Despite the stunning variety of photoreceptor organs, every animal uses the same kind of light-capturing molecule to do this job. Insects, humans, clams, and scallops all use opsins. Not only can we trace the history of eyes through differences in the structure of their opsins, but we have good evidence that we can thank bacteria for these molecules in the first place.

The bacterial past can be used to our advantage in studying the diseases of mitochondria — in fact, some of the best experimental models for these diseases are bacteria. This is powerful because we can do all kinds of experiments with bacteria that are not possible with human cells… [European researchers] were able to simulate parts of a human mitochondrial disease in a bacterium, with virtually the same change in metabolism. This is putting a many-billion-year part of our history to work for us.

Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body

Paul Davies authored The Cosmic Blueprint. Like most of his work this book is thoughtful and well written. I want to focus on a small part of it for the purpose of this blog entry. On page 131 Davies discusses how life has modified earth's environment over geologic timescales. He illustrates his point with the specific example of the sun's luminosity which has increased by about 30% during the earth's history. Despite this significant increase, the temperature of the earth has remained within a small range that is hospitable to life. Davies uses the phrase "equability of conditions" in alluding to this.

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By analyzing the recently-sequenced choanoflagellate genome, the researchers discovered another similarity between choanoflagellates and most metazoans–their genetic code caries the markers of three types of molecules that cells use to achieve phospho-tyrosine signaling proteins.

Animals depend on tyrosine phosphorylation to conduct a number of important communications between their cells, including immune system responses, hormone system stimulation and other crucial functions. These phospho-tyrosine signaling pathways utilize a three-part system of molecular components to make these communications possible.

Tyrosine kinases (TyrK) 'write' messages between cells by adding phospho-tyrosine modifications, protein tyrosine phosphatases (PTP) are molecules that modify or 'erase' these modifications, and Src Homolgy 2 (SH2) molecules 'read' these modifications so the recipient cell gets the message.

Without these three molecules to help our cells 'write,' 'read' and 'erase' chemical messages between them, our bodies would never be able to conduct the complex tasks needed to survive such as reproduction, digesting food or even breathing.

Other genome analysis showed that some microorganisms contain some of these molecules in small levels, but never all three. This makes sense considering these organisms don't need the tools to communicate between cells since they are made up of only one cell. What makes choanoflagellates unique, however, is that they have all three of these molecules. What's more, they have relatively large quantities of them in amounts commonly seen in larger metazoan organisms.

The researchers conclude that the presence of the full three-component signaling system may have played a role in the development of metazoan organisms whose cells could communicate with each other in complex ways.

Here

HT: fifth monarchy man

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One thing that has always interested me about computer simulated evolution of networks is that virtually (pun intended) all of them turn out to be non-modular. This has been pointed out in the literature (Thompson et. al 1998).

Modularity itself is something that the front-loading hypothesis predicts:

If life was designed and our analogy to human design is substantial, then we would predict life would be modular…Modularity enhances evolution and thus the perpetuation of design.
The Design Matrix p.167-168

The researchers running these sort of simulations make use of duplication, recombination, mutation, selection until they see the relevant result. However, there is a lot more to the evolution of life-like networks.

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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.

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?

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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The sea urchin has been mentioned before at Telic Thoughts and elsewhere. More recently an article was linked to in which this was said:

Look, when Sherman stresses that the sea urchin has, in-expressed, the genes for the eyes and for antibodies (genes that are well known and fully active in later species), how can we not agree with him that canonical neo-Darwinism cannot begin to explain such facts?

Although this paper is not new there is also:

Embryonic development in the sea urchin requires trophic actions of the same neurotransmitters that participate in mammalian brain assembly

The rabbit seems to have the terrestrial mascot position sewed up but maybe the sea urchin can find a niche at Telic Thoughts.

Guts posted this video before, but I thought I would repost it. I especially enjoyed the comments from Sean Carroll (according to Michael Ruse, "Of all the scientists in the world today, there is no one with whom Charles Darwin would rather spend an evening than Sean Carroll."):

So what this means is in some ways, some sense, evolution is a simpler process than we first thought. When you think about all of the diversity of forms out there, we first believed this would involve all sorts of novel creations, starting from scratch, again and again and again. We now understand that, no, that evolution works with packets of information and uses them in a new and different ways, and new and different combinations, without necessarily having to invent anything fundamentally new, but new combinations.

My, that's a pretty radical change in the way we view evolution. The old way was far more friendly to non-teleology and also failed to prepare scientists for the more accurate understanding of evolution, an understanding that is now much more friendly to teleology.

Given the likelihood that the ctenophore lineage is the deepest branch among metazoans, let's have a closer look at the toolkit contained by these creatures to determine if the basic theme of front-loading evolution continues to hold up.

Consider two classes of transcription factors that are known to play crucial roles in metazoan development: the T-box proteins and the SOX proteins. Both factors activate a variety of genes involved in body plan formation, organ formation and cell specification. And as we might expect from a front-loading perspective, PCR analyses have retrieved a rather complex array of both transcription factors from the comb jellies.

Consider the conclusions from two different studies:

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