Self-Org. Theory

Following are some insightful extracts from G.K.Chesterton that still ring true.
Doubts About Darwinism by G. K. Chesterton, 17th July 1920

. . .I am confronted with a very reasonable retort that I know nothing about the subject. . .it would be equally true if I ventured to throw out the suggestion that the Kaiser has suffered a defeat. If I were to insinuate that the armies of the German Empire were ultimately out-manoeuvered and forced to a surrender, it might be said that I was wholly ignorant of the technical strategy of soldiering, . . .But these cases alone will be sufficient to suggest, to anybody of the smallest commonsense, that there is a fallacy somewhere in the simple argument that only an expert in detail can perceive that there is a difficulty, or declare that there is a defeat. Read More ›

More details of DNA repair have been revealed.
See: Human DNA repair process recorded in action (Video)

(PhysOrg.com) — A key phase in the repair process of damaged human DNA has been observed and visually recorded by a team of researchers at the University of California, Davis. The recordings provide new information about the role played by a protein known as Rad51, which is linked to breast cancer, in this complex and critical process.
. . . In 2006, the researchers recorded a portion of the bacterial DNA repair process, a system considerably less complex than its human counterpart.. . .

This filament composed of a fluorescently-labeled DNA molecule and the repair protein Rad51 grows progressively brighter and longer as more and more Rad51 molecules assemble onto the DNA.

Human DNA is under constant assault from harmful agents such as ultraviolet sunlight, tobacco smoke and a myriad of chemicals, both natural and man-made. Because damage can lead to cancer, cell death and mutations, an army of proteins and enzymes are mobilized into action whenever it occurs. Read More ›

ScienceDaily reports on an interesting experiment relevant to OOL scenarios.

With the aid of a straightforward experiment, researchers have provided some clues to one of biology’s most complex questions: how ancient organic molecules came together to form the basis of life.

Specifically, this study demonstrated how ancient RNA joined together to reach a biologically relevant length. Read More ›

The other day I made an offhand comment that the chirality problem was nowhere being solved. Yellow Shark was nice enough to provide a link to new research published in November, 2008. Now I was referring to scenarios which could occur in nature, not in lab conditions, and so I contacted some friends to see what they thought and to see if the research was indeed relevant to OOL scenarios.
Read More ›

Over at Access Research Network, British physicist David Tyler asks, “Did meteorite impacts help to spawn life?”, as per the theory of the week:

The Scientific American report emphasized the tentative nature of the research: meteorites “may have helped spawn life” and “Did heat, pressure and carbon from meteorite impacts create biological precursors?” An astrobiologist is said to fear “that theories of life’s origin may never move beyond the hypothetical”. Astronomer Donald Brownlee found the research interesting but added: “If the body is too large, generated materials are probably destroyed by impact processes.” One of the authors of the paper cautioned that the meteorite-impact theory “is not ready to supplant the vaunted Miller-Urey experiment”.

It is one thing to generate organic molecules but quite another to label them as “precursors of life”. Life does not exist without biological information, and until abiogenesis research takes information seriously, it will continue to explore cul-de-sac avenues.

(Biomolecule formation by oceanic impacts on early Earth Yoshihiro Furukawa, Toshimori Sekine, Masahiro Oba, Takeshi Kakegawa & Hiromoto Nakazawa Nature Geoscience, Published online: 7 December 2008 doi:10.1038/ngeo383)

To me, the fundamental insight of the intelligent design theorists has been to apply insights from information theory to biology. The results were disastrous for Darwinian theory, of course – and especially ruinous for the New Atheism movement (Dawkins, Dennett, Harris, Hitchens, et al.) that depends so heavily on Darwinism as its creation story. Read More ›

David Deamer, a distinguished professor of zoology at UCSC, in an interview with Susan Mazur gives us his theory of information as it relates to genetics. Deamer: I think genetic information more or less came out of nowhere by chance assemblages of short polymers. Am I being unfair in interpreting the phrase “more or less came out of nowhere” as “poof”? I report. You decide.

Experimenters have recently found that genes–whereby they mean particular sequences of DNA–can “find” one another without the intervention of proteins or other factors. It appears to be strictly an effect caused by electrical charges along the DNA strand; the longer the ‘gene’ (that is, sequence length), the greater theapparent ease in ‘finding’ one another. The experimenters feel that this finding is a help for figuring out what happens during homologous recombination.

Here’s part of what they say: The researchers observed the behaviour of fluorescently tagged DNA molecules in a pure solution. They found that DNA molecules with identical patterns of chemical bases were approximately twice as likely to gather together than DNA molecules with different sequences.

