Deciphering Life’s Regulatory Code

To : Robert P. Zinzen, EMBL Heidelberg

Re : “Deciphering the regulatory code”

A. From “EMBL scientists take new approach to predict gene expression”
http://www.embl.de/aboutus/communication_outreach/media_relations/2009/091104_Heidelberg/index.html

“What’s exciting for me is that this study shows that it is possible to predict when and where genes are expressed, which is a crucial first step towards understanding how regulatory networks drive development”

B. Organism’s behaviour, its reactions to its environments, are “regulatory networks”?

The above statement by Furlong, translated to 22nd century comprehension, amounts to:

What’s exciting is that this study shows that it is possible to predict when and where organisms react to their environments, which is a crucial first step towards understanding how evolution proceeds.

C. Please consider the following suggestions of the origin and nature of life and organisms, and of the origin and nature of cosmic and life evolution

- Genes, Earth’s primal organisms, and all their take-off organisms – Life in general – are but one of the cosmic forms of mass, of constrained energy formats.

- The on-going cosmic mass-to-energy reversion since the Big-Bang inflation is resisted by mass, this resistance being the archtype of selection for survival by all forms of mass, including life.

- The mode of genes’, Earth’s primal organisms, response to the cultural feed-back signals reaching them from their upper stratum take-off organism is “replicate without change” or “replicate with change”. “Replicate with change” is selected in case of proven augmented energy constrainment by the the new generation, this being “better survival”. This mode of Life’s normal evolution is the mode of energy-mass evolution universally.

Suggesting for your consideration,

Dov Henis
(Comments From The 22nd Century)
Updated Life’s Manifest May 2009
http://www.the-scientist.com/community/posts/list/140/122.page#2321
Implications Of E=Total[m(1 + D)]
http://www.the-scientist.com/community/posts/list/180/122.page#3108

i.e. when the Robertson parameters alpha = 1 and gamma = 1/3.

Though this would seem not to be the case for z < 1

http://arxiv.org/abs/gr-qc/0302088 (eq. 60).

Now let us see if this test of reading for comprehension can be passed.

As for your report, NOBODY CAN READ IT. It is password protected. And expecting people to pay you money to substantiate your arguments is high order stupidity.

You are repeating the same unfair accusations on Taganov, the same incorrect factors and misguided errors analysis, etc. that were already replied in the sci.physics.research links of my above message (before you were finally blocked by moderators in that thread who rejected your further posts).

The same moderators recently approved a post about the recent report CSR:20092

http://groups.google.com/group/sci.physics.research/browse_thread/thread/e27983b2fae018ed#

ignoring the ad hominems and vitriolic ‘evaluations’ of the report you are doing in last days in several places, including this blog now.

I will only add that the analysis that you mis-attribute to Taganov were using Weisberg & Taylor (2002) not “literature from 1991″ as you say.

Also your arXiv:astro-ph/0407149v1 is the reference (Relativistic Binary Pulsar B1913+16: Thirty Years of Observations and Analysis by Weisberg and Taylor) given in

http://www.canonicalscience.org/en/publicationzone/canonicalsciencereports/20092.html

As can be easily checked at the bottom part of that page.

A discussion of binary pulsars is given in page 13 of the report, which also includes quotations from Weisberg and Taylor on the issue.

Article comments:

The paper is starting off by imposing a Newtonian perturbation on top of the usual FRW anzatz. I find the choice of eta to be, overall, quite interesting. The forcing of eta being equal to one falls out through the boundary conditions that define the weak field limit, or in this case, perturbation theory on top of FRW.

The quantity being considered is not the “curvature” of space-time, which is horrifically misleading, but rather the ratio of two potentials used to define perturbation theory on top of the FRW manifold which is typically used to model the large scale universe.

