A process sequence chart view of the ribosome in action — a guest post by EP

For some months now, I have been having a behind the scenes correspondence with a regular viewer of UD, whom we shall call EP. He works with industrial robots, and has been fascinated by the way the ribosome works as a nano-scale automated machine cell. Accordingly, a process sequence diagram (‘map”) has been developed, based on accessible descriptions of the ribosome in action. The result is a fascinating look at the ribosome as industrial robot work-cell. (The tRNA’s are molecular scale position-arm devices with a universal CCA coupler — yup, the AA bond is universal, it is the loading enzyme that sets up which tRNA gets what AA — to load and click AAs to a protein chain.)

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 . . . ):

_____________________

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 . . .

embedded by Embedded Video

vimeo Direkt

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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47 Responses to A process sequence chart view of the ribosome in action — a guest post by EP

  1. F/N: It is worth the while to add this thought exercise, from my always linked online note, App 1 point 6 (do read the whole appendix):
    ________

    >> 6] It is worth pausing to now introduce a thought (scenario) experiment that helps underscore the point, by scaling down to essentially molecular size the tornado- in- a- junkyard- forms- a- jet example raised by Hoyle and mentioned by Dawkins with respect in the just linked excerpt in Section A above. Then, based on (a) the known behaviour of molecules and quasi-molecules through Brownian-type motion (which, recall, was Einstein’s Archimedian point for empirically demonstrating the reality of atoms), and (b) the also known requirement of quite precise configurations to get to a flyable micro-jet, we may (c) find a deeper understanding of what is at stake in the origin of life question:

    NANOBOTS & MICRO-JETS THOUGHT EXPT:

    i] Consider the assembly of a Jumbo Jet, which requires intelligently designed, physical work in all actual observed cases. That is, orderly motions were impressed by forces on selected, sorted parts, in accordance with a complex specification. (I have already contrasted the case of a tornado in a junkyard that it is logically and physically possible can do the same, but the functional configuration[s] are so rare relative to non-functional ones that random search strategies are maximally unlikely to create a flyable jet, i.e. we see here the logic of the 2nd Law of Thermodynamics, statistical thermodynamics form, at work. [Intuitively, since functional configurations are rather isolated in the space of possible configurations, we are maximally likely to exhaust available probabilistic resources long before arriving at such a functional configuration or "island" of such configurations (which would be required before hill-climbing through competitive functional selection, a la Darwinian natural Selection could take over . . . ); if we start from an arbitrary initial configuration and proceed by a random walk.])

    ii] Now, let us shrink the Hoylean example, to a micro-jet so small [~ 1 cm or even smaller] that the parts are susceptible to Brownian motion, i.e they are of about micron scale [for convenience] and act as “large molecules.” (Cf. “materialism-leaning ‘prof’ Wiki’s” blowing-up of Brownian motion to macro-scale by thought expt, here; indeed, this sort of scaling-up thought experiment was just what the late, great Sir Fred was doing in his original discussion of 747′s.) Let’s say there are about a million of them, some the same, some different etc. In principle, possible: a key criterion for a successful thought experiment. Next, do the same for a car, a boat and a submarine, etc.

    iii] In several vats of “a convenient fluid,” each of volume about a cubic metre, decant examples of the differing mixed sets of nano-parts; so that the particles can then move about at random, diffusing through the liquids as they undergo random thermal agitation.

    iv] In the control vat, we simply leave nature to its course.

    Q: Will a car, a boat a sub or a jet, etc, or some novel nanotech emerge at random? [Here, we imagine the parts can cling to each other if they get close enough, in some unspecified way, similar to molecular bonding; but that the clinging force is not strong enough at appreciable distances [say 10 microns or more] for them to immediately clump and precipitate instead of diffusing through the medium.]

    ANS: Logically and physically possible (i.e. this is subtler than having an overt physical force or potential energy barrier blocking the way!) but the equilibrium state will on statistical thermodynamics grounds overwhelmingly dominate — high disorder.

    Q: Why?

    A: Because there are so many more accessible scattered state microstates than there are clumped-at -random state ones, or even moreso, functionally configured flyable jet ones. (To explore this concept in more details, cf the overviews here [by Prof Bertrand of U of Missouri, Rolla], and here — a well done research term paper by a group of students at Singapore’s NUS. I have extensively discussed on this case with a contributer to the ARN known as Pixie, here. Pixie: Appreciation for the time & effort expended, though of course you and I have reached very different conclusions.)

    v] Now, pour in a cooperative army of nanobots into one vat, capable of recognising jet parts and clumping them together haphazardly. [This is of course, work, and it replicates bonding at random. "Work" is done when forces move their points of application along their lines of action. Thus in addition to the quantity of energy expended, there is also a specificity of resulting spatial rearrangement depending on the cluster of forces that have done the work. This of course reflects the link between "work" in the physical sense and "work" in the economic sense; thence, also the energy intensity of an economy with a given state of technology: energy per unit GDP tends to cluster tightly while a given state of technology and general level of economic activity prevail. (Current estimate for Montserrat: 1.6 lbs CO2 emitted per EC$ 1 of GDP, reflecting an energy intensity of 6 MJ/EC$, and the observation that burning one US Gallon of gasoline or diesel emits about 20 lbs of that gas. Thereby, too, lies suspended much of the debate over responses to feared climate trends (and the ironies shown in the 1997, Clinton era Byrd-Hagel 95-0 Senate resolution that unless certain key "developing" nations also made the sacrifice, the US would not sign to the Kyoto protocol [they refused to amend the draft to include non-Annex I countries, and the US has refused to sign; signatories then have gone on to bust the required emissions cuts . . .], but that bit of internationalist “folly-tricks” and spin-doctoring is off topic, though illuminating on the concept of work and how it brings the significance of intelligent direction to bear on energy flows once we get to the level of building complicated things that have to function . . .)]

