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

@maxdancona,

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1. Cellular process are not anything like a processor.

That's just an assertion, not counter argument.

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2. Evolution (which would be the process of programming) is certainly not deterministic. Nor would an alleged God be deterministic (if you don't believe in evolution). DNA is not deterministic either, organisms with the same DNA (aka twins) end up with differences. Transcription is certainly not deterministic. Reproduction is not deterministic. I have three kids with the exact same parents.

Technically, evolution is not the programmer according to the theory. It says nothing about that. Evolution is only the blind editor who jiggers the program he received from an unknown source. Evolution just says that once in awhile the programmer (blind chance) comes up with a winner.

True, the results are not carbon copies other than the basic body plan. Mostly due to the mixing up two recipes for the cosmetic details. I would love to get into psychological differences and why they exist but we can’t even agree on these obvious similarities between DNA and software. The nature of consciousness will be for another day.

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3. I don't know what you are talking about in your point about memory providing a deterministic "state". Software can be represented by a state machine, there is nothing similar in biology.

Not sure I’m following you here. My example of determinism in biology was the exact same place (address) in the chromosome (in the BRACA 1 gene I think it is) being responsible for breast cancer. It is pretty determinist but we don’t know all the factors, but we know it’s directly related to this particular gene error and location. Is that not true?

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4. You made this claim up... nobody that I know of makes this claim; "This is exactly the claims made for evolution, this biological hardware architecture is infinitely variable (programmable)."

If DNA were Turing complete, then it could be used to define anything... for example an automobile. This is not what biologists say at all.

No, evolution says we all have a common ancestor. We all share this DNA defined (software defined) architecture. A small deer can easily be reprogrammed to be a whale. That is the claim. Unless you want to negate evolution, I did not make it up.

You are stretching Turing's statement to absurdity. But indirectly making my point. Turing was not claiming the software could BE anything, just that it could control anything that you have the physical means to do or perform any information based function imaginable.
Software IS used to control virtually everything in my latest car. The same computer and software in my car could be used to control a washing machine if one wanted to.

There is Software being written to control biological muscle functioning in paralyzed people. Crude right now but it is possible.

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@farmerman,

from Molecular Biology of the Cell 2000

STRUCTURES OF THE DEVELOPMENT OF THE PRE RNA WORLD

Purines and pyrimidines occur in Isua Formation rocks which are several Billion years old and give us indiications of earliest life because the CARBON is all C12

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@Leadfoot,

Let's try this a different way. I have been involved in both process; creating a new program and starting a new DNA based life.

To create a new program, I generally start with what is called a "functional spec" which is a set of features that the new program should perform. This specification is often not as well thought out as it should be, and a frustrating part of my job is chasing down stakeholders to figure out what is important.

Once I have the requirements, I create a design. Often this is a diagram that I share with other people for their approval. Sometimes no one cares about my design, and I just use it to guide myself.

Then I sit down and start coding, according to the design. Sometimes the design changes while I am coding... but I generally have a very good idea of how the finished product will work.

After the coding is finished, I test (actually I write a lot of tests as I am coding). But the coding isn't finished until the tests are all written, run and pass successfully. If something doesn't work according to the requirements, I consider that a bug... and I go back into the code and fix it.

The process for starting a DNA based life is quite different. I knew I wanted a kid, and I knew it would be human. I didn't have any specific requirements, or any control over the outcome. My kids were all planned... but the process was quite spontaneous... me and my wife had a chemical reaction in our brains that led us to become aroused. After fooling around, my penis became erect and her body also responded. The process involved just doing what felt right until I ejaculated inside of her.

This ejaculation put about 100 million sperm into the reproductive system of my wife, all unique... most of which were capable of starting a new life. The one that made it was largely driven by chance.

The life the started was based on whatever DNA happened to be in the sperm and egg that started it. There was no design, no functional specification and no way to control the outcome.

I am very happy with the outcome, and I greatly enjoyed the process.... but it is absolutely nothing like the careful, methodical process of programming.

