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An alignment-based approach to protein shape determination

Among 7600 proteins we find that the average of maximum intersection in substrings is 51% of the length of individual proteins which gives a quantitative estimate of the redundancy in substrings of amino acids.  Since folded proteins are rigid, this is an interesting empirical result for the problem of shape determination of proteins using a database of known folded protein shapes.

Proteins are sequences of amino acids but are interesting biologically only in folded states. The problem of determining the shape given the sequence of amino acids is nontrivial. The problem is considered hard and current methods employ extensive computational machinery. My approach is to simplify the problem by reducing the shape of a protein to the backbone N-atoms as proxy for the folded shape and take twofold approach: study distribution of angles for fixed amino triples where a sharp concentration reduces possibilities for the triples and on the theoretical side study the possibility of shape determination as a consequence not of subtle thermodynamics but of the fact that EM has SU(2) rather than U(1) symmetry. On the practical side that this approach has merit can be established quite simply. Here is the typical concentration we can expect: if we put a 10 degree grid on angles from 0 to 360 and histogram the angles observed in hinges of CYS-THR-GLU in 7600 folded proteins, we will see percentage concentration as in:
\$ cut -f5 -d, cys-thr-glu.txt | ./hist.pl
210 —> 8.31
220 —> 8.63
230 —> 7.99
250 —> 5.11
310 —> 5.11
320 —> 8.31
Total concentration: 0.434504792332268

So 43% of the angles fall in a narrow set of 6 points in 36. This is a nontrivial result for protein folding algorithms using statistical methods because we can expect that these can reduce possibilities at every step for angles. If a protein is described by amino sequence A1-A2-A3- … then we can reasonably expect that for each triple we have a small table of angles and their weights we could use for shape determination as an elementary method.

Another approach that suggests itself from considering the data of folded protein shapes is an alignment-based approach by which I mean to consider large sequences of amino acids and consider database match to pre-existing folded proteins.   S4 theory tells me, in a nutshell, that proteins fold rigidly BECAUSE electromagnetism has SU(2) symmetry in 4D. Therefore the rigidity of protein folds is fairly stable, therefore ALIGNMENT algorithms can use known protein shapes as rigid, and can easily fill in the “gaps” using maximum likelihood on triple amino twist distributions.  The longest common sequence between proteins can be found by established techniques such as Hirschberg’s algorithm.  This is a reasonable resolution of the protein folding problem that is most definitely going to be polynomial complexity.

We are faced with the problem of determining the longest substring given two strings, for which the most efficient algorithm uses a suffix tree.  We are in luck because the CPAN contained the Tree::Suffix module which reduces workload.  The following simple piece of code then can be used to spot check substrings in common with proteins:

```#!/usr/bin/perl

my %altr =
( 'ALA' => 'A',
'ARG' => 'R',
'ASN' => 'N',
'ASP' => 'D',
'GLN' => 'Q',
'GLU' => 'E',
'GLY' => 'G',
'HIS' => 'H',
'ILE' => 'I',
'LEU' => 'L',
'LYS' => 'K',
'MET' => 'M',
'PHE' => 'K',
'PRO' => 'F',
'SER' => 'S',
'THR' => 'T',
'TYR' => 'Y',
'VAL' => 'V' );

# Read a file and produce a protein string

my \$pname1 = \$ARGV[0];
my \$pname2 = \$ARGV[1];

use Tree::Suffix;

my \$string1 = &get_pstring( \$pname1 );
my \$string2 = &get_pstring( \$pname2 );
my @strings = ( \$string1, \$string2 );

my \$tree = Tree::Suffix->new( @strings );
my (\$common) = \$tree->longest_common_substrings;

print "String 1: \$string1\n";
print "String 2: \$string2\n";
print "Common: \$common\n";

sub get_pstring
{
my \$pname = shift;

my \$file = "rots/\$pname.txt";

my \$string = '';
my @data;

open (FILE, "<\$file");
while (<FILE>) {
chomp;
@data = split ",";
\$string .= \$altr{\$data[2]};
}
close(FILE);
return \$string;
}```

Generically the longest substring between proteins is short but here is an example of a nontrivial substring in common:

```\$ ./pstring.pl 130l 137l
String 1: NKEMLRIDEGLRLKIYKDTEGYTIGIGHLTKSFSLNAKSELDKAIGRNTNGVITKDEAEKLKNQDVDAVRGILRNAKLKFVYDSLDAVRALINMVKQMGETGVAGKTNSLRMLQKRDEAVNLAKSRYNQTFNRAKRVISTKRTGTDAY
String 2: NKEMLRIDEGLRLKIYKDTEGYTIGIGHLTKSFSLNAKKELDKAIGRNTNGVITKDEAEKLKNQDVDAVRGILRNAKLKFVYDSLDAVRALINMVKQMGETGVAGKTNSLRMLQKRDEAVNLAKSRYNQTFNRAKRVITKRTGTDAYKMNIKEMLRIDEGLRLKIYKDTEGYTIGIGHLTKSFSLNAKKELDKAIGRNTNGVITKDEAEKLKNQDVDAVRGILRNAKLKFVYDSLDAVRALINMVKQMGETGVAGKTNSLRMLQKRDEAVNLAKSRYNQTFNRAKRVITKRTGTDAYKN
Common: ELDKAIGRNTNGVITKDEAEKLKNQDVDAVRGILRNAKLKFVYDSLDAVRALINMVKQMGETGVAGKTNSLRMLQKRDEAVNLAKSRYNQTFNRAKRVI```

Now we are interested in the question of the extent to which a randomly selected protein’s subsequences can be found in a stored set of protein sequences because the rigidity of protein folds give us some confidence that the shapes for such subsequences can be used from the database.  This idea is not particularly innovative but what is new in our approach even here is the significant simplification produced by twist decompositions of protein shapes because splicing sequences with twists is a simple operation.

