He obeys my every command.

I'm excited to do my part to help conserve energy.

Anyone wanna ride in my new wheels?

Viewpoint features two consecutive entries relevant to discussions of Intelligent design. Microscopic Clutch refers to the familiar bacterial flagellum and notes a construct, analogous to the clutch of an automobole transmission, enabling rotation stoppage. Arguments, pro and con, about irreducible complexity are well known. Critics of Behe have argued that Behe's selection conundrum can be overcome through evolutionary cooption of systems within which distinct IC parts already existed replete with biological function albeit not necessarily function presently observed. The issue of interrelatedness of parts to function is pushed back in time. The evolutionary cooption alternative obviates the necessity of a telic process. Or does it? If we retrace an evolutionary process we eventually arrive at a single cell; the basic unit of living organisms but irreducibly complex nonetheless.

Was that cell loaded with modular cellular constructs designed to adapt to the variations of earthly environments or can a reductionist approach be traced back to extra-cellular chemistry on prebiotic earth? There are multiple variants of "front loading" the author points out. Front loading a process can be viewed as a series of steps in which each one in the series was enabled by the preceeding one traced back to an initial starting unit- a pre-wound mechanism to use a metaphor.

Is active information required to find targets in search space and does the vast size of protein sequence space assure us that the evolution of protein sequence, structure and function is a given in the absence of front loading?

The God Delusion, Ch 7 (partII) is a second Viewpoint entry accurately debunking the nonsense holding that non-religious value systems are intrinsically preferable. Those convinced that God is a delusion are front loaded with conceptual barriers to an objective assessment of the sufficiency of a non-telic process.

John Moore from the National Post attempts to define ID. Yet when his claims are viewed from the perspective of The Design Matrix, he's shooting blanks:

ID is often referred to as Creationism light. In fact it's more Creationism in drag.

Cute, but false. The Design Matrix does not argue against evolution, it explores the manner in which evolution may have been shaped by design.

Though its proponents claim scientific neutrality, they are usually overtly religious people affiliated with overtly religious institutions.

False. While I am a theist, I am not overtly religious. Furthermore, I am not affiliated with any overtly religious institution, any religious institution, or any institution. I come to the table as a truly independent voice.

They have written essays and books about why ID is science.

False. I have never written an essay about why ID is science. The Design Matrix acknowledges that ID is not science and moves beyond this culture war dispute.

And yet when all the sophistry is boiled down, the theory amounts to "living things are complicated. Some-one must have made them."

False. The Design Matrix does not boil down to "living things are complicated. Some-one must have made them."

It may be a sublime idea worthy of religious and philosophical contemplation, but it fails to meet the definition of science.

Irrelevant. There is no compelling reason to think science is capable of determining whether or not life was designed. Because science has not come up with a objective methodology for resolving this issue, I move on and begin contemplating alternative methods of inquiry.

Sh*t, p*ss, c*nt, f*ck, cocks*cker, motherf*cker and tits.

The Seven Deadly Words, all but one of which still require asterisks in 2008 on public inter-tubes forums. What an earth-shattering bit of comedy that was all those years ago!

An inspiration to millions and what my friend Bill Hamilton (Boss Clown at Ringling) approvingly pronounced, "F*cking Funny." His own words, used at the close of every show…

"Take care of yourself. And take care of someone else."

R.I.P. George Carlin.

Let's now consider cnidarians:

Jellyfish have traditionally been considered simple and primitive. When you gaze at one in an aquarium tank, it is not hard to see why.

Like its relatives the sea anemone and coral, the jellyfish looks like a no-frills animal. It has no head, no back or front, no left or right sides, no legs or fins. It has no heart. Its gut is a blind pouch rather than a tube, so its mouth must serve as its anus. Instead of a brain, it has a diffuse net of nerves.

A fish or a shrimp may move quickly in a determined swim; a jellyfish pulses lazily along.

But new research has made scientists realize that they have underestimated the jellyfish and its relatives – known collectively as cnidarians (pronounced nih-DEHR-ee-uns). Beneath their seemingly simple exterior lies a remarkably sophisticated collection of genes, including many that give rise to humans' complex anatomy.

[...]

