Saturday Musings - Building Blocks, Actin and Acting on my faith

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A short commentary about this blog follows today's articles concerning life at the microscopic level

Origin of life: instability of building blocks

by Jonathan Sarfati

Evolutionary propaganda often understates the difficulty of a naturalistic origin of life. Production of traces of ‘building blocks’ is commonly equated with proving that they could have built up the required complicated molecules under natural conditions. The instability of ‘building blocks’ in non-biotic environments is usually glossed over.

The RNA/DNA base cytosine is not produced in spark discharge experiments. The proposed prebiotic productions are chemically unrealistic because the alleged precursors are unlikely to be concentrated enough, and they would undergo side reactions with other organic compounds, or hydrolyse. Cytosine itself is too unstable to accumulate over alleged geological ‘deep time’, as its half life for deamination is 340 years at 25°C.

Populist RNA-world propaganda

A pro-evolution booklet called Science and Creationism, recently released on the Internet by the National Academy of Sciences (NAS),1 summarized the origin of life section as follows:
‘For those who are studying the origin of life, the question is no longer whether life could have originated by chemical processes involving nonbiological components. The question instead has become which of many pathways might have been followed to produce the first cells.’ 2
No one disputes the existence of living organisms on earth, and that cells indeed are capable of using simple building blocks to generate the required complex biochemicals at the necessary time, location and concentration. The question is whether the massive co-ordination of the metabolic processes which perform such feats could have arisen without intelligent guidance and driven by only statistical and thermodynamic constraints.

The NAS book glosses over the enormous chemical and informational hurdles which must be jumped to go from non-living matter to even the simplest living cells (see also Q&A: Origin of Life).3,4,5 It’s not too surprising, considering the heavy atheistic bias of the NAS, which was documented in the journal Nature,6 and which was probably partly responsible for their demonstrable scientific unreliability in the area of origins.7 It is even less excusable to ignore the difficulties documented in their own journal—Proceedings of the National Academy of Sciences (PNAS), USA, as will be shown here.

Production of ‘building blocks of life’

Science and Creationism argued:
‘Experiments conducted under conditions intended to resemble those present on primitive Earth have resulted in the production of some of the chemical components of proteins, DNA, and RNA. Some of these molecules also have been detected in meteorites from outer space and in interstellar space by astronomers using radiotelescopes. Scientists have concluded that the “building blocks of life” could have been available early in Earth’s history.’2
Even if we granted that the ‘building blocks’ were available, it does not follow that they could actually build anything. For example, under plausible prebiotic conditions, the tendency is for biological macromolecules to break apart into the ‘building blocks’, not the other way round.8 Also, the ‘building blocks’ are likely to react in the wrong ways with other ‘building blocks’, for example, sugars and other carbonyl (>C=O) compounds react destructively with amino acids and other amino (–NH2) compounds, to form imines (>C=N), a common cause of browning in foods.9

Furthermore, some of the building blocks are very unstable. A good example is ribose, which is obviously essential for RNA, and hence for the RNA-world hypothesis of the origin of life.10 A team including the famous evolutionary origin-of-life pioneer Stanley Miller, in PNAS, found that the half life (t½) of ribose is only 44 years at pH 7.0 (neutral) and 0°C. It’s even worse at high temperatures—73 minutes at pH 7.0 and 100°C.11 This is a major hurdle for hydrothermal theories of the origin of life. Miller, in another PNAS paper, has also pointed out that the RNA bases are destroyed very quickly in water at 100°C—adenine and guanine have half lives of about a year, uracil about 12 years, and cytosine only 19 days.12
 
Most researchers avoid such hurdles with the following methodology: find a trace of compound X in a spark discharge experiment, claim ‘see, X can be produced under realistic primitive-earth conditions’. Then they obtain pure, homochiral, concentrated X from an industrial synthetic chemicals company, react it to form traces of the more complex compound Y. Typically, the process is repeated to form traces of Z from purified Y, and so on.13 In short, the evolutionists’ simulations have an unacceptable level of intelligent interference.14
Much of the populist evolutionary propaganda resembles the following hypothetical theory for the origin of a car:
‘Design is an unscientific explanation, so we must find a naturalistic explanation instead. Now, experiments have shown that one of the important building blocks of the car—iron—can be produced by heating naturally occurring minerals like hematite to temperatures which are found in some locations on earth. What’s more, iron can be shown to form thin sheets under pressures which are known to occur in certain geological formations ….’
If this seems far-fetched, then note that even the simplest self-reproducing cell, which has 482 genes,15 has a vastly higher information content than a car, yet self-reproduction is a pre-requisite for neo-Darwinian evolution.

