February 23, 2024 | David F. Coppedge

Archive: Your Model Train Set

Model trains in your cells? Yes: read about this and other wonders from 21 years ago.

Note: Some embedded links may no longer work.

Your Model Train Set   02/25/2003
Model train enthusiasts never had it so good. Imagine five different models of finely-crafted engines, all in perfect working order, and enough track to cover a city. That’s what each of us has, right now, inside our cells. But don’t feel top dog; even lowly bacteria have them, too. To prove we’re not making this up, read “The Molecular Motor Toolbox,“ a Review article in the current issue of the journal Cell, by Ronald D. Vale of the Howard Hughes Medical Institute.  He begins,

A cell, like a metropolitan city, must organize its bustling community of macromolecules. Setting meeting points and establishing the timing of transactions are of fundamental importance for cell behavior. The high degree of spatial/temporal organization of molecules and organelles within cells is made possible by protein machines that transport components to various destinations within the cytoplasm.

Vale reviews the five major motor engine families that ferry cargo around the cell: actin, dynein, conventional homodimeric kinesin, heterotrimeric kinesin II, and Unc104/KIF1. These engines show remarkable flexibility and diversity in living things, from plants to sea squirts to fungi to worms, and are highly conserved from the smallest organisms to the largest. What about the switching? What keeps the engines from colliding on the tracks?

To achieve law and order on the intracellular highways, the multiple cargo-carrying motors in a single cell must be regulated. In the majority of animal cells, individual organelles switch frequently between anterograde (microtubule plus-end-directed) and retrograde (minus-end-directed) movement …. In most cells, relatively little is known about the regulation and coordination of bidirectional motion. … individual cargoes move primarily unidirectionally in these extended processes, and a switch in direction occurs when cargoes reach the ends of these elongated structures.

There is an unknown switching mechanism at so-called “turnaround zones” on the microtubules that dynein and kinesin engines travel on.

The microscopic observations of cargo transport in axons and flagella raise a number of similar questions. How do the opposite polarity motors, kinesin and dynein, coordinate their activities? What kind of machinery processes the incoming cargo and switches motor direction at the ‘turnaround’ zones? Molecular answers to these questions are beginning to emerge but are far from complete.

As a sidelight, another review article in the same issue of Cell by a team from UC San Diego describes how these motors are involved in tugging the chromosomes apart during cell division (mitosis). In fact, the whole Feb. 21 issue is a good source for current knowledge about the cell’s inner workings: mitochondria, cell division, signalling, transport, etc. But back to our story.

Vale points to fascinating indications that the motors signal each other and coordinate their actions. After discussing some of these possibilities, he concludes,

Fifteen years ago, only a few molecular motors were known. In contrast, complete inventories of molecular motors are now available in a number of diverse organisms. While these remarkable accomplishments have answered many questions, the genomic inventories also have exposed many areas of ignorance.

Well, back to the lab; gotta get to “work.” Biochemistry can be fun.  You get to play with miniature railroads.

Nature Science Update reports that NASA engineers are studying the intracellular railroad for spacecraft ideas. UCLA got a $30 million NASA grant to begin the Institute for Cell Mimetic Space Exploration, whose mission is to “come up with biology-inspired devices that could facilitate space travel 30 years from now.” Some of the plans include imitating actin.

Vale’s article is another of many we have reported that seems schizophrenic. On one side of his brain, he marvels at the engineering and design, and on the other side, attributes it all to chance. Here is Vale’s storytelling about how this coordinated transportation system arose: “The complexity of these ‘Toolbox’ motors expanded in higher eukaryotes through gene duplication, alternative splicing, and the addition of associated subunits, which enabled new cargoes to be transported.” Impressed? Well, for crying out loud, how did the motors get there in the first place? Marvel at this explanation: “Recent genomic and functional studies suggest that five cargo-carrying motors emerged in primitive eukaryotes and have been widely used throughout evolution.” There you have it, folks. They just “emerged”. The miracle alarm just went off. It’s time to declare an “emerge”ncy and kick the evolutionary gullibility out of science.

Footnote: In the same issue of Cell, an Austrian team discusses the state of knowledge about meiosis (cell division for sexual reproduction). They note that there is no evidence for evolution of this highly complex series of processes (emphasis added):

In summary, the behavior of chromosomes in meiosis is much more complex than in mitosis.  Additional demands such as chiasmata formation, mono-orientation of sister kinetochores, protection of centromeric cohesion, and prevention of DNA replication between the two divisions are imposed upon the chromosome segregation machinery. These processes are discussed in detail in the following sections. Despite its greater complexity, there is no clear evidence that meiosis evolved later than mitosis. There are, for example, no extant lineages that appear to have split off the eukaryotic tree before the evolution of meiosis (Cavalier-Smith, 2002).

So here is another wonder that just “emerged.” Evolution is the religion of miracles that emerge out of the foaming sea of purposelessness.

