Constructing a Theory of Life

What about enzymes? They are able to exhibit catalytic function because of their particular shape. Shape resulting from folding of the sequence of amino acids. the individual amino acids or ions they are contain do not have the necessary shape to function as the whole enzyme does. So the function is only present at the scale of the whole enzyme. Making catalytic function of the enzyme an emergent property.

What is Joe Fisher? Why do you persist in differentiating it as if it is a separate thing?

OK (re enzymes) but that is just using a word - emergence - to cover effects that are a net result of several combined interactions. I am not sure using such a word takes us any further forward in understanding.

I agree with Andrew.

As AI researcher Eliezer Yudkowsky said in The Futility of Emergence (https://www.lesswrong.com/posts/8QzZKw9WHRxjR4948/the-futility-of-emergence):

"The phrase "emerges from" is acceptable, just like "arises from" or "is caused by" are acceptable, if the phrase precedes some specific model to be judged on its own merits.

However, this is not the way "emergence" is commonly used. "Emergence" is commonly used as an explanation in its own right...

[A] fun exercise is to replace the word "emergent" with the old word, the explanation that people had to use before emergence was invented:

Before: Life is an emergent phenomenon.

After: Life is a magical phenomenon.

Before: Human intelligence is an emergent product of neurons firing.

After: Human intelligence is a magical product of neurons firing.

..."Emergence" has become very popular, just as saying "magic" used to be very popular. "

Georgina, when you you the word "emergent", are you suggesting that magic has occurred?

The last line should read:

Georgina, when you use the word "emergent", are you suggesting that magic has occurred?

Dear Anderson S,

There am no such a real thing as emerging or "re-emergent phenomena." All real phenomena always have a real VISIBLE surface.

Dear Georgina Woodward,

At the moment, Joe Fisher has a VISIBLE surface. Although he might appear to be separated from you, you too have a VISIBLE surface. It would be physically impossible for Nature to devise different kinds of VISIBLE surfaces. Unnatural invisible enzymes have never existed.

Dear Lorraine Ford,

All living creatures and vegetation have a VISIBLE surface. All inanimate entities have a VISIBLE surface. All dinosaur bones have a VISIBLE surface. This is because Nature only devised one unified VISIBLE infinite surface occurring in one infinite dimension that am always mostly illuminated by finite non-surface light.

Joe Fisher, Realist

Lorraine,

Magic is a kind of deception that happens when an observer has incomplete information from which to construct their understanding of what has occurred. As performed by magicians. Or, as I think you may be using the word, a supernatural occurrence brought about by some kind of will. Such as in the belief system of Wicca. The emergence of the catalytic ability of enzymes fits neither sort of magic. Its function happens because of its shape. That functional shape is not a property of its constituents but only of the whole.

Georgina,

Are you talking about a universe where every outcome has a cause? A cause means that an outcome was determined by a relationship representable by a mathematical equation, a number assignment, or an algorithm [1].

If you are talking about "systems whose high-level behaviors arise or "emerge" from the interaction of many low-level elements" [2], then you are talking about a system where every outcome has a cause, a system where nothing new has actually "emerged". Instead, a pattern of behaviours has been labelled with a word.

"Temperature", "cyclone" and "hurricane" are words describing outcome patterns that have a cause. Despite our word-usage, these patterns themselves cause nothing, it is the underlying relationships (representable as equations, numbers and algorithms) that cause outcomes.

It's the same with enzyme behaviour/outcomes. Or are you are saying that the shape of an enzyme did not have a cause?

...................

1. What, in turn, created these relationships in the first place is a separate issue.

2. The Futility of Emergence, (AI researcher) Eliezer Yudkowsky, https://www.lesswrong.com/posts/8QzZKw9WHRxjR4948/the-futility-of-emergence

The shape comes from the protein's folding. It isn't mechanical folding but involves not just the protein itself but interaction with the environment; in which it is buffeted until parts that will bind together come into proximity. So each folding event of a particular protein could play out somewhat differently but result in the same folded configuration. There will be variation in the time taken to fold I expect. There is some seeming randomness or complexity involved in the interaction with the environment which means it isn't just rote playing out of an instruction that is the same every time. While the sequence of the unfolded protein's amino acids is important for folding, it isn't by itself the cause of the folding occurring.

Quantum mechanics theory gives no real mechanism for going from probable to actual and concentrates on the effects of measurement but seems to neglect size limits for superposition.

The efficiency of photosynthesis in converting light energy into chemical energy tends to make me skeptical of the intelligent observer transformation concept's age-old wisdom. It seems that there are a lot of micro-macro interactions in light energy being absorbed by pigment molecules in leaves and then making 2 molecules, ATP & NADPH, to produce chemical energy, seemingly at a superposition efficiency -- this w/o observation.

I would tend to favor the gravitational decoherence idea of growing assembled quantum systems and the introduction of temperature and spectral density to their environment as additional causes of decoherence.

I always look with interest for new explanations of this process.

In the universe, there is no relationship between things (like particles) as such (except maybe coherence): there is only relationship between information categories, where the relationship is itself an information category. Examples of information categories are energy, momentum, relative distance, and time. We represent these information relationships as equations, number assignments and algorithms.

