6
   

Biological organisms are [i]primarily[/i] Software Defined Lifeforms. - Yes or No?

 
 
Aurora Maybe
 
  1  
Reply Fri 7 Sep, 2018 04:59 pm
There's an app for that.

Oh wait, you said biological organisms...

*type* *delete* *type* *delete*
Leadfoot
 
  1  
Reply Fri 7 Sep, 2018 05:01 pm
@maxdancona,
Quote:
Farmerman and I seem to disagree with each other on whether this is a biology thread, or a software thread. Wink It is like we are discussing two completely unrelated topics.

... I guess that is the point.

Bingo. If we can’t fluidly move between the two, what I was hoping to discuss can’t happen.
0 Replies
 
Leadfoot
 
  1  
Reply Fri 7 Sep, 2018 05:08 pm
@farmerman,
Quote:
try to focus in pn the issue of "how can I prove my point"?

I would welcome that

Good. As I said in a previous post, that is part of what I’m hoping to learn. Obviously, so far I suck at it. This paper could take awhile.

So what would you point to as the problem. You mention my 'passive agressive style' but I’m not sure what you mean by that. Can you give me an example.
0 Replies
 
Leadfoot
 
  1  
Reply Fri 7 Sep, 2018 05:12 pm
@Aurora Maybe,
Quote:
There's an app for that.

Oh wait, you said biological organisms...

Software alone can’t do it. Your iPhone must have an especially strong vibrate function.
Aurora Maybe
 
  1  
Reply Fri 7 Sep, 2018 05:52 pm
@Leadfoot,
Leadfoot wrote:

Software alone can’t do it. Your iPhone must have an especially strong vibrate function.

Software and mindfulness.
Leadfoot
 
  1  
Reply Fri 7 Sep, 2018 06:07 pm
@Aurora Maybe,
Well you got me. That is the most important sex organ.
Olivier5
 
  0  
Reply Sat 8 Sep, 2018 01:29 am
@Leadfoot,
Quote:
It translates the copied code (just like in a computer) but it makes absolutely no changes to the original copy. 

Pluricellular organisms constantly tweaks and edits their own DNA.

Why do you think a skin cell is different from a liver cell, itself different from a neuron or a blood cell? Because their DNA has been tweaked so that certain genes get expressed and others not.

In the case of red blood cells, the DNA has been removed entirely. And them red blood cells keep trucking without any DNA... How do you reconcile that with your little metaphor? The hardware gets rid of its software and keeps on working???

How do you think your immune system is able to produce radically new antibodies to control entirely new pathogens? It's not because your DNA includes a library of all possible viruses and bacteria out there and a liust of efective antibodies to use against them (that would be impossible since pathogens keep mutating). Simply, some specialised cells of your immune system actively mutate their own DNA in a process aptly called "somatic hypermutation" to produce random new DNA code, as a way to produce random new antibodies. And when one new antibody is found to work on the pathogen, the whole system then mass-produces it. Your immune system is a sort of miniaturized Darwinian evolution.

Life is more amazing than you seem to think. It's never simple, never straightforward or unidirectional. There are feedback loops all over it, and this is another one: DNA shapes the soma, which in turns shapes DNA. A two-way street.

Olivier5
 
  0  
Reply Sat 8 Sep, 2018 02:31 am
@Olivier5,
In front of this amazing, mind-boggling complexity of biology, we can react in several ways. We can say:

1. "I don't care why or how life emmerged. It exists, and that's good enough for me." But then, we're left without an origin story.

2. "Some god or alien race must have designed it." But then the question arises: "who designed our designer?"

3. "It's just some chemistry trick." But then, how come said chemicals can succeed or fail, live or die? Chemicals don't technically 'die'; they just break down. They don't end up exchanging their ideas about themselves and evolution on an internet board called able2know either. Something radically new happened with life.

4. "Science, not religion, has revealed this amazing, splendid complexity of life. In the future, it will keep shedding more and more light on the question of the origins of life, until a satisfying fact-based answer is found. Or not, but in any case we keep trying to understand this thing rationally."

I see no problem with the latter option.




farmerman
 
  1  
Reply Sat 8 Sep, 2018 04:01 am
@Olivier5,
I can live with that as a decent basis for understanding the origins. However, I still isistant that the chemistry of pre life almost has nowhere to go but arrive at life via many simple hemical teps.
Of course I have no idea how, but thats the entire point of this thread, nobody really does.

