thinking behind this law in a recent article over at Evolution News and Views entitled, Conservation of Information Made Simple (28 August 2012). First of all, the concept of information that Dembski is employing here is a very straightforward one. Information can be defined broadly as anything which assists a search to locate its target:

Conservation of information, as we use the term, applies to search. Now search may seem like a fairly restricted topic. Unlike conservation of energy, which applies at all scales and dimensions of the universe, conservation of information, in focusing on search, may seem to have only limited physical significance. But in fact, conservation of information is deeply embedded in the fabric of nature…

Search is a very general phenomenon. The reason we don’t typically think of search in broad terms applicable to nature generally is that we tend to think of it narrowly in terms of finding a particular predefined object. Thus our stock example of search is losing one’s keys, with search then being the attempt to recover them. But we can also search for things that are not pre-given in this way. Sixteenth-century explorers were looking for new, uncharted lands. They knew when they found them that their search had been successful, but they didn’t know exactly what they were looking for…

Another problem with extending search to nature in general is that we tend to think of search as confined to human contexts. Humans search for keys, and humans search for uncharted lands. But, as it turns out, nature is also quite capable of search.

(As an aside, I’d like to point out that Dembski’s “target” metaphor is similar to that used by Aquinas in his celebrated Fifth Way, where he uses the example of an arrow directed by an archer in order to illustrate how all things tend towards their respective ends.)

This brings Dembski to his next point, that evolution itself can be considered as a search, even though it is commonly conceived as a blind process:

Evolution, according to some theoretical biologists, such as Stuart Kauffman, may properly be conceived as a search (see his book Investigations). Kauffman is not an ID guy, so there’s no human or human-like intelligence behind evolutionary search as far as he’s concerned. Nonetheless, for Kauffman, nature, in powering the evolutionary process, is engaged in a search through biological configuration space, searching for and finding ever-increasing orders of biological complexity and diversity…

Mathematically speaking, search always occurs against a backdrop of possibilities (the search space), with the search being for a subset within this backdrop of possibilities (known as the target). Success and failure of search are then characterized in terms of a probability distribution over this backdrop of possibilities, the probability of success increasing to the degree that the probability of locating the target increases.

The generic structure of an alpha amino acid. Image courtesy of Yassine Mrabet and Wikipedia.

To illustrate his point, Dembski cites an example which should be familiar to all Uncommon Descent readers: the formation of the first proteins on Earth. Proteins are sequences of amino acids (typically, over 100) which are all L-amino acids (unlike those found in non-living things, which come in two varieties, L and D) and which are joined by chemical bonds known as peptide bonds. Only a tiny proportion of all the possible sequences of 100 amino acids that could exist, actually fold up and do a useful job. These are the ones we call proteins. Thus if Nature were capable of building a protein without any outside intervention, it would be like finding a needle in a haystack. Hence the “search” metaphor. As Dembski puts it:

For example, consider all possible L-amino acid sequences joined by peptide bonds of length 100. This we can take as our reference class or backdrop of possibilities — our search space. Within this class, consider those sequences that fold and thus might form a functioning protein. This, let us say, is the target. This target is not merely a human construct. Nature itself has identified this target as a precondition for life — no living thing that we know can exist without proteins. Moreover, this target admits some probabilistic estimates. Beginning with the work of Robert Sauer, cassette mutagenesis and other experiments of this sort performed over the last three decades suggest that the target has probability no more than 1 in 10^60 (assuming a uniform probability distribution over all amino acid sequences in the reference class).

The next concept we need to grasp, in order to grasp Dembski and Marks’ argument, is the notion of a fitness landscape – a biological term which is helpfully explained in an article entitled, Evolution 101: Fitness Landscapes, by Michigan State University postdoc student Arend Hintze and MSU graduate student Randy Olson, and posted by Dr. Danielle Whittaker on the Beacon Center blog. A fitness landscape can be understood in terms of the genotypes which comprise it. (Professor John Blamire defines a genotype as ‘the “internally coded, inheritable information” carried by all living organisms.’)

If we enumerate every possible genotype (and every genotype has its own fitness value), we can start drawing a fitness landscape, where the height of the landscape is defined by the fitness, and the place on the map is defined by the mutational distance from the original genotype…

There are peaks and valleys, and by examining this landscape you can imagine the direction a genotype may evolve. Every time the genotype mutates, it alters its location in the landscape a little, and experiences the fitness value assigned to its new genotype. The higher the fitness value, the better the genotype performs, and the more likely it will create offspring into the next generation. By continuing this process over many generations, the genotype will eventually end up on a peak in the landscape… The shape of the landscape and how far mutations can move the genotype across it will determine the evolutionary path and the final peak the genotype will end up at.

