Tag: biology

Science-Watching: Nature webinar

Cryo-EM and artificial intelligence: A marriage made in cell extracts

Date: Thursday, June 16, 2022

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About this webcast

Deep insights into how cellular proteins interact have been out of reach, especially in a native context. In this webcast, Dr. Panagiotis Kastritis of Martin Luther University Halle-Wittenberg will describe how analysis of endogenous cell extracts with cryo-EM and artificial intelligence methods can provide integrated biological analysis of protein communities in a closer-to-native setting.

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Meaningfulness versus Informativeness

The Decoding Reality book is a classic contemporary analysis of the foundations of physics and the implications for the human world. The scientists don’t see that physics and science are the infrastructure on which the human “quest for meaning” takes place. Ortega (Ortega y Gasset, died in 1955) tells us that a person is “a point of view directed at the universe.” This level of meaning cannot be reduced to bits or qubits or electrons since man is a “linguistic creature” who invents fictional stories to explain “things” that are not things.

The following dialog between Paul Davies (the outstanding science writer) and Vlatko Vedral (the distinguished physicist) gropes along on these issues: the difference between science as one kind of story and the human interpretation of life and self expressed in “tales” and parables, fictions and beliefs:

Davies: “When humans communicate, a certain quantity of information passes between them. But that information differs from the bits (or qubits) physicists normally consider, inasmuch as it possesses meaning. We may be able to quantify the information exchanged, but meaning is a qualitative property—a value—and therefore hard, maybe impossible, to capture mathematically. Nevertheless the concept of meaning obviously has, well… meaning. Will we ever have a credible physical theory of ‘meaningful information,’ or is ‘meaning’ simply outside the scope of physical science?”

Vedral: “This is a really difficult one. The success of Shannon’s formulation of ‘information’ lies precisely in the fact that he stripped it of all “meaning” and reduced it only to the notion of probability. Once we are able to estimate the probability for something to occur, we can immediately talk about its information content. But this sole dependence on probability could also be thought of as the main limitation of Shannon’s information theory (as you imply in your question). One could, for instance, argue that the DNA has the same information content inside as well as outside of a biological cell. However, it is really only when it has access to the cell’s machinery that it starts to serve its main biological purpose (i.e., it starts to make sense). Expressing this in your own words, the DNA has a meaning only within the context of a biological cell. The meaning of meaning is therefore obviously important. Though there has been some work on the theory of meaning, I have not really seen anything convincing yet. Intuitively we need some kind of a ‘relative information’ concept, information that is not only dependent on the probability, but also on its context, but I am afraid that we still do not have this.”

For a physicist, all the world is information. The universe and its workings are the ebb and flow of information. We are all transient patterns of information, passing on the recipe for our basic forms to future generations using a four-letter digital code called DNA.

See Decoding Reality.

In this engaging and mind-stretching account, Vlatko Vedral considers some of the deepest questions about the universe and considers the implications of interpreting it in terms of information. He explains the nature of information, the idea of entropy, and the roots of this thinking in thermodynamics. He describes the bizarre effects of quantum behavior—effects such as “entanglement,” which Einstein called “spooky action at a distance” and explores cutting edge work on the harnessing quantum effects in hyper-fast quantum computers, and how recent evidence suggests that the weirdness of the quantum world, once thought limited to the tiniest scales, may reach into the macro world.

Vedral finishes by considering the answer to the ultimate question: Where did all of the information in the universe come from? The answers he considers are exhilarating, drawing upon the work of distinguished physicist John Wheeler. The ideas challenge our concept of the nature of particles, of time, of determinism, and of reality itself.

Science is an “ontic” quest. Human life is an “ontological” quest. They are a “twisted pair” where each strand must be seen clearly and not confused. The content of your telephone conversation with your friend, say. is not reducible to the workings of a phone or the subtle electrical engineering and physics involved. A musical symphony is not just “an acoustical blast.”

