Let's get back to biology. The latest from Mike Gene's blog:

[Caveman ask that somebody do that magic thing with links]

Setting up a culture of cells is a relatively simple task. All you need is some media, which would be a solution that contains all the ingredients needed for cell growth, and some cells, obtained from another previous culture. Put simply, you fill a container with media and add a small amount of cells. These cells then do what cells do – they divide and form a large population of cells over time. In other words, the machinery within the cells converts the simple biomolecules in the media into new cells.

But now I have a puzzle for you. Read the rest of this entry »

Discussion on the lengthy Remarkable Nucleotides thread has become unwieldy, as well as not much about remarkable nucleotides anymore. This thread serves for continuing sidelines off-topic there - OoL and ET scenarios primarily, as well as physical diversions.

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Mike Gene doesn't post here any more, for family reasons. So I thought I would post the latest from his blog, The Design Matrix:

Recent research concerning tyrosine kinases continues to strengthen the case for front-loading evolution:

When it comes to cellular communication networks, a primitive single-celled microbe that answers to the name of Monosiga brevicollis has a leg up on animals composed of billions of cells. It commands a signaling network more elaborate and diverse than found in any multicellular organism higher up on the evolutionary tree, researchers at the Salk Institute for Biological Studies have discovered. Read the rest of this entry »

I've been reading Kirschner and Gerhart's The Plausibility of Life, which so far is a fascinating read. I'm not done, but it appears that their view is that there have been sudden appearances throughout natural history of "core processes" in living organisms, which then allow the organisms to evolve by relatively small, simple steps. But what they haven't done, so far, is explain where these core processes come from. Perhaps they will offer an explanation later in the book.
But you think they would offer at least a passing mention of Lynn Margulis's ideas of endosymbiosis and symbiogenesis. She knew about the sudden appearances of core processes, and suggested that they came about by acquiring the genomes of other organisms. This happened, according to her view, by either bacteria or protists engulfing other bacteria (endosymbiosis), or more recently, by multi-cellular organisms being infected by bacteria or viruses (symbiogenesis). Read the rest of this entry »

Previously, it has been shown that genes that duplicated in the same time window and are clustered in the MHC regions suggests that a proto-MHC region was present in the last common ancestor of chordates, this is further supported by conservation of clusters with the urochordates.

The conservation of the clustering with arthropods suggests that a proto-MHC region was even older, present in Urbilateria.

Several studies now suggest that many important genes for the Adaptive Immune System were "waiting" for recruitment.

Our studies support the general statement that AIS appears after the jawless/jawed vertebrate split. However our study further reveals the fact that AIS is in its twilight in amphioxus and the evolution of the molecules in amphioxus are waiting for recruitment by the emergence of AIS.

see here, here , and here

Hydra vulgaris is a member of the phylum Cnidaria. It appears to be a relatively simple animal and has a small number of cell types (you can read more about its basic biology here). Yet, as we have seen, it turns out that cnidarians actually possess a rather complex genetic tool kit.

We have also seen that receptor tyrosine kinases (RTK) would play important roles in facilitating the evolution of multicellular life. Added to this is the recent discovery that one example of an RTK, the insulin receptor, plays an important role, along with its ligand insulin, in the development of the nervous system.

So let’s begin the process of tying this together.

Could it be possible that the protein hormone insulin, that is spread throughout the body of mammals via the circulatory system, would actually play a role in the development or life of Hydra? In 1996, Steele et al. (1) identified a gene for a receptor tyrosine kinase that was very similar to the insulin receptor in mammals, called HTK7. They found that is was expressed in ectodermal cells (the cell type that can generate nervous tissue) at both ends of Hydra’s tube.

But what is most striking of all is that they found insulin, obtained from cows, had the ability to induce both DNA replication and cell division in Hydra’s ectodermal cells.

Okay, from the perspective, there is nothing all that surprising about finding insulin receptors, and responsiveness to mammalian insulin, in cnidarians. This is just another example of deep homology that is consistent with such a system being in place with the last common ancestor of all animals.

What’s more interesting this time around is that we are talking about a hormone and its receptor. Here, the function is simple - BIND. What makes this interesting is that cows and Hydra last shared a common ancestor at least 600 million years ago. This in turn means there are 1.2 billion years of evolution that separate the Hydra insulin receptor and the bovine insulin.

Each lineage would possess an independent history of mutations in the receptor followed by secondary, suppressor mutations in the ligand. Each lineage would possess an independent history of mutations in the ligand followed by secondary, suppressor mutations in the receptor. Yet despite two separate spans of co-evolution between receptor and ligand, the ligand from cows retains the ability to function with the receptor from Hydra.

All that this indicates a fairly strong selective constraint on a seemingly simply biochemical function (BIND). So where do we go from here?

1. R. E. Steele, Pauline Lieu, Ninh H. Mai, M. Andrew Shenk and Michael P. Sarras Jr. 1996. Response to insulin and the expression pattern of a gene encoding an insulin receptor homologue suggest a role for an insulin-like molecule in regulating growth and patterning in Hydra Development Genes and Evolution 206:247-259

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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