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

@Olivier5,

Should read: "DNA is not functionally equivalent to computer software.

@Olivier5,

Another trick in which the immune systems plays with DNA is class-switch recombination. It looks like this at DNA level:

https://upload.wikimedia.org/wikipedia/commons/b/b3/Class_switch_recombination.png

The DNA strand is effectively edited by proteins cutting out a segment.

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@Olivier5,

In front of this amazing, mind-boggling complexity of biology, we can react in several ways. We can say:

Quote:

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.

That is for the incurious. It describes a lifeform that I can’t relate to in any way. I'm not sure it describes any human. If they really exist, they don’t need an origin story.

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

That is at least one leap to conclusion. First we would need to look at life and determine what it is, if we're curious. I am, that’s what we’ve been doing.

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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.

We know how chemical reactions proceed naturally. We have no idea how they came to life, but it was not through any natural process we know about. Even our most intelligent scientists have tried their best to get inanimate chemicals to make simple life forms 'naturally' and failed every time. If it’s a trick, it’s a pretty good one.

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
This is ironic.

Me either. Science has already revealed more than we can explain from natural causes. I hope it will be noticed that it is exactly the things science has discovered that I’m using to argue for the equivalency of DNA and software. I have not used one argument in favor that is not a fact discovered by science. If anyone can refute that, please do.

Asking who the programmer is is not a refutation, it is a dodge, an act of intellectual cowardice, an admission that you have no argument. Thank you for not joining the crowd doing that.

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@Aurora Maybe,

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Apologies for briefly hijacking the post

None needed Aurora.

This may sound like a thread for bio geeks but the question could be restated as - Could Shakespere's play 'Hamlet' have written itself when you stir a giant bowl of 'primal' alphabet soup? You have ~14 billion years to try.
So far I’m the only one betting on 'no' .

It boils down to a problem of probability. What are the chances? They are not zero so either answer is possible. I’m just going with the odds. The other guys must feel lucky.

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@Olivier5,

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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.

You are apparently using 'soma' to describe epigenetics, a new field that is only in the infant stage of being understood, which is actually true of biology in general but especially true of epigenitics. If you google the terms 'soma curates DNA' you get a bunch of references to religious groups. Yes epigenetics regulates gene expression, but it Never alters either DNA internons or other code segments.

I call BS on this. The ONLY source of DNA change (other than sex mixing two sets) is random mutation. All your references to self editing of DNA are bogus until you can cite a reliable source for your claims. I have always done that when requested.

And yes, life is a slave to its DNA. The recipe tolerates very little alteration. Change it only a tiny bit and you get birth defects, disease or cancer.

As farmerman once brilliantly put it,
You are only a delivery mechanism for your genes.
Your every action is controlled by genetic software to spread itself. It’s such a beautiful picture of life!

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@Olivier5,

Quote:

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.

This, this right here is what I’m trying to understand.

If you really understand what you are saying here (and I think you do) and you were knowledgeable about the software world, you would be shocked to realize you have exactly described the hirearchcacal (sp?) structure of modern software. I mean, how many levels of abstraction do you think random chance can accomplish in 4 billion years?

But you apparently don't know the software world, won't take my word for it and the other software heads either don’t understand your bio language or don’t give a **** about the argument.

Anyone else here speak both languages?

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@Leadfoot,

Ok. This is fun. Let's summarize Leadfoot's argument.

1) There is a God... Therefore there is order in Nature.
2) DNA is a complex part of Nature... therefore there is order in DNA
3) Computer programs have order... Therefore DNA is a computer program.
4) Computer programs are Turing complete and DNA is a computer programs... Therefore DNA is Turing Complete.
5) DNA is complex... Therefore there is a God.

Leadfoot is taking Google, completely out of context, to support his circular argument without having any real understanding of either the biology or the computer science. This is argument by Google, and it is amazing how often people who argue by Google clash with people with real expertise in the field.

But ultimately this is a circular argument that starts with the premise that there is a God, and then twists itself in a circle to "prove" the original premise. In general, an honest education will often bring you in the opposite direction.

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@Leadfoot,

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All your references to self editing of DNA are bogus until you can cite a reliable source for your claims.

I have already done so. Check out 'somatic hypermutation'.

DNA is just a recipe book for proteins. It can be edited (randomly) and gene expression can be modulated by proteins, so in this sense it's a two-way street. Which is to say: there are feedback loops, cause-to-effect relationsips from proteins to DNA.

Can some hardware edit its software?

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@Olivier5,

Quote:

Leadfoot Quote:
“All your references to self editing of DNA are bogus until you can cite a reliable source for your claims.”

Olivier replied:
I have already done so. Check out 'somatic hypermutation'.

DNA is just a recipe book for proteins. It can be edited (randomly) and gene expression can be modulated by proteins, so in this sense it's a two-way street. Which is to say: there are feedback loops, cause-to-effect relationsips from proteins to DNA.

Can some hardware edit its software?

OK, jury is still out on somatic. Still looking at it. I’m predicting that there is a limited data set involved or a random search would not work in the time available. Otherwise it would take supercomputer speeds to arrive at the antibody required by that method.

Still, assuming you have presented an accurate picture, the incorporation of a random search mechanism to develop antibodies to the already complex macro organism of an animal is a trick I don’t believe is statistically likely by evolution in the time available.

In the past I’ve approached the problem of complexity by means of math and been accused of 'using creationist math', whatever the **** that is. You just can’t win when even math is accused of being religious.