The “meaning of meaning” is evocative and not logically expressible. There’s a “spooky action at a distance” between these levels of meaning versus information but they are different “realms” or “domains.”

Essay 51: “The Whole:” a Quick Second Look

We started this book with a quote from Wittgenstein “Light dawns gradually over the whole” and argued that the meaning of the “whole” is and will be elusive forever.

That is as it should be:

Think of the final pages of John Dewey’s classic book, The Quest for Certainty.  You’ll sense how Dewey oscillates between the “pin-down-ability” of the “whole” and its eternal slipperiness:

“Diversification of discoveries and the opening up of new points of view and new methods are inherent in the progress of knowledge.  This fact defeats the idea of any complete synthesis of knowledge upon an intellectual basis.  The sheer increase of specialized knowledge will never work the miracle of producing an intellectual whole.  The astronomer, biologist, chemist, may attain systematic wholes, at least for a time, within his whole field.

“Man has never had such a varied body of knowledge in his possession before, and probably never before has he been so uncertain and so perplexed as to what his knowledge means, what it points to in action and in consequences.”

(Dewey, The Quest for Certainty, Capricorn Books, 1960, pages 312/313)

Wholeness, Dewey senses, like the white whale in Moby-Dick, “won’t sit for a portrait.”   That is why the student should take an eternally “non-rigid” answer to these questions which are “arguments without end” and that’s fine.

Essay 36: What We Mean by “Epochal Waters”

We sometimes use the phrase “epochal waters” to refer to the deepest layers of the past which we “swimmers” at the surface of the ocean don’t see or know. “Epochal waters” are latent, currents are closer to the surface.

There’s a similar idea from the French philosopher Michel Foucault who died in 1984. In his The Order of Things, classic from 1966, he talks about the “episteme” (as in epistemology) that frames everything from deep down. (The Greeks distinguished between “techne” (arts, crafts, practical skills and “episteme” (theory, overview).

“In essence, Les mots et les choses (Foucault’s The Order of Things) maintains that every period is characterized by an underground configuration that delineates its culture, a grid of knowledge making possible every scientific discourse, every production of statements. Foucault designates this historical a priori as an episteme, deeply basic to defining and limiting what any period can—or cannot—think.

Each science develops within the framework of an episteme, and therefore is linked in part with other sciences contemporary with it.

(Didier Eribon, Michel Foucault, Harvard University Press,  1991, page 158)

Take a simple example. A discussion comes up about what man is or does or thinks or knows. In today’s episteme or pre-definition, one thinks immediately not of man in terms of language or the invention of gods, but in terms of computational genomics, big data, bipedalism (walking upright on two legs). Its assumed in advance via an invisible episteme, that science and technology. physics, genetics, big data, chemistry and biology hold the answer and the rest is sort of outdated. This feeling is automatic and reflexive like breathing and might be called “mental breathing.”

One’s thoughts are immediately sent in certain directions or grooves, a process  that is automatic and more like a “mental reflex” than a freely chosen “analytical frame.” The thinker has been “trained” in advance and the episteme pre-decides what is thinkable and what is not.

There are deep episteme that underlie all analyses: for example, in the Anglo-American tradition of looking at things, the phrase “human nature” inevitably comes in as a deus ex machina (i.e., sudden way of clinching an argument, the “magic factor” that has been there all along). If you ask why are you suddenly “importing” the concept of “human nature,” the person who uses the phrase has no idea. It’s in the “epochal water” or Foucault’s episteme, and it suddenly swims up from below at the sea floor.

Another quick example: In the Anglo-American mind, there’s a belief from “way down and far away” that failure in life is mostly about individual behavior (laziness, alcoholism, etc.) and personal “stances” while “circum-stances” are an excuse. This way of sequencing acceptable explanations is deeply pre-established in a way that is itself hard to explain. It serves to “frame the picture” in advance. These are all “epochal water“ or episteme phenomena.