Genetic entropy...

scordova writes at uncommondescent about genetic entropy, the idea that genomes are degrading:

For example, a fundamental consequence of Sanford’s Genetic Entropy thesis is that there will be an unabated rise in Single Nucleotide Polymorphisms (SNPs) per generation per individual. If confirmed, this data will be more nails in Darwin’s coffin, and then Darwin Day might have to be renamed Darwin Bashing Day...

It would seem that scordova claims that ID predicts that there will be an increase in SNPs (single bases in DNA are changed) between generations and that this is bad for evolution. Why this would be bad news for evolution, I don't know. After all, if there weren't any mutations, evolution would be quite difficult. Rather than being a nail in the coffin, it would be a confirmation of something that evolution requires. Or maybe I have misunderstood what the heck scordova is on about...

Peer-reviewed testable ID claims?

Quizzlestick at overwhelmingevidence asks if ID has provided any peer-reviewed testable claims. The answer appears to be yes and a link is supplied to an article (written by a Kazmer Ujvarosy) that appears in an online magazine that is not peer-reviewed(!). OK you might say. Maybe the article is not peer-reviewed - but surely it provides testable claims. I'll give you five predictions the article makes:

•By virtue of its eternity human intelligence constitutes the cosmological constant.

•Human intelligence has quantum properties because it exists in both particle and field states. Human intelligence in its potential or seed state is a particle, but in its state of expression takes on field characteristics, and thus provides the morphogenetic field or quantum vacuum of the universe for the development of the creatures it has in mind.

•Dark energy, that drives the expansion of the universe, is one of the deepest and most exciting puzzles in modern science. We posit that dark energy is the field manifestation of the parent seed of the universe, just as the cosmic vacuum’s zero-point energy. They all originate from the cosmic seed’s biophoton emissions, which blackbody radiation provides a holographic biofield for the generation of the physical universe. Based on the fact that the biophotonic radiation emitted by DNA is coherent, we predict that the cosmic seed's biophotonic field or "dark energy" is equally coherent.

•The universe is a living system, dynamically managed by the parent seed’s unbounded and conscious holographic biofield, and regulated by the process of information feedback.

•The elusive Higgs boson – so vital to the Standard Model of particle physics that it is dubbed “the God particle” – is identical with the genotype of the phenotype universe, and each human genome is its reproduction. Based on this identification we posit that mass-giving is life-giving because the elementary particles that come into contact with the cosmic seed's biofield or quantum vacuum receive their mass and property as a result of that interaction.

I would be keen for either quizzlestick or Kazmer himself to (please do) tell us how we are supposed to test these predictions. Myself, I have a hard time separating this from most other new-age clap-trap.

quizzlestick says this of Kazmer:

I would like to introduce Dr. Kazmer Ujavorsy, chief scientist of the Frontline Science Institute, one of the most prestigious research organizations dedicated to Intelligent Design.

From what I can see, the Frontline Science Institute has published six articles - all in American Chronicle. From what I can see, none of the articles provide any testable claims and of course, none of them appeared in a peer-reviewed journal. So, the claim that it is a prestigious research organization would appear to be nothing short of a big fat lie.

A commenter (HaEris) has this to say about Kazmer:

.....What can I say other that I am glad he is on our side.

Given the nonsense prediction he supplied (above), I'm glad he's on your side too.

So, all in all, no peer-reviewed testable claims are supplied, which is bizarre, given that that was the reason quizzlestick wrote the article. Oh, well...

Bad poetry

In his book "Unweaving the rainbow", Richard Dawkins explains how the use of analogies and metaphors can be a useful tool to understand scientific ideas and concepts. He also describes why doing this can sometimes be bad and actually make something more difficult to understand and even make you understand things wrong. Dawkins himself refers to this as using either good poetry (when better understanding is reached) or bad poetry (when understanding is hindered) respectively. Reading through intelligent design (ID) material on the web, it strikes me that ID proponents are quite fond of bad peotry. Most importantly, they seem to think that analogies are actually a good descriptor of the way things really are. The analogies become, then, not mere analogies but literal truth. The best example I have seen so far is from none other that William Dembski:

William Dembski quotes an Ivan Amato who talks about mutations that are usually thought to be silent (i.e. have no phenotypic effect): "The more scientists study the genetic code, the more it reads like poetry. In a poem, every word, every line break, even every syllable can carry more than a literal meaning. So too can the molecular letters, syllables, and words of the genetic code carry more biologically relevant meanings than they appear to at first." Amato's poetry is "good" (heck, he even used poetry as an analogy) IMO, but of course Dembski has to take it literally. The reason is obvious: poets write poetry. Poets intelligently designed the poems. But it's just an ANALOGY. Bill took a good piece of poetry and presented bad poetry to his readers.

Gollum... no GOLEM!!!