Essential building block missing—cytosine

The evolutionary biochemist, Robert Shapiro, published a detailed study of the ‘prebiotic’ synthesis of cytosine in the Proceedings of the NAS.16 Previous studies of his had noted that neither adenine17 nor ribose18 were plausible prebiotic components of any self-replicating molecule, but the problems with cytosine are even worse. Together, these studies raise serious doubts about whether a prebiotic replicator with any Watson-Crick base pairing could have arisen abiotically.

Shapiro noted that not the slightest trace of cytosine has been produced in gas discharge experiments, and nor has it been found in meteorites. Thus, he notes, either it is extremely hard to synthesise, or it breaks down before detection. So ‘prebiotic’ productions of cytosine have always been indirect, and involve the methodology alluded to above. That is, cyanoacetylene (HC≡CC≡N) and cyanoacetaldehyde

(H3CCOC≡N) have been found in some spark discharge experiments. Organic chemists have obtained pure and fairly strong solutions of each, and reacted each of them with solutions of other compounds which are allegedly likely to be found on a ‘primitive’ earth. Some cytosine is produced. This then apparently justifies experiments trying to link up pure and dry cytosine and ribose to form the nucleoside cytidine. However, these experiments have been unsuccessful (although analogous experiments with purines have produced 2% yields of nucleosides),19 despite a high level of investigator interference.

Unavailability of cytosine precursors

Shapiro also critiqued some of the ‘prebiotic’ cytosine productions. He pointed out that both cyanoacetylene and cyanoacetaldehyde are produced in spark discharge experiments with an unlikely methane/nitrogen (CH4/N2) mixture. The classical Miller experiment used ammonia (NH3), but NH3, H2O and hydrogen sulfide (H2S) greatly hindered cyanoacetylene and cyanoacetaldehyde formation. However, most evolutionists now believe that the primitive atmosphere was ‘probably dominated by CO2 and N2.’20

Furthermore, cyanoacetylene and cyanoacetaldehyde would undergo side reactions with other nucleophiles rather than produce cytosine. For example, cyanoacetylene and cyanoacetaldehyde both react with the amino group, which would destroy any prebiotic amino acids. And there is one destructive molecule which is unavoidably present: water. Cyanoacetylene readily hydrolyzes to form cyanoacetaldehyde (t½ = 11 days at pH 9, 30°C),20 although one should not count on this as a reliable source of cyanoacetaldehyde because cyanoacetylene would more likely be destroyed by other reactions.20 And cyanoacetaldehyde, while more stable than cyanoacetylene, is still quite quickly hydrolyzed (t½ = 31 years at pH 9, 30°C).21

The implausible production scenarios and likely rapid destruction means it is unrealistic to assume that the concentration of cyanoacetylene and cyanoacetaldehyde could remotely approach that needed to produce cytosine.

Instability of cytosine

As pointed out above, cytosine is deaminated/hydrolyzed (to uracil) far too rapidly for any ‘hot’ origin-of-life scenario. But it is still very unstable at moderate temperatures—t½ = 340 years at 25°C. This shows that a cold earth origin-of-life scenario would merely alleviate, but not overcome, the decomposition problem. And a low temperature also retards synthetic reactions as well as destructive ones.

On single-stranded DNA in solution, t½ of an individual cytosine residue = 200 years at 37°C, while the double helix structure provides good protection—t½ = 30,000 years.22 Such C→U mutations would be a great genetic hazard, but cells have an ingenious repair system involving a number of enzymes. It first detects the mutant U (now mismatched with G) and removes it from the DNA strand, opens the strand, inserts the correct C, and closes the strand.22 It seems that such a repair system would be necessary from the beginning, because a hypothetical primitive cell lacking this would mutate so badly that error catastrophe would result. And the far greater instability of cytosine on single-stranded nucleic acid is yet another problem that proponents of the RNA-world must account for.

Also, cytosine is readily decomposed under solar UV radiation, which requires that prebiotic synthesis should be carried out in the dark.21

An efficient prebiotic synthesis of cytosine?

This was claimed by Robertson and Miller.23 They rightly disagreed with a previous suggested synthesis of cytosine from cyanoacetylene and cyanate (OCN-) because cyanate is rapidly hydrolyzed to CO2 and NH3. Instead, they heated 10-3 M cyanoacetaldehyde with various concentrations of urea ((NH2)2CO) in a sealed ampoule at 100 oC for five hours with 30-50% yields of cytosine. Urea is produced in spark discharge experiments with N2, CO and H2O.

