Cells Designed To Use Important Physical Mechanisms

It’s an amazing thing that cells are designed to use physics or otherwise we would not be able to exist. Two papers (here and here) were published in PNAS not long ago. Harland, Bradley, and Parthasaranthy studied the forces working in cell membranes. Lipid bilayers provide the structural framework which gives the cell membranes movement. It was previously believed that simple Newtonian fluids were able to keep them intact.

But researchers have found evidence to the contrary…“we find that membranes are not simply viscous but rather exhibit viscoelasticity…” which is a type of deformation which exhibits the mechanical characteristics of viscous flow and elastic deformation. The membrane is stretchy and it requires something to pull it apart. “The fluidity of membranes is crucial to functions such as the assembly of proteins into signaling complexes and the controlled presentation of macromolecules at cell surfaces…”

In other words, we could not live without membranes that are designed on how to take advantage of viscoelastic properties. Last September, UC Davis studied quantum mechanics – the Complex I macromolecular complex which was recently discovered machinery that resembles intelligently man-made in having a railroad-like piston and coupling-rod mechanism. The piston creates a proton gradient which then drives the ATP synthesis. It requires energy from food and stores it as chemical energy in ATP molecules for energetic activities in the cell. From humans to one-cell animals like bacteria, this is a vital important process for the existence of life!

Hayashi and Stuchebrukhov discovered that Complex I takes advantage of electron tunneling – a phenomenon in quantum mechanics…

“The whole electronic wiring of complex I is obtained by combining tunneling pathways of individual processes, as shown in Fig. 3.  It is clear that specific peptide residues serve as electronic wires connecting neighboring Fe/S clusters; individual electron tunneling paths involve up to three protein residues, including two cysteine ligands and one additional key residue (Table 1).  Notably, the clusters in the protein are oriented in a specific way—corner to corner—with Cys [cysteine, an amino acid] ligands mostly pointing toward each other, which is clearly the most efficient way to transfer electrons from one cluster to another.”

Did scientists drag into this incredible discovery the evolutionary story to remind us that this came from a non-thinking process?  Well, they did decide to show it could not happen by observing what happened with mutants when they tested them and then came out with this conclusion…

“The key residues identified in this study as mediators of electron transfer (Table 1) are remarkably conserved among different organisms.”

These cells are designed with precision of these machines.  The efficiency of electron transfer in Complex I , for example, it depends on precisely-placed amino acids and water molecules down a fairly long chain. The fact is these amino acids are unevolved which means altering them would cause major problems including causing death. Creationists and evolutionists recognize mutations as a process that occurs but genetic drift and stabilizing selection are level or downhill processes.

Another Uncontested Origin of Life Theory

Climate change theories are not the only issues in science that became an uncontested concept (until recently) in the media, the origin of life theories too, go vastly uncontested by the mainstream media but not here…

Michael Yarus and team had a paper published in PNAS with which had a research grant worth $415,610 dollars from the National Institutes of Health. The paper is called; “Tiny RNA Molecule With Big Implications for the Origin of Life.” Costing over 400,000 dollars in research money you better believe it would have “big implications” or claim to have them. So what is the fuss? The smallest ribozyme yet, with only five nucleotides, is able to “catalyze a key reaction that would be needed to synthesize proteins.”

Yarus who is a strong advocate of the RNA hypothesis, believes that ribozymes didn’t have to be complex to function. This is because specialized complexity would not be able to function under an origin of life theory. However, natural selection is unable to function as well because there is no replicator.  A system able to duplicate its parts accurately in order for natural selection to work. Yarus admits that no tiny replicator has been found and goes on to say no experiments or imagination have been formulated and processed yet.

Is there evidence to support Yarus hypothesis? Let’s take a look…

“RNA was synthesized by Dharmacon. GUGGC = 5’-GUGGC-30 ; GCCU – 5’P-GCCU-3’ ; 5’OH-GCCU = 5’-GCCU-3’ ; GCCU20dU = 5’-GCC-2’-dU; GCC = 5’-GCC-3’ ; dGdCdCrU = 5’-dGdCdCU-3’ . RNA GCC3’dU was prepared by first synthesizing 5’-O-(4,4’- Dimethoxytrityl)3’-deoxyuridine as follows: 3’-deoxyuridine (MP Biomedicals; 991 mg, 0.434 mmol) was dissolved in 5 mL anhydrous pyridine and pyridine was then removed under vacuum while stirring.

Solid was then redissolved in 2 mL pyridine.  Dimethoxytrityl chloride (170 mg, 0.499 mmol) was dissolved in 12 mL pyridine and slowly added to 3’-deoxyuridine solution.  Solution was stirred at room temperature for 4 h.  All solutions were sequestered from exposure to air throughout.”

“Reaction was then quenched by addition of 5 mL methanol, and solvent was removed by rotary evaporation.  Remaining solvent evaporated overnight in a vacuum chamber.  Product was then dissolved in 1 mL acetonitrile and purified through a silica column (acetonitrile elution).  Final product fractions (confirmed through TLC, 1.1 hexane:acetonitrile) were pooled and rotary evaporated.”

“Yield was 71%. Dimethoxytrityl-protected 30dU was then sent to Dharmacon for immobilization of 30-dU on glass and synthesis of 5’-GCC-3’-dU. PheAMP, PheUMP, and MetAMP were synthesized by the method of Berg (25) with modifications and purification as described in ref. 6.  Yield was as follows: PheAMP 85%, PheUMP 67%, and MetAMP 36%.”

