Protein Squinting

What’s the use?

Don’t dismay!  The structure of amino acids will help you infer!

                Determined by the sequence from different species, like primates, like bacteria, 2 proteins can perform the same function, an evolutionary relationship? An evolutionary relationship! The implication of this individual functional unit we find in nature, complex sequencing, beyond its normal function, pro-proteins, an extra sequence, like glycosylation, or a cell that says ‘no’ outside the cytoplasm, like an anti-body, recognition? Edman degradation fragments indirectly, routinely sequence, rapidly, DNA, decode into the protein sequence.  Reiteration, if the functional sequence spits out initially, can we tell post translationally?  Some side-chains cannot be changed at the end of the day, you can still check by mass spectrometry if this is ‘good enough.’ The Gene, The Proteome, the functional aspect of the nucleic acid, the origin.

                Nature acts to protect us.

              

                Stimulating anti-body production (get-away-from-me)

                The epitope is the part of the protein sequence that is going to represent the antibody, politically.

             

   Heavy-chain, light-chain, everything is covalent, produced from 4 separate polypeptide chains, the tertiary structure, a why-like shape, it doesn’t function in recognition at all, it helps the binding interaction take place.  Zoom in on that structure so you can see where it binds.  Red and Blue chains, both peptides are present in this domain, my FAV.  Flexible domains have more than two events take place. How do we make use? Immunity? We can form risky antibodies in your own rabbit, Polly Clonal. The rabbit (Polly) gets injected as you were once boosted.

We don’t know what’s appropriate.

Nature can do this efficiently.

The antibodies are built up in Polly’s blood. Higher-order species have developed many efficiencies.  Centrifuge serum, anti-serum, anti-bodies, all anti-gens to which Polly’s been exposed, they just exist there, figure that out.  Pictured up here are Polly Clonal’s rabbit anti-bodies, differently colored epitopes, red triangles, blue squares, green circles, a non-uniform (racemic) mixture, heterogeneity, why would we use these?

Pictured down here are Mona Clonal’s antibodies.  We’ve selected one predictable dose and response with different affinity. Most cells that produce antibodies have a very short lifetime.

Cancerous yeasts are immortal.  They don’t die.

Multiple myeloma is what we take advantage of.

We generate Polly Clonal’s antibodies, red cells, these will die, these (others) live, hybrids…Just blue, just red, blue and red together, the hybridoma cell line, one type of DNA, one type of antibody.  Polly Clonal is different from Mona Clonal.

Why do we care?

We can make use of precise analytical or preparatory chemistry, very small amounts, quantification, a read-out, fluorescence spectroscopy, affinity tag, the way that would work: a column format chromatography. Detection fits in with tracing.

E.L.I.S.A.: Enzyme-Linked ImmunoSorbent Assay.

The connection between enzyme and an antibody.

Signal detection? Tracer enzyme. Link. Better. Smaller. Direct. Backwards. If it sticks, we have a catalyst. Schematically what’s happening? Red dots are antigen, stuck to the walls of the vessel. Wash. Introduce antibodies. Wash. Introduce enzyme. Wash. Use the laser-dick. (A lot of steps are required to get it up.  That’s why we have designed Elisa. She’s good to us. She’s easy. Routine. Less work.  Sold easily. My precious…) Sandwich Elisa, she recognizes 2 antibodies, same antigen.  Make an elaborate assay, spectral readout, western blotting liked to electrophoresis (SDS-PAGE). You think that one of these bands is a specific protein? Radioactivity tag/auto-radiogram or Elisa, or fluorescence can also be used. That’s it for antibodies.

Cubans are pretty good synthetic chemists.  Not as good as nature. Nature puts out (more than Cubans?). But you can play tricks on nature that nature doesn’t do, unnatural substitutions. Synthetic peptides, short stretches of proteins can be made in a day, like a plant function, formylly, with Formylmethionine.  Higher-order mammalian (live-birthing teet sucker) cells intentionally make polypeptides. Vasopressin. ADH. Increase or decrease urination? Whatever’s functionally useful! Induce for treatment, roses full of loaded thorns. Desamino (take away) remove N term, split. We can do tricks like this to what was otherwise a natural material.