However, Shapiro criticised this experiment on the grounds of the unavailability of cyanoacetaldehyde and instability of cytosine, as above. Robertson and Miller avoided the latter problem by stopping the reaction after five hours. But in a real prebiotic world, such a reaction would most likely continue with hydrolysis of cytosine.

Shapiro also shows that urea is too unstable to reach the concentrations required (>0.1 M). Urea exists in equilibrium with small amounts of its isomer, ammonium cyanate, and since cyanate is hydrolysed readily, more urea must convert to maintain the equilibrium ratio (K = 1.04 x 10-4 at 60°C).21 Robertson and Miller’s sealed tube thus provided a further example of unacceptable investigator interference, because this prevented escape of NH3, thus unrealistically retarding cyanate and urea decomposition. In an open system, ‘half of the urea was destroyed after 5 hr at 90 oC and pH 7’,21 and t½ is estimated at 25 years at 25°C.21

The usual cross-reaction problem would intervene in the real world. For example, urea can react with glycine to form N-carbamoyl glycine,21 which would remove both urea and amino acids from a primordial soup.
Also, the primordial soup would be far too dilute, so Robertson and Miller propose that seawater was concentrated by evaporation in lagoons. But this would require isolation of the lagoon from fresh seawater which would dilute the lagoon, evaporation to about 10–5 of its original volume, then cytosine synthesis. However, such conditions are geologically ‘rare or non-existent’ today.24 Concentrating mechanisms would also concentrate destructive chemicals.

The conditions required for cytosine production are incompatible with those of purine production. Therefore this scenario must also include a well-timed rupture of the lagoon, releasing the contents into the sea, so both pyrimidines and purines can be incorporated into a replicator.

Shapiro’s materialistic faith

Shapiro concluded:
‘the evidence that is available at the present time does not support the idea that RNA, or an alternative replicator that uses the current set of RNA bases, was present at the start of life.’ 25
But unwilling to abandon evolution, he suggests two alternative theories:

1. Cairns-Smith’s clay mineral idea,13 which seems to be driven more by dissatisfaction with other theories than evidence for his own.
‘Cairns-Smith cheerfully admits the failings of his pet hypothesis: no-one has been able to coax clay into something resembling evolution in the laboratory; nor has anyone found anything resembling a clay-based organism in nature.’26
[Update: recent research shows more difficulties with this idea: Darwin’s warm pond idea is tested, 13 February 2006:
‘Professor Deamer said that amino acids and DNA, the “building blocks” for life, and phosphate, another essential ingredient, clung to the surfaces of clay particles in the volcanic pools.
‘“The reason this is significant is that it has been proposed that clay promotes interesting chemical reactions relating to the origin of life,” he explained.
‘“However,” he added, “in our experiments, the organic compounds became so strongly held to the clay particles that they could not undergo any further chemical reactions.”’]
2. Life began as a cyclic chemical reaction, e.g. Günter Wächtershäuser’s theory that life began on the surface of pyrite, which Stanley Miller calls ‘paper chemistry’.27
‘Wächtershäuser himself admits that his theory is for the most part “pure speculation”.’28,29
Shapiro’s dogmatism is illustrated in his interesting popular-level book Origins: A Skeptic’s Guide to the Creation of Life in the Universe, where he effectively critiques many origin-of-life scenarios. But he says, in a striking admission that no amount of evidence would upset his faith:
‘some future day may yet arrive when all reasonable chemical experiments run to discover a probable origin of life have failed unequivocally. Further, new geological evidence may yet indicate a sudden appearance of life on the earth. Finally, we may have explored the universe and found no trace of life, or processes leading to life, elsewhere. Some scientists might choose to turn to religion for an answer. Others, however, myself included, would attempt to sort out the surviving less probable scientific explanations in the hope of selecting one that was still more likely than the remainder.’30

Conclusion

  • No plausible prebiotic synthesis of cytosine yet exists.
  • Vital ‘building blocks’ including cytosine and ribose are too unstable to have existed on a hypothetical prebiotic earth for long.
  • Even if cytosine and ribose could have existed, there is no known prebiotic way to combine them to form the nucleoside cytidine, even if we granted unacceptably high levels of investigator interference.
  • Building blocks would be too dilute to actually build anything, and would be subject to cross-reactions.
  • Even if the building blocks could have formed polymers, the polymers would readily hydrolyse.
  • There is no tendency to form the high-information polymers required for life as opposed to random ones.