Sketch of a fitness landscape. The arrows indicate the preferred flow of a population on the landscape, and the points A and C are local optima. The red ball indicates a population that moves from a very low fitness value to the top of a peak. Image courtesy of Claus Wilke and Wikipedia.

In his essay, Conservation of Information Made Simple (28 August 2012), Professor Dembski quotes a passage from theoretical biologist Stuart Kauffman. Kauffman is no friend of Intelligent Design, yet he is happy to describe the process of evolution as being engaged in a search for higher and higher levels of biological complexity and diversity, as it explores a vast space of possible configurations. Unlike Darwinian biologists, however, Kauffman is prepared to acknowledge that there is a problem with the claim that the Darwinian mechanism of random variation culled by natural selection is capable of generating new biological information. As he puts it in his Investigations (Oxford University Press, 2000, p. 19):

If mutation, recombination, and selection only work well on certain kinds of fitness landscapes, yet most organisms are sexual, and hence use recombination, and all organisms use mutation as a search mechanism, where did these well-wrought fitness landscapes come from, such that evolution manages to produce the fancy stuff around us?

In other words, Kauffman recognizes that Darwinian evolution can only work in special kinds of fitness landscapes. Dembski uses this insight of Kauffman’s to illustrate his point (which has been rigorously proved in his and Marks’ paper on the Law of the Conservation of Information), that any information we see coming out of the evolutionary process must have already been contained in the “fitness landscape” in which evolution occurs.

Bulgarian Orthodox Easter eggs. Image courtesy of Ikonact and Wikipedia.

An Easter Egg hunt provides a useful analogy that helps us understand why evolution cannot hit targets such as functional proteins, or complex life-forms, simply by following a blind search. Some sort of “guided search” is required, but the information that guides the search still has to come from somewhere:

Take an Easter egg hunt in which there’s just one egg carefully hidden somewhere in a vast area. This is the target and blind search is highly unlikely to find it precisely because the search space is so vast…

The Easter egg hunt example provides a little preview of conservation of information. Blind search, if the search space is too large and the number of Easter eggs is too small, is highly unlikely to successfully locate the eggs. A guided search, in which the seeker is given feedback about his search by being told when he’s closer or farther from the egg, by contrast, promises to dramatically raise the probability of success of the search. The seeker is being given vital information bearing on the success of the search. But where did this information that gauges proximity of seeker to egg come from? Conservation of information claims that this information is itself as difficult to find as locating the egg by blind search, implying that the guided search is no better at finding the eggs than blind search once this information must be accounted for…

Most biological configuration spaces are so large and the targets they present are so small that blind search (which ultimately, on materialist principles, reduces to the jostling of life’s molecular constituents through forces of attraction and repulsion) is highly unlikely to succeed. As a consequence, some alternative search is required if the target is to stand a reasonable chance of being located. Evolutionary processes driven by natural selection constitute such an alternative search. Yes, they do a much better job than blind search. But at a cost — an informational cost, a cost these processes have to pay but which they are incapable of earning on their own…

[C]onservation of information says that increasing the probability of successful search requires additional informational resources that, once the cost of locating them is factored in, do nothing to make the original search easier…

The reason it’s called “conservation” of information is that the best we can do is break even, rendering the search no more difficult than before.

The thrust of Dembski’s argument should by now be clear. Let’s imagine (for argument’s sake) that there’s an evolutionary process that leads from a simple cell to the dazzling variety of life-forms that we find on Earth today, via a series of small transitional steps. What the law of conservation of information tells us is that increasing the likelihood that this evolutionary process will succeed in reaching its various targets, can only be achieved by reducing the likelihood of evolution’s being able to occur in the first place. In other words, the more successful we make Darwinian evolution, the less antecedently likely we render it:

…[D]esign proponents have argued that even if common ancestry holds, the evidence of intelligence in biology is compelling. Conservation of information is part of that second-prong challenge to evolution. Evolutionary theorists like Miller and Dawkins think that if they can break down the problem of evolving a complex biological system into a sequence of baby-steps, each of which is manageable by blind search (e.g., point mutations of DNA) and each of which confers a functional advantage, then the evidence of design vanishes. But it doesn’t. Regardless of the evolutionary story told, conservation of information shows that the information in the final product had to be there from the start.

It would actually be quite a remarkable property of nature if fitness across biological configuration space were so distributed that advantages could be cumulated gradually by a Darwinian process. Frankly, I don’t see the evidence for this… The usual response to my skepticism is, Give evolution more time. I’m happy to do that, but even if time allows evolution to proceed much more impressively, the challenge that conservation of information puts to evolution remains.

