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Kirk Durston on “God and Science – Is there a Conflict?” . . . food for thought

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I think we need to watch a video by Friend of UD, Kirk Durston.

But first, a loop-back note: I have been rather busy elsewhere with issues like AS-AD, Kondratiev waves, Hayek’s investment triangle, SD and Schumpeterian creative destruction.(Pardon the resulting absence.)

BTW, this line of thought leads me to hold that the oh- so- dominant . . . and too often, domineering . . . evolutionary materialism of the past few generations has run its course and is about to be overtaken by ideational creative destruction in an information age.  A patently superior idea — we live in an obviously designed world, and we and other living creatures show further compelling signs of design — is going to prevail, never mind what the materialist establishment entrenched in key halls of power thinks.

Never mind the scorched earth bitter ender retreat.

Sooner or later, for instance, it is plain that a critical mass of people will put two and two together on the world of life and realise that we are looking at an utterly sophisticated, subtle and algorithm-rich, code using molecular nanotech system when we look at the living cell.

You don’t have to take my word for this, reflect for a few moments on what Stanford investigators have shown and said about our old friend M. genitalium:

mg_pathways{Let’s add an image from the project site (HT: Mung) giving the context of the Sim:}

wholecell_sim

 

A mammoth effort, led by bioengineer Markus Covert, has produced a complete computational model of the bacterium Mycoplasma genitalium, opening the door for biological computer-aided design

By Max McClure

In a breakthrough effort for computational biology, the world’s first complete computer model of an organism has been completed, Stanford researchers reported in the cover story of the current issue of Cell.

A team led by Stanford bioengineering professor Markus Covert made use of data from over 900 scientific papers to account for every molecular interaction that takes place in the life cycle of Mycoplasma genitalium – the world’s smallest free-living bacterium.

By encompassing the entirety of an organism in silicon, the paper fulfills a longstanding goal for the field. Not only does the model allow researchers to address questions that aren’t practical to examine at the bench, it represents a stepping-stone towards the use of computer-aided design in bioengineering and medicine . . . . Mycoplasma genitalium is a humble parasitic bacterium, known mainly for showing up uninvited in human urogenital and respiratory tracts. But the pathogen also has the distinction of containing the smallest genome of any free-living organism – only 525 genes [–> 525 genes, not bits!], as opposed to the 4,288 of E. coli, a more traditional laboratory bacterium . . . .

Despite the difficulty of working with this sexually transmitted infection (STI), the minimalism of its genome has made it the focus of several recent bioengineering efforts. Notably, these include the J. Craig Venter Institute’s 2009 synthesis of the first artificial chromosome.

“The goal hasn’t only been to understand M. genitalium better,” said co-first author and Stanford biophysics graduate student Jonathan Karr. “It’s to understand biology generally.”

Even at this small scale, the quantity of data that the Stanford researchers incorporated into the virtual cell’s code was enormous. The final model made use of more than 1,900 experimentally determined parameters.

To integrate these disparate data points into a unified machine, the researchers modeled individual biological processes as 28 separate “modules,” each governed by its own algorithm. These modules then communicated to each other after every time step, making for a unified whole that closely matched M. genitalium’s real-world behavior . . .

As in, reverse engineering a living cell. For simulation purposes. And in a context where intelligent design of cells or sub-systems in the cell is a  reality. As in, vera causa.

So, I have every right to highlight the key words above, and to infer their significance.

And, all of this is in a world — an observed cosmos — where, from basic fine tuned physics on up, the world sets a base for such cell based life. Just consider how the first four elements in abundance are H, He, O, C, the latter pair being due to the resonance that so struck Sir Fred Hoyle from the 1950’s on. Stars, the periodic table, water, organic chemistry, beyond, N is close to this level, and that gives us proteins. With the elegant sophisticated simplicity of the water molecule, locked into core parameters of our cosmos, is itself a clue. All tied into the core physics of the cosmos we live in — the only one we actually observe.

In that context, Durston’s video is well worth reflecting on as food for thought:

[vimeo 64365800]

As his videos page comments:

God and Science – Is there a Conflict?: There is a popular notion that as science advances, religion retreats. This is true of Greek mythology and superstitious beliefs, but is it true of Christianity? In this lecture given March, 2013 at Wilfrid Laurier University-Laurier Brantford, biophysicist Dr. Kirk Durston shows that science has not only failed to push back the major claims of Judeo Christianity [–> i.e. Judaeo-Christian theism] pertaining to God and nature but, surprisingly, as science advances the evidence in support of the major claims has actually increased.