Further reading

References

  1. Science and Creationism: A View from the National Academy of Sciences, Second Edition, , 28 July 1999. Return to text.
  2. , 28 July 1999. Return to text.
  3. Aw, S.E., The origin of life: A critique of current scientific models , Journal of Creation 10(3):300–314, 1996. Return to text.
  4. Thaxton, C.B., Bradley, W.L. and Olsen, R.L., The Mystery of Life’s Origin, Philosophical Library Inc., New York, 1984. Return to text.
  5. Bird, W.R., The Origin of Species: Revisited, Thomas Nelson, Inc., Nashville, Tennessee, Vol. I Part III, 1991. Return to text.
  6. Larson, E.J. and Witham, L., Leading scientists still reject God, Nature 394(6691):313, 1998. The sole criterion for being classified as a ‘leading’ or ‘greater’ scientist was membership of the NAS. [See also National Academy of Science is godless to the core — survey — Ed.] Return to text.
  7. For example, the NAS teacher’s guidebook Teaching about Evolution and the Nature of Science, National Academy Press, Washington DC, 1998. This has been shown to be severely flawed by Sarfati, J.D., Refuting Evolution, Master Books, Green Forest, AR, USA, 1999. Return to text.
  8. Sarfati, J.D., Origin of life: the polymerization problem, Journal of Creation 12(3):281–284, 1998. Return to text.
  9. Thaxton et al., Ref. 4, p. 51. Return to text.
  10. See Mills, G.C. and Kenyon, D.H., The RNA world: A critique, Origins and Design 17(1):9–16, 1996. Return to text.
  11. Larralde, R., Robertson, M.P. and Miller, S.L., Rates of decomposition of ribose and other sugars: Implications for chemical evolution, Proc. Natl. Acad. Sci. USA 92:8158–8160, 1995. Return to text.
  12. Levy, M and Miller, S.L., The stability of the RNA bases: Implications for the origin of life, Proc. Natl. Acad. Sci. USA 95(14):7933–38, 1998. Return to text.
  13. The evolutionist A.G. Cairns-Smith has raised the same objections against the typical ‘origin of life’ simulation experiments in his book Genetic Takeover and the Mineral Origins of Life, Cambridge University Press, New York, 1982—see extract. Return to text.
  14. Thaxton et al., Ref. 4, ch. 6. Return to text.
  15. Fraser, C.M., et al., The minimal gene complement of Mycoplasma genitalium, Science 270(5235):397–403, 1995; Perspective by Goffeau, A., Life with 482 genes, same issue, pp. 445–446. Return to text.
  16. Shapiro, R., Prebiotic cytosine synthesis: A critical analysis and implications for the origin of life, Proc. Natl. Acad. Sci. USA 96(8):4396–4401, 1999. Return to text.
  17. Shapiro, R., The prebiotic role of adenine: A critical analysis, Origins of Life and Evolution of the Biosphere 25:83–98, 1995. Return to text.
  18. Shapiro, R., Prebiotic ribose synthesis: A critical analysis, Origins of Life and Evolution of the Biosphere 18:71–85, 1988. Return to text.
  19. Orgel, L.E. and Lohrmann, R., Prebiotic chemistry and nucleic acid replication, Accounts of Chemical Research 7:368–377, 1974; cited in Cairns-Smith, Ref. 13, pp. 56–57. Return to text.
  20. Shapiro, Ref. 16, p. 4397. Return to text.
  21. Shapiro, Ref. 16, p. 4398. Return to text.
  22. Lindahl, T., Instability and decay of the primary structure of DNA, Nature 362(6422):709–715, 1993. Return to text.
  23. Robertson, M.P. and Miller, S.L., An efficient prebiotic synthesis of cytosine and uracil, Nature 375(6534):772–774; correction 377(6546):257. Return to text.
  24. Shapiro, Ref. 16, p. 4399. Return to text.
  25. Shapiro, Ref. 16, p. 4400. Return to text.
  26. Horgan, J., In the beginning, Scientific American 264(2):100–109, 1991; quote on p. 108. Return to text.
  27. Horgan, Ref. 26; Miller cited on p. 102. Return to text.
  28. Horgan, Ref. 26; Wächtershäuser cited on p. 106. Return to text.
  29. Sarfati, J.D., Ref. 8, extensively critiques one of Wächtershäuser’s latest experiments that supposedly supports his theory. Return to text.
  30. Shapiro, R., Origins: A Skeptic’s Guide to the Creation of Life in the Universe, Penguin, London, p. 130, 1986,1988. Shapiro then wishfully continues: ‘We are far from that state now.’Return to text.