If biological evolution proceeds by a gradual accrual of functional advantages, instead of finding itself deadlocked on isolated islands of function surrounded by vast seas of non-function, then the fitness landscape over biological configuration space has to be very special indeed (recall Stuart Kauffman’s comments to that effect earlier in this piece). Conservation of information goes further and says that any information we see coming out of the evolutionary process was already there in this fitness landscape or in some other aspect of the environment or was inserted by an intervening intelligence. What conservation of information guarantees did not happen is that the evolutionary process created this information from scratch.

In this passage, Dembski describes the Intelligent Designer as “intervening” and as having “inserted” information into the fitness landscape, but as I’ll argue below, Behe and Liddle both show that there is no need to envisage an actual insertion of information; a selection made by the Designer, outside space and time, would do the trick equally well.

In any event, the key point that Dembski makes in the foregoing passage is that when it comes to the biological information we find in the genomes of living things, you can’t get something from nothing. Information doesn’t create itself.

Citing the work of Simon Conway Morris, a Christian evolutionary biologist who maintains that the information which guides the evolutionary process is embedded in Nature, Dembski goes on to argue that the very metaphors invoked by Morris to describe the manner in which this information is stored in Nature point to Nature’s having been designed. Even if we grant that evolution is capable of “climbing Mount Improbable” (to use a phrase popularized by Professor Richard Dawkins, the world’s best-known contemporary atheist), it is still a very remarkable
fact (unexplained by Darwinism) that evolution possesses the tools required to get it to the top of the mountain and generate such a variety of complex life-forms:

If evolution is so tightly constrained and the Darwinian mechanism of natural selection is just that, a mechanism, albeit one that “navigates immense hyperspaces of biological alternatives” by confining itself to “thin roads of evolution defining a deeper biological structure,” then, in the language of conservation of information, the conditions that allow evolution to act effectively in producing the complexity and diversity of life is but a tiny subset, and therefore a small-probability target, among all the conditions under which evolution might act. And how did nature find just those conditions? Nature has, in that case, embedded in it not just a generic evolutionary process employing selection, replication, and mutation, but one that is precisely tuned to produce the exquisite adaptations, or, dare I say, designs, that pervade biology…

…This is the relevance of conservation of information for evolution: it shows that the vast improbabilities that evolution is supposed to mitigate in fact never do get mitigated. Yes, you can reach the top of Mount Improbable, but the tools that enable you to find a gradual ascent up the mountain are as improbably acquired as simply scaling it in one fell swoop. This is the lesson of conservation of information.

At the conclusion of his 2012 essay, Conservation of Information Made Simple, Professor Dembski addresses the question of where the information we find in the fundamental properties of Nature ultimately comes from: an Intelligent Designer Who was not designed by anyone else.

One final question remains, namely, what is the source of information in nature that allows targets to be successfully searched? If blind material forces can only redistribute existing information, then where does the information that allows for successful search, whether in biological evolution or in evolutionary computing or in cosmological fine-tuning or wherever, come from in the first place? The answer will by now be obvious: from intelligence. On materialist principles, intelligence is not real but an epiphenomenon of underlying material processes. But if intelligence is real and has real causal powers, it can do more than merely redistribute information — it can also create it.

Indeed, that is the defining property of intelligence, its ability to create information, especially information that finds needles in haystacks.

Professor Felsenstein’s beef with Dembski and Marks’ Law of the Conservation of Information

Felsenstein writes:

I think that ordinary physics, with its weakness of long-range interactions, predicts smoother-than-random fitness surfaces. But whether I am right about that or not, Dembski and Marks have not provided any new argument that shows that a Designer intervenes after the population starts to evolve. In their scheme, ordinary mutation and natural selection can bring about the adaptation. Far from reformulating the Design Inference, they have pushed it back to the formation of the universe.

I’d like to make a brief comment here on Felsenstein’s critique of Dembski’s claim that evolution only works in a very unusual fitness landscape. The basis for this claim is a mathematical one: the Law of the Conservation of Information, which Dembski established by a process of rigorous logical argumentation, in his paper with Marks. Since there has been no credible critique of the mathematical reasoning contained in this paper since its publication, I shall take it that the result stands. Consequently, if Felsenstein wants to argue that evolution would work in a much larger proportion of fitness landscapes than Dembski claims, then he should do one of two things: either critique Dembski and Mark’s mathematical argument for the Law of the Conservation of Information (LCI), or attempt to argue that it doesn’t apply to evolution. Felsenstein does neither. Instead, Felsenstein puts forward an argument that evolution isn’t sensitive to tiny changes in the fitness landscape (as Dembski maintains it is), based on an appeal to “ordinary physics”, which is simply irrelevant to the case in question. If LCI is true, and if it applies to biological evolution, then evolution must be a fine-tuned process. it’s as simple as that.

