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The Inconvenient Truth About Genetics

genetics self-assembly design development organism cell genome

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#35 DanielBoyd

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Posted 24 June 2019 - 12:45 AM

Alright your reasons 1 to 4 along with reason 9 are fallacies, it is nonsense these 5 reasons you have stated the others are fine though, initially I wasn't going to say anything because I assumed you had just worded it wrongly but as the others have pointed out there are serious problems with those reasons. When I originally was reading this paper I kinda was skim reading it and missed these reasons you have but some of them are outright incorrect. The body is a bit wordy with blurbs about religion which is fine but however I would suggest revision to the article in the sense it needs to be less wordy.

Hi Victor, I tried to keep it as compact as possible, but even at this level you run up against the limitations of being able to explain things thoroughly. You could write a book on the subject! Maybe I should have split it into separate topics, but they are all so interconnected that would be tricky. I suppose I could ditch the (short) paragraph on religion. 

 

Glad to hear that you agree with half of my reasons (which are sufficient to justify the conclusion). Could you ask you to choose one of the others and explain why you consider it to be wrong? Then we can start a content-based discussion.



#36 exchemist

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Posted 24 June 2019 - 03:01 AM

The question is: How much information would a design of your body require? To make a comparison: the blueprints for a car needs to define where about 30,000 parts need to be placed. Your body, on the other hand, is created by getting some 40,000 billion cells in the right place. Your genome only contains about 3 billion base pairs. So even if each base pair were to contain the location of one cell it would not contain nearly enough information even at this morphological level.

 

In reality, there is a lot of repetition which vastly reduces the amount of information required. A single muscle may contain billions of cells that can be positioned using the instruction: “build a muscles of size x there”. Even at this level, though, the amount of information required is staggering. One approach here is to consider Gray’s Anatomy, which takes 1500 pages to describe our bodies at a reasonable level of detail (through not sufficient to actually build it from cells). The illustrations in this book, as in most blueprints, are the most informative part (since a picture paints a thousand words). In bitmap format, these would also require more than the genome’s 3 billion base-pairs to be stored.

 

The above calculations exclude the instructions that would be needed to build each of the body’s 200 different kinds of cells out of the appropriate molecules. Here the number of parts (molecules) is even greater, but again, we could restrict ourselves to cellular morphology, and be helped out by the fact that many organelles are essentially the same in different kinds of cell and would therefore only need to be specified once. Still, our design would need to specify all the distinguishing features of these cell types, which is a significant additional amount of information.

 

The simple conclusion is that the genome is by far too small to act as a design for the body (even if the information it contains was dedicated to this task, which it isn’t).

I think you are starting from the wrong end of the problem.  The thing is, theoretical arguments about information are all very well but at the end of the day, we actually observe organisms to grow from a single fertilised seed or egg. So, if you contend that the genome does not contain enough information for this to happen, you have to account for where the extra information you say is needed can come from. Do you have a proposal to make for that? You have not offered one so far.  

 

Because if there is no other source for it, the required information must be in the genome.  

 

Regarding your argument about information content, I notice you do not attempt any quantification of the information required or available in the genome, and  that you provide no references to any work on this. Qualitative arguments about information content are pretty unpersuasive, given the observed facts. Has any quantification been done, by you or anyone you know of? 

 

P.S. Are you an engineer by any chance?


Edited by exchemist, 24 June 2019 - 03:02 AM.


#37 DanielBoyd

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Posted 24 June 2019 - 01:11 PM

Hi guys, just want to apologise for my tardiness in replying to your posts. I will get round to it, but hadn't anticipated such a response and have also got a day job... Which fortunately doesn't involve convincing anyone about wild ideas ;-)


Edited by DanielBoyd, 24 June 2019 - 01:49 PM.


#38 DanielBoyd

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Posted 24 June 2019 - 02:13 PM

You remind me of another crank that keeps looking for attention. It's funny how each time his identity is known, its off to create a new one. While primarily, my background has been largely based in the understanding of physics, I have even taken biology courses and some remedial chemistry courses. Trust me when I say, your article is not scientific, nothing close.

 

Not to pull rank, but I studied biology at university, and have a more thorough understanding of genetics and biochemistry than you are indicating in your posts. From your unspecified critique and misquotes I can only conclude that you have not read my article well enough to understand what I am actually saying and provide a constructive contribution. Unless you have any specific point to make that is relevant to the article, I would kindly request that you. refrain.


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#39 DanielBoyd

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Posted 24 June 2019 - 02:33 PM

I think you are starting from the wrong end of the problem.  The thing is, theoretical arguments about information are all very well but at the end of the day, we actually observe organisms to grow from a single fertilised seed or egg. So, if you contend that the genome does not contain enough information for this to happen, you have to account for where the extra information you say is needed can come from. Do you have a proposal to make for that? You have not offered one so far.  