    Q: After a time, will we be likely to get a flyable nano jet?

    A: Overwhelmingly, on probability, no. (For, the vat has ~ [10^6]^3 = 10^18 one-micron locational cells, and a million parts or so can be distributed across them in vastly more ways than they could be across say 1 cm or so for an assembled jet etc or even just a clumped together cluster of micro-parts. [a 1 cm cube has in it [10^4]^3 = 10^12 cells, and to confine the nano-parts to that volume obviously sharply reduces the number of accessible cells consistent with the new clumped macrostate.] But also, since the configuration is constrained, i.e. the mass in the microjet parts is confined as to accessible volume by clumping, the number of ways the parts may be arranged has fallen sharply relative to the number of ways that the parts could be distributed among the 10^18 cells in the scattered state. (That is, we have here used the nanobots to essentially undo diffusion of the micro-jet parts.) The resulting constraint on spatial distribution of the parts has reduced their entropy of configuration. For, where W is the number of ways that the components may be arranged consistent with an observable macrostate, and since by Boltzmann, entropy, s = k ln W, we see that W has fallen so S too falls on moving from the scattered to the clumped state.

    vi] For this vat, next remove the random cluster nanobots, and send in the jet assembler nanobots. These recognise the clumped parts, and rearrange them to form a jet, doing configuration work. (What this means is that within the cluster of cells for a clumped state, we now move and confine the parts to those sites consistent with a flyable jet emerging. That is, we are constraining the volume in which the relevant individual parts may be found, even further.) A flyable jet results — a macrostate with a much smaller statistical weight of microstates. We can see that of course there are vastly fewer clumped configurations that are flyable than those that are simply clumped at random, and thus we see that the number of microstates accessible due to the change, [a] scattered –> clumped and now [b] onward –> functionally configured macrostates has fallen sharply, twice in succession. Thus, by Boltzmann’s result s = k ln W, we also have seen that the entropy has fallen in succession as we moved from one state to the next, involving a fall in s on clumping, and a further fall on configuring to a functional state; dS tot = dSclump + dS config. [Of course to do that work in any reasonable time or with any reasonable reliability, the nanobots will have to search and exert directed forces in accord with a program, i.e this is by no means a spontaneous change, and it is credible that it is accompanied by a compensating rise in the entropy of the vat as a whole and its surroundings. This thought experiment is by no means a challenge to the second law. But, it does illustrate the implications of the probabilistic reasoning involved in the microscopic view of that law, where we see sharply configured states emerging from much less constrained ones.]

    vii] In another vat we put in an army of clumping and assembling nanobots, so we go straight to making a jet based on the algorithms that control the nanobots. Since entropy is a state function, we see here that direct assembly is equivalent to clumping and then reassembling from a random “macromolecule” to a configured functional one. That is: dS tot (direct) = dSclump + dS config.

    viii] Now, let us go back to the vat. For a large collection of vats, let us now use direct microjet assembly nanobots, but in each case we let the control programs vary at random a few bits at a time -– say hit them with noise bits generated by a process tied to a zener noise source. We put the resulting products in competition with the original ones, and if there is an improvement, we allow replacement. Iterate, many, many times.

    Q: Given the complexity of the relevant software, will we be likely to for instance come up with a hyperspace-capable spacecraft or some other sophisticated and un-anticipated technology? (Justify your answer on probabilistic grounds.)

    My prediction: we will have to wait longer than the universe exists to get a change that requires information generation (as opposed to information and/or functionality loss) on the scale of 500 – 1000 or more bits. [See the info-generation issue over macroevolution by RM + NS?]

    ix] Try again, this time to get to even the initial assembly program by chance, starting with random noise on the storage medium. See the abiogenesis/ origin of life issue?

    x] The micro-jet is of course an energy converting device which exhibits FSCI, and we see from this thought expt why it is that it is utterly improbable on the same grounds as we base the statistical view of the 2nd law of thermodynamics, that it should originate spontaneously by chance and necessity only, without agency.

    xi] Extending to the case of origin of life, we have cells that use sophisticated machinery to assemble the working macromolecules, direct them to where they should go, and put them to work in a self-replicating, self-maintaining automaton. Clumping work [if you prefer that to TBO’s term chemical work, fine], and configuring work can be identified and applied to the shift in entropy through the same s = k ln W equation. For, first we move from scattered at random in the proposed prebiotic soup, to chained in a macromolecule, then onwards to having particular monomers in specified locations along the chain — constraining accessible volume again and again, and that in order to access observably bio-functional macrostates. Also, s = k ln W, through Brillouin, TBO link to information, viewed as “negentropy,” citing as well Yockey-Wicken’s work and noting on their similar definition of information; i.e this is a natural outcome of the OOL work in the early 1980′s, not a “suspect innovation” of the design thinkers in particular. BTW, the concept complex, specified information is also similarly a product of the work in the OOL field at that time, it is not at all a “suspect innovation” devised by Mr Dembski et al, though of course he has provided a mathematical model for it. [ I have also just above pointed to Robertson, on why this link from entropy to information makes sense — and BTW, it also shows why energy converters that use additional knowledge can couple energy in ways that go beyond the Carnot efficiency limit for heat engines.] >>
    ________

    Now, remember, the challenge does not start at the level of a full bore Jumbo jet, it begins at the level of say a D’Arsonval galvanometer instrument on its instrument panel. Just 500 bits of explicit or implied functionally specific, complex information is enough to swamp the resources of our solar system on blind search, and 1,000 bits, those of our observed cosmos.