“Quaedam remedia graviora sunt quam ipsa pericula.” – Seneca

(Certain remedies are more grievous than the dangers themselves)

Scio a Carmene

We do well always and everywhere to give You thanks and praise for the glory of His church, who laid the groundwork for the form designs (icons) Whose window blueprint a glory box with radio antennae for a cross on a steeple.  Redress the graves of those who went before us to increase the rates of rolling corpses there, in the system, and thus calculate the rates of disapproval against the binary standard by the invisible Hand of the proper authorities who properly sort papers, action amended.

Persistent in perpetuity, the lucrative species evokes the necessary responses requisite to form desired outcomes. ‘Cause loyalty to the institutional standard that derives power through obfuscation filters, a CREAMy crust that forms on the surface. Erratic logic diagrams of binary log (decision-making prefrontal cortex) of peaks and troughs, signs of logically low posits of uncertainty.

“’Say at last – who art thou?’
‘That Power I serve
Which wills forever evil
Yet does forever good.’”

Goethe, Faust, from Bulgakov, M., The Master and Margarita.

The phrase ‘hooked up’ is an urban colloquialism that comes from the Christian notion of Jesus being a ‘fisher of men,’ and thus, there comes an appreciation for being caught in a net presence of divinity. In science, however, the calque comes from ‘Hooke’s Law,’ which creates dual meaning, wherein the body being acted upon is being upwardly elevated not as from a force from above, but being pulled from a force from below.  The alternate urban notion to having been ‘hooked up’ follows the physical notion of having been ‘sprung,’ wherein the body achieves the physical state of achieving upward mobility in an imagined sense, psychologically associated with an object used to ‘get high.’ Furthermore, in the Christian sense of the word, the alternate position achieved by the body put in motion has an indefinite recurrence to its former position (pendulously), whereas the use of the sense of the word derived from physics presupposes a repositioning due to gravity or some other form of periodicity inherent in the mechanistic act, (where the body having been sprung upwards is sure to fall). Thus comes confusion arising from the religious sense of belief based on orthodoxy (‘right belief’) and the scientific sense of the phrase that is based on method or habit, viz. orthopraxy (‘right action’).  What is the science of ascension?  (Quantum rockets.)

Time is Chaos: We're all Doomed!

All quotes from Spengler, O. from The Decline of the West.

“Yellow and red, on the other hand, the colours of nearness, the popular colours, are associated with the brass timbre, the effect of which is corporeal often to the point of vulgarity.” P133

“Astonishment at alien motion is the source of religion and physics both; respectively, they are the elucidations of Nature (world-around) by the soul and by the reason. The ‘powers’ are the first object both of fearful or loving reverence and of critical investigation.  There is a religious experience and a scientific experience.” P200

“The outcome of a Numen is a Deus, the outcome of a notion is an idea…Every myth of the great style stands at the beginning of an awakening spirituality…” p201

“The Roman felt that the claim Yahweh to be recognized as sole God had something atheistic in it.  One God, for him, was no God, and to this may be ascribed the strong dislike of popular feeling, both Greek and Roman, for the philosophers insofar as they were pantheists and godless. Gods are bodies, of the highest type, and plurality was an attribute of bodies alike for mathematicians, lawyers, and poets.” P203

“All these deities more and more came to be felt as a single numen, though the adherents of a particular cult would believe that they in particular knew the numen in its true shape. Hence it is that Isis could be spoken of as the ‘million-named.’ Hitherto, names had been the designations of so many gods different in body and locality; now they are titles of the One whom every man has in mind.” P206

“That this ‘force’ of ‘energy’ is really a numen stiffened into a concept (and in nowise the result of scientific experience) is shown by the often overlooked fact that the basic principle known as the First Law of Thermodynamics says nothing whatever about the nature of energy, and it is properly speaking an incorrect (though psychologically significant) assumption that the idea of the ‘conservation of energy’ is part of it. Experimental measurement can in the nature of things only establish a number, which we (significantly, again) named work. But the dynamical cast of our thought demanded that this should be conceived as a difference of energy, although the absolute value of energy is only a figment and can never be rendered by a definite number.” P210

“All that has happened on the way from Newton to Faraday – or from Berkeley to Mill – is that the religious deed-idea has been replaced by the irreligious work-idea.” P212

“When Nietzsche wrote down the phrase ‘transvaluation of all values’ for the first time, the spiritual movement of the centuries in which we are living found at last its formula.  Transvaluation of all values is the most fundamental character of every civilization. For it is the beginning of a Civilization that it remoulds all the forms of the Culture that went before, understands them otherwise, practices them in a different way. It begets no more, but only reinterprets, and herein lies the negativities common to all periods of this character. It assumes that the genuine act of creation has already occurred, and merely enters upon an inheritance of big actualities.” P181-2

“Culture and Civilization – the living body of a soul and the mummy of it.”