The other part of Felsenstein’s critique relates to the modus operamdi of the Intelligent Designer: Felsenstein thinks that Dembski and Marks need to show that the Designer intervenes after the population starts to evolve, but what they’ve shown instead is that He fine-tunes the universe at the very moment of its formation. In other words, the Designer doesn’t intervene in the history of the universe; He just winds it up, like a cosmic clockmaker. At best, contends Felsenstein, that’s an argument for Deism.

The persistence of the fitness landscape over time is a fact which needs to be explained

A cul-de-sac in Sacramento, California. Image courtesy of The Mentalist, LeaW, Indolences and Wikipedia.

What Professor Felsenstein is implicitly assuming in his critique is that the fitness landscape, with its smooth surfaces that permit incremental Darwinian evolution to occur, persists over the course of time. But why should it? The Earth has been through several major cataclysms since its formation: huge meteorite impacts which destroyed nearly all living creatures; having its entire surface frozen for tens (and possibly hundreds) of millions of years (according to some geologists); mass extinctions caused by a sudden soaring of global temperatures; and the sudden release of oxygen into the atmosphere, which proved toxic for many anaerobic organisms on the early Earth, to name just a few. Throughout all these upheavals, we are supposed to believe that the fitness landscape that makes gradualistic Darwinian evolution possible maintained its smooth contours, making incremental improvements possible. But that, in itself, is a huge assumption. Who is to say that a fitness landscape, once set up, requires no further maintenance, other than the continued survival of life on Earth? For instance, what’s to prevent radical environmental changes from pushing all terrestrial organisms into an evolutionary cul-de-sac, where no major improvements are possible, even over the course of billions of years? And why couldn’t that have happened on the early Earth?

If the maintenance of a fitness landscape which permits the evolution of complex organisms over the course of time is not a foregone conclusion, then we can no longer rule out an ongoing role for the Designer simply by appealing to the efficacy of “ordinary mutation and natural selection” to bring about adaptations, as Felsenstein contends. Rather, we need a Designer Who can guarantee at every stage of the development of life on Earth that the path leading to sentient and sapient beings remains open.

Behe and Liddle on the possibility of design without intervention

Balls breaking in a game of pool. Image courtesy of No-w-ay, H. Caps and Wikipedia.

In his book, The Edge of Evolution (The Free Press, 2007), Professor Michael Behe writes:

How was the design of life accomplished? That’s a peculiarly contentious question. Some people (officially including the National Academy of Sciences) are willing to allow that the laws of nature may have been purposely fine-tuned for life by an intelligent agent, but they balk at considering further fine-tuning after the Big Bang because they would fret it would require ‘interference’ in the operation of nature. So they permit a designer just one shot, at the beginning – after that, hands off. For example, in The Plausibility of Life Marc Kirschner and John Gerhart hopefully quote a passage from an old article on evolution in the 1909 Catholic Encyclopedia: ‘God is the Creator of heaven and earth. If God produced the universe by a single creative act of His will, then its natural development by laws implanted in it by the Creator is to the greater glory of His Divine power and wisdom.’

This line of thinking is known as ‘Theistic Evolution’. But its followers are just kidding themselves if they think it is compatible with Darwinism. First, to the extent that anyone – either God, … or ‘any being. . . external to our universe responsible for selecting its properties’ – set nature up in any way to ensure a particular outcome, then to that extent, although there may be evolution, there is no Darwinism. Darwin’s main contribution to science was to posit a mechanism for the unfolding of life that required no input from any intelligence – random variation and natural selection. If laws were ‘implanted’ into nature with the express knowledge that they would lead to intelligent life, then even if the results follow by ‘natural development,’ nonetheless, intelligent life is not a random result (although randomness may be responsible for other, unintended features of nature). Even if all the pool balls on the table followed natural laws after the cue struck the first ball, the final result of all the balls in the side pocket was not random. It was intended [via the specific arrangement of the balls on the pool table before the shot was made].

Second, ‘laws’, understood as simple rules that describe how matter interacts (such as Newton’s law of gravity), cannot do anything by themselves. For anything to be done, specific substances must act. If our universe contained no matter, even the most finely tuned laws would be unable to produce life, because there would be nothing to follow the laws. Matter has unique characteristics, such as how much, where it is, and how it’s moving. In the absence of specific arrangements of matter, general laws account for little.