    Don’t let anyone bamboozle you with dismissive talking points about the “Hoyle Fallacy.”

    Sometimes, the fallacy of label and dismiss is the real fallacy at work. Anyone who poses this should be invited to show, empirically, a case where an entity with just 500 bits of functionally specific complex info has been formed by blind chance and mechanical necessity, without intelligent guidance, control or intervention.

    To show just what I am talking about, let us choose a particularly simple case, the infinite monkeys algorithm of random text generation. As Wikipedia, testifying against interest will admit:

    One computer program run by Dan Oliver of Scottsdale, Arizona, according to an article in The New Yorker, came up with a result on August 4, 2004: After the group had worked for 42,162,500,000 billion billion monkey-years, one of the “monkeys” typed, “VALENTINE. Cease toIdor:eFLP0FRjWK78aXzVOwm)-‘;8.t” The first 19 letters of this sequence can be found in “The Two Gentlemen of Verona”. Other teams have reproduced 18 characters from “Timon of Athens”, 17 from “Troilus and Cressida”, and 16 from “Richard II”.[25]

    A website entitled The Monkey Shakespeare Simulator, launched on July 1, 2003, contained a Java applet that simulates a large population of monkeys typing randomly, with the stated intention of seeing how long it takes the virtual monkeys to produce a complete Shakespearean play from beginning to end. For example, it produced this partial line from Henry IV, Part 2, reporting that it took “2,737,850 million billion billion billion monkey-years” to reach 24 matching characters:

    RUMOUR. Open your ears; 9r”5j5&?OWTY Z0d…

    500 bits would be about 72 characters of text, and for every ASCII character added, the space of possibilities is multiplied by a factor of 128.

    That should serve to help us understand the challenge of getting to FSCI as is measured by:

    Chi_500 = Ip*S – 500, bits beyond the solar system threshold.

    (And again, use common sense when you find the usual attempts to dismiss by strawmannising and claiming all sorts of clever objections. Information that is at work, i.e. that functions, is measured in bits; as commonly seen as your friendly local PC. S is simply a parameter a so-called dummy variable that allows us to, having empirically examined that the body of information is such that if it is significantly changed at random — toss a noise bomb at it and see what happens — it will stop working. Just remember, there was once a NASA rocket that had to be blown up on launch because someone got a comma wrong. The 500 is there as a reasonable threshold of complexity, on the same grounds as we just saw for random text generation.

    In short, we have excellent grounds for seeing that FSCI as measured by this is a strong empirical sign of the only thing routinely observed to create it, intelligence.

    Those who a=want to dispute this empirical, inductive generalisation from billions of cases, should be asked: p-lease, stop the clever arguments, just simply provide us with a case in point where on our observation, blind chance plus mechanical necessity produced such FSCI. No smuggled-in intelligent action, please. last two times around, we had a clock that in software assembled itself out of “simple parts” but the real world of getting gears etc — as the reels in the OP above show — is not like that at all. next, we had some geoglyphs in Amazonia, and were able to calculate values for FSCI that showed that if you see a 100-m circular 15 foot or so ditch with a consistent profile, it is best explained on intelligence.

    So, just stand your ground.

    KF

  2. I would like to point out that the ribosome is not the complete system for the manufacture of proteins. In addition there is the subsystem that creates mRNA from DNA, including controls that dictate which proteins will be produced and when, the subsystem that transports the mRNA out of the nucleus and to a ribosome, subsystems that reprocess proteins to make their amino acids available for reuse, subsystems that create tRNA and attach the amino acids to them correctly, subsystems that transport the tRNA to the ribosomes, etc. All of this reveals a system of staggering complexity and engineering sophistication, a system that is entirely self-contained, with internal controls, repair and maintenance, error correction, and the ability to reproduce itself. The most complex systems engineered by humans cannot maintain themselves indefinitely without external intervention, and none of them reproduce themselves.

    What is astonishing to me is the fact that so many intelligent, knowledgeable human beings continue to convince themselves that such a system could ever have arisen naturally. This is an example of the highest order of the capacity of human beings to be in denial of any evidence which contradicts their worldview.

  3. Dear Bruce:

    What is astonishing to me is the fact that so many intelligent, knowledgeable human beings continue to convince themselves that such a system could ever have arisen naturally. This is an example of the highest order of the capacity of human beings to be in denial of any evidence which contradicts their worldview.

    Precisely, and superbly expressed. I was nurtured from a young age with Darwinian orthodoxy, and thoroughly indoctrinated in the Darwinian catechism into college and beyond. I thus had a lifetime philosophical commitment to Darwinian materialism as the only rational explanation of origins.

    But eventually it became obvious to me that I had been conned. The “overwhelming evidence” of the creative power of the Darwinian mechanism was nowhere to be found. Much to the contrary, the only overwhelming evidence was that Darwinian speculation about such creative powers was based on blind faith in the hopelessly improbable.

    As evidence continues to accumulate that the Darwinian mechanism cannot possibly account for what is continually and inexorably discovered concerning biological engineering sophistication, we can expect further irrational and emotionally-driven attacks upon those of us who insist that the evidence must be pursued to its logical conclusion: Design.

  4. Strange that evos chide IDists for not presenting positive evidence for ID, yet when we do, as evidenced by this OP, evos are noticeably absent from the discussion…

  5. 5

    Joe, you beat me to it. Are the Darwinists who post regularly on this site struck dumb by the OP? Please, push back. We want to hear your side.

