The Inconvenient Truth About Genetics

[Dubbelosix]

Here's a different example, certain viruses have become immune to the use of antibiotics, that has happened over a short time due to evolution of the system responding to its harsh environment. A gene encodes its environment, will have the information within the genome, especially complex genes like we are made of, are no different.

Edited June 25, 2019 by Dubbelosix

[Vmedvil2]

But surely that means the information that causes the enzyme to be produced is also the information that results in the carbohydrate too.

 

That is true exchemist the information that creates the set of enzymes that make the metabolic pathway for carbohydrates usually it is a set of proteins that create complex reactions such as this one, the chemical itself is not sorted within the genes but the enzymes which create it are stored and their folding patterns for them.

 

 

Here is an example Carbohydrate Metabolism Metabolic Pathway

Edited June 25, 2019 by VictorMedvil

[Vmedvil2]

Here's a different example, certain viruses have become immune to the use of antibiotics, that has happened over a short time due to evolution of the system responding to its harsh environment. A gene encodes its environment, will have the information within the genome, especially complex genes like we are made of, are no different.

 

and dubbel you may want to edit this Viruses do not respond to antibiotics as antibiotics are not used on viruses as they are naturally immune to them I think you are referring to bacteria in this scenario. No Doctor would never prescribe antibiotics for a viral infection but rather a vaccine to the virus ahead of time, bacteria are the ones that mutate to become immune to antibiotics as they are targeted by them.

 

Edited June 25, 2019 by VictorMedvil

[DanielBoyd]

But surely that means the information that causes the enzyme to be produced is also the information that results in the carbohydrate too.

 

There is certainly a causative relationship betwen the two: a different enzyme will lead to a different product, as we see in GADH's reference to  https://www.openplan...ate-engineering . The point is that a design for a machine does not constitute a design for a product that machine makes. 

 

If there is a one-to-one relationship then you could see the protein as a 'translator' of genetic information (amino acid sequence) to carbohydrate structure, but as Victor point out there are also other (non-proteinaceous) components and factors involved in the production process. Consequently, while genetic changes will tweat the outcome, they cannot be considered as a complete determinative explanation.

 

I don't know whether you have noticed, but we are still struggling with the role of the genome inside the cell: the molecular environment that it is a part of. While these factors also apply to the cell, the article is primarily concerned with the morphology of multicellular organisms. This is a massive step beyond the level we are now discussing, and far further detached from direct genetic control. While you could say that there is a gene for an enzyme for a carbohydrate, you cannot make a similar leap from a gene to a knuckle joint or a kidney.

Edited June 26, 2019 by DanielBoyd

[Vmedvil2]

There is certainly a causative relationship betwen the two: a different enzyme will lead to a different product, as we see in GADH's reference to  https://www.openplan...ate-engineering . The point is that a design for a machine does not constitute a design for a product that machine makes. 

 

If there is a one-to-one relationship then you could see the protein as a 'translator' of genetic information (amino acid sequence) to carbohydrate structure, but as Victor point out there are also other (non-proteinaceous) components and factors involved in the production process. Consequently, while genetic changes will tweat the outcome, they cannot be considered as a complete determinative explanation.

 

I don't know whether you have noticed, but we are still struggling with the role of the genome inside the cell: the molecular environment that it is a part of. While these factors also apply to the cell, the article is primarily concerned with the morphology of multicellular organisms. This is a massive step beyond the level we are now discussing, and far further detached from direct genetic control. While you could say that there is a gene for an enzyme for a carbohydrate, you cannot make a similar leap from a gene to a knuckle joint or a kidney.

 

Well, what I was speaking about is just biochemistry that proteins will do reactions upon other biochemicals to transform those biochemicals into other biochemicals, ultimately availability of biochemicals to be reacted can have a vast effect on the ability of the cells to operate, the actual intake of biochemicals is controlled by the cell and environmental availability not just one or the other. For instance, if you have not eaten and have little fat remaining the cell will cease to metabolize despite the actual DNA coding which tells the cell to metabolize a certain amount of sugar to make energy even due to biochemical changes start to metabolize less sugar to have the remaining sugar, the body is a complex machine but all of this action is scripted in DNA then physically carried out by proteins even what you would call a sort of Natural Intelligence carried out by cellular machinery. You know like 99% of DNA code is statements about when to activate genes after what stimulation and conditions something like a knuckle joint or kidney is just the effect of the genetic scripting over long amounts of code. The cells are programmed to make that structure by these Cellular Control genes which are a vast amount of the coding within any multi-cellular organism to say this that the genetic scripting or Cellular control genes do not make these structures is silly as they are truly response for their appearance in the structures that we see and the shape of something like a kidney or knuckle, if the amount of activation of genes was different then the structures would have different forms and compositions too.

