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DanielBoyd

The inconvenient truth about genetics

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2 hours ago, DanielBoyd said:

I have been a staunch atheist all my life, so it completely flummoxes me to be accused of religious motivation. I really am curious: what text in the original article leads you to this conclusion?   

Strange already explained it, but the opening post sounds an awful lot like an irreducible complexity argument, and the factual errors, lack of citation and flawed analogies are archetypical of such arguments. 

To clarify, I'm not accusing you of religious motivation - but the opening post sure looks an awful lot like the standard lead up to a creationist pitch, which might explain some of the reaction you're getting. 

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12 hours ago, DanielBoyd said:

Reading all your comments, it strikes me that we seem to agree on the fact that genes only directly determine protein amino acid sequences, and that the rest is self-assembly or self-organisation.

If I get a bunch of matchsticks and cover them with glue, put them in a box, shake them up into some random arrangement and let the glue dry then they have "self assembled" into that shape.

But it's almost certainly no use.

If I want molecules to self assemble into something useful, I need to "choose"- and specify- those molecules very carefully.

And the way I do that is via the genome.

You seem to be persistently ignoring all the points I make.

May I remind you that the rules of the forum say that you have to address them, otherwise you are engaging in soapboxing, rather than discussion.

 

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2 hours ago, Arete said:

Strange already explained it, but the opening post sounds an awful lot like an irreducible complexity argument, and the factual errors, lack of citation and flawed analogies are archetypical of such arguments. 

To clarify, I'm not accusing you of religious motivation - but the opening post sure looks an awful lot like the standard lead up to a creationist pitch, which might explain some of the reaction you're getting. 

Thanks for the explanation. I'm new to this forum and was expecting, since its a science forum, that I wouldn't need to explain that I'm not some religious zealot in disguise. Are there really such types in abundance here who aren't here for the science but to undermine it?

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Posted (edited)
16 hours ago, DanielBoyd said:

we seem to agree on the fact that genes only directly determine protein amino acid sequences

No, we do not agree. In any case, surely genes only directly determine RNA sequences. And not all of those RNA's are used to pattern proteins from. I provided images of working examples of combinations of RNA and proteins. RNA's have enormous biochemical potential - able to bring proteins together as a catalyst for example, as well as combine directly with them, as well as provide the pattern for making those proteins.

If you are seeking better understanding then sticking to the belief that DNA only determines proteins when it has been pointed out clearly and repeatedly that is not the case is not a good start. And you still haven't told us your reasoning for concluding that DNA doesn't contain enough information - just repeated that conclusion.

 

17 hours ago, John Cuthber said:

You don't need gluten.
What you need is food.

Not a good example perhaps. On consideration, all species share so much DNA that the total is not going to include enormously more than one species has. However I still absolutely depend on the DNA of other species, including for molecules my own body and cells can make. And my mother provided the ovum with all the cellular 'machinery' and epigenetic triggers, patterned from her DNA - which I may well have good copies of, for later.

17 hours ago, John Cuthber said:

Well, where is it then?

I'm not convinced a design specification exists, or more correctly that it is an appropriate conceptual framework for describing what is happening - the structures and their form look like an emergent outcome, not a specification.That may be arguing semantics. But I suspect this whole thread is about semantics.

 

Edited by Ken Fabian

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4 hours ago, DanielBoyd said:

Are there really such types in abundance here who aren't here for the science but to undermine it?

You have no idea...

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10 hours ago, John Cuthber said:

If I get a bunch of matchsticks and cover them with glue, put them in a box, shake them up into some random arrangement and let the glue dry then they have "self assembled" into that shape.

But it's almost certainly no use.

If I want molecules to self assemble into something useful, I need to "choose"- and specify- those molecules very carefully.

And the way I do that is via the genome.

You seem to be persistently ignoring all the points I make.

May I remind you that the rules of the forum say that you have to address them, otherwise you are engaging in soapboxing, rather than discussion.

 

It's a shame you should feel that way. I must say that I share the feeling: that you are failing to respond to the arguments I present concerning the limited role of the genome, simply repeating your own viewpoint.

