Feeds:
Posts

## The noisy channel model and protein shape determination problem

This note is simply a simplification and repetition of ideas that I had been pursuing for around a year.  Let us recall the noisy channel model in the simplest form.  Signal from a source is transformed in this model into a target signal.  In the discrete memoryless case, the source consists of a sequence from an alphabet of letters $a_1, \dots, a_K$ and the target consists of alphabet of letters $b_1,\dots, b_M$.  Each letter in the target sequence is statistically dependent only on the input sequence and is specified by the conditional probability assignment $P(b_j|a_k)$ defined for each letter $a_k$ in the input alphabet and each letter $b_j$ in the output alphabet.  This model is not quite sophisticated enough to handle the protein shape determination problem but we can place the protein shape determination problem in this setting as follows.  The input sequences are triples of amino acids and the output consits of sequences of elements from a fixed discrete grid on $SO(3)$ which is the space of rotations in three dimensions.  Since there are 20 distinct amino acids and therefore counting repetitions 8,000 amino triples, and for each of these there is a separate conditional probability table that must account for a fixed grid on $SO(3)$ that is sufficiently fine to produce accurate representation for the entire universe of protein shapes, there is a priori even the memoryless discrete model in this case can produce a priori around in the order of 8,000 conditional probability tables each with order of size of the $SO(3)$ grid entries.

In order for this approach to be tractible, one needs sparsity results that could reduce the size of the computational machinery.  It is in this direction that we have made substantial progress over the past few years.  In the language we have developed, the input alphabet are amino-triples and the target alphabet are twists.  From an empirical sample of 39,000 protein shapes we have found that that the average size of the intersection of twist distributions conditioned on the previous twist in the sequence with the conditional distribution of twists given the amino-triple corresponding to it is on average no larger than several hundred distinct points.  In particular, we avoid the problem of size explosion for the noisy channel approach to protein shape modelling.

We proceed by the analogy with a successful application of the noisy channel model to natural language translation.  In natural language translation, the noisy channel model has been employed with success by modeling natural language translation by an n-gram language model and by phrase tables.  In the example of translating French sentences into English, one proceeds solving the optimization problem

$argmax_e P( e | f ) = argmax_e P(e) P(f | e)$

Our approach is the same with English replaced by twists and French replaced by amino-triple words in protein sequences.  Our simplifying assumption is that the 2-gram dependence is sufficient for modeling both the amino sequence space and the protein shape space composed of twists.

## What sort of revolution is necessary for the human race?

Although people are generally unhappy with the injustice of the current planetary political system both in the west and the rest of the world, there are several pressures on people which keeps their vision and ambition small.  There are obvious pressures where people’s focus is on their private lives.  The systemic structures to buoy them are the religions and the remaining structure pushes them down, such as stagnant wages and unemployment around the globe.  There are obvious fears of radical changes to the system because people have been fed horror stories of Hitler’s Germany, both true and fictionally exaggerated along with many other atrocious results from attempted revolutionary changes.  The 9/11 Mossad operation was carefully calibrated to produce a specific world order where Islam could be demonized and Muslims could be marked for the global untermensch.  As with other such attempts, the results are decidedly mixed.  Since I am interested in a revolutionary change, the 9/11 spark for a new planetary order can be seen as a type of operation that relied on the extant good-and-evil order that was put in place after America won both hemispheres after the Second World War, with its prime document NSC-68.  But clearly there still needs to be a new world order not only to reverse the damage done to the human race by the 9/11 Mossad operation but quite generally because the system of neoliberal capitalism has failed to deliver on its promises even to the explicitly privileged.  This is why there is a strong Occupy Wall Street movement in America, a short J4 movement in Israel and left surge in Europe which is battling with increased panic for alleged Iranian plans for building nuclear bombs.

