So, enough introduction, let’s get the show on the road (apologising in advance for the thumbnail, and noting that English is not first language . . . ):

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EP: >> To fully understand an automated system, several representations of that system are necessary. Normally, technical drawings or blueprints are used for this purpose.  Blueprints could be considered maps to simplify the concept because they contain a layout of components with all the measurements and data related to the system represented.

For understanding modern automated systems several maps are usually necessary: mechanical, hydraulic and air equipment layout, electrical power distribution and control layout, data acquisition and other communication networking, safety circuit etc. These are maps of physical aspects of the machine, which are super imposable to represent or describe the whole automated system.

Components of an integrated automated system are physically interrelated in a specific way which enables them to interact in an organized and logical manner.

Figs 1 - 2: The concept of a process sequence chart

The chart breaks a sequential task down into steps, transitions and actions. These are presented graphically to describe a sequence of interactions as shown in Fig 2. above. Convention requires that flow through the chart is from top to bottom unless indicated by an arrow. The sequence is broken down into steps (or states) where actions are carried out. Each step can include one or more actions. Transitions define logical conditions that cause the process to move from the existing step to the next step.

Molecular machine, for example, a ribosome(Fig.3)  is a chemical, nano sized integrated system, organized into interrelated subsystems or components. It possesses a set of interacting discrete chemical units with relationships among them enforced by chemical forces. The state of each unit is constrained by or dependent on the state of other units.

Some of  ribosome’s  recognizable features are: physical proximity of its chemical units; specialization of its units; cooperative nature of interactions of its units; and distinct patterning of its chemical units.

Fig. 3: A layout view of a Ribosome in action, with mRNA tape and three successive tRNA's, showing as well a protein being assembled; note how the ferried-in amino acids are on the opposite end to the anticodons that match the codons in the mRNA tape

Let’s add Vuk Nikolic’s astonishing video of the process, so we can see what is going on . . .

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To fully understand this system a map of physical components in not enough. Another map, one showing steps of process flow is necessary. To produce this kind of map, repetitive interactions between ribosome subunits and subunit components should be studied and recognized and presented in the form of a process flow chart.

Fig. 4: The EP ribosome process sequence chart, reduced to the size of this page. Pardon, to see the full sized chart, please click here, then click on the image to go to the PNG in your browser window, then click to magnify. It may be useful to simply save and print the image on a sheet of paper. (Alternate site.)

Sequences of interactions, energy and material usage and error control are all easily recognizable on the flow chart type of representation. The advantage of visualizing the process is an instant general overview and easy understanding of process organization.

The process flow is enforced by chemical interactions of ribosome’s  components. Interactions in turn are achieved by special arrangements of ribosomal proteins and RNA. Some sections of ribosomal proteins and RNA are coupled to proper influx of energy and material.

During ribosome’s main mode of operation  matching amynoacyl tRNA (material deliverer) are accurately attracted from the crowded conditions around ribosome’s A site.  Error control is capable of rejecting accidentally attracted non-matching amynoacyl tRNA so that should be the secondary mode of operation.  A high error rate would slow protein production.

Footnotes

1. Basic principles of mapping interactions are the same regardless of the domain being mechanical, electro-mechanical or biochemical and regardless of sizes. Interactions of interest are sequential, logical in relation with each other and repetitive. Interactions may proceed in series, in parallel or the combination of two, depending on the components arrangement.

2. Diagram describing ribosome process is Sequential Function Chart (SFC) standard IEC 61131, one of the automation programming languages. Most of the main steps of ribosome’s process were included but some corrections are needed. It is possible to go further and include details down to the last molecule involved.  Unfortunately, high detail would make the chart enormous. That was not the purpose of this exercise. Instead, the purpose was meeting a challenge of  combining  two different fields, biology and automation.

3. Monitoring of third codon-anticodon  position is not included in the chart. Scientists explain in the reference article0  “third position is monitored less stringently “.