In the universe, these known relationships between information categories have the status of law because they determine the outcome numbers. The reverse situation is not true: sets of outcome numbers do not determine relationships; relationships do not emerge from an objectively observed set of outcome numbers, even if the set of outcome numbers is given a label of "attractor". And relationships do not emerge from situations, where a situation is a subjective point of view on the outcome numbers.

In the universe, all information has context, there is no information without context: any new category of information is necessarily a new relationship built out of existing information categories. So when it comes to living things, it becomes more apparent than ever that we need to understand what it is that builds/creates/constructs information relationships, and what knows these information relationships. The only candidate is things: particles, atoms, molecules and living things.

So Georgina, did any new information arise, i.e. did any new information emerge that was not entirely accounted for by the existing physics of the situation (where chemistry underlies the biology/behaviour of enzymes, and physics underlies the chemistry)?

You seem to be saying that the enzyme folding indicates that a new spatial information relationship has somehow been created, that is not entirely accounted for by the physics.

This begs the question: a new spatial information relationship has been created by whom?

A shape is formed that did not previously exist, and that enzyme shape has a function that the unfolded protein does not have. I am not saying the folding isn't accounted for by the physics that happens but that it isn't following a set prescription of what must be done step by step, that is the same every time. The parts of the protein that must come together are the same but what happens in the environment is not fully controlled by the protein. If you mean by 'a new spatial information relationship' a new shape, i.e. a new distribution of the matter in space including relations of parts to each other then yes that is formed; not created, but by 'self assembly', not by someone

Perhaps "environment driven self assembly" is a useful descriptive phrase. As the energy for motion, which results in the finished folding, comes from interaction with molecules and ions in the environment. Most probably water molecules, as the inside of the cell is an aqueous solution, and ions dissolved in it. As well as the effects of fields generated by charged particles that are part of the protein sequence.

Georgina,

Either the enzyme configuration is 100% determined by the physics (i.e. by laws of nature), or it is not 100% determined by the physics.

If the configuration is 100% determined by the physics, and all interactions of other molecules with the enzyme are 100% determined by the physics, then nothing has emerged.

But more correctly, molecules themselves don't interact: all interactions are information interactions. And all information is a relationship (representable as equations, algorithms, and/or number assignments) that exists in a context of other information relationships. So the real question is: has a new information relationship been created or not? Does a new information relationship exist from the point of view of the enzyme; and does a new information relationship exist from the point of view of other molecules, atoms and particles? A new information relationship is equivalent to a new law of nature because it determines some of the outcome numbers.

Has new information emerged/been created or not? From whose point of view does the information exist? Who created the information?

A catalytic function has been enabled that did not previously exist. I don't see anything wrong with calling that an emergent function. That function changes the relationship of the protein sequence to the molecules or ions that are catalyzed by interaction with it. The topology is altered. That's lots of new spatial relations if all of the relations of individual constituent particles are considered. The enzyme doesn't have a point of view, nor do the reagents with which it interacts. If by point of view you mean opinion. But if they did they would notice their relationship is different upon interaction if the reagent attaches to a binding site. Yes outcome numbers are also altered. As by catalysis involving the enzyme the chemical reaction is sped up.

Georgina,

If new information has not been added to this tiny part of the universe that we are discussing, then there is no new function. Every detail of a hurricane is explainable in terms of lower-level information-processing events; and every detail of enzyme interactions are also explainable in terms of lower-level information-processing events unless new information has been added to the system. New function, i.e. new lawful power over the outcome numbers, means that one or more new information relationships have been added to the universe-system.

I know you don't understand this, but if mathematics (which we use to represent the universe-system) has shown us anything, it is that situations/outcomes are a consequence of rules/laws/relationships. The reverse is not true: rules/laws/relationships do not emerge from situations/outcomes. Only those who refuse to face facts claim that rules/laws/information relationships can emerge from situations/outcomes.

So, who created the new information relationship? And who knows about it? This enzyme-related information certainly does not exist from our human point-of-view (it is only science that has brought this information to our attention): this capacity of an enzyme or a cell, to know about new information, existed long before human beings existed.

Who created the new information relationship? And who knows about it?

Rules and Laws describing or mathematically representing relationships can be 'distilled' from observation of outcomes of particular circumstances. The distilled rules or Laws can then be used predicatively, applied to similar circumstances. That does not mean nature has a rule book in some platonic realm (additional to material reality) from which it is able to receive instruction of what to do.The rules are a characterization of what happens not necessary instruction of what to do, so it can happen.

The enzyme can act ass a catalyst because of its 3D shape and topology, it does not need permission from a new rule. The shape is not formed by someone but by 'environment driven self assembly'. No one need know about it for it to function. An experiment can be conducted and the function of the enzyme characterized by an equation if wanted.

So Georgina,

You are saying that an enzyme is like a hurricane: every detail of its interactions are explainable in terms of lower-level information-processing events.

I.e. no new function has emerged: just like the word "hurricane" is nothing but a label we give to something that is fully explainable in terms of lower-level information-processing events, the word "enzyme" is nothing but a label we give to something that is fully explainable in terms of lower-level information-processing events.

You are saying that, with an enzyme, nothing new has emerged except the label we give it. You seem to be contradicting yourself because you have previosly asserted that the "catalytic function of the enzyme [is] an emergent property" (Georgina Woodward replied on Aug. 8, 2018 @ 00:35 GMT).