“Only a sick man feels his limbs.”

“As soon as life is fatigued, as soon as a man is put on to the artificial soil of great cities – which are intellectual worlds to themselves – and needs a theory in which suitably to present Life to himself, morale turns into a problem… It had become necessary to discover, to invent or squeeze into form, as a rule of being, that which was no longer anchored in instinct; and at this point therefore begin the civilized ethics that are no longer the reflection of Life but the reflection of Knowledge upon Life.” P183

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                All of my belongings, my indelibly ascertained objects of management ideals strewn efficiently in a blinking bucket for all-time’s sake. So current it’s almost predictive of the future status of things as they lie. Lying blinking inert.

                The albino horrorshow freak, face all mouth, no eyes. There was a time when I canvassed forests, mountain ponds, and hours of walking trail; back when? Back before the freak roamed. Much like the freak, whose judgment is blind and whose punishment is swift if he sniffs out a couple campers unawares in a pitch tent making whoopee racket when the freak upends the polyester from the terpene tarpaulin and tin stakes and sends a camper rolling back down whatever height climbed to get there, short way to the bottom, rock, tree, and then down the gaping wet white maw that is the albino’s mouth all slobbery for sapiens. Man’s knowledge of the freak extends all the way back to the Garden whence Adam tamed it and named it Gary.  Gary et apples from a particular tree that gave Gary an appealing reek, ponderously from the very fruit he consumed. Adam had leashed Gary the freak to the forbidden tree where he maintained happily blind and tethered. The fruit from the tree was known as Gary’s fruit, not simply because Gary ate from the tree, but because Gary ate whatever or whosoever haplessly gobbled the possessive apples in his sleep.  Whatever ate from the tree would subsequently produce a signature scent with which the freak associated his appetite. Gary would loosen himself and sometimes run a marathon in pursuit of whatever creature was unfortunate enough to nibble its way into Gary’s grove. Gary mostly feasted on worms, boogers, and apples, until one day…

Sun Tzuzaphones converse.
Terror: an advanced state of panic.
Terrorist: a vertiginous construction worker.
Terrorism: a monument dedicated to the panicking.
Skyscraper: Long-term scaffolding.

Dissenter to the Times Literal translation pled ignorance to knowing antennae stations of the cross with syntactic religious iconoodles executing smellings alt. Delete screen with me falling asleep in front of it.

“Since Newton, the assumption of constant mass – the counterpart of constant force – has had uncontested validity. But the quantum theory of Planck, and the conclusions of Niels Bohr therefrom as to the fine structures of atoms, which experimental experience had rendered necessary, have destroyed this assumption. Every self-contained system possesses, besides kinetic energy, an energy of radiant heat which is inseparable from it and therefore cannot be represented purely by the concept of mass. For if mass is defined by living energy it is ipso facto no longer constant with reference to thermodynamic state. Nevertheless, it is impossible to fit the theory of quanta into the group of hypotheses constituting the ‘classical’ mechanics of the Baroque; moreover, along with the principle of causal continuity, the basis of the Infinitesimal Calculus founded by Newton and Leibniz is threatened. But, if these are serious enough doubts, the ruthlessly cynical hypothesis of the Relativity theory strikes to the very heart of dynamics. Supported by the experiments of A.A. Michelson, which showed that the velocity of light remains unaffected by the motion of the medium, and prepared mathematically by Lorentz and Minkowski, its specific tendency is to destroy the notion of absolute time. Astronomical discoveries (and here present-day scientists are seriously deceiving themselves) can neither establish nor refute it. ‘Correct’ and ‘incorrect’ are not the criteria whereby such assumptions are to be tested; the question is whether, in the chaos of involved and artificial ideas that have been produced by the innumerable hypotheses of Radioactivity and Thermodynamics, it can hold its own as a useable hypothesis or not. But however this may be, it has abolished the constancy of those physical quantities into the definition of which time has entered, and unlike the antique statics, the Western dynamics knows only such quantities.” p419