  6. Barry,

    Maybe you could push it back to the top/ headline post for a couple days-

  7. Well, there are an awful lot of threads! I do suggest that fewer posts might actually benefit this site.

    OK, I’ll have a go?

    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?

    There is a problem with this premise: whether they are “reasonably likely to form” depends very much on the environment you are talking about. Water is “reasonably likely to form” in the presence of hydrogen and oxygen. It’s very unlikely to form in the absence of one or the other!

    The big OOL question (and indeed questions regarding the origins of protein synthesis) is not “are proteins reasonably likely to form”? but “under what conditions are proteins reasonably likely to form?” We know that they do form under the “Rube-Goldbergian” conditions that exist within cells; but are there any other conditions in which they might also form? And if the answer is yes, the straightforward Darwinian answer would to your question would be: if a Rube-Goldbergian tweak makes the process more controlled/reliable/whatever, then any Rube-Goldbergian tweak that comes along is going to be retained in the gene pool. Darwinian evolution tends to produce Rube-Goldbergian results, in fact, unlike (some) engineers, because it is a continuous process of retro-fitting.

    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?

    Well, as I’ve said before, we don’t have a definitive, or, as yet, terribly persuasive detailed account of the origin of DNA coding, although the consensus seems to be that it was preceded by RNA coding. That would make sense, given that so much of the reproductive machinery consists of RNA.

    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.)

    Again, we don’t know, but I do think Jack Szostak has promising findings.

    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.

    OK. Don’t think it tells me much about mine. Certainly doesn’t tell me whether there is a Creator God or not, nor whether I should love my neighbour as myself, nor whether I shall have some kind of existence beyond my death.

    It does tell me that there are some very interesting mysteries to solve about the origin of life. I’m looking forward to the next thirty years (and hope I survive them!). My gut tells me we will have managed to produce life-forms from non-living ingredients in the lab by then. I also think we may be wondering whether our robots are conscious.

    Still won’t tell me whether there is a Creator God or not.

    :)

  8. Is there something new here?

    What is astonishing to me is the fact that so many intelligent, knowledgeable human beings continue to convince themselves that such a system could ever have arisen naturally.

    What astonishes me is that, assuming it didn’t arise naturally, there are otherwise intelligent people who think a non-omniscient designer could poof together 500 bits of non-connected sequence without using evolution or GAs.

    On the evolution side one merely accepts the fact that incremental change is the only known method of reaching such sequences and methodically testing scenarios. It’s a slow and painful process, but it’s what we’ve got.

    The travelling salesman problem demonstrates that GAs can easily assemble sequences from a search space of 10^150 possibilities. The only provision required of such a space is that it supports incremental stepping.

    That is why current formulations of ID will stand or fall on whether sequence space is connected, or can be connected by the various modes of genetic change. Fortunately that’s an empirical question.

  9. Just a general point:

    There seems to be a fairly widespread assumption on the part of many posters on this site, that the reason “Darwinists” don’t find it difficult to accept that life probably emerged from non-life by perfectly natural, but also fascinating and awe-inspiring, means, is that they are terrified of the religious implications if it didn’t.

    In my experience that is simply not the case. The reason is much more likely to be (and is in my own case): the world makes a huge amount of sense, and appears to follow discernable laws; why would we expect this norm to be departed from in the case of life? Especially when we have an excellent theory that accounts for so much biological data?

    We don’t fear the possibility that there may be some weird violation in the case of life, it’s just that we see no more reason to think there will be than that there is a teapot orbiting the sun somewhere near Mars. We can’t definitely prove there isn’t, but why would we think there is?

    Naturalism can be true (in the sense that phenomena within the world are explainable in terms of the world itself) and God can still exist. Naturalism does not imply atheism.

    So why would we have any vested interest in it being true? Even if we were terrified of God?

  10. Petrushka,

    The travelling salesman problem demonstrates that GAs can easily assemble sequences from a search space of 10^150 possibilities. The only provision required of such a space is that it supports incremental stepping.

    Easily. All it requires is 70+ years of computer technology just to get the hardware and software to create a platform for writing symbolic code to execute instructions and solve problems. And then a programmer to write the GA. And a traveling salesman. And here’s the slightly harder part – someone must subjectively determine that a shorter route is better than a longer one.

    If that is your evidence that a process devoid of purposeful intelligence can navigate such search spaces, then it is refuted, black and white, case closed, never to be mentioned again (wishful thinking.)

    If it is your position that no intelligent agent could reach a prespecified target by folding proteins then yours is an argument from ignorance in the truest sense. I’m confounded that given the history of learning and the very existence of the concept of science you would measure the capabilities of technology and the potential for knowledge against the state of technology and knowledge at one moment in time. It is a simultaneous refutation of intelligence, learning, and science!

  11. Elizabeth,

    There seems to be a fairly widespread assumption on the part of many posters on this site, that the reason “Darwinists” don’t find it difficult to accept that life probably emerged from non-life by perfectly natural, but also fascinating and awe-inspiring, means, is that they are terrified of the religious implications if it didn’t.

    That’s not how I would state it. I believe that people develop a particular worldview based on their upbringing and education. That worldview can be grounded in atheistic naturalism, religious fundamentalism (of any particular stripe), religious belief of a non-fundamental nature, agnosticism, or non-religious forms of theism. Most people, once this worldview has solidified, stick with it for the rest of their lives. It becomes part of their identity, of who they think they are, and part of the fundamental bedrock of belief upon which they base their lives. Thus, it is defended against any and all attacks, ie., any evidence that might call it into question. I think that fear can be involved, but it is the fear that they have been wrong all their lives, and possibly fear of loss of identity.

