More Complex than Previously Thought – Part IX – The Ribosome

The ribosome is a nanomolecular factory that uses genetic instructions and amino acids to build proteins.  If the previous understanding of the functions of the ribosome were not enough evidence for design, new technology has enabled researchers capture nanoscale movements inside the structure and found that the functioning of the ribosome was complicated than previously thought.1

In the protein manufacturing process, the genetic code – or instruction manual – for making proteins lies inside a cell’s double-stranded DNA. When the cell needs to produce more proteins, the DNA unzips into two separate strands, exposing the protein code so it can be duplicated by single-stranded messenger RNA (mRNA). The mRNA dutifully delivers that code to the ribosome, which somehow reads the instructions, or “data tape,” as each amino acid is added to a growing protein chain.

At the same time, other RNA molecules, called transfer RNA (tRNA), bring to the ribosome amino acids, the raw building blocks needed for protein construction.

To help elucidate the ribosome’s movements as it interacts with mRNA and tRNA, the researchers used X-ray crystallography to obtain a highly detailed picture of the ribosome – a mere 21 nanometers wide – from an Escherichia coli bacterium. In addition to revealing atomic level detail, the technique allowed the researchers to capture the ribosome mid-action, a challenge because it acts fast, adding 20 new amino acids to a protein chain every second.

“Scientists used to think that the ribosome made a simple two-stage ratcheting motion by rotating back and forth as it interacts with mRNA and tRNA,” said Cate, who is also a member of the California Institute for Quantitative Biomedical Research (QB3) at UC Berkeley. “What we captured were images of the ribosome in intermediate stages between the rotations, showing that there are at least four steps in this ratcheting mechanism.”

“We suspect that the ribosome changes its conformation in so many steps to allow it to interact with relatively big tRNAs while keeping the two segments of the ribosome from flying apart,” said Cate. “It’s much more complicated than the simple ratcheting mechanism in a socket wrench.”

Cate said that while this study marked a major accomplishment in cracking open the “black box” of ribosomal function, there are far more details yet to be revealed. Advances in imaging techniques over the next decade should allow researchers to go beyond the snapshots taken in this study to high-resolution movies of a ribosome’s movements, he said. (emphasis mine)

1 New Images Capture Cell’s Ribosomes At Work, ScienceDaily, 8/23/09

Advertisements

More Complex than Previously Thought-Part I

I’ve written before about how Ocam’s razor consistently slices the wrong way in biology…meaning that there is a continuous trend of discovering that the machinery of life is more complex than previously thought. 

Scientists have recently discovered,(1) that ribosomes have a “proofreading step,” which is said to recognize errors shortly after making them and has an analog to a computer’s delete button. 

It turns out, the Johns Hopkins researchers say, that the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products which, as workhorses of the cell, carry out the very business of life.

“What we now know is that in the event of miscoding, the ribosome cuts the bond and aborts the protein-in-progress, end of story,” says Rachel Green, a Howard Hughes Medical Institute investigator and professor of molecular biology and genetics in the Johns Hopkins University School of Medicine. “There’s no second chance.” Previously, Green says, molecular biologists thought the ribosome tightly managed its actions only prior to the actual incorporation of the next building block by being super-selective about which chemical ingredients it allows to enter the process.

Joey Campana discusses this subject (more complex than previously thought) in detail(2):

“More complex than once thought”

 

 

A revealing reason that Darwinian thought has not been helpful is that it tends to see biology in simplis-tic terms that are, well, too simple. When searching Google for phrases such as “more complex than pre-viously thought,” over a million-and-a-half hits cur-rently result. Some things that were “more complex than thought” from the first few pages include re-search findings in the following areas:

  1. communication among cells
  2. the oldest animal genomes
  3. bird flight orientation
  4. genes
  5. patterns of neuronal migration during cortical development
  6. the relationship between evolution and embry-onic development
  7. p53 ubiquitination and degradation
  8. human memory
  9. the fetal immune system
  10. the mouse genome
  11. visual processing in the brain
  12. regulation of neuronal survival in the retina
  13. COX enzymes
  14. the human genome
  15. the female human body
  16. cerebellar circuitry and learned behaviors
  17. estrogen receptors
  18. neural induction (list truncated)

 ….

Currently, “less complex than once thought” only returns two hits. The data coming out of the labs would suggest that we begin to expect that things are more complex. We would stand a greater chance of being correct.

So, the science of biology would be well served by a paradigm shift focusing on design analogs and assuming design rather than assuming chance. When an information recording and trascription system is involved in biology, scientists should first start with all they know about information recording and transcription systems. Error detection and correction is an integral part of these types of systems designed by humans, and engineers can also benefit from the analysis of the machines of life.

(1). The Ribosome: Perfectionist Protein Maker Trashes Errors
(2). http://www.arn.org/docs/article_the_design_isomorph_and_isomorphic_complexity.pdf