Finally, a particular, complex outcome cannot be ensured without a high degree of specification. At the risk of overusing the analogy, one can’t ensure that all the pool balls will end up in the side pocket just by specifying simple laws of physics, or even simple laws plus, say, the size of the pool table. Using the same simple laws, almost all arrangements of balls and almost all cue shots would not lead to the intended result. Much more has to be set. And to ensure a livable planet that actually harbors life, much more has to be specified than just the bare laws of physics. (2007, pp. 229-230)

Behe then proceeds to address a “theological” objection to Intelligent Design on the part of some religious believers:

Some people who accept design design arguments for physics, but not for biology, nurture an aesthetic preference that our universe should be self-contained, with no exceptions to physical laws after its inception. The prospect of the active, continuing involvement of the designer rubs them the wrong way. They picture something like a big hand flinging a Mars-sized orb at the nascent earth [in order to generate the moon - VJT], or pushing molecules around, and it offends their sensibilities. (2007, p. 230)

In order to assuage the concerns of these religious believers that belief in Intelligent Design commits us to a demeaning view of the Designer, Behe then provides what he describes as a “cartoon example” of how an Intelligent Being with a perfect understanding of physics (or an uberphysicist, as Behe calls Him) might design the evolution of life down to the last detail, without having to intervene in the history of the cosmos. At the beginning, Behe envisages that the uberphysicist has “a huge warehouse in which is stored a colossal number of little shiny spheres,” where “[e]ach sphere encloses the complete history of a separate, self–contained, possible universe, waiting to be activated.” Behe explains that “the warehouse can be considered a vast multiverse of possible universes, but none of them have yet been made real.” Most of these possible universes will be inhospitable to life, but a tiny proportion will be life-friendly:

One enormous section of the warehouse contains all the universes that, if activated, would fail to produce life. They would develop into universes consisting of just one big black hole, universes without stars, universes without atoms, or other abysmal failures. In a small wing of the huge warehouse are stored possible universes that have the right general laws and constants of nature for life. Almost all of them, however, fall into the category of “close, but no cigar.” For example, in one possible universe the Mars–sized body would hit the nascent earth at the wrong angle and life would never commence. In one small room of the small wing are those universes that would develop life. Almost all of them, however, would not develop intelligent life. In one small closet of the small room of the small wing are placed possible universes that would actually develop intelligent life. (2007, p. 231)

From among the (relatively few) life-friendly universes, Behe’s uberphysicist then makes a selection: He brings one of them into being, in a single creative act, thereby setting in motion the entire course of evolution, culminating in the appearance of intelligent human beings. The mutations that occur during the evolution of life may appear random, but in fact, they were deliberately selected by Behe’s uberphysicist. Behe argues that this selection amounts to an act of design, without the need for any interference.

One afternoon the uberphysicist walks from his lab to the warehouse, passes by the huge collection of possible dead universes, strolls into the small wing, over to the small room, opens the small closet, and selects on the extremely rare universes that is set up to lead to intelligent life. Then he “adds water” to activate it. In that case the now–active universe is fine–tuned to the very great degree of detail required, yet it is activated in a “single creative act.” All that’s required for the example to work is that some possible universe could follow the intended path without further prodding, and that the uberphysicist select it. After the first decisive moment the carefully chosen universe undergoes “natural development by laws implanted in it.” In that universe, life evolves by common descent and a long series of mutations, but many aren’t random. There are myriad Powerball–winning events, but they aren’t due to chance. They were foreseen, and chosen from all the possible universes.

Certainly that implies impressive power in the uberphysicist. But a being who can fine–tune the laws and constants of nature is immensely powerful. If the universe is purposely set up to produce intelligent life, I see no principled distinction between fine–tuning only its physics or, if necessary, fine–tuning whatever else is required. In either case the designer took all necessary steps to ensure life.

Those who worry about ‘interference’ should relax. The purposeful design of life to any degree is easily compatible with the idea that, after its initiation, the universe unfolded exclusively by the intended playing out of the natural laws. (2007, pp. 229-230, 231-232)

In her post, Is Darwinism a better explanation of life than Intelligent Design? (14 May 2013), Elizabeth Liddle puts forward a similar theory, although it is somewhat less detailed than Behe’s:

Here’s an ID theory that any IDist who likes it is welcome to:

Let’s say that a Designer (and I’m going to assume a divine designer, because, as Dembski says, any material designer just moves the problem back a notch, as it would itself require a designer) wanted to create a universe in which life would appear. This designer knows that of the trillions of possible universes, only one will unfold according to the Divine Plan and bring forth life and human beings, and yet such beings are her Divine Purpose.

And so she causes to exist just that one in a trillion universe, in which each event unfolds as she intends. From within the universe, all we observe are natural causes, which, nonetheless, against all apparent odds, happen to result in us. And so the only way of inferring the Designer is to apprehend just how many possible universes might have been created, and how few of those would have resulted in us.

Nothing has occurred that is not possible given the rules we infer about this universe. But the probability that of all possible events, the ones that lead to intelligent life are those that occurred is infinitesimal, unless we posit that we were intended – that of all hypothetical universes in the Divine Mind, the one she chose to actuate was the one that would lead to us.

We will find nothing but apparently fortuitous chemistry in the formation of novel proteins – but such unlikely chemistry that trillions of alternative chemical reactions must have been considered and rejected as being not on the path to us.