 

 

 

 

 

Edited June 26, 2019 by VictorMedvil

[exchemist]

There is certainly a causative relationship betwen the two: a different enzyme will lead to a different product, as we see in GADH's reference to  https://www.openplan...ate-engineering . The point is that a design for a machine does not constitute a design for a product that machine makes. 

 

If there is a one-to-one relationship then you could see the protein as a 'translator' of genetic information (amino acid sequence) to carbohydrate structure, but as Victor point out there are also other (non-proteinaceous) components and factors involved in the production process. Consequently, while genetic changes will tweat the outcome, they cannot be considered as a complete determinative explanation.

 

I don't know whether you have noticed, but we are still struggling with the role of the genome inside the cell: the molecular environment that it is a part of. While these factors also apply to the cell, the article is primarily concerned with the morphology of multicellular organisms. This is a massive step beyond the level we are now discussing, and far further detached from direct genetic control. While you could say that there is a gene for an enzyme for a carbohydrate, you cannot make a similar leap from a gene to a knuckle joint or a kidney.

But these people seem to think they can farm kidneys: https://www.sciencedirect.com/science/article/abs/pii/S0272638618305067

 

Where do they get the information from to construct them?

[Dubbelosix]

Victor 

 

I do apologize, I actually meant bacteria however a prophylaxis of antibiotics for HIV have cured them a few occasions which is probably why I got a bit mixed up. But when I am in a frustration to write something out I do tend from time to time, give out the wrong information, but hopefully the basis of what I meant was understood. 

Edited June 26, 2019 by Dubbelosix

[Vmedvil2]

Victor 

 

I do apologize, I actually meant bacteria however a prophylaxis os antibiotics for HIV have cured them a few occasions which is probably why I got a bit mixed up. But when I am in a frustration to write something out I do tend from time to time, give out the wrong information, but hopefully the basis of what I meant was understood. 

 

Tis fine, the message was still received as intended, I understood the mistake. The position you took was the correct one just about the wrong micro-organism.

Edited June 26, 2019 by VictorMedvil

[DanielBoyd]

But these people seem to think they can farm kidneys: https://www.sciencedirect.com/science/article/abs/pii/S0272638618305067

 

Where do they get the information from to construct them?

 

It's clever stuff, where genetics really comes into its own. They're working with experimental bits of kidney (organoids) that can be grown in the lab from the appropriate stem cells. These are cells with exactly the same genetic information as differentiated cells, but in which the cell state is such that they are capable of dividing and developing to form tissues and organs.

 

The self-organising growth process is comparable to what takes place in the foetus..However, the fact that most of the external (non-genetic) factors that are present in a developing foetus are missing means that going beyond the organoid stage to a complete kidney is not easy. And not necessary for the purpose at hand. By meddling with the genes of key proteins they can test whether this helps in models of particujlar disease states that are caused by faulty proteins. Having found out which parts work best in the system, gene therapy could be used to solve medical problems in patients with the defective proteins.  

[DanielBoyd]

Here's a different example, certain viruses have become immune to the use of antibiotics, that has happened over a short time due to evolution of the system responding to its harsh environment. A gene encodes its environment, will have the information within the genome, especially complex genes like we are made of, are no different.

 

The susceptibility of bacteria to antibiotics is all about proteins in their outer membranes. Changes in the genes used to build these proteins can therefore make them resistant. This is not because a gene has changed the structure of the bacterium or the way it grows, divides or works, just a single component that is key to this particular situation, in which genetic information does play a directly causative role.

[Vmedvil2]

The susceptibility of bacteria to antibiotics is all about proteins in their outer membranes. Changes in the genes used to build these proteins can therefore make them resistant. This is not because a gene has changed the structure of the bacterium or the way it grows, divides or works, just a single component that is key to this particular situation, in which genetic information does play a directly causative role.

 

I want to put this forward that a mutation causes the antibiotic resistance this can be found by the inherit-ability of antibiotic resistance in bacteria, secondly antibiotic resistance can be moved by plasmid too showing that the change is definitely genetic. Though what you say about the protein expression is correct that the outer membrane begins to reject antibiotics which shows a level of chemical change based on the genetic change proving the idea that genetic changes can create chemical changes. (https://www.ncbi.nlm.nih.gov/pubmed/17127523) 

Edited June 26, 2019 by VictorMedvil

[Dubbelosix]

Mutation, I would like to add, is a small evolutionary step which is known as punctuated equilibrium, instead of large genetic mutations. Mutations are just genes responding to an environment and/or located to bad genes - for instance, in quantum biology, a double helix strand can become mutated by losing a proton through quantum tunneling. The underlying mechanism here, is that the genetic code alters slightly, but will passed on from generation to another.

