we live instead in a place called phase space.” That, we are told, is a “curious eight-dimensional world that merges our familiar four dimensions of space and time and a four-dimensional world called momentum space.”

The first question I asked was, “do they have any empirical evidence?”, and found,,

Big questions still remain. For instance, how can we know if momentum space is really curved? To find the answer, the team has proposed several experiments.
One idea is to look at light arriving at the Earth from distant gamma-ray bursts. If momentum space is curved in a particular way that mathematicians refer to as “non-metric”, then a high-energy photon in the gamma-ray burst should arrive at our telescope a little later than a lower-energy photon from the same burst, despite the two being emitted at the same time.
Big questions still remain. For instance, how can we know if momentum space is really curved? To find the answer, the team has proposed several experiments.
One idea is to look at light arriving at the Earth from distant gamma-ray bursts. If momentum space is curved in a particular way that mathematicians refer to as “non-metric”, then a high-energy photon in the gamma-ray burst should arrive at our telescope a little later than a lower-energy photon from the same burst, despite the two being emitted at the same time.
Just that phenomenon has already been seen, starting with some unusual observations made by a telescope in the Canary Islands in 2005 . The effect has since been confirmed by NASA’s Fermi gamma-ray space telescope, which has been collecting light from cosmic explosions since it launched in 2008. “The Fermi data show that it is an undeniable experimental fact that there is a correlation between arrival time and energy – high-energy photons arrive later than low-energy photons,” says Amelino-Camelia.
Still, he is not popping the champagne just yet. It is not clear whether the observed delays are true signatures of curved momentum space, or whether they are down to “unknown properties of the explosions themselves”, as Amelino-Camelia puts it. Calculations of gamma-ray bursts idealise the explosions as instantaneous, but in reality they last for several seconds. While there is no obvious reason to think so, it is possible that the bursts occur in such a way that they emit lower-energy photons a second or two before higher-energy photons, which would account for the observed delays.
http://www.newscientist.com/ar.....tml?page=2

But alas, it appears that the champagne will have to remain corked for them:

Quantum Foam Paper Suggests Einstein Was Right About Space-Time Being ‘Smooth’ – January 2013
Excerpt: It appears Albert Einstein may have been right yet again.
A team of researchers came to this conclusion after tracing the long journey three photons took through intergalactic space. The photons were blasted out by an intense explosion known as a gamma-ray burst about 7 billion light-years from Earth. They finally barreled into the detectors of NASA’s Fermi Gamma-ray Space Telescope in May 2009, arriving just a millisecond apart.
Their dead-heat finish strongly supports the Einsteinian view of space-time, researchers said. The wavelengths of gamma-ray burst photons are so small that they should be able to interact with the even tinier “bubbles” in the quantum theorists’ proposed space-time foam.
If this foam indeed exists, the three photons should have been knocked around a bit during their epic voyage. In such a scenario, the chances of all three reaching the Fermi telescope at virtually the same time are very low, researchers said.
So the new study is a strike against the foam’s existence as currently imagined,,, “If foaminess exists at all, we think it must be at a scale far smaller than the Planck length,”
http://www.huffingtonpost.com/.....49734.html

Note as to higher dimensions that we have actual empirical evidence for:

The ‘Top Down’ Theistic Structure Of The Universe and Of The Human Body
https://docs.google.com/document/d/1NhA4hiQnYiyCTiqG5GelcSJjy69e1DT3OHpqlx6rACs/edit

One of the problems I have with the notion of “natural genetic engineering” is the word natural. Suppose a discovery is made where a new protein emerges through domain shuffling. Great. If it were the result of a signalling response, triggered by the environment, such a function that could respond to the trigger by building a “novel” protein would be dependent on an existing mechanism, probably an irreducibly complex one. Under the rubric of natural genetic engineering, this event would be considered natural, and I think that begs the question. What force or law motivates such a triggered response? None do. It would be the result of programming, not physical law.