    Like Gil, Michael Behe, Douglas Axe, and others, I look at the incredible complexity and obvious engineering of life, from the machinery of the cell on up to the systematic interconnections of the subsystems of large multicellular organisms, and it’s simply obvious that it was designed and built by some incredibly talented engineer (or engineering team). While it’s true that all of the analysis that has been done by ID proponents—irreducible complexity, probability calculations, CFSI, experimental verification, analysis of the fossil record—supports the conclusion, that work really isn’t even necessary. One has only to look carefully at what we’re dealing with, like in the OP, to see that it’s so. Frankly, Elizabeth, the only way that I can explain to myself how someone as intelligent and knowledgeable as you, for example, can not see something so totally obvious is that you are too committed to your materialist worldview to allow for the possibility.

    I mean no disrespect in this. I think you’re human, just like the rest of us.

    All that said, I do also believe that there is a concern (“terrified” is too strong a word) on the part of many who defend a naturalistic view of creation that if one allows for the truth of ID it could support efforts on the part of religion to reassert the power it once wielded over society, power which people fear (rightly, in my view) would result in a diminution of individual freedom.

  12. My mother was obsessive about cleanliness. I won’t bore you with the details, but she was beyond having high standards and well into OCD. As silly as this is, years later I feel the tiniest bit of empowerment every time I walk across my own living room in my shoes or eat dinner on the sofa. (Jesus reclined. Why shouldn’t I?) It doesn’t matter whether she was right or wrong. I felt oppressed, and now I feel empowered by casting it off.

    I suspect that’s a part of what underlies the atheistic/evolutionist worldview. (Sorry if I’m psychoanalyzing in general. I understand that we are all different.) It’s empowering to take the beliefs and practices of generations past, many of which may have actually been quite irrational or even harmful, and minimalize them. Perhaps it’s doubly so when done in the name of science and enlightenment. Why boost ourselves in comparison to our next door neighbor when we can do so against people who have been dead for hundreds of years?

    I don’t mean to offend by suggesting that what people hold to be reasonable may have a psychological undercurrent. But it’s quite often there.

  13. Frankly, Elizabeth, the only way that I can explain to myself how someone as intelligent and knowledgeable as you, for example, can not see something so totally obvious is that you are too committed to your materialist worldview to allow for the possibility.

    Well, of course, that’s how it looks from this end of the telescope too :)

    It fascinates, me, actually, how good people can be so convinced that the other lot are the ones not seeing the obvious! It’s a perfectly symmetrical situation. My conclusion is that nothing is as obvious as we think it is :)

    Still, I must supply a discrepant data point for your model re me:

    I was brought up by a mother who was both a scientist (gave up her PhD to have me, sadly, although remained a physician) and a devout Christian. So while you might blame her for my “materialist” outlook, you could just as easily credit her for my “scientific” one, because neither of us ever thought of it as “materialism”, just science. And you can scarcely blame her for my atheism, because, like her, I was a devout Christian myself*, for half a century or more. Indeed, I still regard myself (as I’ve said elsewhere) more as a theist than a non-theist, and one of Christian flavour, though I think “pantheist” is a better description. So to say I am “too committed to [my] materialist world view to allow for the possibility [of ID]” just doesn’t seem to me to fit the facts.

    It is true, I guess, that I am committed (as I have indicated in vjtorley’s thread on it) to “methodological naturalism” but I regard that as a methodology, not as a “world-view” – and I’d defend it on what I’d regard as entirely logical grounds: the scientific method concerns natural causation, and simply does not have a way of testing non-natural/supernatural/non-material/non-physical hypotheses (in which I do NOT include design by intelligent agents, of which you and I are two, and we are perfectly material beings :))

    But there was never any conflict in my mind between my theism and my science; it simply never occurred to me that the two were not compatible (I was not, of course, a YEC!) I simply regarded the world as God’s creation, and science as the business of figuring out how it worked.

    And I still love this song:

    http://www.echoschildren.org/CDlyrics/WORDGOD.HTML

    So, while I don’t expect to convince you of my view of the origins of life, let me at least try to convince you that it is not derived from “commit[ment] to [my] materialist worldview”, but because I actually find the evidence for it convincing. I’d rather you thought less of my intelligence than of my integrity :)

    *I mean that in all seriousness, not as a boast, but as a simple fact: I had a very profound religious experience at quite a young age (about four, I would guess) and still recall it vividly as a moment of utter bliss and one-ness with the world; I was lying in the heather on Caldy Island, off Pembrokeshire, Wales, smelling the thyme, hearing the bees, and then what must have been the Angelus, followed by the Cistercian monks chanting. All my senses felt utterly saturated by the entire universe, it seemed. Although my family were Episcopalians (Scottish), and although I subsequently was educated at a Quaker school and became a Quaker, I never lost that sense that moment, was confirmed at university in a very High Church Anglican parish (smells and bells), and subsequently became a Catholic, about a year after I married in a Catholic church (i.e. not just to get a fancy wedding!) I did the music for mass for years, and ran Sunday schools. I even wrote stories about God for children, and one was published in several languages and did quite well (though I see the US edition is now out of print).

    http://www.amazon.com/Pip-Edge.....0802852572

    And when I did change my mind (I guess you’d call it), it was not willingly. If anything, my commitment was to the worldview I was leaving, not the one I was joining.

    Anyhoo. I rest my case :)

    cheers

    Lizzie

  14. Oh, I would agree, Scott :)

    (Not being snarky, I really agree: even the most reasonable views – and I include ones I share – can hide unchallenged assumptions and emotional anchors.)