 

Because if there is no other source for it, the required information must be in the genome.  

 

Regarding your argument about information content, I notice you do not attempt any quantification of the information required or available in the genome, and  that you provide no references to any work on this. Qualitative arguments about information content are pretty unpersuasive, given the observed facts. Has any quantification been done, by you or anyone you know of? 

 

P.S. Are you an engineer by any chance?

 

No, I'm not actually an engineer but a biologist frustrated by the rather mechanical explanations for the dynamic complexity of living systems provided at university level. So kinda surprised if I come across as a mechanist!

 

Your argument is what the assumption of genetic determinism is based on: organisms must be built using instructions, the genome is the only set of instructions available, therefore the genome must be contain the instructions to build an organism. This is entirely logical, The problem is that while the genome does contain instructions (for making proteins) it cannot actually provide the instructions to build the organism, for the reasons given. 

 

Since there is no other information available, the only alternative is for the organism to build itself through self-assembly. Which should not really sound as wild as it does, considering the fact that practically everything in the universe self-assembles and organisms are so good at homoeostatic control, which is closely related to self-assembly. 

 

I get your point that more robust numerical evidence would provide a sounder footing, but we are talking orders of magnitude here, not just a percentual difference. Still, even that could do with more substantiation I guess..



#40 exchemist

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Posted 24 June 2019 - 02:51 PM

No, I'm not actually an engineer but a biologist frustrated by the rather mechanical explanations for the dynamic complexity of living systems provided at university level. So kinda surprised if I come across as a mechanist!

 

Your argument is what the assumption of genetic determinism is based on: organisms must be built using instructions, the genome is the only set of instructions available, therefore the genome must be contain the instructions to build an organism. This is entirely logical, The problem is that while the genome does contain instructions (for making proteins) it cannot actually provide the instructions to build the organism, for the reasons given. 

 

Since there is no other information available, the only alternative is for the organism to build itself through self-assembly. Which should not really sound as wild as it does, considering the fact that practically everything in the universe self-assembles and organisms are so good at homoeostatic control, which is closely related to self-assembly. 

 

I get your point that more robust numerical evidence would provide a sounder footing, but we are talking orders of magnitude here, not just a percentual difference. Still, even that could do with more substantiation I guess..

I don't see how self-assembly solves the problem. The self-assembly has to rely on components made according to the template in the genome. So it all goes back to the genome. 



#41 Dubbelosix

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Posted 24 June 2019 - 09:41 PM

Not to pull rank, but I studied biology at university, and have a more thorough understanding of genetics and biochemistry than you are indicating in your posts....

 

Then prove it, because I am not satisfied you have demonstrated such a thing.



#42 Dubbelosix

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Posted 24 June 2019 - 09:44 PM

I don't see how self-assembly solves the problem. The self-assembly has to rely on components made according to the template in the genome. So it all goes back to the genome. 

 

I suppose self-assembly of living organisms can tell only one truth, or possibility, in-so-much that consciousness could be cosmic itself. A second idea behind consciousness itself would probably require quantum entanglement, all human beings are like giant quantum machines in which their particles are quantum entangled - we have been unable to find consciousness to any certain region of the brain and this may have something to do with how a large collection of particles interact coherently, acting as one system alone.



#43 DanielBoyd

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Posted 25 June 2019 - 11:43 AM

I suppose self-assembly of living organisms can tell only one truth, or possibility, in-so-much that consciousness could be cosmic itself. A second idea behind consciousness itself would probably require quantum entanglement, all human beings are like giant quantum machines in which their particles are quantum entangled - we have been unable to find consciousness to any certain region of the brain and this may have something to do with how a large collection of particles interact coherently, acting as one system alone.

Well excuse me! You're criticising me for being unscientific, and are then leaping from organismal developmental morphology to cosmic consciousness and then to humans as giant quantum machines? Perhaps you should leave this thread and start one of your own on those topics, since they don't belong here. 



#44 DanielBoyd

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Posted 25 June 2019 - 11:53 AM

I think you need to learn about information compression. Computer science is learning a lot about that from the very bit you're criticizing. As you say, every cell has the same basic structure, and only differences between them need to have information. DNA is actually very messy and replete with duplicate information (mostly used to control how much of any one protein is produced at a time in the chaos theory environment of random reads and writes) and can probably function just fine if you clip it down..for a short while.

The neat thing about cell differentiation is that it's controlled externally from the cell, not internally. Most of the organelles respond to an "if then" sort of reflex when they are in the body, that's how you can take a chunk from one part of the body and have it respond properly when you move it elsewhere.