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@farmerman,

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Jut cause DNA LOOKS like a barcode diesnt men that its a done deal .

I haven’t mentioned how it looks. You are the one talking about natural structures looking like DNA that are not. You claiming that nucleotides started jumping on the crystal helix one day and life was born?

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tarting with the fact that lifes 'ladders of information are tetradecimal not binary.

Holy ****, how many times do I have to say that it’s the information that is significant, not the material or encoding scheme. Have you read all the articles out on encoding binary data onto lab grown DNA in 'quadary'. Quadary is twice as space efficient at storing data and software. No matter, The difference is irrelevant to the argument.

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till we must define an example of how such systems as you propose even act .

What did life do before the "bar code you propose" existed Remember life predate RNA and DNA. Thats a fact.

What do you mean? The examples are every lifeform you've ever seen.

We have not established that non DNA life forms existed. RNA world is just a theory and has many technical problems as I think you know.

We can’t go back and prove pre DNA life but the subject is what is the life we see in front of us now. Is it Software Defined or not, that is the question. So far you haven’t shown one reason not to make an easily seen comparison.

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@Leadfoot,

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No, evolution says we all have a common ancestor. We all share this DNA defined (software defined) architecture. A small deer can easily be reprogrammed to be a whale. That is the claim. Unless you want to negate evolution, I did not make it up.

You are stretching Turing's statement to absurdity. But indirectly making my point. Turing was not claiming the software could BE anything, just that it could control anything that you have the physical means to do or perform any information based function imaginable.

I am not stretching the definition of Turing-complete at all. It is clear that evolution can create a deer, because it did create a deer. This doesn't even mean that every conceivable animal is possible. There are no deer with wings and no evidence that such an animal is possible to reach using evolution.

I program in Java (a Turing complete language). I am currently using it for an AI system based on understanding human speech. The same language is used for flight simulators, for games, to make robots walk, and run elevators. I can also make any combination... I can insert speech recognition into an elevator.

Software is Turing complete in a way that DNA is not. I can use the same language to understand human speech that I use to create an airplane.

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@maxdancona,

Come on Max, don’t you see where the breakdown in your comparison is?

In the first case, you are the programmer.
In the second, you're just a user.

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@Leadfoot,

I am the one ejaculating... spraying 100 million sperm, each with unique DNA, at random toward an egg (which also has unique DNA). If the programming is the DNA, it is my sperm and the mothers egg that create the new DNA. The sperm that succeeds in fertilizing the egg determine the "programming" of the result. I do have a part in determining the result of the process... but only in choosing the egg donor.

Who is the programmer in this case? And exactly what is his or her role in this process?

I don't see how the programming metaphor fits at all. There is nothing in programming that involves spraying 100 million possible outcomes and just accepting the one that happens.

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@maxdancona,

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I am not stretching the definition of Turing-complete at all. It is clear that evolution can create a deer, because it did create a deer.

So you drive a java car do you? My C++ can kick your Java’s ass. Sorry.

Not sure how those two sentences are related but the second one starts with an assertion and ends in circular logic. Nothing I can get into there.

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@maxdancona,

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I am the one ejaculating... spraying 100 million sperm, each with unique DNA, at random toward an egg (which also has unique DNA). The sperm that succeeds in fertilizing the egg determine the "programming" of the result. I do have a part in determining the result of the process... but only in choosing the egg donor.

Who is the programmer in this case? And exactly what is his or her role in this process?

I don't see how the programming metaphor fits at all.

For the software comparison, A user can load a piece of software on disk into any computer he or she wants. That’s the only choice they’ve got at that point. Requires no programming chops at all.

The only thing I can say about your mating analogies and how it relates to software, is that we know you are not the programmer and you did not code that app.

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@Leadfoot,

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We can’t go back and prove pre DNA life

ignoring all the chemical system is like saying "we can only argue life chemistry by avoiding it"
Enjoy your masturbatorium

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@Leadfoot,

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You claiming that nucleotides started jumping on the crystal helix one day and life was born?