William Dembski at uncommondescent writes (Jan 17th, 2007):

Does the following point up disconfirming evidence against the creative power of unguided evolutionary processes? What has become of this project to vindicate standard evolutionary theory?

• The golem@Home project has concluded. After accumulating several Million CPU hours on this project and reviewing many evolved creatures we have concluded that merely more CPU is not sufficient to evolve complexity: The evolutionary process appears to be hitting a complexity barrier that is not traversable using direct mutation-selection processes, due to the exponential nature of the problem.
  

Well, from what I have seen in ID writings, evolutionary algorithms all fail to mimic Darwinian processes for some reason or other. One common objection is that these programs strive for a preset goal - i.e. they have teleology. Teleology, they claim, is what an intelligent designer has and evolution doesn't, so all these algorithms really show is that intelligent designers are able to design the algorithms that lead to the solution - i.e. the programs really support ID.

Golem basically works as follows:

The organism will attempt to move across an infinite plain, and its fitness is determined by how successful it is at locomotion. The construction details are then stored, and another creature allowed to develop. The fitter "robots" can pass their "genes" on to the next generation, and as time passes, the more successful combinations are permitted to survive.

Golum's teleologic goal is thus to be able to move better than before. The success of this approach would thus (by ID standards) have been support for ID and this is what IDists would have claimed had the program been successful. But the program failed and thus the project really points up disconfirming evidence against the creative power of intelligently designed processes.

If IDists were consistent, they should read the above as:

The golem@Home project has concluded. After accumulating several Million CPU hours on this project and reviewing many intelligently designed creatures we have concluded that merely more CPU is not sufficient to intelligently design complexity: The intelligently designed process appears to be hitting a complexity barrier that is not traversable using direct intelligently designed mutation-selection processes, due to the exponential nature of the problem.

Well, this is what IDists themselves should be saying.

Designing iterated

Uncommondescent has a list of arguments they don't want commenters to use. One of these is:

Who Designed the Designer

This argument points out that, by inferring a designer from complexity in machines, the designer must also be complexity. Why? Well just because it seems like he/she/it would. This of course then plunges into an infinite loop of who designed the designer. This infinite loop makes Intelligent Design somehow impossible. The really weird part is the argument is broadcast to us using a computer that was the result of intelligent design. Intelligent design does not speak to the nature of designers anymore than Darwin’s theory speaks to the origin of matter.

More properly, the argument is that it takes (by ID's definition) intelligence to build complexity (well, specified complexity, at least). Idists would be foolish to suggest that intelligence is not complex. So, the question remains: how did the designer become complex? Dembski et al often claim that intelligence is non-material - so maybe non-complex non-material stuff can design complex material stuff? If the designer would not even have to be complex, then we would have complexity arising from non-complexity - which is pretty much what evolution (and abiogenesis) claims anyway. So why the need for ID?

This issue can be debated back and forth - and it should be!

All these ID reasearch papers...

idnet.com.au at uncommondescent claims (re certain papers he reads in Nature):

Almost every time I read the abstracts and even the titles, or spend more time delving into the detail, I hear “Intelligent Design” silently screamed from the pages. Am I deluded, or do others hear it too? Here is a recent example.

He then quotes from an article about cell signalling and leg morphogenesis in Drosophila. He seems to think that the article in question screams design since it contains words such as "specifies", "signal" and "information" (well, he bolded these words and added no further comments). But how on Earth does presenting some research that examines something complicated containing a few ID buzz-words support ID? The answer as far as I can tell is "I think something looks intelligently designed, so therefore it was intelligently designed". So, I guess that the article supports ID just because an ID supporter thinks it does.

Maybe I'm deaf, or maybe I'm reading this in outer space, because I can't hear the screaming. Or maybe idnet.com.au really is deluded(?).

Beating that old dead ungulate

William Dembski at uncommondescent wonders (Jan 8th, 2007) why, with the publication of two new anti-intelligent design books, do evolutionists keep beating a dead horse. I assume that Dembski asks this question after having heard some evolutionist claiming that ID as a science is dead in the water. Well Bill, ID as science is dead (or rather, it was never alive in the first place) - but it is alive and kicking in the religious, political and commercial arena. This is of course where ID is trying to get a legitimate standing, hence the beating.

Or maybe....
...
...
maybe the horse is non-materialistic and every time it dies it reincarnates in some other form...
...
(sorry, just rambling)

Evolution says nothing about...

Dembski's pal Denyse O'Leary is quite amusing. She seems to have very little understanding about logic and science. The post of interest is again the one dated (Jan 5th, 2007). Writes she:

In Commentary magazine, Eric Cohen's "The Human Difference" offers to explain why most North Americans do not accept the current science pundits' vision of the world:

On the evidence provided by nature, Darwin’s claim of common descent seems undeniably compelling; man’s emergence via genetic mutation and natural selection seems likely; and the possibility of man’s never emerging seems all too possible. Yet for all its insights into the development of complex life, the theory of evolution ends before the most interesting questions begin. Where did matter come from in the first place, and with it the latent possibility of man? What is the source of nature’s fixed laws, by which the chance process of evolution plays itself out? Why do animals seek to survive and reproduce at all, hungering for life even with its manifold sufferings?