Food for thought. So, now, let us think together. END

Comments
Regarding the Springer Handbook of Bio-/Neuro-Informatics, I found the opening ironic in the extreme. The first sentence of the bible simply assumes the existence of God. Although the bible contains some deistic apologetics, they are largely tangential: the presumption of God's existence is consistent. So I found it quite amusing to read the first sentence of the Springer Handbook of Bio-/Neuro-Informatics:
Life is a striking state of material that emerged 3.6 billion years ago on our earth.
plus ça change, eh? This is progress? This is what we collectively pay tens of billions of dollars every year, for? A materialist philosophy that bears all the identifying characteristics of the religion it seeks to supplant? Meh. Color me distinctly unimpressed.ScuzzaMan
April 20, 2014
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kf:
PS: I did a Good Friday post building on VJT’s highlighting of Babbage on testimony of witnesses to miracles, here. That is relevant to the topic of this thread.
Nice article!Mung
April 19, 2014
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D: Springer Verlag is a famous science publisher. KFkairosfocus
April 19, 2014
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Mung @ 40 Is this "Springer Handbook of Bio-/Neuro-Informatics" a creationist publication? Is this publication allowed in public schools? If so, then how did it go undetected by the censorship police of the Neodarwinian Center to Save Evolution (NCSE)? Springer sounds German. Do they have creationist publications in Europe too?Dionisio
April 19, 2014
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Mung @ 40
The brain is the most complex information processing machine… …the information is encoded through the excitation of neural action potentials. The information is encoded using the average of pulses or the time interval between pulses. This process seems to follow a common pattern for all sensory modalities, however there are still many unanswered questions regarding the way information is encoded in the brain. – Springer Handbook of Bio-/Neuro-Informatics
Does anyone seriously believe all that came up from a primordial soup through unguided RV+NS+T?Dionisio
April 19, 2014
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PS: I did a Good Friday post building on VJT's highlighting of Babbage on testimony of witnesses to miracles, here. That is relevant to the topic of this thread.kairosfocus
April 19, 2014
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Mung, good stuff, mon. The circles of thought practically beg to be highlighted. KFkairosfocus
April 19, 2014
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Is information encoded in the brain?
The brain is the most complex information processing machine... ...the information is encoded through the excitation of neural action potentials. The information is encoded using the average of pulses or the time interval between pulses. This process seems to follow a common pattern for all sensory modalities, however there are still many unanswered questions regarding the way information is encoded in the brain. - Springer Handbook of Bio-/Neuro-Informatics
HT: News Information killed the Central Dogma tooMung
April 18, 2014
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Attention Upright BiPed!
The marriage of information and matter makes it possible to implement the evolutional mechanism.
Of course, that absolutely begs the question, without the "marriage of information and matter" what would be left of "the evolutional mechanism"? What does it mean for "evolutionary theory" if the evolutionary mechanism is informational? Is there a mechanical theory of information?Mung
April 18, 2014
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Life is a striking state of material that emerged 3.6 billion years ago on our earth. It has the ability of self-reproduction, by keeping information about itself in itself. The marriage of information and matter makes it possible to implement the evolutional mechanism. Thus, life has developed to achieve a variety of amazing structures and functions. In particular, we humans have appeared, with the characteristics of intelligence and consciousness, constructing societies and culture. Now the time is ripe to understand the mechanisms of living systems, where information is kept and processed efficiently and robustly. These mechanisms are highly complex and exquisite; their structures range from the molecular level to the higher level of the brain function. Advanced information science/technology is required to decipher the information mechanisms of life.
hereMung
April 18, 2014
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I am against blind watchmaker evolution because the very idea is self-contradictory and therefore absurd. But if logic doesn't matter... Got another one for you kf! The Human Brain Project Forget cell simulation, let's simulate the brain! SP6 - Brain Simulation That's simulate, not stimulate.Mung
April 18, 2014
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In response to Dawkins' quote, how about this? "I'm against institutional science because teaches us to be satisfied with speculation, to conform to authority and consensus, and to deny any value to spiritual values such as kindness, honesty, and ethics." -QQuerius
