from M Wainwright | Fri, 25 Jul 2008

22:01:47 +0100: Dear Brig, I have created a web site which has an arcticle of Darwin and Wallace (i.e. that they did not originate natural selection etc) which may be of interest to your website viewers. Can you let them know of its existence? It's at http://wainwrightscience.blogspot.com, or via google at wainwrightscience. Best Wishes, Milton

08:57 PM: Hi Brig, I'm struggling with this one, but thought you might find it interesting.... Ken
Vasily V. Ogryzko, "A quantum-theoretical approach to the phenomenon of directed mutations in bacteria (hypothesis)" [abstract], doi:10.1016/S0303-2647(97)00030-0, p 83-95 v 43, ScienceDirect - Biosystems, Jul 1997.

16 Jul 2008, 08:18 AM: Ken, thanks. Glad to know you're there! In the 1970s my hobby was quantum theory. My final opinion was that nobody understands the phenomena behind quantum theory. Richard Feynman agreed. Lots of fantasy like the Many Worlds theory, and quantum theory to explain consciousness gets published. I think that a superposition of states is sometimes only a mental fiction used to explain what we don't understand. (Sorry to be grumpy this morning.)

I do think that directed mutation needs more attention. And I think that it would be pretty easy to make a computer model that exhibits directed mutation. Thanks for alerting me. I definitely want to hear from you when you see something interesting....

09:15 PM: Brig, Ogryzko has a more recent paper at http://arxiv.org/ftp/arxiv/papers/0805/0805.4316.pdf, and a 1999 presentation at http://arxiv.org/ftp/arxiv/papers/0802/0802.2271.pdf

It might be a good time for you to reactivate your former hobby. Because of the tremendous prestige of Einstein, physicists were reluctant to buy into entanglement effects even when they were first demonstrated in the early 1980's. But now quantum engineering is just getting started, and it includes more than just quantum computing and quantum cryptography. We (me and 5 others) broke away from General Dynamics and started the Ann Arbor office of www.sri.com in January, 2008, and a big part of our plan is quantum sensors and other advanced device concepts based on exploiting superposition and entanglement.

Once you get back into it, you just have to take superposition as real - there are just too many real effects that one can use for practical purposes. I'm not a physicist, nor a historian of science, but I think its just like atoms, field, earth-as-a-sphere, and other mental constructs that weren't accepted as real for a long time because one could not perceive them directly. I want our group also to get into quantum biology, and if you know any academics who might want to collaborate with us, please let me know....

17 Jul 2008, 08:19 AM: Dear Ken -- As I recall, there was spooky action-at-a-distance that seemed to violate the speed of light limitation. And there was the suggestion that causality does not hold. The latter I couldn't get over. Was it Bell's inequality that first proved entanglements? Anyway, I'll browse that section of the science shelf and see if I can get back into it. Thanks for the links. ...Thanks. Brig

03:40 PM: Well, there is no possibility of controlling an event at a distance faster than the speed of light; that is, one cannot send a signal (containing information) faster than light speed. But there is, nevertheless, an instantaneous consequence at point B of doing something at point A independent of the spatial separation whenever an entangled particle pair is created and one part moved to A and the other part to B and a measurement is done at A. This is called a "non-local" effect, or sometimes an "EPR phenomenon" after a famous paper by Einstein, Podolsky, and Rosen of 1935, where they did a 'thought experiment' which seemed to show quantum mechanics must be wrong because it predicted non-local effects (i.e., the very effects that were demonstrated starting in the 1980's) which they judged to be "unphysical" (google on EPR).

The experimental violation of Bell's inequality shows that you can't solve the observed EPR phenomena by postulating that the entangled particles traveling to A and B carry some kind of "hidden variables".

I've never seen it suggested that causality does not hold. What apparently does not hold is determinism, the idea that past and future are all part of one big block. Actually, determinism IS compatible with QM but at a very high price: the multi-worlds interpretation, which some very big physicists actually believe in (e.g., David Deutsch). But the more common interpretation of QM is that the Schroedinger equation computes "probability amplitudes" for the future (perfectly deterministically!) but that the square of a probability amplitude is the probability of that measurement outcome happening in the future. So the future is constrained by the past and present, but is not rigidly determined by it.