One obvious question is then what sort of spark can produce a movement for real change?  The Ron Paul phenomenon in America is interesting in its attempt for gaining popular support for a radical shift of the status quo.  And I believe that it will nevertheless fail to produce a political victory in America, and then the question will be whether the Ron Paul popular movement’s failure is due to its radical departure from the current power structure of the planet or whether its failure is due to insufficient radical departure from the current power structure.  While it is considered normal in America that one navigates the political landscape by carefully avoiding explosive topics — and just as the Zionists have amassed an enormous stockpile of nuclear weapons and the most sophisticated military technology in abundance since 1948 they also have produced some of the most explosive political weapons in America although in America Zionism is a larger political stream including the Christian evangelical Zionists.   Just so that one realizes the seriousness of this issue, one can look at Chris Hedges’ book on the dangers of Fascism that are appearing from this stream.  If one is concerned only in analyzing the situation passively, one can see how Samuel Huntington’s “Clash of Fundamentalisms” seem to have been a self-fulfilling prophesy or indeed even consciously guided by the tools of the power elite.  While in fact the “Clash of Fundamentalisms” is gigantically deceptive rather than flawed because Islamism as fundamental political ideology is something that could have been avoided altogether and instead it has been quite consciously been encouraged by the western political elite.  The clearest example of this of course is the creation of Hamas as a counter to PLO to sabotage the Oslo peace process presumably for the “Greater Israel” project.  But the precedent for this is obviously the funding of Islamic fundamentalists in Afghanistan to counter communism and continued support in Libya and Syria to destabilize reasonably secular regimes.  Here Ron Paul was right and was the only person to object to the almost unanimous vote in the US Congress supporting Israel after the Operation Cast Lead massacre that killed hundreds of Palestinian children and more than a thousand civilians.

Arab Spring showed the face of democracy seeking parties in the Middle East and this has been attacked from all sides.  The million killed by America in Iraq and now the military preparations for a regime change in Iran are clearly provocations that sideline secularists and moderates and strengthen hardline Islamists.  But we are faced today with a broader concern about the sort of world order we could expect that is not driven by Fascist imperatives driven by Zionist evangelicalism and a revival of Crusades.

It is not an exaggeration to consider the current global spiral deeper into Hell to be a function generally of the duality of Good and Evil.  The 9/11 Mossad operation was essentially equivalent to taking the NSC-68 good-and-evil story and amplifying it by a thousand fold.
Today I overcame the metaphysical barrier produced by some agencies that kept 9/11 as a Mossad operation or deviation from the completely false story of al Qaeda’s primary role in 9/11 as incredible.  This includes Noam Chomsky who had drawn lines of truth for 9/11.  Those who had done this perhaps had different ideas about the reasonable expectations of what can seriously change in the planetary political system and which narratives are worthwhile challenging and which narratives are better left alone for more important issues affecting people.  Both 9/11 and the standard narrative of the Holocaust have the same treatment by them.  There is a serious problem with this approach because the dystopia is global and to speak the truth means to speak the truth regardless of agenda.  My criticism of Noam Chomsky’s views of both US and Britain as examples of terror states is that the mythologies that justify this behavior cannot be sustained with the expectation that with these active mythologies that there is any genuine chance of this behavior changing.