4. (Musings). It is mindboggling how ribosome manages to accurately attract matching tRNA from crowded conditions in front of A site. All 20 different tRNAs must be available for ribosome’s operation otherwise it will have to pause often. Fortunately, pausing is not costly in terms of energy usage as the elongation factor9 EF Tu delays hydrolyzing  of GTP.

Physicist Vlatko Vedral and his team investigated quantum entanglement effects which influence the shape of DNA. I can speculate there is a possibility of the same effects in high accuracy of complementary tRNA attraction. Another possibility is there is a form of amplification of mRNA template codon’s chemical forces via ribosome sub units. >>

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The process sequence map, of course, is a nodes and arcs map, and itself reveals an astonishing functionally specific complex organisation, with implied information.

The ribosome is not merely analogous to a process unit, it is a process unit, only, with a degree of miniaturisation we can only dream of accomplishing. Just for fun, let us compare the innards of a Spinning reel (which is far less complex):

Fig 5: A top quality rear-drag adjusting front drag manual bail surf spinning reel, showing the innards to achieve that (HT: Free Patents, fair use; and why not let the hard-working clever boys over at Van Staal have a free mention in exchange for fair use of an image . . . ?)

For even more fun, let us look at an exploded view — which is of course a nodes and arcs diagram — of a classic Abu Cardinal:

Fig 6: An exploded view of a classic ABU Cardinal [Fair use, sadly, these babies are no longer made so far as I know . . .], showing how functionality arises from a highly specific, tightly constrained complex arrangement of matched parts according to a Wicken “wiring diagram.” Such wiring diagrams are objective (the FSCO/I on display here that we may become consciously aware of when we see the reel work or fail, is certainly not “question-begging,” as some — astonishingly — are trying to suggest!), and if one is to build or fix such a reel successfully, s/he had better pay close heed. Taking one of these apart and shaking it in a shoe-box is guaranteed not to work to get the reel back together again. As for tornadoes in a junkyard over in Sweden assembling one of these classic babies, not a chance.  (That is, even the assembly of such a complex entity is functionally specific and prescriptive information-rich. FSCO/I is objectively real, get over it.)”]

So, now let us ask ourselves, soberly: on our experience of (i) searching for needles in haystacks, and (ii) the routinely observed source of such FSCO/I, what best explains the cell’s protein factory — BTW, the observed source of bio-functional proteins?

Then also, let us ask ourselves a few pointed questions:

1 –> If proteins are reasonably likely to spontaneously form, why would we end up with such an almost Rube Goldbergian apparatus for making proteins in the cell, in a controlled fashion?

2 –> And, given the mRNA code tape that drives the whole process, stored in DNA, then transcribed, snipped up and stitched together [in eukaryotes], then passed to the ribosome, then going through such a complex assembly process, how can we best explain the origin of codes, algorithms, data structures and algorithms implied in that code tape?

3 –>What is all of  this trying to tell us about he best explanation for the origin of the metabolising, self-replicating C-chemistry aqueous medium living cell? (Given, that this is the protein-making factory used in the cell hijacked by viri when they want to replicate themselves.)

Then, let us reflect on what our answers tell us about our worldviews and how open we are to reflect on what empirical evidence is revealing to us. END

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(And for those wanting a narrated version of the famous XVIVO vid, cf here.)

Remember, we are looking at these videos in light of Denton’s remark of 1985:

Sometimes, seeing is believing. END

Here is a nice, short summary of the kinesin microtubule highway “walking truck” protein in action:

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This vid gives a bit of context:

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Especially notice the role played by Brownian motion, and that played by ATP.

So, post turkey and pudding vid no 3: ATP Synthase in action:

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Walking trucks in the cell, fuelled by batteries made in a molecular factory that uses a nanotech motor  . . .

And, a highway network that has to go where it is needed, with need for directions — that delivery truck has to know where to go, when!

