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

The Applied Science of Intelligent Design-Part III

ARN correspondent, Robert Deyes, has written an interesting post entitled, The Designs That Human Endeavors Can Only Approximate And Rarely Surpass. He writes:

Throughout history man has looked to the natural world as the source of inspiration for some of the most exquisite inventions ever seen. Perhaps most famous of all is the Eiffel tower which, originally conceived by Gustav Eiffel as a temporary edifice, had at its foundations the design of already-existing natural structures notably the curvature of bones (Ref 1). Velcro was likewise inspired by already-existing biological contrivances as was perhaps Charles Paxton’s water lilly-based design of the Crystal Palace in London (Ref 2).

As I’ve written before, considering life from a teleological perspective can make this process more explicit leading to beneficial inventions that help the lives of people. Darwinists would have you to believe that such things as chance and necessity are capable of producing biological technology that is beyond our ability to emulate. From an ID perspective, when an apparent design flaw is discovered, the questions do not stop there. In other words, Darwinisim is a science stopper, because it’s more important to them to have ‘evidence’ to hold out that their theory is true. Taking an ID perspective, a more cautious approach would ensue, and the issue would be examined in greater detail before it is concluded that a ‘design flaw’ has been discovered.

There are two major issues at work here. The first issue is that thinking in terms of design in biology can focus researchers on practical applications and inventions with likely benefit to humanity. The second issue is that the scientific process of understanding the function of biological processes can continue to a deeper level without stopping with an apparent design flaw, which would be attributed to the happenstance nature of evolution. The second issue is important in terms of understanding biological processes, which could lead to new treatments for disease.

The article concludes with:

CEO and president of Promega Corporation, Bill Linton, once remarked that “our most well designed human endeavors can only approximate- and rarely surpass- the elegant precision of nature” (Ref 8). Indeed crediting evolution for the engineering of complex systems that lie beyond the capacity of human minds to fully conceive seems thoroughly misplaced. Moreover there is something deeply telling about the observation that the natural world has machines that we, as intelligent agents, are so ready to copy. Defenders of Intelligent Design theory have of course provided their own take on this singular fact, concluding that the work of an intelligent designer and not the blind walk of evolution lies at the heart of biological complexity.

Indeed, crediting evolution for the engineering of complex systems is thoroughly misplaced, and impedes scientific progress in ways that are truly important. That is, applied science is impeded by a happenstance view of natural history.

Nested Hierarchies: Proof of Evolution?

We had a recent drive-by commenter, John, here who purported that nested hierarchies were “proof” of common descent (the holy grail of Darwinism). My friend over at the Italian ID site, Progetto Cosmo, recently wrote a post on nested hierarchies.

Why complex systems of nested hierarchies like cars or living things cannot be produced from the lowest to highest level.

An automobile is an example of a complex system with nested hierarchies. At the highest hierarchical level, a car is a device for transporting people and things. It consists of several sub-hierarchies:

1. Steering mechanism
2. Braking system
3. Engine
4. Transmission Etc.

The most complex of these is the engine. Within the engine we have further sub-hierarchies like the crankshaft assembly, a precisely machined and balanced steel bar which converts rotary to linear motion. Then we have the piston assembly which includes the piston itself, connecting rod, piston pin, and rings. The rings are a hierarchy down from the pistons. They are precision parts and typically sold as sets. The set of spark plugs and wires is yet another sub hierarchy of the engine. And each spark plug is a hierarchy of it’s own consisting of insulator, threads, electrode and so on. And the same applies even to spark plug wires which consist of insulator, copper wire, and connectors.

The car does not function unless all the hierarchies of systems are included in the proper order. Nor can they be included helter-skelter. They have to be in the proper assembly order. The piston rods must be connected to the crankshaft. The cylinders must have spark plugs. The wheels must have tires. A car which has the pistons in the trunk and the tires on the back seat is useless. An engine without piston rings will not function.

And continues…

We now understand that the molecule lying at the lowest level of hierarchy is DNA. The random changes are simply substitutions of one DNA base for another resulting in a mutation. A useful mutation will aid survival and reproduction. The cycle of mutation/selection is the engine that drives evolution. So we are told. But wait: mutation takes place at the lowest level of a living organism’s hierarchy. How can changes at this level be coordinated into the vast array of hierarchies above?

Imagine handing an ancient Roman engineer a spark plug and expecting that by tinkering with it he might eventually develop a car. How could this possibly happen without a vision of a car and how its hierarchies interrelate? Even if that ancient Roman somehow stumbled on a modification that improved the spark plug he would have no way to recognize the improvement because without all the hierarchies that make up a car, the spark plug is useless.

So his notion is that for complex systems of nested hierarchies, there must be a designer who has in mind, a purpose and function of the designs, from the beginning in order to produce a functional nested hierarchy. In other words, random changes in the surface of your concrete floor in your basement will not transform your house into something different. Random changes to a blueprint for a house before it is built would certainly have implications for the outcome, and blueprints that result from random processes would have even further implications. The blind process and necessity worshipers seem to believe that these processes can result in nested hierarchies and even try to use this as proof of evolution. I’m less than convinced…

The Applied Science of Intelligent Design-Part II

In Part I, I introduced the concepts that were set forth by Joey Campana on how a design orientation fosters applied science. William Dembski over at UD linked to a site that has a page titled: The 15 Coolest Cases of Biomimicry. I am much more an advocate of applied science over basic science. That’s not to say that basic science can never eventually be useful, because sometimes the findings of basic science eventually end up finding some applicability. But, the fact is that a choice must be made about what’s the most important. Money doesn’t grow on trees. The equation is simple in my mind. Let’s focus more on things that might actually improve people’s lives.

The site documents 15 of the Coolest things that are based on God’s designs [my words, not theirs]. My point of view is that ID researchers would have more of an orientation toward things that might actually be useful now rather than on processes that purportedly take millions of years to have any effect. Some of the things documented at the site include: velcro, passive cooling, gecko tape, whalepower wind turbines, and more.

More Complex than Previously Thought-Part II

I thought I’d provide a few recent snippets along these lines.

1). The First Animal on Earth was More Complex than Previously Thought

ScienceDaily (Apr. 11, 2008) — A new study mapping the evolutionary history of animals indicates that Earth’s first animal — a mysterious creature whose characteristics can only be inferred from fossils and studies of living animals–was probably significantly more complex than previously believed.

2). Volcanoes function in a far more complex way than previously thought

Washington, Oct 10 (ANI): A new research by a team of US and UK scientists has found that volcanoes function in a far more complex way than previously thought, making future eruptions even harder to predict.

3). Arctic Ice Formation is More Complex Than Previously Thought

Contrary to historical observations, sea ice in the high Arctic undergoes very small, back and forth movements twice a day, even in the dead of winter. It was once believed ice deformation at such a scale was almost non-existent.

4). Research: Bee vision

Bees’ colour vision is more sophisticated than previously thought.

Like humans, bees are sensitive to light at three different wavelengths (trichromatic). Also like humans, they can recognise the colour of objects such as flowers even when their illumination changes (so-called colour constancy).

5). Study: Single muscle far more complex than previously believed

The finding enriches a gradually emerging picture of a single muscle as a far more complex unit than traditionally believed. Research in the late 1970s and early 1980s showed that the amount of work a muscle does can vary along a lone muscle fiber. The most recent research is the first to document a range of activity within a single muscle of a live animal, in this case a helmeted guinea fowl.

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