Remember that rapid evolution of lizards that “evolved” cecal valves? Same issue. To label such an events as examples of evolution, or as natural processes, is misleading at best.

Can it really be that he really believes that is the ONLY principle powerful enough to explain the data? Is he being willfully obtuse? Or can it be that his metaphysical commitments are so powerful that he literally cannot see the gobsmackingly obvious alternative principle that could account for the data?

How Natural Genetic Engineering Solves Problems in Protein Evolution – James Shapiro – May 2012
Excerpt: When I pointed out the potential of domain shuffling by natural genetic engineering to Intelligent Design advocates who claimed protein evolution by natural mechanisms was impossible, they refused to recognize genomic data as irrefutable evidence and insisted on real-time experiments. I disagree with them strongly on the DNA sequence data.
http://www.huffingtonpost.com/.....41180.html

On Protein Origins, Getting to the Root of Our Disagreement with James Shapiro – Doug Axe – January 2012
Excerpt: I know of many processes that people talk about as though they can do the job of inventing new proteins (and of many papers that have resulted from such talk), but when these ideas are pushed to the point of demonstration, they all seem to retreat into the realm of the theoretical.
http://www.evolutionnews.org/2.....55471.html

Shapiro admits he has no ‘real time’ empirical evidence for the origin of novel protein domains and/or genes by Darwinian processes (so as to be able to have the ‘protein domains’ to shuffle around in the first place) but must rely, as do neo-Darwinists, on the DNA/protein sequence similarity/dissimilarity data to try to make his case that novel protein domains were created in the distant past so that ‘natural genetic engineering’ can presently create all the diversity we see in life on earth today. Yet, just as with neo-Darwinists, Shapiro relying on sequence similarity/dissimilarity data to ultimately try to make his case for ‘natural genetic engineering’ has the very same ‘unscientific’ problem that neo-Darwinism has of assuming the conclusion beforehand to try to prove the very question being asked. The primary problem is never addressed! i.e. Can the novel functional information we see in protein domains and/or genes ever be generated in a ‘bottom up’ fashion by the unguided material processes of neo-Darwinism? The answer to that question, as far as empirical evidence is concerned, is a resounding NO.

Now Evolution Must Have Evolved Different Functions Simultaneously in the Same Protein – Cornelius Hunter – Dec. 1, 2012
Excerpt: In one study evolutionists estimated the number of attempts that evolution could possibly have to construct a new protein. Their upper limit was 10^43. The lower limit was 10^21.

These estimates are optimistic for several reasons, but in any case they fall short of the various estimates of how many attempts would be required to find a small protein. One study concluded that 10^63 attempts would be required for a relatively short protein.

And a similar result (10^65 attempts required) was obtained by comparing protein sequences.

Another study found that 10^64 to 10^77 attempts are required.

And another study concluded that 10^70 attempts would be required. In that case the protein was only a part of a larger protein which otherwise was intact, thus making the search easier.

These estimates are roughly in the same ballpark, and compared to the first study giving the number of attempts possible, you have a deficit ranging from 20 to 56 orders of magnitude. Of course it gets much worse for longer proteins.
http://darwins-god.blogspot.co.....1503051454

Moreover, ‘domain shuffling’, which Shapiro mentioned in his ‘natural genetic engineering’ scenario, is far from being as plastic as Shapiro apparently imagines it to be:

Why Proteins (Protein Domains) Aren’t Easily Recombined – Ann Gauger – May 2012
Excerpt: each particular helix or sheet has a distinct set of side chains sticking out from it, requiring a distinct set of chemical interactions with any nearby protein sequence. Thus, helices and sheets are sequence-dependent structural elements within protein folds. You can’t swap them around like lego bricks. This necessarily means that when you bring new secondary structure elements into contact by some sort of rearrangement, they will be unlikely to form a stable three dimensional fold without significant modification.
http://www.biologicinstitute.o.....recombined