I think the best way of understanding the quantity being considered is how well the boundary conditions we choose to apply to perturbation theory match observation, which is a whole lot LESS sexy than ‘a new challenge to Einstein’. {Sorry Sean }

What I’m having difficulty with is getting an exact handle on what is being _measured_. We have the ISW effect, and that is sensitive to the time components of the metric ala Shapiro delay, as it quantifies that little bit of gravitational redshift in CMB photons as they traverse anisotropies on their way to Earth. But the ISW effect, to my knowledge, isn’t done on a per-galaxy basis. And the two individual surveys were simply, as far as I know, doing mass surveys of the sky in some certain region looking for redshifts of objects.

How the hell this translates to a serious test of GR as claimed is something that I’ve been scratching my head on for awhile now. I wonder how circular the data sets are, with the essential cosmic parameters derived from WMAP/2df being fed back into a test of WMAP/2df.

I also wonder how much of a coincidence it is that the low-z objects end up favoring GR more than the higher-z objects. I further wonder if any effort was made to distinguish between freely traveling objects and objects gravitationally bound. Any test of the expansion theory is going to go to shit if you consider objects in the local group, which is a {loosely} bound system.

Basically this doesn’t tell us jack beyond ‘WE REQUIRE MORE VESPENE GAS’, I mean , “DATA”.

Peter Fred: “What am I missing? Why am I alone in considering the flat rotation curves of galaxies as representing a serious anomaly. If dark matter is detected by some means other than gravitationally , then the anomaly of flat rotation curves should rightfully ” go away”.”

What you are missing are gravitational {macro,micro} lensing observations that directly couple to the {mass,energy} density present in a given volume of space. People who argue that dark matter doesn’t exist have to find creative excuses for why dark matter behave as predicted in that respect.

Juan: Thanks for being a cosmic jackass by importing an argument you lost onto a medium that has people who are capable of reading for comprehension. Readers interested in the state of the art on the galactic center should read through the overall thread. As I was reduced to explaining things using small words and pantomime to a child with a learning disability, the overall argument should be simple to follow for people who can read for comprehension.

As for this stupid goddamn argument, this nonsense was dealt with 6 months ago.

http://groups.google.com/group/sci.physics.research/msg/2c6d68195d99b0c8?dmode=source

Taganov’s argument is, quite frankly, as full of shit as you are. Why is he, in 2009, citing literature from 1991 when there has been a factor of 3 reduction in error bars since then?

Could it be because his argument falls to pieces if one reads, say arXiv:astro-ph/0407149v1? I think so, because it becomes remarkably hard to not only butcher statistics and claim a 0.6% _ERROR BAR_ is not just an excess as opposed to an exquisite failure in comprehension of basic error analysis (of which you are complicit by repeating the claim) when an article published 13 years later shows that the error bars are reduced to 0.13% +/- 0.21.

Class, since statistics seems to be under discussion to some degree, how many standard deviations away is a factor of 3 difference in a measurement when one realizes that an error bar represents 1 standard deviation centered upon the measurement? I’ll leave it as an exercise.

And Juan, an extra special thank you for once again citing your many-year unpublished draft in an argument. As you have explicitly denied having done. Hurry the fuck up and publish it, as Sean Carroll will probably be highly interested in your opinions of his work in addition to your complete butchering of the subject. If for no other reason than because you invoke his name all the time.

Hey Sean, since I know you’ll see this, I have a question.Have you heard about Juan’s rather interesting usage of your online lecture notes? Its’ fuuuun to read.

I share the opinion of several of my colleagues that dark energy and dark matter are the aethers of the 21st century. We need a new theory eliminating both from physics.

