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The Inconvenient Truth About Genetics

genetics self-assembly design development organism cell genome

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#69 GAHD

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Posted 27 June 2019 - 01:13 PM

What a cool Lego machine! There's an issue of the definition of 'coding' here. Your CAD design of the machine would clearly not contain a design of the paper plane, but there would be a direct causative relationship between it and the plane that allows the plane to be predicted on the basis of the machine's design. I agree on that.

 

Of course, most metabolic pathways involve several components, not just one protein and one substrate, so things get a bit more complicated: the end result cannot be predicted from one design (gene). Potentially though (with considerable extra effort) it could be predicted by looking at all the genes involved. I'm not claiming this not to be the case.

 

But now imagine the following. You have not one but 10,000 Lego machine designs in a book. You throw this book into a bath tub containing a 3d printer and a heap of raw materials (sheets of paper, bits of wood,...) that the machines described in the book could work on. You're not there to intervene and tell the printer which pages to read, and what we want is not a simple paper plane, but a complex contraption built of hundreds of these little machines. Is the book of CAD designs going to be sufficient to get this done? 

 

It doesn't stop there. Now imagine that we've got millions of these bathtubs, each with the same instruction book and more or less the same raw materials. We want them to make not just one but hundreds of different kinds of contraption, composed of different collections of machines. And then we want the millions of contraptions built to join together in an orderly fashion into one huge entity in which each of them is in just the right place to play its part.

 

Is the book of CAD designs really going to be sufficient to get this done?  

"imagine that we've got millions of these bathtubs, each with the same instruction book...want them to make not just one but hundreds of different kinds of contraption...Is the book of CAD designs really going to be sufficient to get this done?"

When the scale is small enough that Brownian motion and van der waals interactions become major players, yes. Particularly since the "book" is itself a macheine of sorts, and all the contraptions are set up to only connect properly in a single fashion though the BM an VDWF.

There's a very interesting wording you use here "each of them is in just the right place to play its part" as if it matters terribly where things end up. Do Identical Twins have the same moles? Do you think each scutoid is defined in placement? That's just silly. Cells are packed in and shift around constantly. DNA is a set of overall bootstrapping blueprints, and variations will occur because of the way the data unpacks itself.

Much the same way you'll see the exact same house built 50 to 100 times in infill housing, but walls will vary by an inch here or there, none of the nails will be in the same place, and the drywall in some will be vertical standard while others use cross lapped horizontal. Couple might have a dog-flap in the door while others are secure.Of course a body is not a stretch of infill housing, but the analogy is there even with the workers building that infill township: drywallers drywall even if some of them do sloppy corners, electricians hook up the fixtures even if one guy puts the wires along a different joist than the next guy, and plumbers send stuff downhill even if the stack placement moves around between different houses because the city boys were a little off on their sight lines. Same deal goes with vascular/osteoblast/nervous systems; no 2 people's are the same even with a shared master design.

 


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#70 exchemist

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Posted 27 June 2019 - 02:34 PM

What a cool Lego machine! There's an issue of the definition of 'coding' here. Your CAD design of the machine would clearly not contain a design of the paper plane, but there would be a direct causative relationship between it and the plane that allows the plane to be predicted on the basis of the machine's design. I agree on that.

 

Of course, most metabolic pathways involve several components, not just one protein and one substrate, so things get a bit more complicated: the end result cannot be predicted from one design (gene). Potentially though (with considerable extra effort) it could be predicted by looking at all the genes involved. I'm not claiming this not to be the case.

 

But now imagine the following. You have not one but 10,000 Lego machine designs in a book. You throw this book into a bath tub containing a 3d printer and a heap of raw materials (sheets of paper, bits of wood,...) that the machines described in the book could work on. You're not there to intervene and tell the printer which pages to read, and what we want is not a simple paper plane, but a complex contraption built of hundreds of these little machines. Is the book of CAD designs going to be sufficient to get this done? 

 

It doesn't stop there. Now imagine that we've got millions of these bathtubs, each with the same instruction book and more or less the same raw materials. We want them to make not just one but hundreds of different kinds of contraption, composed of different collections of machines. And then we want the millions of contraptions built to join together in an orderly fashion into one huge entity in which each of them is in just the right place to play its part.