To these questions, modern Darwinian theory has no compelling answer, and its methods are poorly equipped even to initiate the right sort of inquiry. Evolution may explain the mechanisms of man’s descent, but not the mystery of his ascent, including the wonder he exhibits about the origins and destiny of the cosmos—a wonder that serves no useful animal function. A theory of man’s origins is not yet a theory of man, let alone a theory about why there is something rather than nothing.

She ends with a comment of her own: "Well, exactly". Well, exactly, Denyse, it's true. Darwinian theory has no compelling answer to these questions. Neither should it. Neither should the theory of gravity, theories about electromagnetism, theories about material stress, theories about the change in global temperatures, theories about... Well, you get the picture. Intelligent design creationists like Denyse seem to seriously think that a theory has to answer ALL questions for it to be valid. This is simply nonsensical and only shows her willful ignorance about science in general. I can only assume that Dembski lets her share his blog because she shares his conclusions and he really couldn't care less how she reached them.

ID says nothing about the designer...

A central tenet of intelligent design (ID) is that it does not address the nature or identity of the designer in question. With this in mind, one has to wonder why ID proponents (Dembski included) constantly claim that there is more to the universe than materialism. For example, Dembski's pal Denyse O'Leary writes in her blog (Friday 5th Jan, 2007):

I wonder how Dyson would feel about materialist scientists just leaving the ID guys alone to just get on with their work: One of them wrote me recently, saying poignantly, "If only they would just leave us alone, but they can't and won't." Of course not. If ID is right in any particular, materialism is dead. (bolding added)

Bearing in mind ID refusal to say anything about the designer, O'Leary's (bolded) comment above rests on bad logic. Since ID says nothing about whether or not the designer is material or not, even if ID is right, materialism would not necessarily be dead. Unless of course ID does say something about the designer...

Evolution: An idea on the verge of extinction?

You can always count on intelligent design creationists to predict the in-the-not-too-distant-future demise of evolution. The lastest(?) to do so is SBWillie at overwhelming evidence. One of his arguments for this is that he claims that evolution is a tautology (i.e. survival of the fittest leads to the fittest surviving). This is simply wrong. Fitness is a probabilistic term where those that are better adapted, compared to others in the same population, are more likely to reproduce and pass on their traits (as an aside, I would personally like to call it "survival of the fitter"). In order for it to be a tautology, the consequence would always have to follow from the premise (also see claim CA500 at talkorigins). Even Answers in Genesis recommend that this argument should not be used. So, the answer to SBWillie's question:

Could Darwinists have been so silly to have based their entire field of study on a glaringly obvious tautology?

would appear to be no. He continues:

What if "Survival of the fittest" were the "engine" that drives life on? Do we really live in a selfish world where only the most ruthless competitors stand a chance of survival? Fortunately this is not the case. When Darwin originally wrote his "Origin of Species" he was completely unaware of the many forms of symbiosis, co-operation and even generosity in the animal kingdom. The only way a Darwinist can continue to believe in this core dogma is by closing his eyes to the last hundred years of biological research.

The only one's who think that Darwinists believe this are strawman-wielding ID creationists. After all, there is nothing quite like misrepresenting your opponents positions, attacking it and then claiming victory.

Unlike Evolutionists, we Proponents of ID do not pretend that we have all the answers. We only wish to humbly point out that scientists who refuse to accept Intelligent Design may be risking lives. For example, it is widely acknowledged amongst AIDS researchers that the reason why the virus is so hard to fight is because it "evolves". Millions of dollars are being spent on researching how this life-form evolves and where has it got us? Perhaps the reason for failure of conventional research has less to do with "bad luck" or "lack of budget", but a fundamentally wrong approach. Is it not possible that life cannot evolve in the way that Darwinists think, but that it only adapts in precisely the way predicted by the theory of Intelligent Design?

And now, Darwinists are risking lives as well. I don't think I've come across a ID creationist claiming this before (not in the sense it's used here anyway [they usually say something along the lines that Darwinism leads to Nazism]). SBWillie, HIV does evolve - no doubt about it. I would love to see SBWillie explain just how scientists have got it wrong and more to the point just how ID theory is getting it right. Of course, no such explanation is given.

There is much work still to do, but as yet mainstream science has not yet managed to argue away this new science. I think this may be proof that our ideas are valid.

Methinks he must mean apart from pointing out that ID is not science, thus showing that his ideas are not scientifically valid.

