So, how can molecules correctly work out each complex step without some crude form of awareness? — Gary Enfield

Indeed, how can this possibly happen? But is this a crude form of awareness? DNA is about 750 mb of data, or roughly the equivalent of 100 encyclopedia volumes . What you have described is equivalent to sifting through 100 encyclopedia volumes, finding the wrong word and replacing it with the right one.

I would say our cartesian estimate of what is going on at that level might be a tad faulty. :smile:

Chemistry!

Sorry - but chemistry says that DNA is no more than a template to produce components. It has no logical capacity/capability. It also does not describe solutions to problems, and even if it did, we should constantly see enzymes (with no apparent logical capability) having to refer back to DNA for guidance. But they don't. they clearly operate just on their own.

they clearly operate just on their own. — Gary Enfield

In another example what happens is DNA via RNA creates the enzymes, which then go on to repair a section of DNA - self awareness!

So, how can molecules correctly work out each complex step without some crude form of awareness? — Gary Enfield

Evolution.

A great many biomolecules that do a great many whizzy things have been computationally modelled for predictive purposes. Do you know what the modellers don't need to add to the models to make them work? Self-awareness.

There's actually several whizzy molecules involved in homologous recombination, not just one. That it can physically occur (which it can according to the models) is the necessary condition to allow nature to explore that as a pathway. No awareness required, just a survival advantage. Since this occurs in microbes and plants, a pretty fundamental one at that.

Sorry - but chemistry says that DNA is no more than a template to produce components. — Gary Enfield

Components with function, which is what you're describing.

It has no logical capacity/capability. — Gary Enfield

That's s circular argument. You can't presume the molecule to be aware when answering the question "How can it do what it does without awareness?"

Even assuming that one could begin to establish that molecules are 'aware' by some kind of god-of-the-gaps fallacy ("this seems very complex and hard to explain... so probs awareness"), the question is what kind of "explanation" this would be at all. Ascribing 'awareness' to molecules doesn't explain anything so much as opens up even more to be explained - it complicates, not simplifies. How are they aware? What enables this awareness? What function would awareness 'add' that would enable it to somehow (how?) 'oversee'(?) the complexity of what happens with DNA repair? Exactly how does "awareness" work as a mechanism to explain the 'downriver' mechanics of it? We know a great deal about how awareness functions in higher-order animals - we can study the way tactile or visual illusions come about, the emergence of spatial and depth perception, the ways in which color properties interact in various ambient settings and so on, much of which can be explained by both physiology and developmental and ontogenic history. Can we do the same or similar for this proposed 'awareness'? 'Awareness' is a black hole of ramifying confusion, not a simplifying explanans.

This is a process, run by enzymes, (single but complex molecules), which are observed to seemingly identify a double break in the DNA strand; then find a suitable piece of alternate DNA to compare it to; align the remnants of the strands with the whole 'template'; perfectly in-fill any gap (which can be of varying length on either strand); and then re-connect the broken strands, without mixing them up. — Gary Enfield

An enzyme is a catalyst. A catalyst is not the cause of a chemical reaction, it is an enabler, accelerating the reaction. It is only because of this faulty representation, that the enzymes are the cause of the activity, that you see the need to posit awareness in the catalyst, as if the enzyme knows what it is doing. But the enzyme is just there as an enabler, it is not actually performing the activity. The problem which your op demonstrates, is the problem with any attempt to separate a specified cellular activity, and represent it as an independent activity, separate from the rest of the cell. This could make it appear like the catalyst is actually the cause of the activity.

I am told that this process only runs on a few enzymes - far fewer than the logical steps we can all appreciate from this process.

There are no known chemical signals to form any known form of feedback loop, and no basic chemistry like a catalyst to explain the varying rationale either.

This is truly remarkable but scientifically proven.

So could this repeatable process, (which resolves problems that can vary on each occasion, yet produce the complex but predictable outcomes), be evidence of a degree of awareness in a single molecule? — Gary Enfield

It really doesn't mean much to say that there is only a few enzymes involved. A protein is an extremely complex molecule, and maybe I need to emphasize 'extremely'. So it's like you're amazed that a complex task can be carried out by just a few computers, when a computer is a very complex thing in itself. But since there is a large number of protein molecules in any given cell, it's unlikely that this process you refer to only involves a few.