## Purgatory

```Unreal City,                                                            60
Under the brown fog of a winter dawn,
A crowd flowed over London Bridge, so many,
Sighs, short and infrequent, were exhaled,
And each man fixed his eyes before his feet.
Flowed up the hill and down King William Street,
To where Saint Mary Woolnoth kept the hours
With a dead sound on the final stroke of nine.
There I saw one I knew, and stopped him, crying "Stetson!
"You who were with me in the ships at Mylae!
"That corpse you planted last year in your garden,
"Has it begun to sprout? Will it bloom this year?
"Or has the sudden frost disturbed its bed?
--T. S. Eliot, "The Waste Land" 1922```

Greyhound bus stations in Oklahoma, in Indianapolis, New York, in Dallas and Chicago with uniform architecture, a sparseness with despondent public with a drugged serenity provided elsewhere by Lithium.  A sleepiness different from the early morning subways in New York with uniformed bureaucrats in ties and suits rushing to their stations.  These are the loci of purgatory, interim public places with incoherent public.  Oppressive gloom that is barely a notch above that of the 30th street homeless shelter whose main discernible difference is a gigantic weapon detector infrastructure at the entrance where one has to take off metallic objects including belts, not very different from the security checks mandated for the concocted threat of Islamist terrorists.  The oppressive chambers of hopelessness are punctuated often by conversations.  In Oklahoma, a devout man explained to me that God loves us all, and to appreciate this love one must water one’s life labors like that of a tree.  Purgatory waiting for a judgment for people whose hopes have been squeezed into a narrow passage.
I have been in an internal metaphysical path that is mostly healing through spirit matter that is mostly dark muck.  My answer to the pervasive gloom is not simply a new adventure for people, which is what 9/11 produced, a military adventure to refocus the national sentiment towards an aggressive project, a rejuvenation of the project of American entry into the Second World War which mobilized the nation into a good-and-evil drama that led to enormous wealth for a few and gave global military hegemony for America.  The 9/11 event did not quite have the same effect on the people and in an ironic turn ended with the American economy in a worse shape than it began.  Thus we see the expanse of purgatory and a decline in the empire on its fringes.

There is a sense in which there is an impossibility of the same pattern twice and there is thus a continuous need for change, and for evolution.  Stories of wealth and poverty are age-old and does not lead to significant change for there is no moral force in social injustice that has not been neutralized before and thus cannot be neutralized again.  Thus one must seek a different path out of this pervasive gloom, and if we, as a race wish to evolve then our global dramatists must consider the drama of our enemies within.  Televisions in purgatory have commercials on how clinically proven techniques can increase one’s testosterone by 61%.  The set of innovative ideas to come out for improvements in our lives for commercial success has a higher chance of sinking us into an inhuman Hell rather than a path to eudaimonia by any standards.  It is art that changes the world because it is art that can present us with the most difficult wars that are necessary.  We must be mobilized not for vampyric destruction and plunder but to overcome our inner demons, for these are much more pernicious, and the lies to produce the external demons are precisely an obstruction to the passage from purgatory to sunlight.

## Power pyramids of Trotsky and Lenin

Last night we captured the power pyramids of Lenin and Trotsky after realizing that Trotsky had applied the Zionist metaphysical power as well.   I quickly saw a succession of hundreds of faces of people under the sway of Trotsky and Lenin.  Also last night as I wanted to make use of my own resentment at having been in humiliating situations, I reached a high level of resentment and it is here that I saw a global network of levels of resentment.  I literally saw a world map with blocks in black that showed concentration of resentment, at least realtime last night it was clear that the pyramid of highest levels of resentment belonged to Islam, and their resentment against America was high.  I saw markings on the world map with arrows pointing from the Middle East to different parts of the world, and a Muslim name was attached to a line to America.  I took a dive into the blocks of resentment which I had learned to transform into energy required for transformation of the human race to a Republic.  I also saw last night that Islam was under attack by other metaphysical means that I deflected as my own path is to ensure that Zionist metaphysical power dissolve before Islam for a planetary Republic metaphysical order.

## Conversation about good and evil 2/21/2012

• Merlin Saint GermainThe “false light” of half truths is one of the great dangers that many fall prey to, unwittingly. Another great danger is unworthy sensual desires. Also, on the mental plane, the great lie of philosophical materialism, with all that it spawns – denial of spirituality, selfishness, ambition, greed, consumerism, the belief in drugs as a spiritual tool, and ruthlessness.

