Odotope Theory

From Wikipedia, the free encyclopedia

Odotope theory, also known as weak shape theory, is a theory of how olfactory receptors bind to other molecules. The theory proposes that a combination of shape factors determine the coupling. The word itself is an analogy to epitopes.”

If you have been following some of my essays concerning the magnificent work of Donald Ingber about tensegrity, I have coined the term, shape sensing as Nature’s way to feel molecules to gain recognition to communicate. It’s quite an extraordinary process. If I were to start thinking of analogies its about touch: how proteins on their own recognize what is literally around them like being in a crowd- you feel the crowd, you feel the emotion, at an instantaneous grasp. The proximity of a stranger especially if you have a loved one nearby mere eye contact, facial expressions can convey messages. We don’t need an iPhone Nature built in these shape sensing apps that function by touch, by contact. The message of our world is that the universe can sense itself right down to two proteins as if they were holding hands in a crowd to exchange information. Shape to recognize- shape to feel -shape sensing is at the core of cellular signaling, the immune system works that way, here’s another definition to help.


“An epitope is known as an antigenic determinant, is part of the antigen that is recognized by the immune system, specifically by antibodies, B cells, or T cells. The part of an antibody that recognizes the epitope is called a paratope. Although epitopes are usually thought to be derived from non-self proteins, sequences derived from the host that can be recognized are also classified as epitopes.

The epitopes of protein antigens are divided into two categories, conformational epitopes and linear epitopes, based on their structure and interaction with the partope. A conformational epitope is composed of discontinuous sections of the antigen’s amino acid sequence. These epitopes interact with the paratope based on the 3D surface features and shape or tertiary structure of the antigen. Most epitopes are conformational.

By contrast, linear epitopes interact with the paratope based on their primary structure. A linear epitope is formed by a continuous sequence of amino acids from the antigen.”

Here’s some more in interesting stuff:

“Epitopes are sometimes cross-reactive. This property is exploited by the immune system in regulation by anti-idiotypic antibodies (This was originally proposed by Nobel Prize winner, Niels Kaj Jerne). If an antibody binds to an antigen’s epitope, the paratope could become the epitope for another antibody that will then bind to it. If this second antibody is of IgM class, its binding can regulate the immune response.; if the second antibody is of IgG class, its binding can downregulate the immune response.” Wow that’s so cool !

If you read these great epitope/odotope definitions, what’s happening here? We’re dealing with words that describe touch. When I touch my wife’s hand to this day I still get a shock, I love her that much. The touch translates into the physical contact. Lips to lips that’s a whole different contact, lots and lots of neurons interacting at that contact, ooo lala….

So we have Nature capable of conformational sequence recognition. Here’s my translation: skin to skin contact, that we understand right away. Conformational antibodies, wow sounds like a committee definition of a touching event, no? Host that can be recognized, you’re back in the crowd, is it a stranger rubbing against you or is it a friend? Easy to tell by smell, by sight, by feel the information at the contact is getting interpreted both at the contact as the local event and the higher centers of integration/interaction our brain. Now let’s throw emotion into the mix. I’ll take an example from a riot yesterday in Montreal. There is an annual tradition of violence against police. This fervent mix got stirred with the students upset at rising tuition fees.The whole scene was a mob being pushed by the police beating their batons marching right down the middle of the street dispersing the crowds. Unfortunately innocent people happened to get caught in the spinning out of public order. One such person had a smoke grenade thrown by the police strike against his forehead as it exploded. A nurse who happened to be nearby was shocked of the viciousness, that the man could lose his eyes as he sat down screaming, I’ll quote todays, March 16, 2012 the Montreal Gazette, written by Sue Montgomery, Justice Reporter.

‘One man, trying to stop some young men from throwing rocks, was hit in the forehead with a tear-gas canister as it exploded. Scottt Weinstein, a nurse in the crowd who was providing first aid when needed, poured water over the man’s eyes, as the man screamed in anger.

“If he hadn’t been wearing ski goggles, he could have been blinded,” Weinstein said. “His hair was singed and his goggles covered in chemicals.

“I’ve never been in a demonstration ever where police threw explosives into the crowd,” said Weinstein, who says he’s been in dozens of demos. “It’s a terrible path to take because these people will lose their eyes.”

The man, who said he had a 20-month old child, sat on the steps of an apartment building trying to comprehend what had just happened.

“I was being peaceful and this is what theory do to me ?” he yelled.

Did your blood pressure surge when you read that piece like mine did? Back to the message getting through the crowd; now the message is jumped into a totally different category of crowd message. It’s smell, its visual, its memory, it’s intellect, it’s social, it’s visceral it’s all instantaneous. The entire crowd senses the arousal, the immune system triggers on just like that in a flash.

So here’s my point. Things contact, proteins are things, proteins have shape, shape contacts, shape is recognition, shape is also sensing, shape is receiving, shape is sending, shape is interpreting, that’s what odotope is all about, it’s the shape at contact messaging information strictly running as a shape based sensing system, between neighbors within a crowd watched by a city reactions spilling out into a country. One scale of shape contact slides smoothly to the next scale. The immune system is on, its odotope theory in practice.

About cerebrovortex

Montreal Grandmother, Agnes Kent was saved by Raul Wallenberg from certain death, when he provided papers for her and her Mom to escape away from the Nazis. Today when asked what that escape meant, she replied,"Remind people, that while statesmen and whole countries remained silent and did nothing, a single individual chose to act, with ramifications that proved enormous. Similar choices confront us today. Write that simple truth she said, it can never be repeated often enough because the world keeps forgetting it."
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1 Response to Odotope Theory

  1. test says:

    *An impressive share, I just given this onto a colleague who was performing a little analysis on this. And he in fact bought me breakfast because I located it for him.. smile. So let me reword that: Thnx for the treat! But yeah Thnkx for spending the time to discuss this, I feel strongly about it and really like reading a lot more on this subject. If possible, as you become expertise, would you mind updating your blog with a lot more details? It is highly beneficial for me. Big thumb up for this blog post!

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