Nano-scale aligning tool used in the assembly of actin filaments

by Giovanie Adams
The structure of filamentous actin. A. A 14-subunit filamentous actin as an isosurface, viewed along its longitudinal axis. B. The structure of 3-subunits of filamentous actin as an isosurface, viewed from the pointed end. The solid lines pass through the center of each actin monomer, showing the position of each actin monomer. The dashed paths travel from the pointed end to the barbed end and show the position of the next monomer with respect to the previous monomer.
Figure 1. The structure of filamentous actin. A. A 14-subunit filamentous actin as an isosurface, viewed along its longitudinal axis. B. The structure of 3-subunits of filamentous actin as an isosurface, viewed from the pointed end. The solid lines pass through the center of each actin monomer, showing the position of each actin monomer. The dashed paths travel from the pointed end to the barbed end and show the position of the next monomer with respect to the previous monomer.

Eukaryotic cells have systems for maintaining their shape and all their movement, and for the transport of molecules within them. Intra-cellular networks of fibers assemble from actin proteins, and are an important part of these systems. This network of actin filaments maintains cell shape by forming a support structure—an important component for cell motility—and provides the paths for the transport of molecules within the cell. The intra-cellular traffic of molecules along these paths is also necessary for cell fission (the division of one parent cell into two daughter cells). Actin filaments are also a major component of the muscle fibers of animals and are essential for the contractile apparatus of muscles.1
 
Actin filaments are made up of two long, twisted chains consisting chiefly of tens to thousands of monomeric or globular actin proteins. The assembly and disassembly of actin filaments is controlled at each step by sets of actin-binding proteins.1 The initial assembly of a short actin filament is a rate-limiting step in filament assembly,2 and a subset of actin-binding proteins has been designed to overcome the relative instability of these short filaments.3 This process of assembling short filaments of two or three subunits from monomeric actin is called actin nucleation.

This complicated mechanism, of actin nucleation and preparation of the nucleated product for elongation by spire, suggests the work of an intelligent designer who engineered it in an incredibly intricate manner.

The spire family of proteins is a family of actin-binding proteins that nucleates a pool of actin monomers and prepares the product of nucleation for elongation.4 Spire overcomes the relative instability of short filaments made up of actin dimers and trimers, by helping to overcome the kinetic barrier to nucleation.2 Spire also attaches the newly synthesized actin filament to a membrane and aligns the filament to a nano-scale machine, a dimer of formin proteins.

The formin dimer then proceeds to extend the filament by adding actin monomers, assembling long double-helical-twisted actin filaments. This complicated mechanism, of actin nucleation and preparation of the nucleated product for elongation by spire, suggests the work of an intelligent designer who engineered it in an incredibly intricate manner.

Structure of filamentous actin and spire proteins

Actin filaments appear in electron micrograph images as thin, dense lines of approximately 7 nm in diameter.1 The filaments are made up of two chains of monomeric actin with each actin monomer rotated 166.15º from the other. This produces two helical chains that lie almost back to back and wind into a right-handed, double-helical structure with a very long pitch with respect to its diameter (figure 1).

Filamentous actin is polar and, therefore, the two ends of the filament are different. Because of this polarity, the filaments often fit into other cellular structures in only one orientation, in a similar manner to how many of the parts of man-made structures are assembled. Growth, the addition of monomeric actin to the filament, occurs predominantly in one direction; the plus direction. This end of the filament (where the majority of growth occurs) is known as the barbed end and the other end is called the pointed end (figure 1).

The domain organization of spire family of proteins.
Figure 2. The domain organization of spire family of proteins. The kinase non-catalytic C-lobe domain (KIND), the four WASP-homology domains 2 (WH2), the Spir-box (S-box) and the FYVE zinc finger domain of spire.

