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

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

The Applied Science of Intelligent Design-Part I

I recently read a brilliant paper(1) written by Joey Campana, in which he details what he terms the Figure 1-Design IsomorphDesign Isomorph and Isomorphic Complexity. His ideas have practical applicability to both applied technology research and the applied science of biology. As I’ve stated before, Darwinism has little practical utility beyond designed algorithms (i.e., genetic algorithms) utilized for optimal design (this is basically an advanced trial and error system). Then, there is the design isomorph, which has practical implications for biology and technology.

From its beginnings, the empirical study of life has been earmarked by the idea that tiny machines are at work in living tissues. The discovery of protein machines and the illumination of the genetic code during the 20th century revealed a profound similarity between many aspects of technological devices and biological components, and this fulfilled many of the musings of early biological thinkers. The stronger similarities between biology and engineering are so clear that there are pervasive cases of design isomorphs, where precise technological designs are found to preexist in living organisms. This isomorphic congruence has been thought by many to be a mere coincidental outcome of undirected evolutionary processes, making the similarities superfluous to scientific practice, and inconsequential to the question of the cause of life.

The author also details several design isomorphs and explains in detail how considering biological components from a design perspective can be an effective strategy in understanding biology. Likewise, utilizing the tried and true methods of design oriented fields (e.g, engineering) in tandem with considering the analogous nature of machines designed by humans, we can greatly increase our understanding of how biological systems work. Reverse engineering was mentioned as one specific approach (e.g., remove a part to see what happens to get an idea of its function). Also, when one considers biological systems as analogous technology, it may lead to breakthroughs in applied technological science. This has already happened in a number of areas, but I won’t detail those things in this brief introduction.

The author also has started compiling a list of design isomorphs.(2) I am planning to work with some other IDers to develop a database of design isomorphs, which may be useful for inventors as well as biological scientists….to be continued….

(1). The Design Isomorph and Isomorphic Complexity

(2). Catalog of Design Isomorphs in the Wild

Recent Harvard Cellular Animation

I can’t help but consult homology on this one with respect to bipedalism. I’m mean seriously. Look at that little bugger walking the tightrope. Perhaps humans evolved from that molecule. In all seriousness, this video is great, and furthers my appreciation of Creation. I realize that is probably not the intent of the folks at Harvard, but it’s a great video nonetheless. For those without broadband, you can see a few stills.1

I can’t help but see the sentience expressed in these “nano-machines.” Although they are not sentient themselves, they appear to be an expression of sentience in my opinion (a sentience far beyond that of our own). I think this really goes to the point my coauthor DB has made a number of times in the past about appreciating the beauty in science.


1 http://www.studiodaily.com/main/searchlist/6850.html

For a longer excerpt of the video without the lecture, go here:
http://aimediaserver4.com/studiodaily/videoplayer/?src=ai4/harvard/harvard.swf&width=640&height=520

Digital Coding in DNA

One way of thinking about DNA is it’s information storage ability. DNA has an information storage capacity that is far beyond anything devised by humans for the amount of space that is used (information storage density). The information stored in DNA is essentially digital in nature. With computer technology, information is stored as a series of 0’s and 1’s. With DNA, the information is stored as a series of 4 different types of base molecules. All information needed for the construction of a biological organism is contained in DNA. But DNA does nothing on it’s own. Imagine taking your hard drive out of your computer. It’s useless. The same with DNA removed from a cell. There are many more functional components of a cell that are required to read the information, construct proteins from information contained in DNA, power generation, and so forth. Cells also contain error correction processes for reading DNA, just as computer technology contains processes for error correction.

Utterly, any analogy that we might try to utilize to explain the complexity of what happens in a living cell will fail. We have designed nothing of that comes close to the sophistication of a living cell. All of these functions on a cellular level are carried out with no intelligence actively guiding the process. However, all of these functions exhibit what I would call hallmarks of intelligent processes. In other words, intelligence is exhibited in the design and function of life. Life at any level of analysis exhibits something akin to intelligence. Their is an increasing trend in biology toward discovering ever increasing complexity at a cellular level. I happen to believe the miraculous is possible, but the miracle required for life to self-organize from non-living matter to living matter is beyond the level to which I can extend my faith.