Evolution of life

The last time I thought much about abiogenesis, I had a hard time finding good (recent) review articles to summarize things, and relied on the NYT. The past few years have provided many breakthroughs, summarized by Hazen and others. This month's Nature Chemistry has an entire section devoted to the subject. It calls the Grand Challenge of chemistry explaining the emergence of life, similar to a Theory of Everything in physics.

Quantum weirdness and Bell's theorem

Although I was nearly certain I wrote a post about Bell's Theorem in the summer of 2006, it appears I started a post on it then modified it to talk about Hume and creationism. At some point the post got so long and complex I cut out quantum stuff entirely.

At any rate, Wired has an article explaining that a recently-published study has shown quantum entanglement, which is the heart of Bell's Theorem, on a scale never before seen.

In the new study, researchers used a microwave pulse to attempt to entangle the electrical currents of the two superconductors. If the currents were quantum-mechanically linked, one current would flow clockwise at the time of measurement (assigned a value of 0), while the other would flow counterclockwise when measured (assigned a value of 1), Martinis says. On the other hand, the currents’ directions would be completely independent of each other if everyday, classical physics were at work.

After attempting to entangle the superconducting circuits, Martinis and his team measured the directions of the currents 34.1 million times. When one current flowed clockwise (measured as a 0), the team found, the other flowed counterclockwise (measured as a 1) with very high probability. So the two were linked in a way that only quantum mechanics could explain.

Refs:

1. "Is the moon there when nobody looks? Reality and the quantum theory" (PDF, 267k), N. David Mermin, Physics Today (April 1985)
2. Bell's Theorem with Easy Math, by David R. Schneider
3. Quantum Entanglement and Information, Stanford Encyclopedia of Philosophy

New NAS Report on Astrobiology & Abiogenesis

**Update: Carl Zimmer remarks on this in the NYT
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A new National Academies of Sciences publication, The Limits of Organic Life in Planetary Systems, can be read for free in HTML at the site, or downloaded as a .pdf after login. The executive summary may be downloaded here as a .pdf (and the entire book here as a .pdf (1.1MB), if you're too lazy to login and do it yourself). I'm reposting some earlier material on abiogenesis, evolution and the origin of the genetic code below, with updated links that were previously broken.

Repost:

I have compiled a very useful list of papers (continually revised), covering abiogenesis, the evolution of genetic information, the origin of the genetic code, and human evolution. I will list some of those papers below.

For more on the evolution of information in the genome:

1. Natural selection as the process of accumulating genetic information in adaptive evolution, M. Kimura, Genetic Research Cambridge, 2 (1961) 127-140
2. Rate of Information Acquisition by a Species subjected to Natural Selection, D.J.C. MacKay, open-source @ http://arxiv.org/, (1999)
3. Evolution of biological information, T.D. Schneider, Nucleic Acids Research, (2000), 2794-2799
4. The fitness value of information, C.T. Bergstrom and M. Lachmann, open-source @ http://arxiv.org/, (2006)
5. Review of W. Dembski’s No Free Lunch, J. Shallit, BioSystems, 66 (2002) 93-99
6. The Evolution and Understanding of Hierarchical Complexity in Biology from an Algebraic Perspective, C.L. Nehaniv and J.L. Rhodes, Artificial Life, 6 (2000) 45–67
7. On the Increase in Complexity in Evolution I, P.T. Saunders and M.W. Ho, Journal of Theoretical Biology, 63 (1976) 375-384
8. On the Increase in Complexity in Evolution II: The Relativity of Complexity and the Principle of Minimum Increase, P.T. Saunders and M.W. Ho, Journal of Theoretical Biology, 90 (1981) 515-530

In addition to these papers, I wanted to highlight six other recent reviews that give a great overview of the present scientific thinking towards the origin of the genetic code:

1. "Selection, history and chemistry: the three faces of the genetic code.", Trends in Biochemical Sciences, Volume 24, Issue 6, 1 June 1999, Pages 241-247 (full-text .pdf)
   
2. "Genetic code: Lucky chance or fundamental law of nature?", Physics of Life Reviews, Volume 1, Issue 3, Dec 2004, Pages 202-229 (full-text .pdf) [low-quality pub, but expansive overview of the subject]
   
3. "Stepwise Evolution of Nonliving to Living Chemical Systems.", Origins of Life and Evolution of the Biosphere, Volume 34, Issue 4, Aug 2004, Pages 371–389 (full-text .pdf)
4. "The Origin of Cellular Life.", Bioessays, Volume 22, Issue 12, Dec 2004, Pages 1160-1170 (full-text .pdf)
5. "The Origin of the Genetic Code: Theories and Their Relationships, A Review.", Biosystems, Volume 80, Issue 2, May 2005, Pages 175-184 (full-text .pdf)
6. "The Origin and Evolution of the Genetic Code: Statistical and Experimental Investigations.", Robin D. Knight, Ph.D. Dissertation, June 2001.
   