Comparison of the spire family of proteins to other proteins has identified seven domains (figure 2). At the carboxyl-end of the protein is a domain called the FYVE zinc finger,5 and adjacent to this is a domain called the Spir-box (S-box).6 A cluster of four, evenly spaced domains, called the Wiskott–Aldrich syndrome protein homology domain 2 (WH2), are located in the central region of the protein,7 and a domain called the kinase non-catalytic C-lobe domain (KIND) is at the amino-end.8 The FYVE zinc finger domain may bind to the membrane, thus, FYVE may anchor the newly assembled actin filament to a membrane.5 The S-box is a potential binding site for Rab GTPase.9 The four WH2 are connected by linker regions; they bind monomeric actin and are sufficient to nucleate actin4. Finally, KIND has a high affinity for the FH2 domain of formin.10

Nucleation of monomeric actin

Proposed mechanism for actin filament nucleation by spire.
Figure 3. Proposed mechanism for actin filament nucleation by spire. From left to right the schematic shows actin nucleation by spire. Scene one shows the binding of an actin monomer to the carboxyl-end WH2 domain of spire and the binding of the FH2 domains of a formin dimer to KIND of spire. The FYVE and S-box domains of spire and the other domains of formin are not shown in these scenes. Scene two shows a second actin monomer binding to the second most carboxyl-end WH2 domain. Scene three shows the stabilization of two actin monomers by the two most carboxyl-end WH2 domains and the intervening linker region. Scene four shows the stabilization of four actin monomers into a helical structure by the WH2 domains and the intervening linker regions. Scene five shows the formation of an actin filament by four actin monomers binding to the single helical structure formed by four actin monomers. Scene six shows dissociation of KIND from the FH2 dimer and rapid polymerization of the actin filament by the FH2 dimer. All molecules are represented as isosurfaces.

It remains to be established exactly how a pool monomeric actin is nucleated by spire, but it may occur via the following steps (figure 3).4,10 The process is initiated by KIND of spire binding to the FH2 domains of a formin dimer; this step inhibits formin but enhances spire activity. Next, each WH2 domain of spire binds to an actin monomer. The two WH2 domains closest to the carboxyl-end and the intervening linker region align and stabilize the bound actin monomers. Actin monomers bound to other WH2 domains are then aligned to the initial structure by the action of the other linker regions. This results in the formation of a single-stranded helical polymer of four actin monomers. Following these steps, a second helical polymer consisting of another four actin monomers binds on the other side of the helix by self-polymerization. Once an actin filament of about eight monomers has formed, KIND of spire dissociates from the FH2 domains of the formin dimer. This exposes the FH2 domains to catalyze the incorporation of actin monomers into the filament resulting in rapid polymerization of the barbed end of the actin filament by the formin dimer.

Spire is likely to be an elaborate nano-scale alignment tool with some machine-like functions. This would make spire far superior to modern tools engineered by humans.
Actin filaments are highly dynamic structures that rapidly assemble and disassemble.2 To prevent disassembly of the newly synthesized filament from the pointed end, spire caps the pointed end of the filament.4
 
Although spire performs machine-like functions during actin nucleation, the main role of spire is probably to act as a nano-scale alignment tool. A broad definition of a tool is “an entity used as an interface between two or more entities”, that makes it easier for one entity to act upon the other. In the case of the function of spire in actin nucleation, spire probably acts as an interface between the actin monomers and formin dimer entities, facilitating the alignment of these entities. That is, the four WH2 domains of spire align four actin monomers, and the KIND of spire probably aligns the four monomers to the FH2 domains of a formin dimer. Therefore, spire helps to overcome the kinetic barrier to actin nucleation, stabilizing actin dimers and trimers.2

Conclusions

Actin filament nucleation by spire is yet another example of the complexity of the automated systems needed to assemble the nano-scale structures and machines found within living cells. Spire is likely to be an elaborate nano-scale alignment tool with some machine-like functions. This would make spire far superior to modern tools engineered by humans. All this attests to the work of an intelligent designer who engineered these structures and machines in an incredible intricate manner.