Much to their surprise, the scientists found that some genes switched on in embryos were nearly identical to the genes that determined the head-to-tail axis of bilaterians, including humans. More surprisingly, the genes switched on in the same head-to-tail pattern as in bilaterians.

Further studies showed that cnidarians used other genes from the bilaterian tool kit. The same genes that patterned the front and back of the bilaterian embryo, for example, were produced on opposite sides of the anemone embryo.
The findings have these scientists wondering why cnidarians use such a complex set of body-building genes when their bodies end up looking so simple. They have concluded that cnidarians may be more complicated than they appear, particularly in their nervous systems.

[...]

In some ways, cnidarians are a better model for human biology than fruit flies. As strange as it may seem, gazing at a jellyfish in an aquarium is a lot like looking in the mirror.

Here

But where shall we go from here?

Gordy Slack wrote What neo-creationists get right, an article in which he attempts to set aside his gut reactions and dispassionately assess some points made by the opposition. From the article:

First, I have to agree with the ID crowd that there are some very big (and frankly exciting) questions that should keep evolutionists humble. While there is important work going on in the area of biogenesis, for instance, I think it's fair to say that science is still in the dark about this fundamental question. It's hard to draw conclusions about the significance of what we don't know. Still, I think it is disingenuous to argue that the origin of life is irrelevant to evolution. It is no less relevant than the Big Bang is to physics or cosmology. Evolution should be able to explain, in theory at least, all the way back to the very first organism that could replicate itself through biological or chemical processes. And to understand that organism fully, we would simply have to know what came before it. And right now we are nowhere close. I believe a material explanation will be found, but that confidence comes from my faith that science is up to the task of explaining, in purely material or naturalistic terms, the whole history of life. My faith is well founded, but it is still faith.

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OPENTHREAD

You've heard of a Flea Circus… now get ready for the Germ Circus!

Thinking Ahead: Bacteria Anticipate Coming Changes In Their Environment

LOL!!! Something a bit more than Shapiro's "cellular intelligence," researchers at Princeton have demonstrated some interesting intelligence in e.coli per anticipating future conditions and turning genes on or off based on that acquired knowledge.

In addition to shedding light on deep questions in biology, the findings could have many practical implications. They could help scientists understand how bacteria mutate to develop resistance to antibiotics. They may also help in developing specialized bacteria to perform useful tasks such as cleaning up environmental contamination.

Huh. An understanding of evolution as endogenous adaptive mutagenesis looks to "have many practical implications?" Who'd a thunk?

The researchers say that their findings open up many exciting avenues of research. They are planning to use similar methods to study how bacteria exchange genes with one another (horizontal gene transfer), how tissues and organs develop (morphogenesis), how viral infections spread, and other core problems in biology.

By golly, here we have actual biological scientists at an Ivy League institution and publishing in Science reporting that life anticipates the future at the most rudimentary level and adapts itself accordingly. Who was it who predicted years ago that science would eventually come to accept an EAM-ish version of intelligent design in biological evolution because it offers better solutions to 'problems' the RM-NS paradigm simply cannot explain?

Very cool.

A classic example of a receptor tyrosine kinase receptor is the insulin receptor. Most people are familiar with insulin because of diabetes, a disease that is associated with high blood sugar. Basically, insulin is a protein hormone that is secreted by endocrines cells in the pancreas. Once the insulin enters the blood, it can specifically bind to insulin receptors on the cells of various tissues, triggering those cells to import glucose. Diabetes can be caused either by either a defect in insulin production (type I) or a defect with the insulin receptors (type II). Either way, failure to import glucose from the blood leaves high levels of glucose in the blood – high blood sugar.

Well, we can make a slight detour on our trip through the rabbit hole given the announcement of some new research yesterday. It turns out that insulin is a multifunctional signal molecule, highlighting the modularity of the whole system:

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Now that one story is on pause, let's turn to another story and another set of blog entries. I'll begin with something I previously posted a few months ago.

Let's talk about receptor tyrosine kinases (RTKs). We can think of an RTK as a communication device, since these membrane proteins transmit signals from the cell's environment into the cell. Event X outside the cell is translated into Event Y inside the cell. Specifically, the signaling molecules (such as hormones) bind the extracellular portion of the receptor protein. This binding event is then somehow communicated to the contents inside the cell. But how?

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