We already have a theory that explains the “rotation curves” with an accuracy do not matched by dark matter theories

http://www.astro.umd.edu/~ssm/mond/fit_compare.html

Moreover, the theory is predictive and its predictions have been all confirmed

http://www.astro.umd.edu/~ssm/mond/mondvsDM.html

http://www.astro.umd.edu/~ssm/mond/mondpred.html

http://www.astro.umd.edu/~ssm/mond/CMB1.html

It seems that the theory continues providing satisfactory predictions

http://arxiv.org/abs/0909.5184

The goal here is to add relativistic corrections to this theory. One popular approach is revised next

http://arxiv.org/abs/0901.1524

I advance an alternative model to TeVeS in the above cited report (CSR:2009), with the advantage it can also compute what cannot be obtained by any other available model or theory: we can obtain a_0 and its relation to cosmological a_H, we can obtain the correct order of magnitude of the cosmological constant, we can obtain the cluster mass limit…

Your ill-informed assertions about PPC-08 and your ad hominems were already replied in sci.physics.research until moderators there blocked you from posting more in the thread:

http://groups.google.com/group/sci.physics.research/msg/0bca9684bc5e0a3e

http://groups.google.com/group/sci.physics.research/msg/bee924193a0a5b68

http://groups.google.com/group/sci.physics.research/msg/b6c4269a42ddea97

http://groups.google.com/group/sci.physics.research/msg/b2384376b4c5b02c

(…)

This assertion has no support in the literature.

Plus I greatly enjoy your presence here given your opinions about Carroll.

What am I missing? Why am I alone in considering the flat rotation curves of galaxies as representing a serious anomaly. If dark matter is detected by some means other than gravitationally , then the anomaly of flat rotation curves should rightfully ” go away”.

I believe that a multi-team, multi-million dollar effort has been underway at least since 1988 looking for non-gravitational evidence for the dark matter. Even though the need for dark energy concept has only been around for ten years, it raises more serious theoretical difficulties than does the dark matter concept.

So when do good scientists consider the fact the flat rotation curves and the fact of cosmic acceleration a serious anomaly?

I have a hard time thinking that scientist are really “good scientists” if they do not hold the view, at this late stage, that the need for dark matter and dark energy represent in some sense a serious anomaly.

It is worth to start remarking that binary pulsar tests are also challenging general relativity. First, the same tests are also passed out by alternative theories like nonlinear field theory and the recent relational theory (2008: Grav. and Cosm. 14(1), 41—52).

Second, recent works —also presented in conference PPC-08— point out the possibility that the discrepancy of 0.85% between the general relativity prediction and observation can be explained by a nonlinear field theory, which predicts extra radiation of 0.735% thanks to novel radiation mechanisms not available in general relativity.

I want not to discuss about if GR is aesthetically compelling or not. Some people thinks GR is the most beautiful of the theories of physics. Others strongly disagree and consider that the nongeometrical formulations are more beautiful —particle physicists as Feynman and Weinberg have stated their preference by nongeometrical formulation for gravity—. I agree that nongeometrical formulations are more beautiful. But the important question is are they more useful as well?

This important question has been answered in a report presented some few days ago, which rigorously analyzes the geometrical formulation of general relativity and compares —as never before was done— with another five theories of gravity in mainstream journals. The results are somehow surprising: (i) the geometrical formulation behaves poor than nongeometrical ones —the myth of equivalence of both formulations is showed—, and (ii) the deficiencies of the geometrical formulation are the cause of some observational discrepancies —there is a section in the Report specifically devoted to cosmological discrepancies—.

The implications for quantum gravity are deep. Beyond the profound cultural divide between the relativity and the particle physicists’ community in dealing with spacetime, this reports shows that field-theoretic approaches to gravity over a flat background are more correct than attempts like loop theory —deeply rooted into the geometrical language of general relativity—.

It is not strange that experts as M. Pavsic (author of the book “The Landscape of Theoretical Physics: A Global View; From Point Particles to the Brane World and Beyond, in Search of a Unifying Principle”) have praised this work, as reported in some news

http://www.canonicalscience.org/en/publicationzone/canonicalsciencereports/20092.html

http://www.geskka.com/articles/categories/Space-science/

http://digg.com/d316f5a