And three more about evolution and complexity:

1. Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons, Human Mutation, 28(2):99-130, Oct 2006, Download PDF
2. The origin of new genes: Glimpses from the young and old, Nature Reviews Genetics, 4(11): 865-875 Nov 2003, Download PDF
3. Evolution of biological complexity, PNAS, 97(9):4463-4468, April 2000, Download PDF

No one pretends that all questions are sufficiently answered within the complex topics surrounding abiogenesis and the evolution of life. But to pretend that there are no answers is to engage in self-deception.
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Technorati tags: Abiogenesis, Intelligent Design, Evolution, Creationism

Nerd Stuff

Biggest. Periodic table. Ever:

In more nerdy news, ever notice how sleepy you get after eating a large meal? It's because of the activity of orexin/hypocretin, a new study indicates. Turns out the hypothalamus, long indicated as a source of the neuronal misfortune that leads to narcolepsy, plays a role in monitoring our blood glucose levels. When the glucose level spikes, like after you eat, the brain's "get food" activities are turned off, and "preserve energy" kicks in -- leading to lethargy and nap-time.

Here we demonstrate that their inhibition by glucose is mediated by ion channels not previously implicated in central or peripheral glucose sensing: tandem-pore K⁺ (K_2P) channels. Importantly, we show that this electrical mechanism is sufficiently sensitive to encode variations in glucose levels reflecting those occurring physiologically between normal meals. Moreover, we provide evidence that glucose acts at an extracellular site on orexin neurons, and this information is transmitted to the channels by an intracellular intermediary that is not ATP, Ca²⁺, or glucose itself. These results reveal an unexpected energy-sensing pathway in neurons that regulate states of consciousness and energy balance. (Abstract)

From ACS:

[the researchers] found that glucose’s effect on the firing rate of the neurons was well matched to the concentrations of blood glucose that typically oscillate between meals.

This provides the strong suggestion of a link between glucose levels in the blood and a corresponding behavioral output: the orexin/hypocretin neurons cannot only sense small changes in glucose levels, but they can respond to those levels by adjusting their firing rate to those levels. This shows that the neurons are capable of being involved in moment-to-moment readjustments of alertness depending on glucose as a guide. Additional work will be needed to confirm that what can be made to occur in isolated cells really does play a physiological role in the whole animal.

As for the precise steps involved, the researchers were able to show that glucose specifically affected a particular ion channel known as the tandem-pore K⁺ channel in the neuronal cell membrane. This effect was only initiated if glucose was introduced in the external medium. If glucose was added to the interior of the cell, no effects were seen. Glucose, therefore, does not act as an internal messenger. No effects were seen if ATP or Ca²⁺ ions were added either, leaving the intracellular mechanism a mystery yet to be resolved.

The article can be found in Neuron 2006, 50, 711–722
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Technorati tags: Science

Abby and Her Five Senses

Recently I've had abiogenesis on my mind. After reading a PT post on the topic, I started thinking about how abiogenesis is so much like cosmology. I wrote recently about my attitude towards the unknown--that I view rational skepticism as the best approach to both (ab and cos). Some people give up with "goddidit" while others believe the answers are already in hand.

Why is it that so many fundies see methodological naturalism as "faith"? They say things like, "i have faith god made everything, you have faith things made themselves," (which is of course a straw man, considering the 1st Law and cosmology and etc.)...without realizing [one of] the huge difference[s]--that while evidence has shown time and again that observable phenomena are the result of natural law, no evidence has ever shown observable phenomena to be the result of "supernatural" activity. In fact, it is just this line of reasoning that leads me to conclude that life on earth is the result of chemistry and physics. Obviously, god can still fit in the picture as the maker/guider of chemistry and physics, but that doesn't appeal to most theists. And usually they conclude that naturalistic philosophy leads one to dismiss "evidence" that purportedly supports a supernatural cause, yet they acknowledge that rational naturalistic scenarios always fit the bill, and that Occam's razor slices god right out of the picture.

I recently compiled some really good articles on my website in list fashion regarding abiogenesis. I specifically focused on publications reviewing homochirality and other frequently-touted “problems” for abiogenesis (mostly Bonner pubs). For those of you without the access or time to look them up, this could prove a valuable resource. Also, in one of the listed pubs, Lindahl, from TA&M, put together a very good review (2004) that takes us from organic chemistry to extant metabolism via “Quasi-steady state systems”…worth your read. Keep in mind that copyright laws apply to these full-text PDFs.
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Technorati tags: abiogenesis, Faith, God, Religion, Philosophy