8 hours ago · Like · 4
• Zulf AhmedI do not agree. Political and social freedoms, to the extent they can be detected are manifestation of the true inner freedoms of our race.

6 hours ago · Like
• Merlin Saint GermainThat may be so, Zulf. But in order for people to bring into outer manifestation in society a true reflection of their inner values and beliefs, they need to participate in the social life and shape it through their initiative, not just stay at home eating, having sex, reading books, talking, meditating and watching the TV.

6 hours ago · Like · 2
• Zulf AhmedThat’s true, but at the same time, we need to have this happen globally, for which there are great obstructions. Either the entire race will have outer manifestation of inner freedom or the entire race will sink deeper into Hell that was begun by the Mossad operation of 9/11.

5 hours ago · Like · 1
• Merlin Saint GermainYes, so true! Humanity is a singular family, and our fate is one. Humanity needs to dust themselves off, quit drinking and taking drugs as much as possible so that they are in their normal sober state, call on their best selves, and set out to fix the world as best they can, both singly and collectively.

5 hours ago · Like · 1
• Zulf AhmedNow only if these pesky rulers of the world would stop being so obsessed with control and surveillance to use child porn as an excuse to push through their SOPA and PIPA efforts which failed while they point fingers at China and Iran as totalitarian censorship states.

4 hours ago · Like · 1
• Merlin Saint GermainI doubt that those pesky rulers will do anything but continue to step up their program for global fascistification. We can’t control them, but we can control ourselves and employ our faculties and gifts to put them back in their box and retake control over the affairs of humanity in the name of truth, justice, freedom, and goodness.

4 hours ago · Like · 1
• Zulf AhmedTruth, Justice, Freedom above good and evil!! Hear hear!!

4 hours ago · Like · 1
• Merlin Saint Germain

If we reject notions of duality, of truth, of righteousness, justice and goodness, then we are buying into the evil propaganda of the dark brothers who want us to be outside of the realm of goodness, and thus neutralised in the conflict bet…See More
3 hours ago · Like · 1
• Zulf Ahmed What is done out of love always takes place beyond good and evil, said Nietzsche and I cannot agree more.

https://zulfahmed.wordpress.com/2012/02/10/the-human-race-must-overcome-the-duality-of-good-and-evil/

3 hours ago · Like · 1 ·
• Merlin Saint GermainYour argument that the belief in good and evil is the cause of evil is not only false, but self contradictory.

3 hours ago · Like
• Zulf AhmedI did not say the belief in good and evil is the cause of evil. You should read the note I posted for what I am saying. The zealous “Good” are more likely to cause great evil.

3 hours ago · Like · 1
• Zulf AhmedI will give you a very clear example of this: around 54% of American Church-goers believe that it is right to torture suspected terrorists. This is not a trivial percentage.

3 hours ago · Like
• Merlin Saint Germain

The mistaken belief that evil is good, and good evil, has certainly been the cause of many problems in the world, but that is no reason to discard the concept of good and evil, or to try to somehow transcend it, as you seem to be suggestin…See More
3 hours ago · Like
• Zulf AhmedI adhere to the ideals of Freedom and Justice. I personally am beyond good and evil, but the ideal of Freedom tells me to respect your freedom to refuse to cross these lines.

3 hours ago · Like · 1
• Merlin Saint Germain

A person who does not strive to be righteous, moral, ethical, good and virtuous is very dangerous in society. You may call goodness freedom or justice, but if you believe that there is a better way to be that is in alignment with the social…See More
3 hours ago · Like
• Zulf Ahmed

You see, I believe that the human beings are metaphysically primarily the fallen angels in Hell at one level because I have seen the Hell manifest in my own eyes, have seen the suffering of our race. I accept my own darkness and my light a…See More
3 hours ago · Like
• Merlin Saint Germain

The reason that I made this comment is because a huge and seemingly rapidly growing number of people on earth are buying into belief systems that purport to be very profound and spiritual, but I think they are pernicious and also usually ha…See More
3 hours ago · Like · 2
• Zulf Ahmed

I am a minimalist in terms of spiritual constraints. The human race is a single race. Truth, Justice, and Freedom are the fundamental spiritual and simultaneously political — because there is no difference between collective spirituality…See More

zulfahmed.wordpress.com

I did not know about the US massacre of German soldiers in 1945 until I saw Davi…See More
2 hours ago · Like ·
• Merlin Saint Germain

I have a book detailing how in all likelihood the Allied murdered about 6 million Germans in retaliation for the Second World War, after the cessation of the formal hostilities. The Christians, such as the colonialists, the slave traders, t…See More
2 hours ago · Like