And the best explanation for all of this functionally specific, complex organisation and required information is . . . ?

Why?

I guess it would be helpful to reflect here on Denton’s classic word-picture:

And, again, you say the best explanation is . . . ? END

Every cell a densely populated ocean. I’d be interested to know whether wave mechanics can be used to interpret many of the behaviours of life forms.

www.hybridmedicalanimation.com/demoReel.html

Back in September of 2006 I announced at my blog UncommonDescent that a “breathtaking video” titled “The Inner Life of Cell” had just come out (see www.uncommondescent.com/…/the-inner-life-of-a-cell). The video was so good that I wanted to use it in some of my public presentations, but when I tried to purchase a DVD of it (I sent several emails to relevant parties), I was informed it wasn’t ready (to my knowledge the video is still not available for sale in DVD or any other format — if it were, I would gladly purchase it and encourage others to do so). Moreover, at the time, the video did not have a voiceover explaining the biology of what was being shown.

Although the video was at the time and remains to this day widely available on the web (YouTube has many copies — go, for instance, here), most simply have some background music that do not explain the relevant biology. A few months after announcing the video at UncommonDescent, I found on the Internet a version of the video that did add a voiceover, giving the relevant biology, and was in a format that allowed me to incorporate it into my PowerPoint presentations. I used the video a handful of times, including at a talk in Oklahoma this September. In consequence, some biologist(s) in the audience contacted the makers of the video, falsely suggesting to them and on the web:

(1) That I myself had modified the video and given it a new soundtrack.
(2) That I had stripped it of its copyright information.
(3) That I had retitled it “The Cell as an Automated City.”

Each of these allegations is false. Regarding (1), I downloaded from the Internet a version of the video with a voiceover describing the relevant biology. It seemed to me accurate and to have the best educational value for my listeners. The version I used took the original soundtrack, which simply had music, and added a voice. I had nothing to do with modifying or recrafting or authorizing the production of the video (in particular, that is not my voice on the video). The video I showed is the one I downloaded.

Regarding (2), the version I used omitted the opening credits (a fact about which I became aware only in the last few days), beginning instead with the actual animation; however, at the end of the video that I showed, there is the following copyright notice:

Conception and Scientific Content
by Alain Viel and Robert A. Lue
Animations by John Liebler / XVIVO
Supported by the Howard Hughest Medical Institute
Copyright (c) 2006. The President and Fellows of Harvard College

Here is the screen capture of the final thing people saw when I presented the video (note that it is dim, so it might be difficult to make out without a suitable projector and lighting):

Finally, regarding (3), the phrase “The Cell as an Automated City” was simply a caption for the video as it appeared in my PowerPoint presentation (a caption I used in context with the preceding slide). It was never meant to be a retitling of the video. Indeed, that caption never bled into the actual video but was always separate from it in my PowerPoint presentation.

I continue to this day to think that “The Inner Life of the Cell” is the best animation illustrating cellular activity. But there are other videos that make the same point. From now on, I will no longer use it and instead go back to using a clip from “Unlocking the Mystery of Life.”

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I find the phenomenon of the DNA supercoiling problem and its biochemical solution even more compelling than examples like protein synthesis and the bacterial flagellum, since twisted ropes are familiar to everyone. This might make for another highly persuasive ID mascot.

How could random variation and natural selection come up with a pair of biochemical scissors and a repair mechanism that cuts and splices the twisted DNA molecule in order to relieve torsional tension? What would be the functional, naturally-selectable intermediate steps in a hypothetical stochastically generated evolutionary process? It is clear that there could not possibly be any.

I’m suffering from a state of extreme cognitive dissonance. How can educated, intelligent scientists continue to defend the obviously indefensible, in light of what is now known about the nature of living systems (at all levels, not just the biochemical)? Richard Dawkins has remarked that biology was once a mystery, but “Darwin solved that.” Really?