The evidence for life on this planet is a story where very a long period of time was needed to accomplish the first tiny steps, whherein things like cell walls, energy tranformation, and reproduction are only guesses today. After several billion years, due to a "friendly eH/Ph environment and ample oxygen, organisms ,from the late preCambrian through the Triassic(about 400 million years) evolved into all the phyla we see today. We have pretty good evidence and ideas how that happened and under what conditions.
Using the evolution of the phyla as an example of how "opportunistic" and disjointed all this evolving represented (mostly because our planet was never a very stable platform where lif could lazily putz along. Instead there were severl mass extinctions that presented critical decision points that can be interpreted through modern scientific methods(mostly because the "code of life" that resides in our cells has left remarkeable evidence of past episodes that seem to reaffirm this opportunistic helter skelter "invention" of new life forms that successfully reproduce and populate the changing terrain.
We all know that all biological life(based on its ability to adapt to becoming a truly extra solar-system , intra- universe dweller) will otherwise be snuffed out in a billion and a half years as this planet becomes pretty much uninhabitable.(actually we dont really know with any plus or minus range of accuracy since the calculations may have a big error bar based on what point the criticality of Helium fusion will cause that element to "light up')

We sorta know the end of this story and its all dependent on the physics of fusion energy kinetics .


The components of all the proteins , nucleotides and nucleosides are, to biochemistry, easily understood "blocks" in the structural wall of genetic material. With that in mind, Im more amazed at how fucked up our genetic chemistry i, how we as a species LACK so many of the physiological simple minded tools like GULO genes wherein theyve become so overmutated only in primates that , if it werent for vitamin C our diets , wed have gone extinct from scurvy, the story book is full of the trail left in the relict genomes of "pseudigenes" (most all of which , though heavily broken down, still remain as evidence in our genomes as to how erratic an "intellient force" could have been.

I think D Fairbanks wrote the book on the interpretive genetics of the "mistakes" that reside in our genomes and how these belie the possibility of a designer.
So, if life is a computer code, not only does it write itself as its being run , it continually drops huge piles of its accumulated code without any apparent corrections. I think Olivier and Monterey jack can come up with manymore of these apparent mitakes that make the computer code analogy a kind of logical tautology. Im not sure , but Ive always had computers crash based on assaults on their anatomy, not from "randomly re-edited software" while I was on line. Usually it could be fixed or at lleast transferred to a new unit which, like a robotic arm, would carry-on like a clone.
I dont think life does that, but I cant be sure about stuff like ants,who, once pupated, each seem to instinctively know their specific function. Thats sorta puter-like. But even ants have opportunistically evolved new forms within our lifetimes.





Olivier5
 
  1  
Reply Sat 8 Sep, 2018 05:32 am
@farmerman,
Quote:
the chemistry of pre life almost has nowhere to go but arrive at life via many simple hemical teps.

Not sure the steps were that simple but yes, the primeval soup had nowhere else to go than up i.e. towards synthesis of more and more complex stuff.

Whether it happened on earth or elsewhere is another question.

Quote:
the story book is full of the trail left in the relict genomes of "pseudigenes" (most all of which , though heavily broken down, still remain as evidence in our genomes as to how erratic an "intellient force" could have been.

I agree with that too. The paths that evolution took were taken at random, not designed. They're just too messy.

But then, a really smart designer would not design a system that tequires its constant maintenance and intervention to just move along. A real smart designer would build a low-maintenance system that can grow and evolve all by itself, without bothering the designer all the time... :-)
farmerman
 
  1  
Reply Sat 8 Sep, 2018 09:14 am
@Olivier5,
I didnt mean expressly that were dealing with 1st grade simple chemical variants but the fact that we can reconstruct most cell walls via fatty acid polymers and complex esters and the nucelic acids (all of em) are based on purine or pyrimidine chains.

Some of the same **** we see in star spectra.
Leadfoot
 
  1  
Reply Sat 8 Sep, 2018 10:03 am
@Olivier5,
Marvelous stuff Olivier, this is more like it. There are arguments counter to the OP, it was starting to sound like the opposition had nothing but philosophical issues. You are the first to bring a factual argument.

Quote:
Leadfoot Quote:
It translates the copied code (just like in a computer) but it makes absolutely no changes to the original copy. “


Olivier replied:
Pluricellular organisms constantly tweaks and edits their own DNA.

Why do you think a skin cell is different from a liver cell, itself different from a neuron or a blood cell? Because their DNA has been tweaked so that certain genes get expressed and others not.