  15. All that said, I do also believe that there is a concern (“terrified” is too strong a word) on the part of many who defend a naturalistic view of creation that if one allows for the truth of ID it could support efforts on the part of religion to reassert the power it once wielded over society, power which people fear (rightly, in my view) would result in a diminution of individual freedom.

    Yes, I think that is true. But the fear is not simply of “diminution of individual freedom” but of denial of basic human rights.

    Which might turn out to be two ways of looking at the same thing :)

    But I think we can distinguish, all the same: I don’t think we (if “we” is the right word) fear, for example, that a more theocratic society would prevent us from stealing, or murdering, or exploiting other people; it might be better at preventing that, or it might not, but that isn’t what we fear. Most of us would hugely welcome a reduction in crime.

    What we fear is that a more theocratic society would make women wear veils; make homosexuality a crime; require us to carry all pregnancies to term; ban contraception; insist that we live out our days in pain rather than be eased, at our wish, into timely death; ban female education; disallow gay marriage; punish sex with stoning.

    And while you may approve, and even campaign for, some of those things, you must surely share our fears of some.

  16. Folks:

    Thanks for the thoughts, on behalf of EP. (Apparently he does not have full commenting privileges here at UD.)

    There is one thing I need to point out.

    Namely, what is going on here is that the ribosome is implementing a code controlled automated assembly process that can be represented in the same sort of diagram used in the automotive industry or other industries that make heavy use of industrial robots.

    We are not dealing with analogies here, but instantiation.

    So, are we to be invited to think that mechatronic systems of the complexity, sophistication and miniaturisation we are seeing, arose by blind chance and mechanical necessity?

    If so, on just what specific, solid grounds in observation can such an astonishing claim be made?

    Failing that, should we not rather infer that the best explanation for an even more sophisticated mechatronic system that those in our factories, is even more sophisticated engineers?

    GEM of TKI

  17. The evidence is that ants use the travelling salesman GA algorithm and in fact invented it. It does not require a high order of intelligence, just a means of comparing the length of two or more routes.

  18. EP via KF, I really enjoyed this post.

  19. It may be simply obvious to you, but if it can’t be tested empirically it’s not science.

    I think that the following statement: “that work [empirically testing ID] really isn’t even necessary” says it all.

    There are many, many things that are simply obvious to many people. Put together, all of those obvious things that people personally know about the world amount to zero knowledge, unless they can be empirically tested.

    Of explanations with high degrees of empirical support, we can say “we know that ______”. As in “we know that the earth revolves around the sun”, or “we know that life evolved from a common ancestor.”

    Of things that don’t have empirical support, we can only say “we know that some people believe _______” As in “we know that some people believe that the positions of the stars when they were born affect their lives” or, “we know that some people believe in ghosts.”

  20. So, are we to be invited to think that mechatronic systems of the complexity, sophistication and miniaturisation we are seeing, arose by blind chance and mechanical necessity?

    Not exactly. At any rate, I think that is a very poor description of the proposed mechanism.

    Think rather of “a continuous optimisation process of a self-reproducing system, in which any slight variant of the current system that makes reproduction more likely is retained, and anything that makes it less likely is rejected”.

  21. a means of comparing the length of two or more routes

    Yeah?

    Just taking you at face value for argument’s sake, exactly what would that physically entail??

  22. The relevant fact about the travelling salesman problem is that a simple incremental traversal is the only known way of solving it with finite resources.

    Even intelligent designers have to use evolution when the numbers get big.

    Of course there are spaces that can’t be traversed incrementally, such as encrypted data. If sequence space turns out to resemble a cryptogram, then evolution is impossible.

    If it’s not a cryptogram, then intervention by a designer is unnecessary.

  23. 23

    LYO,

    It may be simply obvious to you, but if it can’t be tested empirically it’s not science.

    Just as a point of consistency; any conclusion that the universe had a beginning (Big Bang Theory) isn’t science because we cannot test that conclusion, even though it is based upon what we can and do see and test.

    Correct?

  24. 24

    You didn’t answer the question. It doesn’t appear that you even attempted to

    Are you suggesting numbers are required?

    Answer the question as to what is required to fulfill you statement:

    a means of comparing the length of two or more routes

  25. Thanks Upright Biped

    I love your semiotic argument.

    Dawkins said:

    “Although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist” (Dawkins 1986)

    To rephrase Dawkins now:

    …latest science made it possible to be an intellectually fulfilled theist.

  26. Mrs Liddle (Am I correct ?)

    You stated the following:
    “Naturalism does not imply atheism.”

    First the definition of naturalism (in philosophy)

    Philosophy .
    a. the view of the world that takes account only of natural elements and forces, excluding the supernatural or spiritual.

    b. the belief that all phenomena are covered by laws of science and that all teleological explanations are therefore without value.

    To argue that this does not imply atheism is fraudulent as I believe should be clear to you from reading the posted definitions. Unless, of course, you were using naturalism in another sense apart from that which has been defined above. This is something I doubt.

  27. This may seem like a nitpick but I think it’s important: you don’t “test” a conclusion, you test a hypothesis.

    And you can certainly test the hypothesis that the world had a beginning. Or at least that the duration of the world so far appears to have a finite value. And, if supported, you can provisionally conclude that it did.

    (Although the bigger problem here is expressing both hypothesis and conclusion in language designed (heh) to describe human-scale time and space. “Beginning of time” is a phrase without a referent in any other context than Big Bang, and we cannot therefore extrapolate our every day understanding of time to our understanding of what the phrase “Beginning of time” might mean. Still that’s a topic for a different thread I think.)