There are many other interpretations of QM besides these two, but the latter is the most popular (so-called Copenhagen interpretation) at the moment. Also fair warning: this is all off the top of my head, and I'm not a physicist. Ken

18 Jul 2008, 10:37 AM: For a non-physicist, you seem to know enough! I think I'll confine my comments to directed mutation. Ogryzko apparently thinks that directed mutation would violate the rule that the causal arrow only goes left-to-right. But I think it doesn't violate any rules. The DNA software management system could easily have the capability to do directed mutation, and computers could model it.

Genes need to have some wiggle room in which to become optimized, which it seems they do. The system needs to know where these are, and when to accelerate the rate of mutation in them. "When" could be when environmental events lead to the production of the enzymes that ultimately trigger this accelerated mutation at those places. What's so complicated about this?

Note that the range of capabilities that can be reached this way is limited to the optimization range of the gene. OK, some genes make proteins that can have more than one function, and perhaps these functions, if they require sequence adjustments, could also be switched off/on by directed mutation. Come to think of it, directed mutation could be aimed at regulatory sequences, toggling whole programs off/on. But none of this writes new programs. Of course, these genetic changes are still subject to darwinian natural selection. Comments invited! Best regards. Brig

06:49 PM: I want to do some research about directed mutations and write something in What'sNEW....

Sat, 19 Jul 2008, 16:06:27 -0400: Brig, Since you will be diving into directed mutations, you might as well start with Ted Steele in Australia. He's focused his entire career on trying to make progress on this, been beaten up many times, but never gives up. I've attached his latest letter to Molecular Immunology which gives his take on several models. I don't understand the field well enough to have any comments, but I know Ted and I'm sure he would be happy to correspond with you if you have questions....
Edward J. Steele, "Reflections on the state of play in somatic hypermutation" [preview], doi:10.1016/S0303-2647(97)00030-0, p 2723-2726 v 45, Molecular Immunology, May 2008.
On Ogryzko and the causal arrow, I'm still working on that paper so can't yet say what I think he means. However, there is an element of "backwards in time" settling of affairs in quantum mechanics, at least according to some physicists. For example, experiments by Ben Libet seem to show (at least to some) that free will is an illusion (because freely-chosen movement timings are preceded by neural activity that occurs before the conscious choice). Yet one physicist, Henry Stapp at Lawrence Berkeley, shows that in his interpretation of quantum mechanics there is no conflict at all with free will in these experiments: http://sts.lbl.gov/~stapp/Libet.pdf ...Ken

06:31 PM: Ken thanks -- I reviewed one of Steele's books ...and corresponded a bit with him in 1999. Apparently, I need to see what he's up to now. Thanks.
Lamarck's Signature... is the mentioned book review, What'sNEW, 12 May 1999.
Before I had my quantum theory hobby, I was especially interested in free will versus determinism. It may be an exaggeration, but OK, say I was a strict determinist. "...Past and future are all part of one big block" in your words. I still saw free will as assured. The argument against it required an unnoticed shift in perspective, from ...human to ...call it God's, to choose words hastily. (And for an argument of lesser logical, but more social, value, we simply must hold ourselves responsible.) The insertion of QT into this mix might have made the big block a big soup, but was otherwise no help, I thought. Perhaps more after I read your attachment. Thanks, as always. Brig

20 Jul 2008, 11:40 AM: Thanks again for the article. I am 40% through it and I will have to calm down before I go on. I accepted, long ago, the apparently instantaneous correlations over large distances of the behavior of particle-pairs. OK. But I do not see any need to insert the observer into the mix. Observations that may effect outcomes are always physical events, right? Young's double slit experiment creates an interference pattern on the photograph plate whether anyone actually looks at it or not. (The point of Schroedinger's cat, I guess.) It feels to me like astrology and ESP have suddenly become respectable science. Furthermore, I do not feel any hope for enlightenment if the observer participates in Stapp's manner. Makes it worse, not better. But I will try to read on! I should confess that I have never been very interested in consciousness as a problem. Never heard the problem well-posed, for one thing.