The complexity of living organisms is staggering, and it is quite sobering to note that we currently lack even the tiniest hint of what the function might be for more than 10,000 of the proteins that have thus far been identified in the human genome. — The Shape and Structure of Proteins

https://www.ncbi.nlm.nih.gov/books/NBK26830/

So, how can molecules correctly work out each complex step without some crude form of awareness? — Gary Enfield

'Working out' is actually an anthropomorphism. How it happens is the subject of molecular biology. I agree that it involves something other than what is known to physics and chemistry, which is why I agree with those biologists who say that biology can't be reduced to physics and chemistry. But that doesn't need to introduce 'awareness' as a factor. Have a read of What is Information Marcello Barbieri. He’s introduced the concept of ‘code biology’. It’s not reductionist, but also requires no invocation of ‘awareness’.

No awareness required, just a survival advantage. — Kenosha Kid

On the other hand, the emergence of living organisms also amounts to the emergence of subjectivity, or subject-hood.

On the other hand, the emergence of living organisms also amounts to the emergence of subjectivity, or subject-hood. — Wayfarer

No, vegetable and microbial life could have gotten on just fine without us.

Same schema though:

1. What actually is it?
2. Can we explain what it supposedly does without it?

No, vegetable and microbial life could have gotten on just fine without us.

Same schema though:

1. What actually is it?
2. Can we explain what it supposedly does without it? — Kenosha Kid

Nobody can explain anything without it, nor would there be anything in need of explanation.

It would help you to see where your ingrained methodological naturalism morphs into a worldview. After all, this is a philosophy forum.

Another interesting variant of this theme are Prions.

"Prions are misfolded proteins with the ability to transmit their misfolded shape onto normal variants of the same protein. They characterize several fatal and transmissible neurodegenerative diseases in humans and many other animals." - Wikipedia

"The prion hypothesis, also known as the protein only hypothesis, states that protein, rather than virus or bacteria, is the infectious agent of the prion disease." - Wikipedia

The hypothesis suggests that the prion leaves the cell and infects other cells, and takes on a life of its own as a virus like organism, spreading amongst living creatures through the food chain.

A Prion has its own integrity and momentum as a living organism. A prion evolves from a chance variation in the folding of a protein, and then proliferates along its own independent and self created pathway, much the same as any living organism.

**What often seems to get missed is that enzymes are proteins, and that proteins are the building blocks of a cell. The Prion shows us how even the basic building block of a cell, with slight mutation, has the ability for an independent existence - weaving its way through the possibilities and constraints of a cellular environment whilst maintaining a distinctive self.

How different is this to what humanity does?

Nobody can explain anything without it, nor would there be anything in need of explanation. — Wayfarer

True.

It would help you to see where your ingrained methodological naturalism morphs into a worldview. After all, this is a philosophy forum. — Wayfarer

That's not an argument for blind acceptance of anything. But, yes, *my* worldview is very much ingrained with my methodological naturalism, largely because it seems to explain a lot of the world.

But, yes, *my* worldview is very much ingrained with my methodological naturalism, largely because it seems to explain a lot of the world. — Kenosha Kid

Indeed it does, and I respect it. But methodological naturalism starts with a process of exclusion, then it forgets what it has excluded, then it uses those very methods to claim that what it has excluded in the first place doesn't count, or isn't real.

Of course, from 'inside' the naturalist viewpoint, this doesn't make any sense, but philosophy requires questioning of those things we take for granted as being obviously true.

(None of that has any bearing on the OP, as I agree that there's no need to invoke awareness as a factor in molecular biology. It's a broader comment on the role of naturalism in philosophy of mind.)

philosophy requires questioning of those things we take for granted as being obviously true. — Wayfarer

Something I am also keen on. First, there's ample scope for philosophy grounded in naturalism without having to subscribe to less explanatory ideas. Second, my post above was not a rebuttal; it was an invite to you to address what of subjectivity is left unexplained by naturalism and what you think explains it instead. It's a perfectly open-minded approach. That you did not suggest an answer is not indicative of my close-mindedness.

None of that has any bearing on the OP, as I agree that there's no need to invoke awareness as a factor in molecular biology. It's a broader comment on the role of naturalism in philosophy of mind. — Wayfarer

Agreed, it is rather off-topic.

That you did not suggest an answer is not indicative of my close-mindedness. — Kenosha Kid

I have a good answer but this is not the thread for it. :sad:

I wonder if those molecules with some sort of consciousness have philosophical discussions on to what part of them, and how their consciousness connects to their physical existence.

If only someone could document the discourse between conscious molecules, then the argument would be over.