 

Is the book of CAD designs really going to be sufficient to get this done?  

If it isn't, then you need to suggest what supplementary source of information there is to enable the task to be completed. 

 

So far you have just talked about "self-assembly", without suggesting where the information you consider missing can possibly come from. 

 

As GAHD says, it's a bootstrap process whereby it makes the tools to do the job in stages and uses the nutrient and energy supply to do the construction. I don't see why you consider this impossible.


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#71 Dubbelosix

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Posted 27 June 2019 - 02:53 PM

Of course you could, in a way it has already been done... see, my genetics is related to family, and family is like cloning but with genetic deformations, right down to the fact we are individuals. It doesn't mean twins for example, are always identical, nor is their sexual orientation always identical... but... in most cases, twins often share the same sexual orientation, other twins share the same looks, but not always the orientation, even though the odds for it are very high. 

 

 

We can clone things like dogs it just the original experiments were done on sheep. Hell, dubbel I could clone you given the proper instruments.



#72 Dubbelosix

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Posted 27 June 2019 - 02:55 PM

"imagine that we've got millions of these bathtubs, each with the same instruction book...want them to make not just one but hundreds of different kinds of contraption...Is the book of CAD designs really going to be sufficient to get this done?"

When the scale is small enough that Brownian motion and van der waals interactions become major players, yes. Particularly since the "book" is itself a macheine of sorts, and all the contraptions are set up to only connect properly in a single fashion though the BM an VDWF.

There's a very interesting wording you use here "each of them is in just the right place to play its part" as if it matters terribly where things end up. Do Identical Twins have the same moles? Do you think each scutoid is defined in placement? That's just silly. Cells are packed in and shift around constantly. DNA is a set of overall bootstrapping blueprints, and variations will occur because of the way the data unpacks itself.

Much the same way you'll see the exact same house built 50 to 100 times in infill housing, but walls will vary by an inch here or there, none of the nails will be in the same place, and the drywall in some will be vertical standard while others use cross lapped horizontal. Couple might have a dog-flap in the door while others are secure.Of course a body is not a stretch of infill housing, but the analogy is there even with the workers building that infill township: drywallers drywall even if some of them do sloppy corners, electricians hook up the fixtures even if one guy puts the wires along a different joist than the next guy, and plumbers send stuff downhill even if the stack placement moves around between different houses because the city boys were a little off on their sight lines. Same deal goes with vascular/osteoblast/nervous systems; no 2 people's are the same even with a shared master design.

 

 

Yes, no two individuals are exactly the same, if they were we would see a direct evidence for it. However, it can come very close.... to the point that it is hardly indistinguishable. 



#73 VictorMedvil

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Posted 29 June 2019 - 08:05 AM

Yes, no two individuals are exactly the same, if they were we would see a direct evidence for it. However, it can come very close.... to the point that it is hardly indistinguishable. 

 

That is because the genetic code does not have the data for the position of every blood vessel or every neuron in the brain, but rather is the underlining data that creates this pattern rather than each blood vessel or each neuron, it is the pattern that creates the blood vessel or creates the neuron that is what is stored within DNA.


Edited by VictorMedvil, 29 June 2019 - 08:18 AM.


#74 GAHD

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Posted 29 June 2019 - 03:25 PM

That is because the genetic code does not have the data for the position of every blood vessel or every neuron in the brain, but rather is the underlining data that creates this pattern rather than each blood vessel or each neuron, it is the pattern that creates the blood vessel or creates the neuron that is what is stored within DNA.

AFAIK it's more that each cell will put out signals when it needs more fuel tan it's currently getting. These signals are then acted upon by neighboring cells to find a nearby area with high fuel and grow new pipes towards the low fuel one. AFAICT that same signal pathway leads to the development of the "standard" vascular structure in humans (and other animals) simply because of the stages of growth that we go though setting up natural signal gradients in uterus and over lifespan. A similar pathway seems to be used by skeletal muscle to control densities and whatnot bot seems absent or different in cardiac muscle. Unsure which pathway is used for neural growth but I'd wager it's similar to if not directly piggybacked onto the other two. This signal pathway is often hijacked by cancers which leads to big and fat vascular systems developing around particularly large globs of cancer. 