This is a "bootstrap" environment you're trying to describe, not a full image state.

 

Since I took up a career in IT after studying biology, I know about data compression too: the thing is that it needs a (de)compression algorithm and mechanism that do not exist in the DNA transcription process, which is a simple one-to-one mapping of codons to amino acids. That's why I quote the pictures in Gray's anatomy in bitmap rather than jpeg (though both are arbitrary, since the genome clearly does not contain pictorial information).

 

And I did apply data compression principles in my calculations: I recognized that to place 40.000 billion cells of 200 types does not require 40.000 billion * 200 bits of information due to the repetitions present. Just like in image compression, this massively reduces the amount of information required - just still not enough to fit into the genome.  



#45 DanielBoyd

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Posted 25 June 2019 - 12:00 PM

I don't see how self-assembly solves the problem. The self-assembly has to rely on components made according to the template in the genome. So it all goes back to the genome. 

 

Absolutely, there is a relationship: different mixes of components will obviously self-organise in different ways. So genetic information will of course have an indirect effect on what happens in the formation of the cell and the organism. This is what we see in many heritable traits. The point, however, is that this is not the same as saying that the genome contains a design for the organism. Furthermore, we need to acknowledge that not just proteins but other molecular components and other non-genetic factors are also influential in determining the outcome.



#46 DanielBoyd

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Posted 25 June 2019 - 12:04 PM

I noted mt DNA because of your bit here:

 

Most metabolic stuff can be found in the mitochondrial loops if I remember my old bio texts correctly, in humans it would be for converting carbs to ATP and the back and forth switch between sugars and fats. I think nuclear DNA codes for the glycolysis metabolic pathway rather than the mitochondrial DNA, but I'm foggy since it's been a while.

Carbs would be fully coded for in the chloroplast DNA or main line DNA of plants since they produce the carbs. It's not really a surprise to be missing code for a thing you don't produce but just use. The factory doesn't need to have blueprints of a fuel refinery to burn gas.

Minerals is also a red-herring to put in there since those aren't produced they are absorbed and used in other process.

 

Carbohydrates aren't coded in DNA, only proteins are. There's at best a very indirect relationship here: genes code for enzymatic proteins, which are involved in carbohydate metabolism.



#47 Dubbelosix

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Posted 25 June 2019 - 01:06 PM

Our ability to process things are certainly coded in genes... otherwise lactose intolerance would not exist. So try again.



#48 Dubbelosix

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Posted 25 June 2019 - 01:07 PM

Well excuse me! You're criticising me for being unscientific, and are then leaping from organismal developmental morphology to cosmic consciousness and then to humans as giant quantum machines? Perhaps you should leave this thread and start one of your own on those topics, since they don't belong here. 

 

Life, the ability to produce life, is not exclusive here on Earth, it applies on cosmic scales.



#49 GAHD

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Posted 25 June 2019 - 01:34 PM

Since I took up a career in IT after studying biology, I know about data compression too: the thing is that it needs a (de)compression algorithm and mechanism that do not exist in the DNA transcription process, which is a simple one-to-one mapping of codons to amino acids. That's why I quote the pictures in Gray's anatomy in bitmap rather than jpeg (though both are arbitrary, since the genome clearly does not contain pictorial information).

 

And I did apply data compression principles in my calculations: I recognized that to place 40.000 billion cells of 200 types does not require 40.000 billion * 200 bits of information due to the repetitions present. Just like in image compression, this massively reduces the amount of information required - just still not enough to fit into the genome.  

That reads quite like a filibuster to me. For one, Ribosome and Vault Oraganels would take up parts of that function. The creation of those tools is coded for in...? That's where the compression and decompression comes into play. It's again not a full image problem (which needs massive data), but a booting one. Much like getting Pi to n decimals takes a lot of storage...or just computation based off a small formula as needed.

Carbohydrates aren't coded in DNA, only proteins are. There's at best a very indirect relationship here: genes code for enzymatic proteins, which are involved in carbohydate metabolism.

and yet... https://www.openplan...ate-engineering


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#50 exchemist

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Posted 25 June 2019 - 02:31 PM

Carbohydrates aren't coded in DNA, only proteins are. There's at best a very indirect relationship here: genes code for enzymatic proteins, which are involved in carbohydate metabolism.

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


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#51 Dubbelosix

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Posted 25 June 2019 - 03:27 PM

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

 

Sure, there is a system-environment connection. A cell responds to its environment and will modify over time. To think that the cell miraculously comes to know its environment, is nothing but hocus pocus, its basic evolution.





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