If I step back and try to look at the thread objectively, I see us both responding to what the other is saying, but maybe our mindsets are so far apart that bridging the distance from either side is nigh impossible. 

At the same time, I have the feeling that there is common ground that we are failing to find. At least we agree that genes determine proteins, that proteins are the most significant types of molecules in the cell, and that which proteins are present will therefore strongly influence the processes (both formative and functional) taking place in the cell.

So fas so good?

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8 minutes ago, DanielBoyd said:

If I step back and try to look at the thread objectively, I see us both responding to what the other is saying

And what you said was that you were not going to answer my point.

WHERE IS THIS INFORMATION STORED, IF IT IS NOT IN THE GENOME?

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7 hours ago, Ken Fabian said:

No, we do not agree. In any case, surely genes only directly determine RNA sequences. And not all of those RNA's are used to pattern proteins from. I provided images of working examples of combinations of RNA and proteins. RNA's have enormous biochemical potential - able to bring proteins together as a catalyst for example, as well as combine directly with them, as well as provide the pattern for making those proteins.

If you are seeking better understanding then sticking to the belief that DNA only determines proteins when it has been pointed out clearly and repeatedly that is not the case is not a good start. And you still haven't told us your reasoning for concluding that DNA doesn't contain enough information - just repeated that conclusion.

 

Not a good example perhaps. On consideration, all species share so much DNA that the total is not going to include enormously more than one species has. However I still absolutely depend on the DNA of other species, including for molecules my own body and cells can make. And my mother provided the ovum with all the cellular 'machinery' and epigenetic triggers, patterned from her DNA - which I may well have good copies of, for later.

I'm not convinced a design specification exists, or more correctly that it is an appropriate conceptual framework for describing what is happening - the structures and their form look like an emergent outcome, not a specification.That may be arguing semantics. But I suspect this whole thread is about semantics.

 

Hi Ken, you're right, I'm oversimplifying the biochemistry, but there isn't space here to be complete on such complexities. My point is (whether we're talking DNA, RNA or protein), we're still on the molecular level here, and need to transcend that to explain the higher levels of organisation that are what life is really about.

Your last sentence suggests that we share common ground. This is exactly what I am saying: that an emergent outcome is not the result of specification.

Some people seem to think I'm making a mountain out of a molehill here: of course there are regulatory processes and stuff which actually determine outcome, but that that is trivial. Because the genome makes the parts it's still in control.

I think this is more than semantics, and that the conceptual framework (self-assembly vs design as formative explanations for observed structures) is fundamental to the discussion. 

If you see the cell (and organism) as an emergent outcome, how do you interpret the role of the genome in that context?

6 minutes ago, John Cuthber said:

And what you said was that you were not going to answer my point.

WHERE IS THIS INFORMATION STORED, IF IT IS NOT IN THE GENOME?

Sorry, I thought I'd answered this question. The point is that self-assembly does not need or use information to create its product. A snowflake does not need some design to create its filligree form: this is simply the result of water molecules interacting. The thermodynamics of this process allow something complex to arise out of something simple (chilly water vapour) without any design information or external mechanism to build it. 

Proteins are different from snowflakes in this sense. They have a design (the gene) and a construction mechanism (gene transcription).

My contention is that the cell and the organism are like the snowflake, not the gene. They spontaneously grow without any external source of information to guide them out of the components (genetically-defined proteins, lipids, carbohydrates etc) that are available. We don't see cells or organisms 'crystallising' out of a random mix of molecules or cells like we do with snowflakes: instead growth and formation take place at the same time. But we do see something similar happening in the butterfly crysalis: All of the caterpillar's internal structures are first broken down into a disordered mush, which the re-forms into an entirely different ordered body. This is a classic case of self-assembly.

Having said this, you are right that there is an 'information gap'. In terms of information theory the entropy of a cell/organism is lower than that of a random collection of molecules/cells, You can see this as: "it requires more information to define it". So where this information come from, if not from the genome, is a good question.