Either way, yeah, the machines are coded with IF/THAN/ELSE/DO that through complex interactions "unzips" into a large bipedal anxiety meta-machine. The major issue is more that environmental strains can completely alter the end product in any one generation because of that process. EG that gen1 and gen 2 study I linked a couple posts back, EG2 Iodine deficiency from environment leading to cretinism.



#75 VictorMedvil

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Posted 29 June 2019 - 10:59 PM

AFAIK it's more that each cell will put out signals when it needs more fuel tan it's currently getting. These signals are then acted upon by neighboring cells to find a nearby area with high fuel and grow new pipes towards the low fuel one. AFAICT that same signal pathway leads to the development of the "standard" vascular structure in humans (and other animals) simply because of the stages of growth that we go though setting up natural signal gradients in uterus and over lifespan. A similar pathway seems to be used by skeletal muscle to control densities and whatnot bot seems absent or different in cardiac muscle. Unsure which pathway is used for neural growth but I'd wager it's similar to if not directly piggybacked onto the other two. This signal pathway is often hijacked by cancers which leads to big and fat vascular systems developing around particularly large globs of cancer. 

Either way, yeah, the machines are coded with IF/THAN/ELSE/DO that through complex interactions "unzips" into a large bipedal anxiety meta-machine. The major issue is more that environmental strains can completely alter the end product in any one generation because of that process. EG that gen1 and gen 2 study I linked a couple posts back, EG2 Iodine deficiency from environment leading to cretinism.

See this proves my point if the DNA had the position of every blood vessel mapped then when cancer formed there would be no blood supply to the cancerous growth but the blood vessels to feed the cancerous cells grow anyways. The nature of this being simple that these pathways do a specific job toward creation of something, not necessarily always being an exact copy even with similar DNA.


Edited by VictorMedvil, 29 June 2019 - 11:01 PM.


#76 Famouseral

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Posted 30 June 2019 - 07:05 PM

I learn a lot from this thread. I am keen to learn about the same subject.

#77 DanielBoyd

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Posted 01 July 2019 - 12:06 AM

If it isn't, then you need to suggest what supplementary source of information there is to enable the task to be completed. 

 

So far you have just talked about "self-assembly", without suggesting where the information you consider missing can possibly come from. 

 

As GAHD says, it's a bootstrap process whereby it makes the tools to do the job in stages and uses the nutrient and energy supply to do the construction. I don't see why you consider this impossible.

 

Sorry, you asked this question before and I didn;t answer. The point is that self-assembly does not need 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 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 disordered components (genetically-defined proteins, lipids, carbohydrates etc) that are available.

 

Still, 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 informatiuon to define it", This information is not provided by the genome, which it busy enough building proteins.

 

This extra information (order) is actually created by the self-assembly process itself. It creates this order through the metabolic use of external energy sources.

 

Does this help at all?


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#78 VictorMedvil

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Posted 01 July 2019 - 12:17 AM

Sorry, you asked this question before and I didn;t answer. The point is that self-assembly does not need 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 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 disordered components (genetically-defined proteins, lipids, carbohydrates etc) that are available.

 

Still, 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 informatiuon to define it", This information is not provided by the genome, which it busy enough building proteins.

 

This extra information (order) is actually created by the self-assembly process itself. It creates this order through the metabolic use of external energy sources.

 

Does this help at all?

 

Cells are constructed of proteins thus saying that proteins on one hand are assembled by design and the cell is assembled without information is kinda silly as they are one in the same a cell is no more than many proteins all working together, thus by extension cells are coded for.


Edited by VictorMedvil, 01 July 2019 - 12:18 AM.


#79 DanielBoyd

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Posted 01 July 2019 - 10:22 AM

Cells are constructed of proteins thus saying that proteins on one hand are assembled by design and the cell is assembled without information is kinda silly as they are one in the same a cell is no more than many proteins all working together, thus by extension cells are coded for.

 

You're saying that if you've explained a thing, you have also explained everything it is a part of? Sorry, but that just doesn't hold.

 

Using that reasoning we wouldn't need a genome: because we know how the atoms are built and a protein is no more than atoms working together.