You are confusing gene expression like in the early blastula stages after fertilization with DNA modification. This is in addition to the 'modification' that occurred during fertilization when the two decks of software were shuffled. That isn’t true DNA modification, only random selection of preexisting traits.

If what you are claiming we’re true, cloning wouldn’t be a thing. Do you remember the first cloned animal (Dolly the sheep)? The cell they cloned a sheep from came from the skin of another sheeps udder. In other words, most all your cells contain the entire software suite needed to build your body. True of all organisms

Quote:
In the case of red blood cells, the DNA has been removed entirely. And them red blood cells keep trucking without any DNA... How do you reconcile that with your little metaphor? The hardware gets rid of its software and keeps on working???


Here you bring up an excellent argument. Exactly how and why red blood cells are enucleated and why production of this particular cell type is done by a separate mechanism is a good question. One reason is obvious, they would not be small and flexible enough to fit through capillaries if they had a nucleus. It adds to the complexity of how such a mechanism and strategy would arise by evolution.

Oxygen transfer in red blood cells (RBCs) still indirectly requires software. The transfer mechanism (Hemoglobin) is a protein (a protein is a molecular machine) that was manufactured by a software driven process. Proteins have limited lifespans and so RBCs only work for a matter of weeks. So you could look at RBCs as not really a cell. It is just a packet of proteins. Calling it a cell is probably a misnomer when looked at this way.

Quote:
How do you think your immune system is able to produce radically new antibodies to control entirely new pathogens? It's not because your DNA includes a library of all possible viruses and bacteria out there and a liust of efective antibodies to use against them (that would be impossible since pathogens keep mutating). Simply, some specialised cells of your immune system actively mutate their own DNA in a process aptly called "somatic hypermutation" to produce random new DNA code, as a way to produce random new antibodies. And when one new antibody is found to work on the pathogen, the whole system then mass-produces it. Your immune system is a sort of miniaturized Darwinian evolution.

This is interesting. I have not studied the immune system very much so I can’t respond with any authority right now. But just based on pure reason and gut feeling for the math, I can predict that there are serious flaws in your argument here. If a mutation is what Darwinian evolution says they are (accidental random changes) then the process you claim is happening would take millions of years (like evolution?) not the 7 to 10 days it’s taken me to get over this miserable cold I just got over.

So let me test the predictive power of my perspective. I’ll bone up on the immune system and come back to this argument.

Quote:
Life is more amazing than you seem to think. It's never simple, never straightforward or unidirectional. There are feedback loops all over it, and this is another one: DNA shapes the soma, which in turns shapes DNA. A two-way street.

Then again, it might be more amazing than you think. It’s certainly more complex that what science currently knows. I’ve never said it was simple. I'm saying it’s more complex than anything that could happen by chance. Even at the cellular level, science does not currently have a clue as to how the first one came about, just guesses.

I know you are talking about biology at a higher level (animal) which complicates the basic issue, that’s why I suggested we talk about it at the single celled level to make discussing it easier. It’s plenty amazing and complex even there.

But these are really good arguments, keep it up.
Leadfoot
 
  1  
Reply Sat 8 Sep, 2018 10:36 am
@Olivier5,
The quote from Wikipedia below is in response to the 'two way street' you mentioned for DNA modifications. They even call it 'central dogma' and it says it’s a one way street'. There is no internal feedback capable of making changes. All you got are evolution's random mutations.

If there was an actual mechanism inside the organism that made intelligent choices about what genetic changes to make, I would gather up my marbles and go home. No further proof of 'this couldn’t be a result of random ****' would be necessary. Yes, I realize you could easily come back and say that I'm completely wrong and that we are now making intelligent changes to DNA and since we are the result of natural causes, the feedback loop is complete.

It all depends on how far you can stretch your ability to believe what random chance and processes can do.

Quote:
The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system. It is often stated as "DNA makes RNA and RNA makes protein,"[1] although this is not its original meaning. It was first stated by Francis Crick in 1958:[2]

“ The Central Dogma. This states that once 'information' has passed into protein it cannot get out again. In more detail, the transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein may be possible, but transfer from protein to protein, or from protein to nucleic acid is impossible. Information means here the precise determination of sequence, either of bases in the nucleic acid or of amino acid residues in the protein. ”
— Francis Crick, 1958
and re-stated in a Nature paper published in 1970:[3]

Information flow in biological systems
“ The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred back from protein to either protein or nucleic acid. ”
Leadfoot
 
  1  
Reply Sat 8 Sep, 2018 11:17 am
@Leadfoot,
I love this qualification of 'information' in Crick's Central dogma I posted earlier. He even puts the word in quotes so you will not think he is talking about real information, it’s just the term they use for “precise determination of sequence”. As I said earlier, the materials used to encode the information is irrelevant.

