May 23, 2020 | David F. Coppedge

Ribosome Self-Assembly Is Not Evolution

So many pieces have to be placed in the right order, chance is ridiculously out of luck.

Scientists at the Weizmann Institute of Science in Rehovot, Israel, tried to do what ribosome does every day routinely: get all the protein and RNA parts together such that self-organization brings them all together into a functioning molecular machine. Writing in Weizmann Wonder Wander, they describe their own attempts to get the parts to self-organize, starting with the smaller of two major subunits that make up the ribosome:

As the cell’s protein factory, the ribosome is the only natural machine that manufactures its own parts. That is why understanding how the machine, itself, is made, could unlock the door to everything from understanding how life develops to designing new methods of drug production. An intensive, long research effort at the Weizmann Institute of Science has now demonstrated the self-synthesis and assembly of the small subunit of a ribosome –30S – on a surface of a chip.

Good thing they didn’t bring Darwinian evolution into the picture. Look at the challenge they faced:

Prof. Roy Bar-Ziv and Staff Scientist Dr. Shirley Shulman Daube of the Institute’s Chemical and Biological Physics Department have been working on this project for around seven years. One of the main challenges to such a project is the sheer number of different molecules the cell must produce to make the subunit: The core is a long strand of RNA, and 20 different proteins must be attached to the strand. These get organized by the weak chemical forces between the protein molecules and the RNA – repelling at some points and attracting in others – and the whole structure thus relies on the proper manufacture and organization of each component. Add to that another six proteins that are not part of the structure, but act as chaperones to assist in the assembly. That makes a total of a least 27 different genes – one to encode each component or chaperone – that must work together to make the subunit.

Simplified portrayal of a ribosome in action: messenger RNA in, protein out. (Illustra Media)

Whew! Twenty-seven genes must be precisely encoded in order to produce 20 proteins, plus six chaperones to fold them, and a long RNA strand – and they must be placed in position so precisely that weak chemical forces will make them come together into a working subunit. Even then, they get only one subunit – not a working ribosome that can translate DNA into proteins. It needs to match the large subunit, which requires even more proteins and RNA!

This is not only a chicken-and-egg problem (which came first, the ribosome or the protein?), but a positioning problem as well. You can’t just put the parts into a sack and shake it. They have to be placed in the correct relative positions to one another, such that the chemical forces assemble them.

To visualize the difficulty of pulling this off, imagine Lego pieces with magnets on them in various points. Try placing the right pieces of the right shape, with the magnets in the right spots, on a table in the right relative positions, such that when you let go of it, the magnets all tug on the appropriate other pieces and spontaneously assemble into a working player piano, ready to read a coded input and play the music.

The scientists recognize that this is a high-level problem that involves multiple problems in a hierarchical system:

In the beginning, Bar-Ziv and Shulman Daube found they could make the components, but getting them to self-assemble, as the natural structures do, was a challenging hurdle. Over the course of the next seven years and hundreds of trials, the scientists tracked down the proper placement of the genes on the chips. Something like the organization of genes in the chromosome, the genes on the chip had to be positioned in the right locations, and in the proper relative quantities. This, it turned out, was crucial to the overall orchestration of the complex assembly process. Each time, the scientists would attach a different constellation of genes to the chips, narrowing down the possibilities until they had a composition that could mimic that natural process of subunit production as well as self-assembly. In nature, subunit assembly is a hierarchal process. In the course of their experiments, the scientists were able to break down the assembly to the individual steps to prove that the end result was a self-assembled subunit, and to observe the roles of the chaperones in this process.

In essence, they reverse-engineered part of the ribosome and imitated the steps that occur in living cells.

They were glad after seven years to get their ‘Lego blocks’ to self-assemble into the small subunit of the ribosome, thinking that their success might lead to “creating all sorts of other complex, molecular structures – existing ones as well as those not yet found in nature.” Nowhere in the press release did they mention evolution – nor does the formal paper in Science Advances (Levy et al, “Autonomous synthesis and assembly of a ribosomal subunit on a chip,” 15 April 2020), where they published their results.

It’s an impressive achievement, for sure, but think about what they did: they used their minds. They applied intelligence to information they had studied through tedious PhD programs. They had a goal, and a purpose, They thought, practiced, used trial and error, and learned from repeated failures for years until they reached their goal. That is the opposite of natural selection!

It would beggar the imagination to think that these scientists could achieve this result using the Stuff Happens Law – just tossing the raw materials into a tumbler and waiting for a ribosome to pop out. On the contrary, they illustrated numerous principles of intelligent design:

  • Irreducible complexity
  • Foresight
  • Artificial selection
  • Reverse engineering
  • Goal-directed behavior
  • Hierarchical organization
  • Recognition of success

If it took these highly-gifted and well-trained scientists seven years of applied intelligent causation to achieve the assembly of the small part of a complex machine, why on earth would anyone ever imagine that chance could do it? Remember, Illustra Media, in their short film “First Life” (watch it here), calculated that the chance formation of one small protein is so vastly improbable, that in the time required to self-assemble, an amoeba, moving one foot per year, carrying one atom per round trip, could haul 56 million universes of matter across a bridge the width of the observable universe!

This partial machine needs twenty proteins with 6 chaperones, and a long RNA transcript, each part matching its neighbors, in the right places at the right time, to self-assemble. And the simplest conceivable cell needs hundreds of proteins, plus a genetic code, metabolism, and a membrane to hold everything together. Folks, chance is never going to do such a thing. When that fact becomes burned into your consciousness, the magnitude of unbelievers’ willful ignorance and ingratitude becomes painfully evident. We must get people to discard their irrational faith in what unguided nature can do. And when people repent of that evil, it starts a different path that changes everything.

 

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