  28. I agree, and I would add, ban any speech that is viewed as heretical or “ungodly”, ban the right of anyone to have relationships with members of their own sex if that is their wont, ban opening business on the Sabbath, and I’m sure I could think of some more if I devoted more time to it.

    I view myself as spiritual but not religious. One of the tenets of my “faith” is that God grants us perfect freedom, not just free will, but freedom itself. In other words, no punishment, no matter what we choose to say or do. The granting of freedom to each human being by the society in which he or she lives is as important to me as it is to you.

  29. 29

    Liz: “Beginning of time” is a phrase without a referent in any other context than Big Bang, and we cannot therefore extrapolate our every day understanding of time to our understanding of what the phrase “Beginning of time” might mean.”

    This is why people get accused of worldview corrupting science. You liz, the empiricist, the clear authority on scientific methodology, is now pivoting from the empirical evidence for t=0 into a philosophical treatment. Into a …what… does it…can it… all mean…stoner rant.

  30. Elizabeth:

    Water is “reasonably likely to form” in the presence of hydrogen and oxygen.

    That’s a joke, right? It takes more than just the presence of hydrogen and oxygen to get water.

    That said there isn’t any evidence that proteins can form without a ribosome, which needs proteins to form.

    The reason is much more likely to be (and is in my own case): the world makes a huge amount of sense, and appears to follow discernable laws; why would we expect this norm to be departed from in the case of life?

    Umm that is exactly why we infer design wrt living organisms.

    Especially when we have an excellent theory that accounts for so much biological data?

    Where is this alleged “excellent” theory, then?

  31. Ah, Lizzy, you never cease to amaze!

    I accused you of being a materialist because that is how you characterized yourself in an earlier post. I retract the accusation.

    My spiritual journey has been the complement of yours. I started out life as an atheistic materialist, having been raised by an agnostic father and a mother who believed in God because “there must be something to give life to newborn babies”. It was the evidence that didn’t fit the paradigm, much of which I have recounted in other threads, that caused me to re-evaluate that position. The particulars of my spiritual beliefs have been in a continual process of evolution ever since. I do not, however, consider myself religious.

    Regarding methodological naturalism, how do you respond to Stephen Meyer’s carefully reasoned argument that the scientific method used in the historical sciences (archaeology, cosmology, paleontology, etc.) seeks the best explanation for the phenomena they study, based on causes that are known from experience to be acting in the present. Therefore, in the case of the origin of life, since the only known cause of complex specified functional information (which is found in abundance in even the simplest cell) is the action of an intelligent agent, that must be the best explanation. In other words design is a conclusion that is reached via the scientific method which is used in the historical sciences.

    In still other words, it is entirely within the province of science as it is practiced to draw the conclusion that design is the best (indeed the only reasonable) explanation for the existence of some phenomenon. Note that this does not preclude additional data at some later date overturning that conclusion. No conclusion is science is ever irrevocable.

    And by the way, I am aware that my argument (it really isn’t an argument anyway) regarding the obviousness of the design of living systems cuts both ways. However, I’ll stick to those guns. To me (and to an awful lot of other very bright people) it is obvious. And frankly, Lizzy, I’m still puzzled by the fact that you can’t see it.

    Or am I wrong about that? Do you accept that design is the best explanation, but hold that the designers were somehow physical beings subject to physical law?

    Here’s another question that just occurred to me: Given that you are something of a theist, why do you insist that you and I are totally physical beings? Why don’t you allow for the possibility that at least some aspects of our nature cannot be fit into a materialist paradigm?

  32. “Just comparing” is a lot. It is the essence of intelligence. In the case of ants, collective intelligence. No means is known to exist apart from intelligence to coerce nature to spontaneously begin to choose between two or more options in order to optimise a function.

  33. hat’s a joke, right? It takes more than just the presence of hydrogen and oxygen to get water.

    I didn’t say it didn’t.

    Where is this alleged “excellent” theory, then?

    Oh, I dunno, start with Darwin, and then read on :)

  34. lastyearon:

    It may be simply obvious to you, but if it can’t be tested empirically it’s not science.

    Well, you have just invalidated all the historical sciences (origins biology, paleontology, archaeology, etc.) None of the hypotheses or conclusions of these sciences can be tested empirically for the simple reason that we can’t go back into the past and run the experiments. You can’t even test the assertion that the origin of all species is the result of Darwinian processes. Thus, by your definition, Darwinian evolution isn’t science either.

    And anyway, I never said that the conclusion I drew is science. It is a conclusion I draw from knowledge of the structure and function of living things. It’s obviously true. It doesn’t have to be science.

  35. Self replicating systems of the sort in the cell — vNSRs — are of course FSCO/I and IC. They give every evidence of design, KF

  36. I started with darwin, read on and all I have read are vague speculations.

    The “theory” of evolution can be summed up as -

    “Once living organisms appeared some things happened some time in the past, other things kept happening which led to diverging branchs of descent with modification, and here we are because we traversed the fitness landscape thus diversifying into the emerging diversity of variability.”

    Hey if you don’t believe me just go the The Smithsonian Nat Museum of Natural History in DC- right at the beginning they have this show with a talking amoeba who gives you basically that.

    We do know that genes control traits. Beyond that it’s anybody’s guess.

  37. Thanks for your gracious post (again!) Bruce :)

    You asked me three good questions:

    Regarding methodological naturalism, how do you respond to Stephen Meyer’s carefully reasoned argument that the scientific method used in the historical sciences (archaeology, cosmology, paleontology, etc.) seeks the best explanation for the phenomena they study, based on causes that are known from experience to be acting in the present. Therefore, in the case of the origin of life, since the only known cause of complex specified functional information (which is found in abundance in even the simplest cell) is the action of an intelligent agent, that must be the best explanation. In other words design is a conclusion that is reached via the scientific method which is used in the historical sciences.