Professor Alexei Kornyshev from Imperial College London, one of the study’s authors, explains the significance of the team’s results: ‘Seeing these identical DNA molecules seeking each other out in a crowd, without any external help, is very exciting indeed. This could provide a driving force for similar genes to begin the complex process of recombination without the help of proteins or other biological factors. . . .’

The article from ScienceDaily is here.

I have an OOL question: This study strongly suggests that similar DNA sequences have a preferential attraction for one another. And the longer the similar sequence, the greater the attraction. If that is the case, then, if a particular ‘gene’ began to ‘replicate’, wouldn’t the replicated ‘genes’ congeal together?

Read More ›

“The energy in the ATP molecule powers all biological processes. Thus, the synthesis of ATP is essential for life.” Sir. John Walker, The ATP Synthase Group, MRC Dunn Human Nutrition Unit ATP Synthase has been frequently discussed at Uncommon Descent including Intelligent Engineering or Natural Selection 15 July 2006 “Our job is to follow the money, track and document the flow of funds, and thereby help prove the underlying criminal activity.” Eileen Mayer, Chief, Internal Revenue Service, Criminal Investigation Division I propose that one of the most important concepts in Intelligent Design vs evolution is to “follow the energy trail“. This will be especially important in examining the origin of life. Energy processes are central to design of dynamic systems. Read More ›

There is a new paper on Irreducible Complexity by renowned mathematician Gregory Chaitin: The Halting Probability Omega: Irreducible Complexity in Pure Mathematics Milan Journal of Mathematics, Vol. 75, 2007.

Ω is an extreme case of total lawlessness; in effect, it shows that God plays dice in pure mathematics.

On the surface Chaitin’s notion of Irreducible Complexity (IC) in math may seem totally irrelevant to Irreducible Complexity (IC) in ID literature. But let me argue that notion of IC in math relates to IC in physics which may point to some IC in biology…

First, of consider this article archived at Access Research Network (ARN) by George Johnson in the NY Times on IC in physics:

Challenging Particle Physics as Path to Truth

Many complex systems — the very ones the solid-staters study — appear to be irreducible.

The concept of “irreducible complexity” has been used by Alan Turing, Michael Behe, and perhaps now by physicists. Behe’s sense of irreducible is not too far from the sense of irreducible in the context of this physics. If biological systems take advantage of irreducible phenomena in physics (for example, what if we discover the brain uses irreducible physical phenomena ) we will have a strong proof by contradiction that there are no Darwinian pathways for biolgoical systems to incorporate that phenomena.

The possibility of IC in physics may be tied to IC in math and this may have relevance to IC in biology.
Read More ›

Accepted July 2006

Physics of Life Reviews

[Update: thanks to Todd for a link to the full paper:]

Self-organization vs. self-ordering events in life-origin models

[Update: IDers Charles Thaxton, Walter Bradley, and R.L. Olsen were cited as well!! They wrote the book in 1984 which is considered the beginning of the modern ID movement. Also, critical remarks were made indirectly of Dawkins.]

Self-organization vs. self-ordering events in life-origin models

by David Abel and Jack Trevors

Self-ordering phenomena should not be confused with self-organization. Self-ordering events occur spontaneously according to natural “law propensities and are purely physicodynamic. Crystallization and the spontaneously forming dissipative structures of Prigogine are examples of self-ordering. Self-ordering phenomena involve no decision nodes, no dynamically-inert configurable switches, no logic gates, no steering toward algorithmic success or “computational halting”.
Read More ›

When it comes to discussing open systems aren’t we getting a little ahead of ourselves here? There are still some very basic problems to solve before getting into hand-waving over the evolution of computers and human minds.

http://www.pnas.org/cgi/content/abstract/0605863103v1

Solutions with as little as 1% enantiomeric excess (ee) of D- or L-phenylalanine are amplified to 90% ee (a 95/5 ratio) by two successive evaporations to precipitate the racemate [mixture]. Such a process on the prebiotic earth could lead to a mechanism by which meteoritic chiral {alpha}-alkyl amino acids could form solutions with high ee values that were needed for the beginning of biology.

Read More ›

http://www.ffame.org/sbenner/cochembiol8.672-689.pdf

The opening discussion:

To decide whether life has a common chemical plan, we must decide what life is. A panel assembled by NASA in 1994 was one of many groups to ponder this question. The panel defined life as a ‘chemical system capable of Darwinian evolution’ [16]. This definition, which follows an earlier definition by Sagan [17], will be used here. Read More ›

Go here to read the article.

http://www.fields.utoronto.ca/audio/05-06/public_lectures/kadanoff