April 18, 2014
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F/N: I note, Dawkins:
I am against religion because it teaches us to be satisfied with not understanding the world
Nice example of a broad-brush stereotyping smear, one directly contradicted by say Proverbs -- which teaches the opposite, to seek wisdom. That is, profound and accurate insight leading to right thought and action. Of course, part of that wisdom exposes Dawkins' presumptions. For, in fact, we can scarcely honestly claim to actually understand the world, or to know beyond reasonable doubt its deep, unobserved past of origins, especially given the inherent limits of science and more broadly of induction. Ironically, Dawkins reveals his arrogance and ignorance about a major part of seeking to understand our world -- philosophy. KFkairosfocus
April 18, 2014
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franklin:
good point, mung. I was wondering if you think that the data suggest the protein's you are speaking about completely interdigitated within the membrane? Or do these proteins have a few membrane-spanning segments leaving the majority of the protein contained in the extracellular and intracellular domain?
Hi franklin, thanks for your questions. I don't have access to the original source cited for the table. Source: Based on Jain, M.K., and R.C. Wagner Introduction to Biological Membranes, 2nd ed. New York: Wiley, 1988 p. 34. So I don't have the information at hand to answer that specific question. But I'm not sure it matters all that much, really. If you think it matters I'd like to know why. Specifically, if the proteins on or near or protruding through the outer surface of the membrane, or on or near the interior, are any less necessary for the functions of the membrane.
In short, the biomembrane consists of amphiphilic molecules that respond to the hydrophobic effect by spontaneously assembling into the bilayer. The bilayer is fluid and mosaic with respect to both lipids and proteins and contains dynamic lateral domains, or rafts, which appear to be critical to many biological functions. The central nonpolar region that excludes virtually all water molecules spans about half the bilayer, sandwiched between the two interfacial layers where considerably more activity takes place. The surface of the bilayer is often crowded with peripheral proteins, some coming and going and others providing mechanical support. Many functions of the membrane are carried out by molecular assemblies that are large multicomponent complexes, some of which even span two membranes. ...many functions of the membrane are carried out by large protein complexes. - Membrane Structural Biology p. 11
What concept do you have of a membrane for a simple proto-cell and how do you get to an actual cell membrane from there? What sense does it make to speak of a biomembrane that has no function? And given that protein complexes are essential to biomembrane function, what sense does it make to speak of the biomembrane as if it could function without proteins? By what process did proteins become essential to membrane function?Mung
April 17, 2014
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Jerry, more to come -- a lot more! I suspect Moore is speeding up a tad. Years ago in designing a 4y u/grad tech degree one of the challenges was the 1/2 life of tech, what was new at the start was old hat at the end. But I suspect there is a lower limit, perhaps 1 - 2 y, due to limits of diffusion in markets . . . which looks suspiciously familiar. Schumpeter and Kondratiev are looking over Heaven's balcony and are chuckling. KF PS: Use my handle and contact me through the linked page. Feel free to talk econ and tech transformation in this thread. I am confident the connexions are there, tech revos in the economy vs those in life forms.kairosfocus
April 17, 2014
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People were flying in from across a continent to see the million dollar memory in action.
When my kids were little I helped their swim coach run swim meets and use his computer and a Basic program to enter and tabulate results. His computer had only 10 MB of storage and the program was stored on a floppy. His comment was we hardly use any of this 10 MB to run the meet or anything else on the computer. So why all this storage needed? He and I at the time never heard of Moore's law or Schumpter. Moore's law certainly has been responsible for a lot of creative destruction.jerry
April 17, 2014
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PS: An old engineer here who used to work for Sony I think it was, did a design as an RD effort, with 1 MBytes of RAM back in the must be early 70's. People were flying in from across a continent to see the million dollar memory in action. (Did they insure the RAM and the power supply to drive it?) Now, we do the same thing on Youtube without batting an eye. KFkairosfocus
April 17, 2014