Purification and isolation steps under controlled conditions. The multiple solvents were also used at various temperatures, which were needed to prevent cross-reactions. Where was the media on this? Questions like this should have been asked…“How would nature sequester the desired compounds from damaging cross-reactions without the techniques you used?” Not surprisingly, creationists and intelligent design proponents are the only ones asking these critical questions. Producing something in a lab doesn’t mean it can happen in nature allegedly millions of years ago…

New Paper Advocates The “Genetics First” Hypothesis

Last year, William Dembski who is one of the key figures in the modern intelligent design movement recently debated Lewis Wolpert who is a developmental biologist. It was an interesting debate, but they were not the only ones butting heads, there was another ID proponent who reviewed the debate and found it to be not that impressive, he states…

“I am afraid I will have to disagree with the impression of the debate. While I give Wolpert a failing grade or at best a D, I cannot give Bill Dembski’s responses better than a C…”

“One glaring example was when Bill was asked whether Chemistry was designed. There was hesitation and then an attempt to get into the design of the universe. The better answer would have been that the laws of Chemistry flow from the characteristics of the elements and that these flowed from the basic laws of physics. To try to move it immediately to the design of the laws of physics left the impression that there was a designer behind every door.”

Dembrski takes issue with a fellow contributor of ID…

“Jerry, We have some history in which you find fault with my presentations, and in which you cite your Duke and Stanford degrees and experience in business communications as qualifications for offering up your criticisms.

As I point out in the debate, the arrangement of stones can signify design even if the stones themselves can’t be said to be designed. The same point can be made for chemistry — basic chemistry may be undesigned (I don’t believe this) but chemical arrangements might be. Thus there are nuances to the design question in chemistry and physics that I was not willing to slide over in my discussion with Wolpert.”

Obviously, Dembski went into is comfort zone which is physics rather than chemistry. Most likely Stephen Meyer could have addressed the chemical aspect. But this brings up the “Genetics First” hypothesis (chance formation of nucleic acids) verses metabolism coming into existence first. The later has been rising in popularity in certain camps. Evolutionists believe replication of chemicals must be in play before natural selection can pick the best material so it can build it into elephants, sharks, humans, you name it.

Two Darwinian schools of thought on origins butting heads and falsifying each other. Three European scientists who published a paper in PNAS, said stated the following…

“A basic property of life is its capacity to experience Darwinian evolution.  The replicator concept is at the core of genetics-first theories of the origin of life, which suggest that self-replicating oligonucleotides or their similar ancestors may have been the first “living” systems and may have led to the evolution of an RNA world.”

“But problems with the nonenzymatic synthesis of biopolymers and the origin of template replication have spurred the alternative metabolism-first scenario, where self-reproducing and evolving proto-metabolic networks are assumed to have predated self-replicating genes.  Recent theoretical work shows that “compositional genomes” (i.e., the counts of different molecular species in an assembly) are able to propagate compositional information and can provide a setup on which natural selection acts.”

“Accordingly, if we stick to the notion of replicator as an entity that passes on its structure largely intact in successive replications, those macromolecular aggregates could be dubbed “ensemble replicators” (composomes) and quite different from the more familiar genes and memes.”

We know metabolism-first scenario is plagued with many problems of its own as indicated in this paper. Anyone can generalize the notion of a replicator up to a system or network of molecules instead of requiring a genetic code but replication has to be accurate! In a designed world we live in, there is not much room for error, in the story of evolution there is plenty room for errors which supposedly result in updates or upgrades.

The “Genetics First” hypothesis have it’s problems as well. Leslie E. Orgel of the Salk Institute for Biological Studies who has spent a lifetime studying origins from an evolutionary framework.  His final paper published in 2007 in PLOS, was not very encouraging for evolutionists, it was called; “The Implausibility of Metabolic Cycles on the Prebiotic Earth.”

The caption reads like this…“In this essay, the final contribution of his scientific career, Leslie Orgel explores the severe difficulties that arise when these proposals are scrutinized from the standpoint of chemical plausibility.”

Their hope is fading, the story of  complex polymers to arise naturally. Rather, they are starting to settle for more on untested ideas such as simple compounds arising instead. Orgel in his final criticisms of the field are so broad and so damaging to the ability of natural processes to produce life at all by any method.  He states…

“It must be recognized that assessment of the feasibility of any particular proposed prebiotic cycle must depend on arguments about chemical plausibility, rather than on a decision about logical possibility.”

Does this sound familiar? I have repeated this theme many times in various topics when it comes to the scientific method concerning data. Just because there is a claim that it could happen, doesn’t mean it ever will. For example, some might believe O2 levels increased sizes of animals and could test O2 levels in tanks to see if it had effects on smaller animals. Then say well we haven’t found it yet, but we believe it will show results. This doesn’t mean certain O2 levels can evolve by a million-fold.

“Whatever the original input, one would finish with an equilibrium mixture, the composition of which is determined by thermodynamics.” Equilibrium means you are at a standstill and nothing more will happen.

Back to the ID debate which I opened up with. Even though Jerry was vague in his assertion that the laws of chemistry  should have been included in the debate for ID, it’s certainly in the debate for creationism. Science has said “no” countless times to evolutionary prediction, assumptions, and other stories. But science has said “yes” to a creator, an intelligent designer, namely God!