 

Nope: each level of organisation needs to be explained, and in emergent systems (the whole is more than the sum of the parts) explaining the parts is never going to sufficient to understand the whole.  



#80 exchemist

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Posted 01 July 2019 - 10:40 AM

Sorry, you asked this question before and I didn;t answer. The point is that self-assembly does not need 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 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 disordered components (genetically-defined proteins, lipids, carbohydrates etc) that are available.

 

Still, 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 informatiuon to define it", This information is not provided by the genome, which it busy enough building proteins.

 

This extra information (order) is actually created by the self-assembly process itself. It creates this order through the metabolic use of external energy sources.

 

Does this help at all?

Yes, a bit. You are claiming, in effect, that processes analogous to crystallisation play a role in the assembly of biochemical structures and that this cuts down on the amount of information the genome itself needs to carry. I'm sure that must be true, for example in the secondary and tertiary structure of enzymes. Is this the sort of thing you have in mind? 



#81 DanielBoyd

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Posted 02 July 2019 - 11:39 PM

Yes, a bit. You are claiming, in effect, that processes analogous to crystallisation play a role in the assembly of biochemical structures and that this cuts down on the amount of information the genome itself needs to carry. I'm sure that must be true, for example in the secondary and tertiary structure of enzymes. Is this the sort of thing you have in mind? 

 

I hadn't yet dared to bring up secondary and tertiary structures since they are so closely related to amino acid sequences that you could argue design, at least for secondary structure, is present in the gene. After all, this is the functional product that evolution works on, which allows neutral mutations in codons and amino acid substitutions that do not alter secondary structure.

 

For those not in the know: the gene defines the sequence of amino acids that are strung together, but functional proteins are not just loose strings. After being strung together, these chains spontaneously fold and wrap themselves into very specific 3D shapes (secondary structure). The way they do this is dependent on the chemical environment they find themselves in. For instance, in a too acidic or alkaline solution they will not fold in the right way, because this disturbs the interactions between the amino acids in the chain. Secondary structure, then is not explicitly coded for in the genome, and is determined partially by non-genetic influences.

 

Frequently, several of these moolecules have to bind together to form the functional protein, sometimes together with non-protein components. This is tertiary structure. For instance, hemaglobin consists of a number of globular proteins and a porphyrin ring that holds the iron atom that actually binds to oxygen. Genes have no causative relationship with the the porphyrin ring and the iron, and do not instruct the modules to self-assemble.   

 

@exchemist: So yes, this is the first level of organisation that is not expicitly coded for in the genome but is created through self-assembly. Above this, we get the organelle; the cell; the tissue; the organ and the organism. Since few organisms are independently viable, explaining life fully also requires explanations for the organisation seen in populations, communities, ecosystems and possibly the biosphere itself,

 

So again, we see that the genome is a useful little toolbox, but that a toolbox doesn't build a shed.



#82 Dubbelosix

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Posted 03 July 2019 - 05:30 AM

In a way... yes, cells, proteins form like crystals, but its not a self-assembly from an ultimate spaghetti monster, it is encoded in the gene itself.



#83 DanielBoyd

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Posted 04 July 2019 - 09:03 AM

In a way... yes, cells, proteins form like crystals, but its not a self-assembly from an ultimate spaghetti monster, it is encoded in the gene itself.

 

Funny you should bring up the spaghetti monster. That's kinds the image I get of your impression of the genome. It spews out these long strands, that get all tangled up and drift off into the distance, yet somehow it manages to keep control of where they go and what they do. Personally, I don't see how it could. But perhaps I'm missing a nuance here or taking things too literally.  



#84 fahrquad

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Posted 04 July 2019 - 08:44 PM

We can clone things like dogs it just the original experiments were done on sheep. Hell, dubbel I could clone you given the proper instruments.

 

Lord no.  One is more than enough.



#85 DanielBoyd

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Posted 07 July 2019 - 03:05 AM

Hi people, up till now, we've been mostly discussing the first couple of points, about what the genome does and does not code for.

 

Does anyone have any ideas about the systemic arguments I present (numbers 7 - 10)?

 

I'd be interested to hear your thoughts on those.





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