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TJ: interwoven codes is one of the highest arts in micro design. When I heard of it, I said a silent prayer of thanks that I did not have to try, there being enough fairly cheap ROM and RAM in my day! Poly constrained designs like that embedding interwoven codes are a DOUBLE specification, each probably beyond the FSCO/I limit. Together, I suspect we are dealing with exponentiation here. The evidence of design is fairly shouting from the housetops now -- cf the vid and clips I posted here [HT BA77 I think], including that from Mr Dawkins himself, on the reasonableness of an experienced designer using judgement to recognise the presence of a design. As in: >> "We may say that a living body or organ is well designed if it has attributes that an intelligent and knowledgeable engineer might have built into it in order to achieve a sensible purpose . . . [A]ny engineer can recognize an object that has been designed . . . just by looking at the structure of the object." [The Blind Watchmaker, 1986, p. 21.] >>. Interwoven codes meets that condition, in spades. KFkairosfocus
April 17, 2014
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http://www.icr.org/article/7870/ Duons: Parallel Gene Code Defies Evolution by Jeffrey Tomkins, Ph.D.
The human mind struggles to comprehend the overall complexity of the genetic code—especially the emerging evidence showing that some genes have sections that can be read both forward and backward.3 Some genes overlap parts of other genes in the genome, and now it has been revealed that many genes have areas that contain dual codes within the very same sequence.1,4 [Try and evolve that now guys!] Even the most advanced computer programmers can’t come close to matching the genetic code’s incredible information density and bewildering complexity. An all-powerful Creator appears to be the only explanation for this astounding amount of seemingly infinite bioengineering in the genome.
tjguy
April 17, 2014
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OT: Here's a guy who truly is clueless, and in for a most unpleasant surprise -> "“I am telling you if there is a God, when I get to heaven I’m not stopping to be interviewed. I am heading straight in. I have earned my place in heaven. It’s not even close,” Bloomberg told the Times. http://www.weeklystandard.com/blogs/michael-bloomberg-i-have-earned-my-place-heaven_786943.htmlbornagain77
April 17, 2014
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The egg shell emerged from the egg. There isn't any egg and egg shell, they are one in the same. Or at least I am sure that is the canned evo answer. It's a secretion thing. In the primordial soup there wasn't any need for a membrane. The entire soup was a group of chemical reactions. It is only when those reactions produced membranes around certain chemicals did life get its starting chance. Any questions? :)Joe
April 17, 2014
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Q: a sobering point. KFkairosfocus
April 17, 2014
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EA: Actually, overnight, I added a pic from the site as pointed out by Mung. Their code is available via the link and onward links. Quite refreshing, no where's the Weasel games. So, figure out interfaces and any interested party can have a go. But what is interesting is: this is a reverse engineering project, led by a "bioengineer." Think about where that points. Notice, too where the highlighted phrases point. Then observe the studious silence from the usual suspects. Notice, this project is not a focal point for controversy and accusation, even though it is a demonstration of the feasibility and reality even of intelligent design of bio-forms. As in, vera causa. Any actual demonstration of such forms being created by blind chance and mechanical necessity? Nope. So, we have a perfect right to challenge advocates of such: put up, or admit want of crucial empirical support. KF KFkairosfocus
April 17, 2014
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Kairosfocus noted:
Save, it seems that things are obvious
Yes, they are. But some people choose to be blind as in "Oh that formation over there isn't a building, it's a rock formation that musta been carved by differential erosion over millions of years." -QQuerius
April 16, 2014
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kairosfocus: Thanks for highlighting this exceedingly important Stanford project. This represents the first (perhaps still the only?) real concerted effort to understand a complete organism -- really understand how every aspect of the organism works from the ground up. (Sorry, Avida lovers.) What I don't know is whether they have done any subsequent work to ascertain exactly what kinds of perturbations/mutations the organism can undergo and still remain viable. More to the point, after all manner of mutations, what kinds of new information has arisen, what kinds of new capabilities and biological features have arisen? I could probably Google it as well as the next person, but I'm wondering if anyone happens to be aware of any particular results coming out of this project yet that might give us a sense as to the "edge of evolution" of M. genitalium. ----- Mung:
It’s no longer, which came first, the chicken or the egg, it’s which came first, the egg or the egg shell!
That's a keeper! Excellent point.Eric Anderson
April 16, 2014
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Jerry@7: Thanks, this is what I wanted. KFkairosfocus
April 16, 2014