Whatever became of the pilot-wave theory?

7 Jul 2008: The Design Matrix: A Consilience of Clues — the subject book review.

20 Jul 2008, 04:02 PM: Hi Brig, Thank you for both the review and reply. Yes, the book did not address the issue of panspermia. The book is intended as the first part of a three part series, where I lay out the logic of my approach. The book argues for an investigative approach, lays out the clues that suggest design might be associated with the origin of life, explores how design and evolution might interface (from both the subjective and objective angles) and then lays out a methodology to assess a design inference.

The topic of panspermia would fit much better in the second or third volume, where one could distinguish between undirected and directed panspermia. Both hypotheses could account for any indicators of discontinuity, but the latter, IMO, better explains any indicators of analogy, rationality, and foresight. In essence, my approach is that of a teleologist. You ask if I am trying to prove a miracle. No. The relationship between my religious views and ID views are spelled out clearly in the following essay: http://telicthoughts.com/neither-science-nor-religion/ ...Or you might want to read through this essay: http://www.idthink.net/biot/rational/index.html

If you think about the subtle argument I am making, it does not in any way depend on a particular mode of becoming - whether life was ultimately spawned naturally on Earth or from space, or whether it came into existence through a creative act of God, the same argument applies.

As for any agenda, I have none other than the line of thinking laid out in The Design Matrix. I sincerely lay my cards on the table with regards to the clues for design, its relationship with evolution, and how we might proceed from there. My "agenda" is to make people aware that there are other unexplored ways of thinking about these issues, as this is an area of inquiry where neither science nor religion can function as the final authority.

I fully understand that this whole issue has become so thoroughly politicized from all sides, but the fact remains that I find this topic to be intrinsically interesting and 2500 years of Western thinking backs me up on this. Yes, people will continually suspect that people like you and I are closet creationists with hidden agendas. It is part of the superficial thinking and stereotypes that play well in a culture dominated by group think, sound bites and pop media. Regards, Mike

07:24 PM: ...A TEAM of Australian scientists has discovered the earliest known example of a creature able to have sex and give birth -- http://www.theage.com.au/articles/2008/05/28/1211654123040.html
Why Sexual Reproduction? is a related CA webpage.

Thanks for the wonderful site. You do a great job of presenting a very interesting alternate origin of life theory.... Sincerely, Vince Wuellner | Lakeland, FL USA
Hoyle and Wickramasinghe's Analysis of Interstellar Dust is the referenced CA webpage.

6:17 AM: Hi... I don’t know if nanobacteria are part of the cosmic ancestry theory, but I felt they might hold some place, hence this link to an article on nanobacteria.... Regards, Sean
Nanobacteria - Are They Alive?, by Lisa Zyga, Physorg.com, 23 Apr 2008.

4:38 PM: Brig... See ["Nanobacteria theory takes a hit" at] http://www.nature.com/news/2008/080417/full/news.2008.762.html. Mike
What'sNEW: Nanobes has updates on this subject, discussed on our Life on Mars! webpage.

19:51:24 +0000: Brig - So, back to the drawing board about how objects enter the atmosphere?!? So, meterorites (rock) CAN survive the decent.... and life forms in them???
Streamlined meteorite hit Peru fast and hard, Concast.net News, 11 Mar 2008.
A meteorite caused illness in Peru? is our original story about this meteorite, in What'sNEW, 20 Sep 2007.
Comets: The Delivery System is a related CA webpage.

[...Genetic information can be passed on to following generations via RNA, in addition to DNA, according to research at Princeton University studying the reproduction of the singled-celled ciliate Oxytricha trifallax, whose cells have two nuclei.]
New route for heredity bypasses DNA, Physorg.com, 4 Jan 2008.
Neo-Darwinism: The Current Paradigm is a related CA webpage.