Quote:
Information means here the precise determination of sequence, either of bases in the nucleic acid or of amino acid residues in the protein. ”


I could make the same claim about a complex piece of software. It’s just a 'precise determination of sequenced' magnetic bits on a disc, with no indication of any intelligent intervention.' But if I did you could rightfully say I was a complete loon.

This complete avoidance of the meaning, if not the unavoidable word (because there is no other word for it) exposes the philosophical bias. He is saying it can't be information because the only source of information is an intelligence. So he is forced into ludicrous euphemisms like 'precisely determined sequences'.

it is the precisely determined sequence that is at issue. Random chance does not precisely arrange things to convey information.
0 Replies
 
maxdancona
 
  1  
Reply Sat 8 Sep, 2018 11:19 am
@Leadfoot,
This thread started out as slightly amusing diversion. Now it has become just another religious guy claiming to disprove established science.

You kids have fun. I have been in far too many of these threads... they all end up the same.
Leadfoot
 
  1  
Reply Sat 8 Sep, 2018 11:24 am
@maxdancona,
Show me one piece of science that I have tried to disprove or shut the **** up.

(Note to farmer - is this an example of what you mean by my passive agressive behavior?)
0 Replies
 
Aurora Maybe
 
  1  
Reply Sat 8 Sep, 2018 09:05 pm
@Leadfoot,
Apologies for briefly hijacking the post.
Twisted Evil
Olivier5
 
  1  
Reply Sun 9 Sep, 2018 02:33 am
@Leadfoot,
You keep misunderstanding what I (and others, including Crick) say, on purpose I suspect.

I never said that proteins were transcribed into DNA. Try and focus.

It's a two way street in the sense that the soma currates the DNA, suppresses the expression off certain genes, enhences others', mutates DNA at random to produce antibodies, etc.

Life uses DNA as a recipe book, it is not slave to its recipe book.
Olivier5
 
  1  
Reply Sun 9 Sep, 2018 03:46 am
@farmerman,
Yes, the building blocks are easy to make, and an RNA world seems plausible to me as a way to explain the emergence of the structure. I'd love to see attempts at reconstructing an RNA world in a tank.

The central question is statistical / mathematical: how much time is needed for useful (and idealy self-replicating) combinations of nucleic acids to emerge randomly? Seems to me there wasn't enough time for that to happen only on earth, reason why I see early life as more of a cosmic thing.

0 Replies
 
Olivier5
 
  1  
Reply Sun 9 Sep, 2018 04:51 am
@Leadfoot,
Quote:
You are confusing gene expression like in the early blastula stages after fertilization with DNA modification. 

DNA can be chemically modified (methylation for ex.) as a way to stop its expression. The underlying code is not modified, and is still retreivable after de-methylation, but another, higher-order code now superseeds its expression, like a tag saying : "don't read this part". That tag has been affixed there on the DNA by the body of the cell, often under instruction by yet another biological language: the hormonal system. So it's a two-way street of action-reaction from DNA to the broader organism, a dialogue between them.

Quote:
Red Blood Cells

The case of red blood cells illustrates why DNA is not functionally equivalent to DNA: a computer cannot operate without a set of instructions called 'software'. But a cell can operate for a while without its DNA. DNA ain't a code to operate the cell; it's a set of instructions to repair it, a recipe book of proteins. So when a cell needs a specific protein (e.g. current stock is damaged and depleted) it can 'read' the corresponding recipe on its DNA and synthetize the proteins it needs.

Quote:
If a mutation is what Darwinian evolution says they are (accidental random changes) then the process you claim is happening would take millions of years (like evolution?) not the 7 to 10 days it’s taken me to get over this miserable cold I just got over. 

A mutation needs not be 'accidental'. If you expose an organism to highly radioactive material for a long-enough time, the DNA in its cells will be affected randomly by many mutations, but that is not what I would call 'accidental'.

In the case of the immune system's somatic hypermutation, the mutations appears to be induced by editing a very specific loci of the DNA of B cells randomly by error-prone enzymes. It's done simultaneously by many B cells so the process may yield as many antibody trials as B cell made per day, probably millions during an infection.
 

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