 

Besides, as I have already said, if genes did not express the entire body or system, then the questions remains how we are able to clone not just sheep, but a whole range of other species, just like dogs.

[Vmedvil2]

Mutation, I would like to add, is a small evolutionary step which is known as punctuated equilibrium, instead of large genetic mutations. Mutations are just genes responding to an environment and/or located to bad genes - for instance, in quantum biology, a double helix strand can become mutated by losing a proton through quantum tunneling. The underlying mechanism here, is that the genetic code alters slightly, but will passed on from generation to another.

 

Besides, as I have already said, if genes did not express the entire body or system, then the questions remains how we are able to clone not just sheep, but a whole range of other species, just like dogs.

 

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.

 

One could even use the method used for dolly on humans even from your male nipples like dolly, though I don't know if I would want to collect the sample, so I would settle for a blood sample with T-cells or B-cells.

 

 

 A few genetic changes using Viral Mediated CRISPR And the clone army begins

Edited June 27, 2019 by VictorMedvil

[GAHD]

...The point is that a design for a machine does not constitute a design for a product that machine makes. ...While you could say that there is a gene for an enzyme for a carbohydrate, you cannot make a similar leap from a gene to a knuckle joint or a kidney.

We're of opposing viewpoints there. If I have a cad file for this, then I print it on some z-printer and assemble, I'm fairly certain the paper airplanes produced by it are encoded in it's very structure even if you don't see the paper or the airplane coded in the design file. I'm thinking you have some arbitrary limits on how you define information encoding?

 

As for gene to protein to micro structure to complex interaction to knuckle...how terribly wrong you are can be shown with a single event. The second-generation study on it seems to confirm that the blueprints remain intact despite the embryonic issues with expression of first-gen. Are you aware of this body of research?

[DanielBoyd]

I want to put this forward that a mutation causes the antibiotic resistance this can be found by the inherit-ability of antibiotic resistance in bacteria, secondly antibiotic resistance can be moved by plasmid too showing that the change is definitely genetic. Though what you say about the protein expression is correct that the outer membrane begins to reject antibiotics which shows a level of chemical change based on the genetic change proving the idea that genetic changes can create chemical changes. (https://www.ncbi.nlm.nih.gov/pubmed/17127523) 

 

I think, then, that we agree here. Antibiotics are molecules that interfere with molecules (mostly proteins) in the cell, Altering these proteins can prevent this.

 

I'm not saying that the genome has no essential role to play! Just that we need to realise what it does not do: provide a design on the basis of which the cell is built.

 

What strikes me is that we're still talking molecular and cell-level structures and processes here, which are at least the same level as DNA and its transcription processes. Consequently, the efffect of genetic changes is fairly direct. My article is not so much about the cell, but about the differentiation, migration and organisation of billions.of cells that is required to build an organism.

 

There is a gene for the protein that is attacked by an antibiotic. There is not a gene for the skin tissue that defends our bodies from the big bad world.

[DanielBoyd]

We're of opposing viewpoints there. If I have a cad file for this, then I print it on some z-printer and assemble, I'm fairly certain the paper airplanes produced by it are encoded in it's very structure even if you don't see the paper or the airplane coded in the design file. I'm thinking you have some arbitrary limits on how you define information encoding?

 

As for gene to protein to micro structure to complex interaction to knuckle...how terribly wrong you are can be shown with a single event. The second-generation study on it seems to confirm that the blueprints remain intact despite the embryonic issues with expression of first-gen. Are you aware of this body of research?

 

Nice points! Hold that thought. Not sure what time zone you're in, but I just arrived at work. Will get back to you later.

[DanielBoyd]

We're of opposing viewpoints there. If I have a cad file for this, then I print it on some z-printer and assemble, I'm fairly certain the paper airplanes produced by it are encoded in it's very structure even if you don't see the paper or the airplane coded in the design file. I'm thinking you have some arbitrary limits on how you define information encoding?

 

As for gene to protein to micro structure to complex interaction to knuckle...how terribly wrong you are can be shown with a single event. The second-generation study on it seems to confirm that the blueprints remain intact despite the embryonic issues with expression of first-gen. Are you aware of this body of research?

 

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?