There. I think I’ve presented myself with a more convincing ID argument than any I’ve read so far.

Is this the clockwork universe by another name?

Tim Wetherell’s Clockwork Universe sculpture at Questacon, Canberra, Australia (2009). Image courtesy of OpheliaO and Wikipedia.

It is important to note here that neither Behe nor Liddle envisages a deterministic universe: both of them posit scenarios in which mutations occur. To a naive onlooker, these mutations might appear random, but in fact, the outcome of these mutations has been carefully planned by the Designer. In other words, we are not dealing with a front-loading scenario here, in which the outcome of each and every mutation could (in principle) be predicted from a knowledge of the laws and initial conditions of the cosmos. Rather, what Behe and Liddle envisage is a Designer who selects not only the laws and initial conditions of the cosmos, but also the outcomes of indeterministic events, such as mutations.

This is an important point, as physicist Dr. Robert Sheldon has argued in a highly persuasive article entitled, The Front-Loading Fiction (July 2, 2009) that front-loading wouldn’t work. The clockwork universe of Laplacean determinism, which endeavors to specify all future outcomes simply by selecting the laws and initial conditions of the cosmos, won’t work because in a quantum universe like ours, “no amount of precision can control the outcome far in the future,” as “[t]he exponential nature of the precision required to predetermine the outcome exceeds the information storage of the medium.” Nor will it do to suppose that the universe unfolded according to a cosmic computer program, since “Turing’s proof of the indeterminacy of feedback; the inability to keep data and code separate as required for Turing-determinacy; and the inexplicable existence of biological fractals within a Turing-determined system” would all render the outcome of any such program inherently unpredictable. In fact, the only kind of universe that could be pre-programmed to produce specific results without fail and without the need for any further input, would be one without any kind of feedback, real-world contingency or fractals – and hence, one devoid of organic life.

For his part, Sheldon envisages an incessantly active “hands-on” Deity, Who continually maintains the universe at every possible scale of time and space, in order that it can support life. That’s perfectly fine by me. But what Behe’s and Liddle’s thought experiments show is that a Deity can be actively involved in the history of life, without necessarily being an interventionist. All the Deity needs to do is select a cosmos with the history He intends, from among countless alternative possible universes.

Would design detection be possible in a non-interventionist universe?

Dr. Liddle, in her thought experiment, makes it quite clear that a Deity’s acts of design could still be detected in the “non-interventionist” cosmos which she envisages. Design could be inferred from the extreme rarity of possible universes that lead to intelligent life:

From within the universe, all we observe are natural causes, which, nonetheless, against all apparent odds, happen to result in us. And so the only way of inferring the Designer is to apprehend just how many possible universes might have been created, and how few of those would have resulted in us.

We will find nothing but apparently fortuitous chemistry in the formation of novel proteins – but such unlikely chemistry that trillions of alternative chemical reactions must have been considered and rejected as being not on the path to us.

This kind of reasoning accords very well with the design inferences that Intelligent Design theorists make by invoking Professor Dembski’s “design filter” – not that I would accuse Dr. Liddle of being an Intelligent Design theorist for one moment, of course! Nevertheless, the scenario she proposes should allay any concerns that people living in a cosmos that was not subject to acts of Divine intervention could never infer the existence of a Designer.

Would a designed universe satisfy the requirements of quantum randomness?

Professor Felsenstein may be inclined to object that the non-random outcomes in the universe selected by Behe’s (or Liddle’s) Deity are at odds with the inherent randomness of quantum physics. In response, I would argue that an act of selection by an Intelligent Designer need not violate quantum randomness, because a selection can be random at the micro level, but non-random at the macro level. The following two rows of digits will serve to illustrate my point.

1 0 0 0 1 1 1 1 0 0 0 1 0 1 0 0 1 1
0 0 1 0 0 0 0 1 1 0 1 1 0 1 1 1 0 1

The above two rows of digits were created by a random number generator. Now suppose I impose the macro requirement: keep the columns whose sum equals 1, and discard the rest. I now have:

1 0 1 1 1 0 0 0 0 0 1
0 1 0 0 0 1 1 0 1 1 0

Each row is still random, but I have imposed a non-random macro-level constraint. Likewise, when the Designer makes a choice of which world to create from among various possible worlds, there is no violation of quantum randomness at the microscopic level.

Could the foregoing scenario actually be true? A philosophical evaluation

It seems to me that the question of whether the scenario proposed by Behe and Liddle is viable or not ultimately hinges on the philosophical question of whether this universe would still be the same individual universe, if its history were different. Philosophers often like to talk about possible universes (although many of them prefer to speak instead of “possible worlds”, which is a somewhat broader term). Disagreement exists as to whether these possible worlds are concrete or merely abstract. But the question of how these worlds should be individuated is a vexed one. It makes sense to say that this world could have been different from the way it is; consequently, not every feature of this world can be essential to it. The question then boils down to this: which features of the cosmos we live in are part-and-parcel of its individual identity?