1. Things that have consciousness know that they have consciousness.
2. As conscious beings, they probably ponder the origin of their physical as well as their spiritual existences.
3. Because they ponder their existence's origins, they have consciousness.
Q.E.D. They have consciousness.

wonder if those molecules with some sort of consciousness have philosophical discussions on to what part of them, and how their consciousness connects to their physical existence. — god must be atheist

Well, the Wikipedia article on homologous recombination describes enzymes as being recruited. So I guess this implies that each particular enzyme makes a free will choice as to whether or not to go into service.

If by "awareness" you have in mind the kind of thing people who use this word take it to mean, then no DNA has no awareness. If you invent a technical term and call it "awareness", then it is liable to be misleading, but it can be done, you'd have to clarify what this term means.

But it's probably safest to steer away, as much as one can, from "mentalizing" language and say that DNA follows patterns or laws. Much of this depends on how you think about teleology.

I wonder if those molecules with some sort of consciousness have philosophical discussions on to what part of them, and how their consciousness connects to their physical existence. — god must be atheist

'A physicist is just an atom's way of looking at itself' ~ Neils Bohr.

So if I build a rube goldberg machine out of rocks, sticks, playing cards, and other things from my garage, that has consciousness?

I wonder if those molecules with some sort of consciousness have philosophical discussions on to what part of them, and how their consciousness connects to their physical existence.

If only someone could document the discourse between conscious molecules, then the argument would be over.

1. Things that have consciousness know that they have consciousness.
2. As conscious beings, they probably ponder the origin of their physical as well as their spiritual existences.
3. Because they ponder their existence's origins, they have consciousness.
Q.E.D. They have consciousness. — god must be atheist

What about sheep? Is bleating a philosophical discussion?

Well, the Wikipedia article on homologous recombination describes enzymes as being recruited. So I guess this implies that each particular enzyme makes a free will choice as to whether or not to go into service. — Metaphysician Undercover

:rofl:

What about sheep? Is bleating a philosophical discussion? — SolarWind

It might be. For all I know.

Well, the Wikipedia article on homologous recombination describes enzymes as being recruited. So I guess this implies that each particular enzyme makes a free will choice as to whether or not to go into service. — Metaphysician Undercover

This assumes that the hard question of free will has a resounding "yes" as to its existence.

Sorry - it isn't practical for me to respond to people individually so I will try to cover off a few points collectively.

There seems to be a fair amount of confusion in these various responses between consciousness and awareness. Awareness is not consciousness and at best is just one of several factors in achieving consciousness.

While I admit that it is unusual to invoke the suggestion of awareness in molecules, people are avoiding the issues raised if they try to dismiss the question by pretending that my OP is in some way trying to promote a God of the Gaps argument. It isn't, and if you run away from the points by using God as a way to deflect from the issue, I think you have lost the argument. This is a serious question, because the computational models which can be applied to a single molecule, or even a few of them, cannot get close to explaining homologous recombination.

Evolution tells us how something may have arisen, it doesn't tell us how a dynamic process is made to work in ever-changing circumstances.

I am not sure that an enzyme is just a catalyst, but they are observed doing things which go well beyond simple chemical matching/enabling. Think about just one of the steps involved....

- the breaks on both stands of the DNA molecule are rarely clean and often result in missing pieces that form gaps of long and varying lengths. Yet enzymes need to establish the size of a gap before attempting to repair each strand. In doing this they seem to go hunting for parts of a different strand of DNA that equates to the full sequence of the correct gene - a different template which is generally not just side by side with the break but potentially curled up in a completely different place.

Neither is this matching process just a case of finding the first nucleobase pair and then continuing from that random point - no - the active molecules in the process go looking for a complete sequence that is appropriate to the unbroken sections of DNA that remain on either side of the break. How does it make that assessment? We can do this with a brain, because we understand the scenario, the objective, and the significance of the coded sequences on the remaining strands of the DNA. How does the matching occur without such awareness?

I do not mind a purely chemical solution emerging, and I am certainly not promoting a God-based solution, but when decades of research fails to even get close to an answer, and what we see is not a fixed process but a variable/dynamic one - aiming for an outcome that we can describe as an objective that we can predict - then I think it is fair to ask where that level of sophistication comes from if it is not from traditional sources.

Basic observation shows that the behaviour of these chemicals is far from the scenario normally predicted by the mathematics of the physical laws, and the deterministic principles commonly applied. There seems to be an additional factor here which has not been identified and if the logic that we humans might apply to mimic what is happing through our manual efforts, can only be achieved by millions of brain cells - and yet it is happening with a handful of enzymes - then we are truly missing something profound.