Footnote 2: Another molecular motor story appeared on EurekAlert Feb 25. Stanford scientists are studying kinesin, the “workhorse of the cell,“ which hauls chromosomes, neurotransmitters and other vital cargo. Joshua Shaevitz describes it: “This is one of the most efficient engines anyone has ever seen. Some estimates put it at near 100 percent efficiency. It’s an amazing little thing.” His colleague Charles Asbury chimes in with elegant prose, “Kinesin is an example where Mother Nature kicks our butt. For me, I’m motivated just by understanding how this fascinating thing works.” One thing is for sure. It’s not the believers in intelligent design that are getting their butts kicked by the accelerating discoveries about molecular machines.


Shoot Bullets at Ice and Create Life   02/24/2003
New Scientist reports that NASA researchers shot bullets at ice and saw sparks. They think this is maybe a way the icy moon Europa could have life. Meteorites bombarded the ice, melting methane and ammonia and water. The shock also produced electricity that might help form amino acids, the building blocks of life, like Stanley Miller did with his spark-discharge apparatus. We won’t know till we send a spacecraft there, maybe around 2011.

This is so lame it hardly deserves a comment. Evolutionists see the forces of destruction as the new creator gods. Lightning, chance and meteor blasts are now the cosmic garden of Eden. Should they teach this nonsense in the schools?

Dr. A. E. Wilder-Smith, organic chemist, used to be outraged that students were never told that amino acids must be optically pure (single-handed), or they are biologically useless. Miller’s results, and those of all other naturalistic experiments, are always 50-50 (racemic) mixtures of left and right handed forms. Even one amino acid of the wrong hand is enough to ruin the enzymatic capabilities of a polypeptide. It requires intelligence to separate them: information must be supplied from the outside to make them all one-handed. But information is precluded by the presuppositions of naturalism.

Along that line, the claimed slight excess of one hand seen in the amino acids found in the Murchison meteorite has been recently suspected as being due to earthly contamination. No natural process ever produces amino acids of a single hand, because the two forms have equal entropy.

Evolutionists have two monstrous hurdles right out of the starting gate with their naturally-formed amino acids and nucleotides: (1) achieving optical purity, which is astronomically improbable, and (2) producing a sequence that has any functional specificity; i.e., writing a coded language by chance. It’s not going to happen, here or in 10100 universes. Chemical evolutionists need to stop spewing their nonsense about impacts and sparks breeding life, and tell the truth: all observational science demonstrates that information requires an intelligence cause.


Another Rotary Motor Found in Cells   02/24/2003
Another member of the ATPase (ATP synthase) superfamily has been shown to rotate and produce three ATP per cycle. The well-known FoF1-ATP synthase was imaged in rotation about five years ago. Another enzyme, VoV1-ATPase, was known to be structurally similar and has been assumed to rotate also, but experimental evidence was lacking. The Japanese have done it again. They attached a bead to the stalk and imaged the tiny molecular machine rotating counterclockwise at about 144 rpm, which they assume is the natural rotation rate without the bead attached.

VoV1-ATPase is responsible for acidification of eukaryotic intracellular compartments and ATP synthesis in Archaea and some eubacteria. FoF1-ATP synthase resides in the mitochondria and chloroplasts; VoV1-ATPase is embedded in various intracellular acidic compartments. This enzyme’s D subunit acts like a rotor shaft, analogous to the gamma subunit of F1ATPase. The experimental results are written up in the Proceedings of the National Academy of Sciences online preprints for Feb. 21.

How they work

The Fo and Vo subunits of the machines are embedded in the membranes and use proton motive force to rotate. The F1 and V1 subunits are where ATP synthesis takes place. They contain six lobes that are acted on by a rotor shaft, or camshaft, attached to the rotating portion. The six lobes come in pairs. As the camshaft turns, it causes each pair to cycle through the manufacturing steps: load the ingredients (ADP and phosphate), squeeze them together into ATP, then eject the ATP into the surrounding medium. Each pair is undergoing one of these stages every 120o turn of the camshaft, so that 3 ATP are produced for every full turn.

ATP is the energy currency used by most processes in the cell. On a busy day, your miniature motors can recycle an amount of ATP equal to or exceeding your body weight.

The discovery of rotary motors like ATP synthase and the bacterial flagellum in living cells has caused a great deal of excitement and astonishment, not just because they are cute, but they are extremely efficient (nearly 100%, utilizing the Brownian motion of the cell to their advantage), and absolutely essential to life. Add this one to the growing list of molecular machines. Did you notice it exists in Archaea and eubacteria, the most “primitive” of lifeforms? How can evolution hope to explain rotary engines with highly efficient, fine-tuned moving parts, in the earliest cells? They cannot.

You never see an evolutionist giving a plausible sequence of steps from a random collection of molecules to a rotary motor like ATP synthase, because the machine is useless unless it is fully assembled. Either everything works, or nothing works. Yet life depends on the ATP generated by these exquisite molecular machines. Don’t forget also that these machines are composed of parts all of one hand, and the motor requires an even more complex set of blueprints and assembly instructions that can be accurately reproduced from cell to cell. Evolutionism retreats into fantasyland trying to explain such wonders without design.

 

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