I produced a gigantic table of intersections of protein sequences, a table that looks like this:

```\$ head intersections.txt
102m.txt 101m.txt 0.583333333333333
103m.txt 101m.txt 0.586206896551724
104m.txt 101m.txt 0.486111111111111
105m.txt 101m.txt 0.486111111111111
106m.txt 101m.txt 0.558620689655172
107m.txt 101m.txt 0.558620689655172
108m.txt 101m.txt 0.5625
109m.txt 101m.txt 0.696551724137931
110m.txt 101m.txt 0.696551724137931
111m.txt 101m.txt 0.696551724137931```

The file contains in the order of 7600×7600 entries and the data becomes unmanageable using straightforward use of hashes in perl scripts.  We can use the DB_File module for further analyses — I mention this because analytic tools without resources is a general problem for many interested in doing work outside well-funded institutions.   CPAN contains the DB_File module which provides methods for treating text files as databases.  One has to install the Oracle Berkeley DB which can be found here.

We found the protein with the maximum intersection for each in a sample of 7600 proteins with known shapes and the average of these is 51% of the length of the protein which gives a coarse quantitative measure of redundancy of substrings.

Some strategic options for the Occupy movement

Any Occupy Wall Street protester should have some basic understanding of the planetary power structure, and I provided a schematic sketch here.  They should also have the following basic knowledge about the Federal Reserve.  The Fed is a private institution owned by a consortium of large international banks that prints money and has the explicit responsibility of ‘maximizing employment’ and ‘stabilizing prices’, i.e. keep inflation under check.  The Fed does not print money and simply give it to the US Treasury.  The standard process is that the large investment banks buy US Treasury debt at auctions, and then sell outstanding US Treasury debt to the Fed who prints money out of thin air to buy these.  This is how new money comes into the economy.  The investment banks are the only clients of the Fed and are jointly the distributors of actual money.  They can lend or invest money in various ways:  corporate debt has a spread in interest rate to the US Treasury as do most national and other debt based on the relative riskiness above the once-risk-free US Treasury.  Since the dollar is not simply a local American currency but the global reserve currency of a planetary Empire, one described in the link above, it is central not only to the American economy but the global economy where the US Treasuries act as the denominator for the other debt.  Basic facts about the system can be found here for example.

The major direct problems facing Americans who had begun the Occupy Wall Street protesters are unemployment, where the headline figure of 9.1% is probably hiding real unemployment close to 20%, the instability in the financial system and gross inequality where the income of the top 1% has tripled over the past three decades.  But the underlying demand of the Occupy movement and the reason that it has sparked resonant protests globally, is against the planetary political system of the dollar itself.  The underlying demand is for revolution rather than reform, which is one reason that the Occupy protests had steered clear of attachment to the traditional “left” political party in America, the Democrats.

There are many proposals accompanying the Occupy movement that have arisen.  Some of these opinions can be found in excellent interviews conducted by Paul Jay in The Real News, which is a non-corporate news and analysis program.  Representative opinions include Bill Black’s idea that the largest 20 banks pose a danger to the global financial system should they fail and should be broken up and Michael Hudson’s idea of a public utility bank which would be of public interest.  These ideas are presented in the backdrop of the power that global finance has exerted in the global economy which strengthened in the last three decades.  A major obstacle to these sorts of ideas arise from the fact that they seem to localize the role of the US dollar finance which I believe cannot be a real solution for two reasons: the banking elite control the government rather than the other way around; and the reach of the finance elite is global rather than local.  For example, Goldman Sachs controls the US Treasury and the banking private elite control the dollar and its finance, a reality that cannot change by demands made to the US government.  I will suggest that a local American solution will simply not work.

I take planetary empire extremely seriously although it is remarkably well-hidden from us in the standard discourse of the learned and the media for obvious reasons: reinforce the divide-and-conquer strategies that were sharpened when this empire included the territories that were before the Second World War the British Empire, and the state propaganda needed for population control.   So from my point of view the interests of the capital elite above all will be to ensure that the global resource supplies such as oil and minerals are undamaged, which is one reason Obama engaged in a clear neocolonial war in Libya for regime change as well as a careful balance in Middle East to find ways of co-opting the Arab Spring (the Muslim Brotherhood in Egypt are cozying up the US apparently). The financial elite can completely ignore the OWS protests if their sole priority was to protect the US dollar global finance because China is clearly backing the dollar (see the rise in US Treasury debt held over 2011 here: there was a rise until July and then a drop but overall it’s reasonably stablehttp://www.treasury.gov/resource-center/data-chart-center/tic/Documents/mfh.txt). If the elite can re-elect Obama, who got much more campaign funds from banks than GOP rivals so far, they can try to ‘pacify’ the OWS crowd while they try to establish firmer business relations in China which they’ve been doing for a while anyway: US Foreign Direct investment in China in 2006 was close to \$50 billion for example. After 9/11 they basically relocated the money power center from New York to London anyway so WS is a symbolic site of protests rather than the literal money power center for planetary empire. Austerity programs exist to break down the socialist wage-increase forces which is clear in the case of Greece where there are privatization programs but in America in Wisconsin, for example, perhaps with an eye for a longer term future where lower wages will allow them to do business more easily.

On the other side, OWS gains most from taking up the Palestinian cause which will give insta-solidarity to OWS from both east and west. They become a real force only when they not only get solidarity from the Middle East and Africa but CHINESE WORKERS.  Forbes recently had an article that describes some of the measures the Chinese government has taken to prevent precisely this possibility, such as censoring the word ‘occupy’ in a popular search engine, but Chinese workers are more radical than American, especially the urban Chinese workers whose parents were in socialist movements, and hence they will respond sooner or later to a credible global Occupy movement.  Then we have an actual force capable of transforming empire to Republic. This is not as far stretch as it may seem because Americans are the LEAST political people in the world for obvious reasons: they’ve been the consumers in the belly of the beast.

Notes on extreme anguish