“Can hardware edit its software? “

Yes, of course it can. So called AI 'learning programs' do just that. They do it in the same way you have been describing gene expression. Only the feedback loops and the kind of changes are carefully 'curated' by the supervising program (just like that DNA process you described) that originated with intelligent programmers. If computers could not do that, there would not even be such a topic and Stephen Hawking would not have been going around spouting about the dangers of AI. (Not that I agree with his fear)

We could easily simulate random life origin and changes in software as well. We don’t because I think people inherently know it would be futile. We could simulate trillions of years of evolution in minutes and watch its marvels unfold in real time on our monitor screens. If that random process really worked. But it doesn’t work in simulations because the statistical odds just are not there in spite of the theoretical possibility that it could.

(Note, the computer hardware is doing the editing under the control of software, but if you are saying it has to be more direct, the hardware could be designed to do that too, but nobody would fund such an unlikely to succeed project.).

The beauty of software is that you can do anything you can think of that does not violate the laws of physics (limited by physical interfaces of course), just like in DNA based Lifeforms.

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@Leadfoot,

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So called AI 'learning programs' do just that.

This is another in a long list of factual errors... a gross misunderstanding of what "machine learning" means.

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@Olivier5,

Really enjoying getting into immune system, glad you brought it up. Obviously this alone is enough to occupy an entire career and not something I can master in a day. But already I can see the direct similarities.

There are different strategies used in the somatic cells right out of computer technology. It checks for the most likely to occur single polymerase errors (single bit error in computers where parity checking is used) and then multi bit errors where different strategies are used, again just like a computer where Hamming codes are used to correct multi bit errors.

Give me some help here. The thing I’m missing so far is what the somatic cell is starting with as a reference to match unless it is the invading microbe. In which case it must 'suspect' that the enemy is a mutant (damaged) strain of normal DNA. This would then reduce by many orders of magnitude the difficulty of finding a match. I see that would make the mechanism practical. Still, for a process like this to develop and then be incorporated by random process is just mind blowing, even at my novice level of understanding. The more I learn of the science, the less plausible random chance seems.

Many, including you I think, have said that given the laws of ordinary (non bio) chemistry the increase in complexity is inevitable. This is just patently false unless you include biology. Examples like crystal growth, iron combining with oxygen etc are not true increases in complexity, they are just chemistry going to a lower energy state. The question I have is why biology is the sole exception to the law of entropy (on any scale of time less than a billion years). The argument that the stars will all burn out eventually does not satisfy me.

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@maxdancona,

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This is another in a long list of factual errors... a gross misunderstanding of what "machine learning" means.

This is another in a long list of empty posts saying “You’re just wrong!” without a single fact or reference to back it up.

I repeat - Put-up or shut up.

PS: I wrote machine learning programs (engine control software) for 20 years and still tinker with it now.

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@Leadfoot,

I will bite. When you say you wrote "machine learning" programs... what exactly do you mean? I must admit, I am a little skeptical given your aversion to mathematics. Do you know what a Markov chain is? I am a software engineer, and my current project involves using AI algorithms to determine meaning from human speech.

You are impossible to discuss things with you, because reject anything that doesn't fit your preconceived notions. You have people on this thread with more knowledge than you about biology and about computer science... you won't budge from your dogma no matter what we say.

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@Leadfoot,

You are the one who made the bogus claim when you said "AI learning programs do just that". You provided no facts or examples of this claim. I am just pointing out since you did not present a "single fact or reference" to back it up, that your point is bogus.

Tell me about the programs you wrote for machine learning and lets see if you have anything there.

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@maxdancona,

I remember the term mentioned along with state machines, but that’s all that recalls.
Fun triggered memory: My only freelance software gig was to do the machine code for the prototype of the “Ive fallen and I can’t get up” system. Wrote it as a state machine. Got paid $1200 but seeing it on TV was priceless.

If you are doing voice rec. stuff you are admittedly doing far more advanced machine learning than engine control. But the points I’m trying to make only require the basics of computer knowledge and about the same in cellular bio. If it sounds like I’m getting into sophisticated AI stuff, I’m not.

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@Leadfoot,

There is a limit to machine learning on a digital computer that is important in this discussion. Modern machine learning maps a specific type of input to a specific type of output. Our systems can learn a new accent... the input is basically an FFT which represents sound samples as a vector (difficult to explain here, but it is math), the output is phonemes->words->N-grams (a set of multiple words). The most advanced systems can't learn a new human language on their own.

The point is predetermined type of input is mapped to predetermined type of output.... the results are impressive. But, it is just calculating a mapping function. It isn't an analogue of what DNA is doing passing from parent to child (if in this metaphor the program is "written" during the process of reproduction).

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@maxdancona,

Quote:

Our systems can learn a new accent... the input is basically an FFT which represents sound samples as a vector (difficult to explain here, but it is math), the output is phonemes->words->N-grams (a set of multiple words). The most advanced systems can't learn a new human language on their own.

I could have used the same sentence and meanings to describe my own end product. Here we go:

Our systems can learn a new intake manifold. The input is basically a spectrum of engine parameter samples ,position, MAP, temps, etc then does some math and looking at history and the output is a set of parameters meant to keep the mixture at optimum. The most advanced ECU systems can’t learn a complete new engine on their own.

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@Leadfoot,

Good, so you understand that that isn't what DNA is doing during the process of reproduction (when new DNA sequences get "programmed").

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@Leadfoot,

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OK, jury is still out on somatic. Still looking at it.

You are not looking at it. You're just in denial. What else is new? Kling to you pet metaphor and your idiotic designer if you need to.

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@Leadfoot,

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The question I have is why biology is the sole exception to the law of entropy

Rest assured that life abides by the laws of thermodynamics, including the second law.

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

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