If we accept that “pure randomness” (i.e. events which “just happen”, without being either causally determined or selected by an intelligent agent) is philosophically impossible, then that seems to entail that there can be no universe whose micro- or macro-level outcomes are not fully specified in some fashion. That, in turn, would seem to imply that when God selects a particular universe to create, God must select one whose history is specified too – at least, up until the arrival of intelligent beings like ourselves, who are capable of making additional specifications by their acts of free choice.

At any rate, we are now in a position to respond to Professor Felsenstein’s objection to the Law of the Conservation of Information, that “Dembski and Marks have not provided any new argument that shows that a Designer intervenes after the population starts to evolve.” As we have seen, no intervention is necessary; a Designer Who is outside time and space could select the entire course of evolution, without needing to intervene even once, if He so wished.

Felsenstein objects that Dembski and Marks’ Law of the Conservation of Information would make evolution a foregone conclusion, from the moment of creation:

In their scheme, ordinary mutation and natural selection can bring about the adaptation. Far from reformulating the Design Inference, they have pushed it back to the formation of the universe.

But this objection presupposes that mutations occur deterministically. If mutations are indeterministic on the physical level, then there is nothing, in the absence of a Designer, which guarantees that the course of evolution will proceed as it does. A universe with the same laws and initial conditions as ours might still remain lifeless, even after 14 billion years, if “random” events happen to go the wrong way for the development of life. Hence the need for selection covering every stage of the history of the universe, on the Designer’s part.

I also argued above that the persistence of the evolutionary “fitness landscape” over the course of time is a highly remarkable fact, which needs to be explained. We are very fortunate that evolution did not get stuck in a cul-de-sac, at a time when the only organisms on Earth were one-celled bacteria. If that had happened, we would not be here today. The fact that we live on a planet where mutations lead to increasing diversity and complexity, over billions of years, requires an explanation, and the only satisfactory one is: design.

To sum up: Felsenstein’s contention that the Law of Conservation pushes the Designer to the very periphery of the picture turns out to be mistaken, and his assumption that design requires intervention rests on a misunderstanding of Intelligent Design theory. It is to be hoped that he will reconsider his views. I’d also like to thank Professor Behe and Dr. Liddle for having demonstrated that belief in an active Designer does not necessarily entail belief in an interventionist Designer.

Let me close with a quote from St. Augustine (The City of God v, 11):

“Not only heaven and earth, not only man and angel, even the bowels of the lowest animal, even the wing of the bird, the flower of the plant, the leaf of the tree, hath God endowed with every fitting detail of their nature.”

Is it true that there is no scientific method, as cosmologist Lee Smolin suggests?

May 20, 2013

Or are some fields mistakenly classified as science?

At Big Think, Lee Smolin, a cosmologist at the Perimeter Institute for Theoretical Physics who has suggested cosmic Darwinism (new universes governed by Darwinian evolution sprout in cosmic black holes), also muses on the idea that there is no scientific method:

Feyerabend thought it was very important to underline that we didn’t know why science works. And so I gave a lot of thought to this problem over the years and my point of view, my proposal, is that science works because scientists form communities and traditions based not on a common set of methods, but a common set of ethical principles. And there are two ethical principles that I think underlie the success of science and I call these the Principles of the Open Future. The first one is that we agree to tell the truth and we agree to be governed by rational argument from public evidence. So when there is a disagreement it can be resolved by referring to a rational deduction from public evidence. We agree to be so swayed.

Whether we originally came to that point of view or not to that point of view, whether that was our idea or somebody else’s idea, whether it’s our research program or a rival research program, we agree to let evidence decide. Now one sees this happening all the time in science. This is the strength of science.

The second principle is that when the evidence does not decide, when the evidence is not sufficient to decide from rational argument, whether one point of view is right or another point of view is right, we agree to encourage competition and diversification amongst the professionals in the community.

The difficulty is that in many fields that is just not what we are seeing.

Incidentally, Smolin himself works largely in an area where evidence wouldn’t seem to matter much. He has espoused cosmic Darwinism, where new universes sprout from black holes:

It seemed to me that the only principle powerful enough to explain the high degree of organization of our universe—compared to a universe with the particles and forces chosen randomly—was natural selection itself. (Lee Smolin, “A Theory of the Whole Universe” in John Brockman, ed., The
Third Culture (New York: Simon and Schuster Touchstone, 1996), p. 294: http://tinyurl.com/4xr9s3u)

He and colleagues have also aimed to take relativity to a brand new level: “They say we need to forget about the home Einstein invented for us: we live instead in a place called phase space.” That, we are told, is a “curious eight-dimensional world that merges our familiar four dimensions of space and time and a four-dimensional world called momentum space.”