In thermodynamic terms, this extra information (order) is created by the self-assembly process itself. It creates this order through the metabolic use of external energy sources. So the extra information is not stored but created.

Does this answer your question?

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1 hour ago, DanielBoyd said:

This is exactly what I am saying: that an emergent outcome is not the result of specification.

If by that, you mean that the genes do not specify how a protein folds (or how larger scale structures are formed) then: Duh. Thank you Captain Obvious.

There is no "inconvenient truth" here. Just the facts that everyone knows. You appear to have worked it out for yourself and there smugly think that no one else knows.

2 hours ago, DanielBoyd said:

Some people seem to think I'm making a mountain out of a molehill here: of course there are regulatory processes and stuff which actually determine outcome, but that that is trivial.

So it is completely unclear what you are adding to this. You keep saying "but there's more" there is the "inconvenient truth that everyone is ignoring". Yet, when pressed all you can do is state the obvious.

2 hours ago, DanielBoyd said:

My contention is that the cell and the organism are like the snowflake, not the gene. They spontaneously grow without any external source of information to guide them out of the components (genetically-defined proteins, lipids, carbohydrates etc) that are available.

Which is obviously nonsense, as we don't get complete cells spontaneously appearing from nowhere.

 

As this thread is going nowhere, and all you can do is repeat the same thing endlessly, I am going to report this thread for closure.

 

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Posted (edited)
On 7/4/2019 at 12:14 AM, DanielBoyd said:

In essence, this is an ultimately reductionistic explanation of life: define the components and you have defined life.

This is to ignore the principles of emergence, which tell us that the whole can be more than the sum of the parts, and the parts therefore cannot explain the whole. The discussion of information quantity is important in this context, since emergence results in the existence of structures (information) at higher levels of organisation that cannot be derived from the parts.  

Your point of view, or the idea that some extra ‘truth’ is needed, might be revised and more congruent with reality if you corrected one misunderstanding about emergent phenomena.  You seem to think, “emergence results in the existence of structures (information) at higher levels of organisation that cannot be derived from the parts.

Just because the whole is “more than” the sum of the parts, it doesn’t mean there are actually “more” parts (somehow magically created).  There may be more functionality than the original parts naturally have, but if you can fully analyze (reductionistic-ally) the whole, working backwards it’s usually fairly easy to see how the original parts interact to generate the emergent phenomenon.

For instance, on page two (in an example of building a car, I think) you said, “Know exactly what's in a toolbox and how it is made does not tell you what will be made using the tools.” 

Right, you can’t predict what will emerge.  However, I bet if you could fully study a car, you’d be able to figure out how to understand “exactly what's in a toolbox and how it is made.”  For a good explanation of emergent phenomena, read The Web of Life: A New Scientific Understanding of Living Systems , by Fritjof Capra                

Evolution doesn’t need to predict what design will work, it only needs to stumble across something that does work.  That is how morphogenesis arises—evolution playing with its toolbox, finding what works, and as Darwin said, through the “cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.”

~

Edited by Essay
clarify 'example'

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8 hours ago, DanielBoyd said:

It's a shame you should feel that way. I must say that I share the feeling: that you are failing to respond to the arguments I present concerning the limited role of the genome, simply repeating your own viewpoint.

If I step back and try to look at the thread objectively, I see us both responding to what the other is saying, but maybe our mindsets are so far apart that bridging the distance from either side is nigh impossible. 

At the same time, I have the feeling that there is common ground that we are failing to find. At least we agree that genes determine proteins, that proteins are the most significant types of molecules in the cell, and that which proteins are present will therefore strongly influence the processes (both formative and functional) taking place in the cell.

So fas so good?

!

Moderator Note

Absolutely not! I'm not sure what kind of blinders you're wearing DanielBoyd, but they're effectively blocking the help that others are offering you. Five pages of comments and you're still ignoring everyone and repeating your mistakes and misunderstandings. 

"Mindset" should be a perspective, NOT fixing your ideas in stone. That's not how science works. 

I'm closing this. Don't open the subject again unless you're prepared to support your assertions with evidence and respond when someone asks you to clarify what you mean.

 

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