I popped into the comments section of an ID news story to post a book blurb. Someone responded with the following argument:

Mike Gene, "Could evolution and Intelligent Design be intimately linked in an elaborate dance we call life?"

No. There is no evidence of design, unless you want to consider the possibility that the the designer is a fucking idiot. The "design" of many organisms is fraught with problems. Our optic nerves are wired backwards from what an intelligent designer would use, although cephalopods got the right design. (I always thought that squid were God's chosen organism).

As I have shown before the "no evidence" claim is mostly rhetorical. But let's consider the argument, as it clearly is part of the Matrix "“ Irrational Design.

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Okay, as if "˜species' and "˜life' were not fuzzy enough, let's consider the rock-solid notion of "˜self-replication':

VENTER: Does it need to be self-replicating?

SHAPIRO: It needs to be reproduced. The idea of a replicator, of DNA copying itself. I have a tie like that: it shows nucleotides swimming up to DNA, and miraculously one strand forms a double helix, but anyone who teaches biochemistry knows that doesn't happen "” no way. There are dozens of proteins that come in and get involved in the action, and untwist the twists of DNA, and prime it and close the gaps in DNA.

VENTER: I wasn't describing a mechanism, just, the term 'self-replicating'.

SHAPIRO: DNA isn't self-replicating.

VENTER: No, I'm not talking about DNA.

SHAPIRO: And RNA as far as I know isn't "” virus needs an entire cell filled with ribosomes and god knows what "” mitochondria.

VENTER: Methanococcus is self-replicating.

SHAPIRO: Methanococcus is self-replicating, and if it lives and grows and changes eventually into different strains, that's alive.

LLOYD: So is a virus alive?

SHAPIRO: That's a question of how you want to define it.

VENTER: Is it not self-replicating.

LLOYD: I'm not self-replicating either. I have children and neither of them look anything like me.

SHAPIRO: The difficulties in these definitions are notorious. Is a nun alive? She's certainly not replicating. Is a mule alive? It has most of other properties, but it's sterile and has no offspring.

CHURCH: Its cells are alive.

SHAPIRO: Its cells are alive.

Okay, we've seen that the important concept of "˜species' comes with a fuzzy definition that does not seem to apply to the majority of organisms on earth, so what about the concept of life? After all, biology is the study of life. How is it defined:

SHAPIRO: There was a wonderful paper written by Chris Chyba and Carol Cleland about three years ago about definitions of life, and how even defining what definition is can get you into philosophical doo-doo. And it's best to look for phenomena that by their properties we would be happy to classify as alive, and to not worry too much about definition.

Here

One could borrow from this logic and also argue, "it's best to look for phenomena that by their properties we would be happy to classify as intelligently designed, and to not worry too much about definition."

Dedicated to those who demand precise, rigorous definitions:

VENTER: I have trouble with some of the fundamental terms. What's your definition of "species" That's something I have great difficulty with lately out of our research.

DYSON: Yes, it is a problem "” it's supposed to be just a population that breeds within the population but not outside, but of course there are all sorts of exceptions.

VENTER: That ignores most of biology.

DYSON: Yes, so I don't know what the real definition is. But that's the conventional definition.

VENTER: It's a human definition.

DYSON: It is fuzzy. Like most things.

[Here]

You'll see what I'm talking about half-way through. But fret not fellow bunnyphiles – watch it to the end.

FREEMAN DYSON:
First of all I wanted to talk a bit about origin of life. To me the most interesting question in biology has always been how it all got started. That has been a hobby of mine. We're all equally ignorant, as far as I can see.That's why somebody like me can pretend to be an expert.

A LITTLE BUNNY:
The most significant unanswered question in biology is the origin of life. How did life first appear on this planet? Not only has this question escaped a non-teleological explanation for decades, it is the most crucial question in biology. The origin of life speaks to the essence of life, and that, in turn, builds context for the rest of biology, including evolution. All else follows from the initial states provided by the original cells and the context they set for subsequent evolution. In comparison, the rest of biology is a footnote.

I was checking through our blogroll and came upon an interesting observation from Lawrence Selden. It then occurred to me that I missed the most delicious opportunity. Given that I used my internet handle for my book, think how funny it would have been if I had instead decided to originally join the ARN forum as "Goldstein." This would have eventually led to:

The Design Matrix: A Consilience of Clues, by Emmanuel Goldstein.

Man, did I blow it.

Freeman Dyson wrote:

The Darwinian interlude has lasted for two or three billion years. It probably slowed down the pace of evolution considerably. The basic biochemical machinery of life had evolved rapidly during the few hundreds of millions of years of the pre-Darwinian era, and changed very little in the next two billion years of microbial evolution. Darwinian evolution is slow because individual species, once established evolve very little. With rare exceptions, Darwinian evolution requires established species to become extinct so that new species can replace them.

Now, after three billion years, the Darwinian interlude is over. It was an interlude between two periods of horizontal gene transfer.The epoch of Darwinian evolution based on competition between species ended about ten thousand years ago, when a single species, Homo sapiens, began to dominate and reorganize the biosphere. Since that time, cultural evolution has replaced biological evolution as the main driving force of change. Cultural evolution is not Darwinian. Cultures spread by horizontal transfer of ideas more than by genetic inheritance. Cultural evolution is running a thousand times faster than Darwinian evolution, taking us into a new era of cultural interdependence which we call globalization. And now, as Homo sapiens domesticates the new biotechnology, we are reviving the ancient pre-Darwinian practice of horizontal gene transfer, moving genes easily from microbes to plants and animals, blurring the boundaries between species. We are moving rapidly into the post-Darwinian era, when species other than our own will no longer exist, and the rules of Open Source sharing will be extended from the exchange of software to the exchange of genes. Then the evolution of life will once again be communal, as it was in the good old days before separate species and intellectual property were invented.