Related articles

Further reading

References

  1. Wolfe, F.L., Microfilaments and microfilament-based cell motility; in: Molecular and cellular biology, Arbogast, M. et al. (Eds.), Wadsworth publishing company, Florence, KY, pp. 451–490, 1993. Return to text.
  2. Sept, D. and McCammon, J.A., Thermodynamics and kinetics of actin filament nucleation, Biophys J 81:667–674, 2001. Return to text.
  3. Chesarone, M.A. and Goode, B.L., Actin nucleation and elongation factors: mechanisms and interplay, Curr Opin Cell Biol 21:28–37, 2009. Return to text.
  4. Quinlan, M.E. et al., Drosophila Spire is an actin nucleation factor, Nature 433:382–388, 2005. Return to text.
  5. Otto, I.M. et al., The p150-Spir protein provides a link between c-Jun N-terminal kinase function and actin reorganization, Curr Biol 10:345–348, 2000. Return to text.
  6. Kerkhoff, E. et al., The Spir actin organizers are involved in vesicle transport processes, Curr Biol 11:1963–1968, 2001. Return to text.
  7. Wellington, A. et al., Spire contains actin binding domains and is related to ascidian posterior end mark-5, Development 126:5267–5274, 1999. Return to text.
  8. Ciccarelli, F.D. et al., The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase fold, Trends Biochem Sci 28:349–352, 2003. Return to text.
  9. Kerkhoff, E., Cellular functions of the Spir actin-nucleation factor, Trends Cell Biol 16:477–483, 2006. Return to text.
  10. Quinlan, M.E. et al., Regulatory interactions between two actin nucleators, Spire and Cappuccino, J Cell Biol 179:117–128, 2007. Return to text.
  11. UCSF Chimera software package from the Resource for Biocomputing, Visualization and Informatics at the University of California, San Francisco (supported by NIH P41 RR-01081) was used in the production of the molecular graphic images. Pettersen, E.F. et al., UCSF Chimera-a visualization system for exploratory research and analysis, J Comput Chem 25:1605–1612, 2004. Return to text.
 ~~~~~~~



Darwinism remains implausible to the extent of absurdity.   Very complex designs and unbreakable barriers to the naturalistic development of life are the findings of 21st Century science.   Get on board the train of Creation because science is eventually going to leave Darwin with no tracks, train engine or destination.   The empty siding of discarded hypotheses has a spot reserved for you...





We get married

ABOUT ME AND MINE, IF YOU CARE

My girls - Wife, three daughters and my granddaughter at Amanda's wedding this May

Dan and Amanda - so happy together!
We are very typical American Christians living the American dream...We are a Brady Bunch become one family.

One of the things I do occasionally and am doing currently is to read the Proverbs chapter that corresponds with the day of the month.   One could see and understand the political situation of both the USA and the City of Chicago summarized neatly by reading and understanding Proverbs 28 and 29.   As far as studying the Bible, my wife and I are in a small group that meets about three times a month to study scriptures, we work in the youth group, where we both have small groups we mentor and just in general work with high school students.   I teach the entire group once a month (used to be twice a month until I was unhappily introduced to MRSA and maybe one day I'll be to the point that twice a month would be fine) and will probably teach another science course this spring.   Then again, I might rather wait until next fall or instead do a summer course, not sure about that yet.

 
Grandsons after the soccer game is won!

My wife and I also pray out loud together every night and we study intentionally a book of the Bible together by reading a chapter out loud and discussing the chapter.  We've just begun 1st Peter after having done Daniel last month.  We have lots of reference books available if needed.   Ussher in particular is very handy when studying Daniel, as are a few commentaries.   I am very blessed to have a wife who is a Bible brain and a political science expert as well as a gifted artist.   We are remarkably happy to be husband and wife and before my health stopped us for awhile we visited Alaska and Hawaii and Seattle and Las Vegas and San Diego and the Appalachians and the surrounding area as well as the Maryland Eastern Shore and parts of Virginia and North and South Carolina and of course various local jaunts throughout parts of Illinois and Indiana and Michigan and Wisconsin and sorties into Missouri and Kentucky.  Hoping to be ready for air travel again by the end of this year at worst.   We have several destinations in mind, but for now our journeys are mostly limited to the exploration of information and we have the internet and scads of book and magazines and journals, etc. Before marriage to Debbie I had traveled to all sorts of interesting places and some I would like to share with her while we both have a few places we've never been that we intend to visit eventually.  Other than Hawaii I have never left the North American continent being limited to the USA and Canada and Mexico.  We intend to change that before too long.

Sara's husband Donny and daughter Sara at reception

We have three sons who live with us.  One is an English major who has his degree but needs to do his teaching semester to be licensed to teach high school English and he ran into money troubles, so he is working and saving and will finally be able to get back to school in the fall.  His older brother did a five year stint in the military, made sergeant, was awarded and on the fast track to make rank if he wanted to continue but he found that serving overseas in a combat area was challenging and interesting but being an MP in at a stateside fort was simply a way to have to deal with man at his worst - drunks, wife-beaters, brawlers, thieves and etc.  So he took his honorable discharge and is also saving money for school this fall, training to teach History to high schoolers.  The first son did work in youth group with us and now the oldest is working in youth group with us.  I think the oldest is just waiting to go back at the same time as his brother so they can sometimes share rides and experience the college life together for one more year.    Our third son is an entrepreneur who is working on building his own small business from scratch.