“Why Proteins Aren’t Easily Recombined, Part 2″ – Ann Gauger – May 2012
Excerpt: “So we have context-dependent effects on protein function at the level of primary sequence, secondary structure, and tertiary (domain-level) structure. This does not bode well for successful, random recombination of bits of sequence into functional, stable protein folds, or even for domain-level recombinations where significant interaction is required.”
http://www.biologicinstitute.o.....ned-part-2

Thus, while I am very pleased that research has advanced to the point of falsifying neo-Darwinism, I’m bothered by the fact that Shapiro, and others who see the inadequacy of neo-Darwinism, have failed to fully appreciate the root of the problem with neo-Darwinism. Namely the sheer inability of purely material processes to generate the functional information we find in life:

The Law of Physicodynamic Incompleteness – David L. Abel – August 2011
Summary: “The Law of Physicodynamic Incompleteness” states that inanimate physicodynamics is completely inadequate to generate, or even explain, the mathematical nature of physical interactions (the purely formal laws of physics and chemistry). The Law further states that physicodynamic factors cannot cause formal processes and procedures leading to sophisticated function. Chance and necessity alone cannot steer, program or optimize algorithmic/computational success to provide desired non-trivial utility.
http://www.scitopics.com/The_L.....eness.html

Verse and Music:

Psalm 139:13
For you created my inmost being; you knit me together in my mother’s womb.

Chris Tomlin – Our God – video
http://www.youtube.com/watch?v=wYJfuFQe4cc

RDfish,

we cannot reduce or translate the full meaning of natural language into logic,

Yup, and that’s why the truthfulness of philosophical and theological statements remains often vague, to the point of making some assertions of little utility.

Practically speaking you just have to assume somethings as true, let others disagree with your assumptions, but as long as its not contradictory, go with it on faith.

You can’t arrive at ultimate truth by reason and logic alone, you will need some providence that your faith axioms are indeed in line with what is ultimately true.

If logic were alone sufficient to discern truth, we wouldn’t have Godel’s incompletess in math, and if we have Godel’s incompleteness in math, how much more will we have incompleteness in evaluating the truth statements in natural language propositions.

What happened in math was essentially, “it’s true or false depending on what you mean”. Russell tried to prove you could execute logic on symbols and thereby avoid the problem of meaning. The problem was that when you got to non-trivial statements, this process crashed. Natural language suffers from the fact statements (although terse) are ultimately non-trivial because every word is subject to being asked “what does that word really mean”. A certain bit of circularity emerges when you realize every word in your vocaublary is cicularly defined by all the other words in your vocabulary, hence formally speaking, you’re stuck if you are unwilling to leave some things unproven and undefined.

Me, I’m a pragmatist. I believe stuff as long as it works for me…..what is ultimately true? Only God knows. Mortals can only access ultimate truth through faith and providence that their faith assumptions are indeed well-placed. Logic is necessary, but not sufficient. Providence is sufficient.

This, though, was a real howler:

It seemed to me that the only principle powerful enough to explain the high degree of organization of our universe—compared to a universe with the particles and forces chosen randomly—was natural selection itself.

Yeah, that’s it. Natural selection. You know, that convenience label that in actuality isn’t a mechanism, isn’t a force. That idea that was proposed and is propped up by “self-replication” being the source of the variation needed to drive the engine of natural selection.

Sure. That’ll help explain the cosmos.

Pause for laughter . . .

In the spirit of full disclosure, and to help RD keep score, I should probably point out that WJM and myself, while almost always in agreement on matters of moral philosophy, do seem to have differing opinions on this finely-tuned point.

For my part, human free will, while being a cause, cannot, strictly speaking, be a causeless cause, since its existence must be accounted for. I hold, therefore, that the existence of human free will, that is, the power and faculty by which we choose, is caused by God.

Yes, Noble did mention redundancies generally, which was why I mentioned it again, but given that the whole junk DNA thing has been justified on the basis of knockout studies it seemed to open pretty well the whole genome up, which he didn’t stress so much.