• Zulf Ahmed Well, I am certainly not a ‘moral relativist’. Justice is a much stronger ideal than Good in my own opinion because the polarity of good and evil inevitably creates conditions for literal physical conflicts between people. Inevitably there is a target evil, and inevitably the zealots are ready for murder.

Consider this:

Gaza, never forget! Video by Max Blumenthal and Dan Luban. Full story here: http://www.alternet.org/story/119372
2 hours ago · Like ·
• Merlin Saint GermainIf you state that justice is good, or that freedom is good, then you are invoking the concept of good and evil. If you refrain from saying that justice is good, or that freedom is good, or that truth is good, then you cannot speak up in favor of any of these. To me, your philosophy is self contradictory, since you refuse to acknowledge good and evil, yet you assert that justice and freedom are good.

2 hours ago · Like
• Zulf AhmedI did not say Justice is Good. Justice is a far stronger spiritual ideal than Good. Divine Love is the ideal of Justice.

2 hours ago · Like
• Merlin Saint GermainYou have just substituted the word “spiritual ideal” for good. They mean the same thing.

2 hours ago · Like
• Zulf AhmedNot at all. I am quite precise when I use the spiritual ideal. Let me repeat the dictum of Nietzsche which provides concreteness to this: What is done out of love always takes place beyond good and evil. I agree that the distinction seems subtle, but I am amoral when it comes to good and evil.

2 hours ago · Like
• Merlin Saint GermainYour philosophy seems absurd to me, Zulf. What is done out of love is often very evil, as when a person is deluded. Take the inquisition for example, and when Catholic parents beat their children out of the mistaken notion that this is good for them. In order for an action to be good, it must be motivated by goodwill, and informed by wisdom, and empowered by effectiveness.

17 minutes ago · Like
• Zulf AhmedWell, I consider people who believe in good and evil to be deluded, and the religions absurd. Catholic inquisition was a product of the good to eradicate evil, and it is unjust to cause physical harm to people.

14 minutes ago · Like
• Zulf Ahmed This is an interesting interview Noam Chomsky gave on terrorism and my philosophy would be in agreement with him in this instance: https://zulfahmed.wordpress.com/2012/02/13/noam-chomsky-interview-in-2010-about-terrorism/

## A conversation about American military and morality of nationalism

This is a basic conversation that brings out a number of issues that requires a coherent discussion regardless of how dispersed the topics seem, because it touches some of the faultlines of America and nationalism.  Sometimes we get caught up in the numbers game on specific broad issues and this is useful but it is also important to quickly glimpse at a large picture because we are individuals beyond nation and ideologies and our individual freedom depends on being able to distance ourselves from a partisan view.  I have myself been extremely critical of Zionism partly for political reasons, as I work towards a planetary Republic based on ideals of Truth, Justice, and Freedom and the condition of the Palestinians is in my view the central political/ideological conflict on the planet, but yet I will claim to be above nations and religions regardless.

• John TeubertThis is an interesting take on that statement, which I’m remembering being said by Bill Hicks. In his version, it was the realization needed to shed the fear that typically keeps otherwise decent people in line; keeps them from challenging the psychos at the top. Any phrase or text, it seems, can be perverted to justify the psycho’s behavior…

4 hours ago · Like · 1
• Mammatus CloudMilitary get the convoluted versions all the time…helps them rationalize and justifies the slaughter. Heard lots of first hand accounts from family…

4 hours ago · Like · 1
• Mammatus CloudNOT saying that “military” automatically equates into “low moral conscience”…but when surrounded by people who Do exhibit lack of one and having to rely upon them under fire, the pull of ‘group think’ programming can be overwhelming.

4 hours ago · Like · 1
• Zulf Ahmed So military in the US is trained to have ‘low moral conscience’ while in fact they may not have it before training:

Josh Stieber: In boot camp we trained with songs that joked about killing women and children
4 hours ago · Like ·
• Mammatus Cloud

That’s a broad brush you’re painting with Zulf. Stereotyping via group is a trap. All ‘isms’ depend upon the ability to overlook individual differences. There’s lots of differing reasons people join any group. Personally, I think groups bli…See More
4 hours ago · Like
• Zulf AhmedMammatus, military is the essence of dissolving individual. It’s a centrally controlled enterprise. This training is not a decision of individuals. Individual differences obviously exist but the military is not a democracy either.

4 hours ago · Like · 1
• Mammatus CloudWhy the suicide rate?

4 hours ago · Like · 1
• Mammatus CloudIf the training were so successful that the ‘individual’ were successfully ‘dissolved’….?

4 hours ago · Like · 1
• Mammatus CloudThe ability to regret, feel guilt, remorse…all Opposite of the psychopathic training. The suicide rate is direct evidence of failure in dissolving the ‘individual’ identity. Repressed or not.

4 hours ago · Like · 1
• Zulf Ahmed