Old couple, new couple! 

Everybody else in the immediate family at wedding

Like the traditional family of human history, we do not seek to kick kids out the door at age 18.  As long as they are willing to toss a little bit into the family money pot and obey the rules of the house we prefer that they stay until job or marriage calls them to start their own family.   The three daughters have gone off to form new families but the sons are not yet gone and that is by mutual choice.  I cry every time one of my kids goes off away from home, whether it be by marriage or for military duty or college

Godson (currently SP4 in NG), godson, son with me at "The Villa" aka my house

One son is a sports enthusiast, a music lover and a history buff, while another collects cultural history in his brain, reads all sorts of books and loves movies.   Both were part of our family band that will, alas, never be reformed other than at holidays around the dinner table.   I am surrounded by lots of people within my own family with wide-ranging interests and therefore the conversations can go in manifold ways.   Some of us truly appreciate puns and well-timed jests, so humor is also a continual guest in our home.   When you include a few young people who are semi-family and come hang out from time to time and the large church family we are a part of in the equation, I am surrounded by lots of smart and creative people who enrich life, so that God's promise to me of an "abundant life" is fulfilled.   I am blessed to have avoided fame and sadly do not have nearly as much money as I would like but I chose family and God over money and that was the correct choice.   With six children and three grandchildren and a few "god-kids" as well, God has richly blessed me and I am very thankful!   We also have many good and faithful friends and it is often hard to find time to share with those we care about because life comes in 24 hour lumps and work demands much of my time so that a roof and walls and all that stuff remain provided for my little corner of the world's population.

First-string godkids before getting old and married

There are so many tugs on the sleeve of my time that I have had to make hard decisions.   I chose to shut down a promising career as a sports writer because it would have forced me to largely or completely abandon this blog.   I have declined positions in politics and political organizations for the most part in order to have enough time for work and family and, again, this blog.   This blog is, after all, much like a column on the editorial page of the internet.   When I was writing, I wrote mostly feature stories as a specialty, which was a step above the straight news reporters, but to ascend to the role of a columnist is the goal of most reporters.  The internet has allowed me to jump up to columnist level.   I much prefer a way to serve God than a few extra bucks discussing screen-and-roll defense or the VORP of a shortstop or the advantages and disadvantages of the cover-two defense.   I can still do that with friends and my wife likes watching games with me and my continual commentaries are actually interesting to her...the perfect woman!  She is cuter than me and loves me like crazy and I want no one else.   That, my friends, is an abundant life!

After basketball son, son, me, another godson (who is now a captain in the Army)

Wisdom comes from God and the Bible is the primary source of Godly wisdom.  Wisdom teaches me therefore to be willing to take a little time with the proverb concerning "heaping coals of fire" because it involves wisdom and to some extent doctrine.   On the other hand, any more time spent on something like "300 versus 800" is unwise by Bible standards:

Don't be fooled by the coats, these are actually our dogs

2 Timothy 2:22-23 (New King James Version)

22 Flee also youthful lusts; but pursue righteousness, faith, love, peace with those who call on the Lord out of a pure heart. 23 But avoid foolish and ignorant disputes, knowing that they generate strife.


Titus 3:8-11 (New King James Version)

8 This is a faithful saying, and these things I want you to affirm constantly, that those who have believed in God should be careful to maintain good works. These things are good and profitable to men.
Avoid Dissension

9 But avoid foolish disputes, genealogies, contentions, and strivings about the law; for they are unprofitable and useless. 10 Reject a divisive man after the first and second admonition, 11 knowing that such a person is warped and sinning, being self-condemned.

There is a clear line to be drawn between discussion and dissension.   There is a clear line to be drawn between discussions of doctrine and foolish disputes.  This is therefore why there are a few commenters who seek to draw me and others into doubtful and foolish disputes that I have often called "rabbit trails" in order to get both me and the readers away from the primary topic.   The clash of worldviews over origins is no foolish dispute but it is rather a foundational one.   The course of every man's life hinges largely on his view of the meaning of life.   Whether there is a God who can be discovered, whether there is a plan ongoing in the Universe or whether there is mostly random meaningless activity is of utmost importance.   If you don't settle in your own heart and mind what is and what is not foundational truth you are walking blindfolded in the dark down the pathway of life and you will fall.  If you make the wrong choice you will take the way where the bridge is out and the rocks are falling and avalanches are commonplace.   I assert that there is only one way to God but that way is both free and available to you as long as you draw breath. 
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