More Alu on the Brain

RNA editing, DNA recoding and the evolution of human cognition.

Mattick JS, Mehler MF.

Trends Neurosci. 2008 May;31(5):227-33.

RNA editing appears to be the major mechanism by which environmental signals overwrite encoded genetic information to modify gene function and regulation, particularly in the brain. We suggest that the predominance of Alu elements in the human genome is the result of their evolutionary co-adaptation as a modular substrate for RNA editing, driven by selection for higher-order cognitive function. We show that RNA editing alters transcripts from loci encoding proteins involved in neural cell identity, maturation and function, as well as in DNA repair, implying a role for RNA editing not only in neural transmission and network plasticity but also in brain development, and suggesting that communication of productive changes back to the genome might constitute the molecular basis of long-term memory and higher-order cognition.

Michael Shermer and Inevitability

Michael Shermer makes an argument that doesn’t strike me as being as strong as he thinks it is.  Shermer writes:

What are the odds that intelligent, technically advanced aliens would look anything like the ones in films, with an emaciated torso and limbs, spindly fingers and a bulbous, bald head with large, almond-shaped eyes? What are the odds that they would even be humanoid? In a YouTube video, produced by Josh Timonen of the Richard Dawkins Foundation for Reason and Science, I argue that the chances are close to zero

and explains:

if something like a smart, technological, bipedal humanoid has a certain level of inevitability because of how evolution unfolds, then it would have happened more than once here.

Not necessarily.  If event X has the likelihood of happening once every 3 billion years, then after 3 billion years, it becomes inevitable and it happens once. It’s like the lottery.  If the odds of winning are a million-to-one, and a million people play, someone will win.  That the winning is inevitable does not mean a thousand people from that million should win.

Methylation – Focusing the Effects of Cytosine Deamination

Back around 2002, I noted that the genetic code appears to funnel one of the most common  base pair substitutions, the C-to-T transitions caused by deamination of the cytosine.  Put simply, codons containing a C specified a wide range of amino acids, but when that C is converted to T, the new set of codons all converge on the most hydrophobic amino acids.  The original analysis is found here.

To see this for yourself, the figure below represents a hydrophobicity scale for the 20 amino acids based on 47 published attempts to quantify hydrophobicity:

Source

Now consider the effect of cytosine deamination using this scale:

Scale on left are the amino acids coded for by C-containing codons which is converted to scale on right by the deamination of those cytosines.

But what if we did the same analysis, but this time restrict our focus to the cytosines that are followed by guanines – the CpG sequences discussed here, given that such sequence is the most likely to exploit the effects of deamination?

A Book Review

Real life is still holding me hostage, so here is a book review that you might find of interest.  No, I do not think cells are conscious, intelligent beings.  But I do think cell’s contain a level of sophistication that is greater than even ID apologists seem to recognize – a level of sophistication that  suggests “thinking” has always been in the cards (independent of any convergence arguments from Conway Morris). We’ll get to that, but in the meantime, I also think this reviewer is correct in his core assessment.  Check it out for yourself:

Inside the Cell

More Brain Nudgin’

Real life is keeping me busy, so here’s a golden oldie:

Hormones control growth, metabolism, reproduction and many other important biological processes. In humans, and all other vertebrates, the chemical signals are produced by specialised brain centres such as the hypothalamus and secreted into the blood stream that distributes them around the body. Researchers from the European Molecular Biology Laboratory [EMBL] now reveal that the hypothalamus and its hormones are not purely vertebrate inventions, but have their evolutionary roots in marine, worm-like ancestors. In this week’s issue of the journal Cell they report that hormone-secreting brain centres are much older than expected and likely evolved from multifunctional cells of the last common ancestor of vertebrates, flies and worms.

Do Cells Think?

The non-teleological perspective has long viewed living things as passive participants of the interplay between stochastic events and environmental pressures, where mutations that just happened to exist are favored in an environment that just happened to exist.  For the non-teleologist, the environment is indeed the driving force and organisms are indeed passive and are being shaped by forces that they do not control.

Yet the hypothesis of front-loading allows us to predict that some aspect of evolution is under intrinsic control.  Evidence that living things  play an active role in their adaptation and evolution would be one way to enhance the plausibility of such control, thus becoming evidence of front-loading.

Recently, I just ran across a fascinating review article.

FL Thoughts Out Loud

It’s often the case that I get an idea but don’t have the time to write up a decent blog to spell it out.  As a result, some ideas come and go.  So I will start a new tag entitled, FLE ruminations.  Here I will jot down ideas for possible future reference and/or expansion.  We’ll kick it off with some stuff that is in the process of connecting genomic shape to front-loading:

Now that’s a Horror Movie

He’s After Ya