On the whole, if this is science, isn’t it just as well that there is no scientific method?

But wait a minute …

See also: Top notch studies commonly report contradictory genealogies today

Evolution: Top notch studies commonly report contradictory genealogies today

May 20, 2013

High profile studies in conflict/ Antonis Rokas, Vanderbilt University

A friend thinks confessions don’t get much better than this screed at ScienceDaily for this paper in Nature:

These days, phylogeneticists — experts who painstakingly map the complex branches of the tree of life — suffer from an embarrassment of riches. The genomics revolution has given them mountains of DNA data that they can sift through to reconstruct the evolutionary history that connects all living beings. But the unprecedented quantity has also caused a serious problem: The trees produced by a number of well-supported studies have come to contradictory conclusions.

“It has become common for top-notch studies to report genealogies that strongly contradict each other in where certain organisms sprang from, such as the place of sponges on the animal tree or of snails on the tree of mollusks,” said Antonis Rokas, Cornelius Vanderbilt Chair in Biological Sciences at Vanderbilt University.

And the further back they go, the less reliable the genetic data becomes.

Keep this story in mind when a coworker splinters the table insisting that Darwinian evolution is supported by “mountains of evidence,” or, better yet, “mountains and mountains of evidence,”or even just plain “fact! fact! FACT!”*

What is the mountain of evidence evidence for, specifically? Nothing the next paper won’t overturn, it seems.

*Michael Ruse, Darwinism Defended: A Guide to the Evolution Controversies, (Addison-Wesley, 1982) 1983, Third Printing, p.58. Emphasis Ruse’s.

Here’s the paper’s Abstract:

To tackle incongruence, the topological conflict between different gene trees, phylogenomic studies couple concatenation with practices such as rogue taxon removal or the use of slowly evolving genes. Phylogenomic analysis of 1,070 orthologues from 23 yeast genomes identified 1,070 distinct gene trees, which were all incongruent with the phylogeny inferred from concatenation. Incongruence severity increased for shorter internodes located deeper in the phylogeny. Notably, whereas most practices had little or negative impact on the yeast phylogeny, the use of genes or internodes with high average internode support significantly improved the robustness of inference. We obtained similar results in analyses of vertebrate and metazoan phylogenomic data sets. These results question the exclusive reliance on concatenation and associated practices, and argue that selecting genes with strong phylogenetic signals and demonstrating the absence of significant incongruence are essential for accurately reconstructing ancient divergences. – Leonidas Salichos, Antonis Rokas. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature, 2013; 497 (7449): 327 DOI: 10.1038/nature12130

Newly on line: Darwinism as a root of make-it-up-as-you-go ethics

May 20, 2013

Richard Weikart of the University of California, Stanislaus, author of (most recently) Hitler’s Ethic: The Nazi Pursuit of Evolutionary Progress (Palgrave Macmillan, 2009), writes to say that he has just posted to his Web site an essay, “A History of the Impact of Darwinism on Bioethics,” originally published in 2011 in the anthology, 150 Years of Evolution: Darwin’s Impact on the Humanities and Social Sciences (ed. Mark Wheeler, San Diego State University Press).
Read it here:

Seeing morality as the product of contingent evolutionary processes was in line with the dominant trend toward historicism that permeated nineteenth-century Western thought. However it was a radical departure from pre-nineteenth century views about ethics as timeless and universal. Darwin clearly contributed to the historicization of ethics in the nineteenth century by portraying morality as changing and by denying its universality. (p. 93) More.

The intriguing part is that so many people who think this an entirely laudable trend in ethics are nonetheless angry and disbelieving when a scholar like Weikart explains the role Darwin played in it. Apparently, it is bad form to embarrass Christian Darwinists by spelling it out?

Weikart explains how he first became interested in Darwin’s role here:

Weikart is sometimes attacked in print for having had a sordid motive for even raising the issue. So why did he do it? And how did he get interested in the first place?

Actually, at first, he wasn’t interested. While living in Germany some years ago to improve his German, he was mainly interested in the nineteenth century. He doubted that he would uncover anything new about the Third Reich. For one thing, in his view, it was an overworked field. But then he discovered one neglected point … More.

Neglected? Shucks.

Video: The Dennis Noble lecture in Suzhou China on physiology and Neo-Darwinian evolutionary biology

May 20, 2013

Between Sal C and Nullasalus, this has come up:

[There is a video that cannot be displayed in this feed. Visit the blog entry to see the video.]

This is meant to support a thread of discussion, so kindly comment here. END