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Folks, I need to just make some points: 1 --> Mung: in thinking about the cell as a system, one starts: "gated, encapsulated," with the implication that the gate is smart, it passes/blocks things under control. Gated, encapsulated, metabolising using molecular nanotech, codes and algorithms, and self replicating per kinematic von Neumann Self replicator. That wrote itself out of chance collocations of molecules that somehow popped up as self replicators and metabolic entities, then incrementally, by blind chance and mechanical necessity managed to invent codes and algorithms out of molecular noise? I have one sentence of advice for such as will swallow that: Get out of the cave and get out of the Ganja-equivalent smoke filled atmosphere that makes the shadow shows seem sound. PS: Thanks for onward links 2 --> TJ, you are right to point to those texts and allude to Rom 1:19 - 32 and Eph 4:14 - 24 on the en-darkened heart and mind. Never mind labels, there is good reason to take such as soundly established, never mind what St Clinton RD says. 3 --> PP: Plainly, Science is not even an independently acting entity, it is a label. 4 --> D: Well spoken as a true Pole, and did I ever state to you my deep admiration for your nation over the years, which has punched beyond its mere numerical weight, ever so many times, and has had to sacrifice so much so often? Of recent sons of your soil, I see John Paul the Great . . . that's what I called him at the time of his passing on, on a local talk show . . . is about to be named a Saint. I say that with respect, never mind my own differences on theological matters. 5 --> F: There are proteins that do all sorts of things in the cell membrane, e.g. sensors. 6 --> Jehu: I mostly missed that, being busy elsewhere, but I was aware that there have been several very weighty posts, especially coming from VJT. 7 --> Q: Save, it seems that things are obvious, starting form the origin of a contingent, complex, fine tuned cosmos set up for C-chemistry, aqueous medium cell based life. I mean, even element abundances and suspicious resonances to get there and the simple elegance of H2O should give us a few clues! We can debate who designed life but a designer and builder of an observed cosmos -- the only actually observed one? Talk about: "the Heavens declare the glory of God and the Firmament shows his handiwork . . ." Okie, KFkairosfocus
April 16, 2014
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Mung
At 70% protein, how could the protein composition be anything but essential to the composition of the membrane? Or simply at the very least if equal importance?>At 70% protein, how could the protein composition be anything but essential to the composition of the membrane? Or simply at the very least if equal importance?
good point, mung. I was wondering if you think that the data suggest the protein,s you are speaking about completely interdigitated within the membrane? Or do these proteins have a few membrane-spanning segments leaving the majority of the protein contained in the extracellular and intracellular domain?franklin
April 16, 2014
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Brilliant video by Kirk Durston! I would add that science being obviously limited to using natural means cannot detect---prove or disprove---the existence of a supernatural God. And what if God wanted to hide from scientific discovery? Do you think you could trap God? ;-) Chaos Theory tells us that a butterfly in Tokyo could be the ultimate cause of a storm in Chicago. So, how would you know which butterfly? And even if you could tell which butterfly, perhaps God could cause the tiniest perturbation in Brazil that caused that Japanese butterfly to do whatever it did, which would be completely undetectable to the physicist and the mathematician. Let's put it another way. Let's say that you and some mathematical friends are playing Monopoly. Let's say that unbeknownst to any of you, I can control the outcome of the die roll (for example, by controlling the display of the spots on the dice by radio signal). You always win and they get suspicious. Looking at the record of die rolls, they can see that there's a close-to-normal (i.e. not perfect) distribution of outcomes both individually and corporately. It's just that some die rolls---not necessarily spectacular, either---by you and them allowed you to win. After all, somebody has to win, but you cannot tell that I'm controlling the game to whatever level I want! And God is likely to be far more subtle than my example. -QQuerius
April 16, 2014
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According to Table 1.1. (p.8) in Membrane Structural Biology, The Lipid composition/Protein composition of membrane preparations by percent dry weight of both Escherichia coli and Bacillus subtilis is 20-30% lipid and 70% protein. At 70% protein, how could the protein composition be anything but essential to the composition of the membrane? Or simply at the very least if equal importance? Are people who think that a spontaneous formation of a lipid bilayer is sufficient to explain the origin of the biomembrane even on the right planet? Is it even relevant to origin of life assertions?
...many functions of the membrane are carried out by large protein complexes. - MSB p.11
It's no longer, which came first, the chicken or the egg, it's which came first, the egg or the egg shell!Mung
April 16, 2014
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