Re-reading some of the posts - can I just add that there is a vast difference between the mechanical and unthinking replication mechanisms which copy a section of genetic code to produce either a protein or RNA, and the processes that we see here.

Nobody denies that the rigid Laws of Physics and Chemistry operate well for the wider environment plus some purely chemical aspects of cellular activity. It is clearly observed that on mechanisms such as homologous recombination, we seem to be dealing with something different.

Similar points can be made about the transportation of proteins from their point of manufacture in a cell to the correct places that they might be used, via a container pulled by motor proteins across an ever-changing network of roads.

If we can identify the principles involved it may help us to explain consciousness. If that is via chemical means then fine, but as we're not even close to doing that, isn't it fair to consider other possibilities?

If we can identify the principles involved it may help us to explain consciousness. If that is via chemical means then fine, but as we're not even close to doing that, isn't it fair to consider other possibilities? — Gary Enfield

But the question of how enzymes combine and how DNA operates is orthogonal to the question of the nature of consciousness or conscious experience. And the two questions can be studied separately.

You said you’re not endorsing any kind of god-of-the-gaps argument, which is well and good. But ‘explanations of the nature of consciousness’ - or could we say, the nature of mind? - are necessarily philosophical. Whereas, explanations for the cellular processes of living organisms are surely within the province of the biological sciences.’

I will mention an emerging discipline which is often discussed on this forum, namely, that of biosemiotics, ‘a field of semiotics and biology that studies the prelinguistic meaning-making, or production and interpretation of signs and codes[1] in the biological realm.

Biosemiotics attempts to integrate the findings of biology and semiotics and proposes a paradigmatic shift in the scientific view of life, in which semiosis (sign process, including meaning and interpretation) is one of its immanent and intrinsic features.’ (Wikipedia). One advocate for this discipline, Marcello Barbieri, who I mentioned up-thread, is a pioneer of what calls ‘code biology’ which is a school within biosemiotics. His approach is not reductionist, in that he believes that the emergence of biological order is genuinely novel and can’t be predicted or explained on the basis of physics or chemistry as such. But he doesn’t seem to feel it necessary to introduce the notion of awareness or consciousness as an agency, which is what I think you’re doing here. There are quite a few biologists who are not reductionist in the old-fashioned sense, who also tend to bracket out the question of the nature of mind or consciousness, except perhaps as seen through the perspective of cognitive science and evolutionary psychology. But I don’t think they feel the need to ‘explain’ the nature of consciousness. That is more the province of the emerging field of consciousness studies, within which philosophy is a discipline.

If we can identify the principles involved it may help us to explain consciousness. If that is via chemical means then fine, but as we're not even close to doing that, isn't it fair to consider other possibilities? — Gary Enfield

Self organization seems the best bet, in my view.

Pop - I think that evolution is a classic form of self organisation, but self organisation builds structures over time. It is not a factor that resolves dynamic problems quickly in the moment. That is something different.

I think Finipolscie was right to build up an argument from undeniable basic logic, and to look for things which seem to break the existing models - for those are the areas which can teach us something new. He identifies the factors that have been shown to deviate from expected principles and tries to find pointers from them. His books are well thought out if you care to read them.

All
Ultimately consciousness needs to be explained in practical rather than purely philosophical terms. As mentioned above, awareness is an unexplained capability that is only one part of the effect we label as consciousness - so an explanation of awareness moves us closer to the ultimate goal. It may also help to reveal other factors at play that we may not have yet identified.

What philosophy can show us, is that some attempts at explanation break down if the principles they use are broken by the examples we find from experimentation, and if the repeated evidence of our eyes tells us that something more is going on. We have to simply begin by accepting the evidence, no matter how strange to our existing beliefs. That's how Quantum Mechanics and Abiogenesis were also started.

Indeed, Quantum Mechanics has now acknowledged that different rules seem to apply to the sub-atomic realm than we experience at our level of existence - but without explanation as yet.

Here we have a choice of whether to only explore purely chemical solutions through blind faith in one philosophy (materialism), or to consider the possibility that other factors may be at play and keep an open mind.

All discoveries are made because people follow the evidence and recognise when something different is happening. The difference here is that life somehow breaks the principles of the normal physical rules. It may follow familiar patterns of activity for living things, but the fact that we have ignored the differences in the past doesn't mean that we have to be blind to them going forwards.

Life is special and is still unexplained after thousands of years of human investigation. The Laws of Physics and Chemistry have served us well in recent centuries, but if we now see things to challenge our perceptions, we can begin by at least recognising those elements that make it special. We can then go looking for an explanation without blinkers.