Human beings have mechanisms and natural reactions to physical pain, grief, and anguish that usually limit our experiences of these clearly uncomfortable experiences.  A question that has been of long interest to me was what to make of the experiences of Christ.  A recent book by Ariel Glucklich addresses the general issue of how pain can be and has been considered in a positive light by particular religious and spiritual traditions.  There are physical situations of wounds and bloodshed that produce reactions of physical pain and discomfort without any deep spiritual effects.  Soldiers in war are toughened to certain types of physical wounds.  Christ’s image with pinned hands by metals and wounds of the flesh and blood can elicit in us an empathetic response but in a sense this physical pain, the bloodletting and the punishment is a superficial physical drama when compared with the spiritual claims made for him.  I am not a follower of Christ by any means, as I know that the mythologies of Abrahamic religions cannot be true.  At the same time, I do not doubt that Christ had a great deal of metaphysical power.  I do not doubt that he had the power at times to calm literal storms in the sea because I have experienced having such direct effects on the environment in certain states myself.  What is more interesting to me is the issue of the “passions” of Christ and their purpose, their method, their effects.  Esoteric cults such as the cult of Pythagoras and others had devised various rituals of spiritual transcendence.  My basic idea is that there are thresholds of anguish, pain, and suffering for human beings one must cross to literally empathise with the pain, anguish and suffering that is of the entire human race, and when one is able to do this, one should be able to affect the entire human race and our collective consciousness/spirit/soul without any physical activity.  The theory is of interest only if it produces a concrete result in change of consciousness/spirit/soul of humanity in a manner that can be verified empirically at least in principle.  This would be an interesting way in which the reality of four macroscopic spatial dimensions of the universe for which I sketched out a physical theory leads to some way of understanding spiritual phenomena that seem superstitious and archaic to those trained under the rubric of modern science.

Jung’s model of the psyche is the division of the conscious and unconscious but also something he calls ‘collective unconscious’. I’ll come to the issue of pain and suffering and why I do not disregard the experiences of Yogis and shamans on pain as a method of spiritual transcendence, but I have to describe a model of the psyche that is different from either the Jungian model or that of the spiritual practitioners. The schematic Jungian model is that of individual consciousness and unconscious as a thin layer beyond which lies the collective unconscious. This picture is coherent with the metaphysical universe which is a single four dimensional space that is objective and hence shared certainly by the human race among all others. On the other hand, the awareness of the individual human beings is limited to a particular region of this metaphysical space. Regardless of the narratives, the task of the spiritual seekers is not only to act in this four dimensional space but to do so in ways that are not purely individual. I believe that although the hagiography of Christ provides a particular narrative of his having sacrificed his blood for the sake of human beings, the dramatic aspects of his pain and suffering are hiding his more serious spiritual accomplishments that did affect the ‘collective unconscious’ if you will or spirit of the universe.

Why I predict that Obama will win a re-election in America

Ron Paul made a great deal of noise about “ending the Fed” and while he is well-respected in many circles with strong libertarian credentials he simply disappeared from the spotlight.  His actual popularity among Americans was strong, so this is a little strange.  Conspiracy theories abound about the corporate media and their deviousness but there is a fairly solid reason for his political misfortune in my opinion.  He believes in the American nationalist mythology of a democratic federal Republic and he is an old-fashioned isolationist of the ilk we had seriously before the Second World War.   He did not respect sufficiently that Pax Americana, which I place in 1945-2008, established a planetary (military) empire with dollar as the global reserve currency.  It so happens that this global currency is administered primarily not by the American government but private corporations and people.  This makes the extremely important issue of the global reserve currency not quite an issue on which the PUBLIC American government has jurisdiction.  He was excised from the presidential hopefuls precisely because of his animosity towards this arrangement.  The American state protects the private ownership and the currency regime of the globe by backing the dollar.

Now as the Occupy protests become more widespread around the globe, whether the protesters produce inarticulate chants and slogans or they produce fleshed-out criticisms of the impulses behind their protests, they are pressing the issue not only of the recent bad behavior of the banks but also the regime of the global reserve currency, the dollar.  There is now an account of the Wall Street direct financial contribution for Obama exceeding that of his GOP rivals.  This is quite expected because a surge of worldwide support for the Occupy movement pushes the elite into supporting a left-wing presidential candidate.  If they supported a right-wing candidate, their decision becomes hostile to this popular surge which is by far stronger than the Tea Party movement — there is 29% support in America for each but Occupy has global support which is more important for American presidency especially after the global distrust after the Bush decision to go to a regime change war in Iraq — which was not spontaneous but organized by corporate interests although they did tap into populist anger about many issues.  Thus regardless of the credentials and popular support for GOP candidates like Perry and Romney, the elite will support a re-election of Obama to keep some control over the sharp left turn perceived by the Occupy movement.  A GOP president is likely to represent a hostile relation with the Occupy protesters which could be tactically viable in a stronger economic environment where these movements could be dismissed as ‘fringe’ but cannot under the current economic state where a ‘double-dip recession’ is almost certain.  Police state measures would only alienate more people and bring the elite under possible physical danger.  Thus the wisest course would be to attempt to co-opt the Occupy movements by the establishment “left” Democrats.  Of course the Democratic party is a right-wing party by standards of the left globally but that has not been voiced or believed in the American popular psyche in the recent past.

Occupy Wall Street represents a shift in consciousness

My first job after graduating from college in 1995 was at Lehman Brothers, which was the most public victim of the Wall Street institutions in September 2008.  The feeling and culture of New York in 1995 is vastly different from it is with the Occupy Wall Street movement today in the sense that at the time, well-dressed Wall Street men and women were generally treated with deference in the city, in the restaurants and public places.  There was a feeling that Wall Street folks were the legitimate regulators of the planet because they were the cream-of-the-crop of talent, and that the system was generally doing a good job in their task of pushing along the global financial system.  There are excellent reasons from the joint failure of the economy and the financial crisis to have an entirely different perception of Wall Street.  But it is misleading to see this primarily as a rational reaction of the people who have had sudden financial hardships that they blame on Wall Street to take to the streets to demand that heads roll.  In evidence in the Occupy protests something much deeper than the superficial complaints that brought them out to the streets against the economic troubles, and that is a completely changed consciousness and an inarticulate rumbling demand for a reorganization of spiritual values of society.  Like plants that grow out of stones cracking them, the changed consciousness is deeper than the specific complaints against what are being called the crimes of Wall Street.  It is precisely this change in consciousness that finds resonance in the protests that have within a month popped up across America and the globe, now in 1500 cities.  This is primarily the manifestation of the painful birth of a new consciousness for humanity that will, I will predict with confidence, engulf the major religions and end nation states themselves.  When we see the people with their sleeping bags and blankets, their painting and singing in New York, people in Zuccotti park which Mayor Bloomberg’s reaction was, “filthy”, we can consider the analogy with the childbirth as almost literal.  The mostly cerebral calls for a changed consciousness that has gone on on social media in the past few years are finally being seen concretely.