Trapped slaves commit suicides because they don’t feel happy about what they are doing. Obviously the training is successful enough that there is not a mass defection from the US military, and disagreements are contained by control mechani…See More
4 hours ago · Like · 1
• Zulf AhmedNationalism is one of the key tools to keep the military in line, and racism is a key tool in imperial operations. Remember that 9/11 was a Mossad operation so a high level of propaganda reality is necessary for the military as well.

4 hours ago · Like
• Zulf Ahmed You can see the actual barbaric policy of US military in Iraq from a down-to-earth account by a veteran. A million mostly civilians were killed in Iraq:

Anderson joined the U.S. Army in January 2003 to get money for college and to se…See More
4 hours ago · Like ·
• Mammatus Cloud

‎”Trapped slaves commit suicides because they don’t feel happy about what they are doing. ” How many ‘trapped slaves’ committed suicide while plowing fields? Cleaning houses? Being raped repeated by ‘owners’? No, Zulf. Conscience has more t…See More

en.wikipedia.org

The Milgram experiment on obedience to authority figures was a series of notable…See More
4 hours ago · Like
• Zulf Ahmed Many more than you would expect. There were suicides in GCC countries because of exactly this reason:

Adam Hanieh: Saudi Arabia and the Gulf states created a super exploited migrant …See More
4 hours ago · Like · 1 ·
• Mammatus CloudCulture is the deciding factor there. Think about it…

4 hours ago · Like
• Zulf Ahmed

You do have a point that not liking slavery restrictions while doing oil work or construction work puts more pressure from the ‘trapped’ portion because there is no moral ambivalence in these jobs except the exploitation aspect, but not lik…See More
3 hours ago · Like · 1
• Mammatus Cloud

‎”So the propaganda tries to adjust this by heroic tales of how great their work is and how beneficial to people and the world, but problems occur when they see through the bullshit for what these operations really are about. What “defense …See More
3 hours ago · Like
• Zulf Ahmed

Well, I don’t have the figures for suicide rate of US military during the Second World War but I would suspect that it was not noticeable. So I highly doubt that people commit suicides simply because of wars and massacres, at least not for…See More
3 hours ago · Like
• Mammatus Cloud

Apply this from a Sociological / societal level : http://counsellingresource.com/lib/therapy/self-help/stockholm/ and then refer to my post above regarding self discrepancy. and consider the “waking up” from such a scenario with no where to…See More

counsellingresource.com

Page 1: If you’re in a controlling and abusive relationship, you may recognize s…See More
2 hours ago · Like
• Zulf Ahmed

So the problem with this sort of personal psychological evaluations are that then one could brand entire societies as psychopathic, which I think would be wrong. Consider the fact that Americans have not felt much remorse for the Hiroshima…See More

www.mtholyoke.edu

Source: Naval War College Review, Vol. XXVII (May-June, 1975), pp. 51-108.  Als…See More
2 hours ago · Like ·
• Mammatus Cloud

‎”to explain the lack of interest in most Americans about these things.” Have you read what I posted above? What do you think societies are made of? INDIVIDUAL people. Zulf, it truly Isn’t that hard. Individuality ‘qwerks’ mean little when …See More

An evolutionary perspective on psychopaths in power. . Apart form the books/ art…See More
2 hours ago · Like
• Zulf Ahmed

Mammatus, societies are not simply made up of individuals. There is an identification of the individual with the nation, which is what nationalism amounts to. Most Americans are extremely insular, so the identification to nation is used f…See More
about an hour ago · Like
• Mammatus Cloud

The identification of the individual with their nation is no different and is simply an extension of the same process of the individual identifying with their family of origin. Again, survival. Ever try getting people to face ‘family of or…See More
about an hour ago · Like
• Zulf Ahmed

So while some of this is true, that there is a sort of tribalism in the national identification, although one has to wonder what ‘survival’ has to do with a military whose explicit policy is ‘full spectrum dominance’ of the globe, I would take exception to your considering this discrepancy between the individuals making the nation who are presumably sane and a leadership that is psychopathic. America was an empire from its birth, from George Washington’s own words, and this psychopathy that you are talking about is the nature of imperial power, and has been the case for every past empire. What is different about America from previous empires is that people have the illusion of popular voice in actual power, and that illusion of freedom is extremely carefully cultivated by a propaganda system. But you can see the disenfranchisement in the tighly controlled duality of neoliberal right parties dominating the “democratic politics” controlled by the major investment banks and lobbies like AIPAC. From my point of view Orwell wrote 1984 describing the National Security State that formed after the Second World War to have military control of the globe.
52 minutes ago · Like
• Zulf AhmedThis is an important conversation for the issues it brings out, so I’ll blog it.

a few seconds ago · Like