All we need to do in order to win this debate is to keep making clear arguments that show the inherent contradictions and absurdities of Darwinism.

And all we get from SBWillie is false claims and strawmen instead.

I believe that ID provides exactly the scientific framework to help simplify the complex problems that continue to puzzle mankind. I personally predict that one or more of the bigger commercial research organisations will come over to our side of the debate within a matter of months: Why wouldn't they accept the truth when there is so much of their own money at stake!

I'm sure someone will continue to issue a few more ID books. There is, after all, money to be made from that.

It looks to me as if SBWillies prediction of evolution's demise is based on rubbish reasoning.

Naturalism: An Obstruction of Justice?

A certain TRoutMac at overwhelmingevidence claims that IDists by necessity oppose methodological naturalism (Definition from wikipedia: Methodological naturalism (MN) is the philosophical tenet that, within scientific enquiry, one can only use natural explanations - i.e. one's explanations must not make reference to the existence of supernatural forces and entities. Note that methodological naturalism does not hold that such entities or forces do not exist, but merely that one cannot use them within a scientific explanation.) and also states:

...but far from relying on "supernatural" causes, this opposition to naturalism merely enables one to objectively weigh the evidence and make rational conclusions based on that evidence. Naturalism actually stacks the deck and only allows evidence for one possible explanation for life to be explored. That's hardly science, and it's hardly objective.

TRoutMac seems to have some problem with definitions here. First of, if you reject MN, you by by necessity rely on supernatural causes - by definition. TRoutMac's claim that naturalism only allows evidence for one possible explanation for life is simply wrong. While the explanation does indeed have to be naturalistic, there can of course be a plethora of these. TRoutMac's second definitional problem is claiming that using only naturalism is not science, is also wrong - by definition (obviously, since science only deals with natual explanations).

TRoutMac continues:

To illustrate the absurdity of the naturalist's position regarding origin-of-life issues, just imagine you're a lead detective in a law enforcement agency, and you've been assigned by your captain to investigate a murder. Due to circumstances around the murder, it's already apparent that there are two prime suspects for the crime. But one of those suspects is your captain's close personal friend. Your captain approaches you privately and instructs you that you are NOT permitted to build a case against his friend and that you must build your case to charge the other suspect.

This is a really bad analogy - just as ID analogies usually are. There are several reasons for this, but the most important one is that we know that people sometimes commit murder and we know that people were around at the time of the murder. What we don't know is whether or not there was anything intelligent around when life first arose on this planet. And if there was, did it design life here or at all. Other reasons for the bad analogy is that he complains about the naturalists position and then only supplies natural explanations. A better analogy would have been to have two other suspects; John Doe and the other something supernatural (call it God, gremlins or leprechauns if you wish). I think that most captains would not entertain the idea of spirits commiting a murder - and neither should they.


TRoutMac finishes:

Naturalists have to explain why they feel compelled to frame the other suspect. They have to explain what they're trying to protect. They have to explain why they wish to obstruct the investigation. I'm glad I'm not in their shoes.

A naturalist would not be framing anyone. He would just reject supernatural explanations. What is being protected? Is rationality enough? Is this obstructing the investigation? No, obviously not. TRoutMac should perhaps try to wear some other shoes.

Front loading???

A pro ID blogger (Nathan) states in one of his posts:

As the articles states, "sea urchins are echinoderms, marine animals" and
the purple sea urchin, "has 7,000 genes in common with humans, including genes
associated with Parkinson’s, Alzheimer’s and Huntington’s diseases and muscular
dystrophy." Of great interest to intelligent design advocates of front loading
is the fact that although the sea urchin has no eyes, nose or ears it does have
genes that are homologous to genes found in humans that are involved in vision,
hearing and the sense of smell.

Are we actually to accept that this is evidence of one-of-many-ways-in-which-the-creator-could-have-done-it? The thinking here is that the common ancestor of mammals and sea urchins would have had these genes and since (the ancestors of) mammals later did develop eyes, the case for front-loading is strengthened. Let's examine that, shall we?

The assumption you have to accept here is that these genes are only useful in vision, hearing and smell (if you do not accept that assumtion, you would reject irreducible complexity, which is after all a cornerstone of ID). Under this assumption, these genes in the sea urchins would have been conserved for some 500 million years (since the last common ancestor of mammals and echinoderms was alive) in the absense of selective pressures to maintain them. That is an extraordinary feat that would be nothing short of miraculous. But maybe you could argue that these genes will become important for the sea urchins in the future when they will acquire vision, hearing and smell themselves. Problem is, this does not get rid of the problem. Since the sea urchins have not got these abilities today, there is no selective pressure to maintain the genes (and again, don't try to argue that maybe the genes also have other functions since this still is an argument against irreducible complexity).

Maybe we should just accept a scientific explanation for why these genes have been conserved instead. Like, the genes have slightly different functions in the two lineages of organisms.