And what has moved us into the post-Darwinan era? Intelligent design. In this case, the intelligent designers are human beings, whose rationality and foresight have not only brought culture into existence, but has enabled them to decipher the machinery and coding of life. Wouldn't it be very interesting if there is indeed a deeper symmetry in the pre- and post-Darwinian eras?

The recent thread about the "Man on Mars" has raised some good questions about The Design Matrix. First, hrun asks:

I am not trying to strike a round-house blow at design detection or the design matrix here. I am asking a genuine question: How do we know that we are operating at the right resolution to detect design? How can we avoid false positives or false negatives due to being at the wrong resolution? Is a single positive result at any resolution sufficient to conclude design?

I think these are excellent and only by asking them, pondering them, and attempting to answer them shall we make progress in trying to infer design in a fair and open-ended manner. So let me address each one.

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Internet forums are buzzing with speculation about a new picture from NASA's Spirit rover that people are calling "Mars Man" or "The Mars Creature" …

Let's start with the most distant view:

Zoom in a bit …

And then a little more …

So how are we to handle this buzz as epistemically responsible creatures? Well, Mike Gene gives us an answer in The Design Matrix.

We need higher epistemic resolution – in this case visual resolution – to infer anything but "rock shaped by atmosphere of Mars". The current image does not provide enough resolution to make a responsible design inference. It's that simple.

Now a question for Mike: When do we know that we have enough epistemic resolution? How deep must we go, how many levels of resolution must we traverse, before we are justified?

Another animal rights extremist unveils his peaceful and tolerant guide to activism. This time, it's Gary Yourofsky in the University of Southern Indiana newspaper, dreaming about inflicting violence on animal researchers, hunters and fur-clad women.

So, while my lifestyle and lectures are based on compassion, those who refuse to stop harming animals force me to support 'eye for an eye' and 'by any means necessary' philosophies. …

Institutionalized violence doesn't simply vanish with a peaceful protest, a dose of logic and whole lotta love. If people continually deny animals their inherent right to be free, radical tactics are necessary and justified. …

Deep down, I truly hope that oppression, torture and murder return to each uncaring human tenfold! I hope that fathers accidentally shoot their sons on hunting excursions, while carnivores suffer heart attacks that kill them slowly.

Every woman ensconced in fur should endure a rape so vicious that it scars them forever. While every man entrenched in fur should suffer an anal raping so horrific that they become disemboweled. Every rodeo cowboy and matador should be gored to death, while circus abusers are trampled by elephants and mauled by tigers. And, lastly, may irony shine its esoteric head in the form of animal researchers catching debilitating diseases and painfully withering away because research dollars that could have been used to treat them was wasted on the barbaric, unscientific practice vivisection.

HT: Secondhand Smoke

Okay, it's just a catchy title I borrowed, but the research looks interesting:

Genes have the ability to recognise similarities in each other from a distance, without any proteins or other biological molecules aiding the process, according to new research published this week in the Journal of Physical Chemistry B. This discovery could explain how similar genes find each other and group together in order to perform key processes involved in the evolution of species.
["¦]
The authors of the new study carried out a series of experiments in order to test the theory, first developed in 2001 by two members of this team, that long pieces of identical double-stranded DNA could identify each other merely as a result of complementary patterns of electrical charges which they both carry. They wanted to verify that this could indeed occur without physical contact between the two molecules, or the facilitating presence of proteins.

Previous studies have suggested that proteins are involved in the recognition process when it occurs between short strands of DNA which only have about 10 pairs of chemical bases. This new research shows that much longer strands of DNA with hundreds of pairs of chemical bases seem able to recognise each other as a whole without protein involvement. According to the theory, this recognition mechanism is stronger the longer the genes are.
The researchers observed the behaviour of fluorescently tagged DNA molecules in a pure solution. They found that DNA molecules with identical patterns of chemical bases were approximately twice as likely to gather together than DNA molecules with different sequences.

- Here

The roundworm C. elegans, a staple of laboratory research, may be key in unlocking one of the central biological mysteries: why we sleep. Researchers at the University of Pennsylvania School of Medicine report in the January 11 advanced online edition of Nature that the round worm has a sleep-like state, joining most of the animal kingdom in displaying this physiology. This research has implications for explaining the evolution and purpose of sleep and sleep-like states in animals.
-Here

In the January 15th issue of G&D, a research team led by Dr. Richard Behringer at MD Anderson Cancer Center reports that they have successfully switched the mouse Prx1 gene regulatory element with the Prx1 gene regulatory region from a bat "“ and although these two species are separated by millions of years of evolution — the resulting transgenic mice displayed abnormally long forelimbs.

While forelimb length is just one of several key morphological changes that occurred during the evolution of the bat wing, this unprecedented finding demonstrates that evolution can be driven by changes in the patterns of gene expression, rather than solely by changes in the genes, themselves.

-Here