    I actually dispute Meyer’s distinction between “historical” sciences and other sciences. Or, at least, I don’t think the methodologies are fundamentally different: both involve deriving hypotheses from explanatory theories and testing those hypotheses against new data, even if that data is from events that occurred billions years ago. So his argument that scientists in these fields “seek… the best explanation for the phenomena they study, based on causes that are known from experience to be acting in the present” is no more (or less) true for any science than it is for what he calls “historical” science. Now it’s true that when studying the remote past we may have to hypotheses factors that existed then and do not exist now, but that is true for any hypothesis (it’s why the word “hypothetical” is derived from “hypothesis”). But what is not true is that we are justified in extrapolating from factors that exist now (human designers) to factors that we have no reason to think existed then (human or otherwise) to explain phenomena that occurred then. Under any kind of science, “historical” or otherwise. So I think Meyer is just plain wrong on this. As for “…in the case of the origin of life, since the only known cause of complex specified functional information (which is found in abundance in even the simplest cell) is the action of an intelligent agent, that must be the best explanation”, I’d disagree that an intelligent agent (if by that we mean an external, intentional designer/artisan) is the only known cause of complex specified functional information. So I’d reject that anyway.

    Or am I wrong about that? Do you accept that design is the best explanation, but hold that the designers were somehow physical beings subject to physical law?

    My position is that life is created by an intrinsically “intelligent” system – not one with foresight, but with what Petrushka the other day called a “tactile” searching facility – in other words the basic Darwinian algorithm. I don’t know how the first Darwinian-capable self-replicators came into existence, but I think they were probably simple enough to have emerged spontaneously in early earth. That is just hunch though, but a sufficiently strong one that I am not inclined to put a “insert miracle here” in that spot :)

    Here’s another question that just occurred to me: Given that you are something of a theist, why do you insist that you and I are totally physical beings? Why don’t you allow for the possibility that at least some aspects of our nature cannot be fit into a materialist paradigm?

    Oh, I allowed for it for fifty odd years :) I thought it was self evident that there was something else going on (Exhibit One: our own awareness of being here). Then I had something of an epiphany and realised that while there is indeed “something going on” and a very interesting something, there’s a perfectly good (if non-intuitive) explanation for it :)

    So I’m still open to the idea in principle, but see no need for it – no mystery that it would explain. But, I have to say, not much more open to it than I am to the possibility that there are ley lines or psi. Possible, but not compelling.

    Anyway, lovely to have such a productive conversation, and good to hear about yourself :) I do miss my old God. But she didn’t actually go far :)

    Cheers

    Lizzie

  38. Golly, sorry about the manic smileys! I tend to type them whenever I smile, so wysiwyg.

    :)

  39. Lizzy,

    I’m glad you’re smiling; I like smiles. :)

    I think it’s really interesting that we two could, from basically the same data, draw such different conclusions. I was a materialist, not for 50 years but maybe 25, believing that activity in the brain could account for human thought, emotion, impulses, etc. Then I had an epiphany: there is no way to get experience (qualia) from inanimate matter. It made no sense to me to say that well, if the neural interconnections are just numerous enough and complex enough, conscious will just “emerge” or “arise”, like magic. This was followed by another one: there is no compelling reason to believe that there is actually any material world “out there” that corresponds to our perceptions of it. Another way to say this is to observe that there is no way that I can prove, even to myself, that I am not dreaming right now. Put these two together, and the only philosophical stance that satisfactorily explains “everything” is a version of Bishop Berkeley’s—we are spirit, and the physical universe is a kind of virtual reality in which God runs the show. An interesting aspect of this is that some physicists and philosophers of science are coming to the same conclusion because quantum physics simply does not make sense in the context of a physical universe that exists independently of our minds.

    A belief in the existence of God, however, does not imply that all of Christian belief is valid, nor, for that matter, any other religious dogma. So the remainder of my life has been a search for the truth of how things really are.

    Based on what I have seen so far, Lizzy, I am convinced that you will meet Her again, after your next transition if not before, and that you will have nothing to fear from Her. She will love you unconditionally, as She does now, and She will welcome you back with open arms.

  40. I should add that the phrase “open arms” is intended to be metaphorical. The only arms She has are ours.

  41. Well, what does it mean? Nobody knows yet.

    Mathematically, it doesn’t work, and we (yet)don’t have laws of physics that cover it.

    There is no “empirical evidence” for “t=0″ AFAIK. There are various mathematical models, from which testable hypotheses can potentially be derived, and tested in various ways (including experimentally, in the LHC). The Hawking-Hartle model, doesn’t have a “t-0″ point, as I understand it – space-time is “bell shaped” as it were, rather than conical.

    At any rate, if you have “empirical evidence” for “t=0″ please link to it :)

    There may be a Nobel in it for you.

  42. And there we can agree :)

    Bless you, Bruce.

  43. Not “of course” at all, kf. That is the very point at issue.

  44. You, too, Lizzy.

  45. Dr Liddle:

    DNA in living systems is past 100 k bits [oops], and is functionally specific and code based. The von Neumann kinematic self replicator in the cell has a core set of necessary and sufficient elements, making it irreducibly complex. It is this property that is a good part of why it is o hard to come up with non-design OOL scenarios. The need for coded info just caps that off.

    KF

  46. Wecome EP

    Hope things are sorting out.

    KF

  47. Thanks Kairos

    hopefully,too.

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