Youre being purpoely obtuse. The structures of more and more simple pre biotics show remarkable similarity to helical COmbined Oxyhydroxide/carbonate/Siderite xlls. To me (and to many scientists who work this street daily). Similarity of shapes can precede functional groupings and can be reproduced in lab xperiments. The Banded iron and clay matrix helicies seem to follow Woese' and Margulis own concepts of lateral transfer of functional groups and yes, Life can appear. The same groupings that are represented by purines and pyrimidines (Chemically produced in extreme reducing nitrogen and iron hydrous environments) also presents a "chemical map" of what other functional groups could be wrt life sustaining polymers.

You dont seem to be discussing this honstly. Im willing to go back and reconsider the chemistry but your just demanding that we take your puter anlogy as the only thing youre bringing up. YET, might I again restate with a bit of rustration, you fail to get ahold of what that all has to do with the chemistry of life.
This is a debate (you said), but youre making it a sermon.

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@Leadfoot,

If DNA is a programming language, sex is the way new programs get written. It's your metaphor, explain who is the programmer, and how does he or she ensure a specific "program" gets written. If someone loads the same software on multiple computers they remain identical in function and code. I have had multiple children, the have different DNA and are quite different.

This metaphor doesn't work even with the most basic questions.

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@farmerman,

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Leadfoot Quote:
“We can’t go back and prove pre DNA life”

ignoring all the chemical system is like saying "we can only argue life chemistry by avoiding it"
Enjoy your masturbatorium

That was a leap.
Point blank - are you saying we know the first lifeform that was capable of reproduction and evolution?
If so, at least give me a reference because honestly I’ve never heard of one that makes this claim that did not also admit that it was speculation based on a lot of guesses. They ALL end in 'we don’t know how life started'. Trust wiki on that?

But in any case, I’m not making an argument about archae, I’m talking about what is here today. It looks like Software Defined Lifeforms to me.

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@maxdancona,

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If DNA is a programming language, sex is the way new programs get written.

I think my analogy of inserting the disk or thumb drive into the slot is infinitely more apt than yours. I can’t concentrate well enough to program during sex.

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It's your metaphor, explain who is the programmer, and how does he or she ensure a specific "program" gets written.

That’s not the question I set out to answer. You have to answer the question of 'what am I seeing here' before beginning to answer the question of where did it come from. We can tackle that one after agreeing about what it is.

Like that'll ever happen.

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@Leadfoot,

I believe that your metaphor breaks down with the simple question. Your claiming that biology is software... yet you are unable to explain who the programmer is, nor what the programmer does to arrive at the desired program.

The metaphor doesn't work at all.

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@Leadfoot,

archaea exit today

The human coding genome contains 20 to 25 K coding genes. The same genome contains about 20K pseudogenes and the entire genome is 3.5 Billion base pairs totl. Turned off genes are those that we will use to reanimate dinochickens or wooly mammoths.
lso the pswudogens and STR's let genes be used as an evolutionary CLOCK wherein we can look at paleo data of a species and compare it to its adaptational history and something that, once a mutation or recombination error(or other tricks). We can map its response as Nat selection (obviously since it is alive today)

PS my comment erlier about pseudogenes was from Fairbanks Relic of Eden

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@Leadfoot,

You used the phrase '...going where science leads..' somewhere above which alludes to the exploration of analogical models. But the computer analogy here has far less credence than say the heliocentric model used in the original study of the atom (which even incorporated elliptical orbits in an attempt to account for differential speed of orbiting electrons) due to its unscientific ID assumptions. The fact that we can talk about genetics in programming terms is no more significant than the semantic shorthand we use in phrases like 'electron orbits' or 'shells'. Such terminology is functional for a limited range of study of a complex system, but cannot be applied to characterise the whole system.
There is subsequently a lot obfuscating word salad here ostensibly about 'science' which is actually about 'ID'. That is all that matters as far as your OP is concerned. The fact that I used to teach kids about Archemedes Principle (upthrusts in a dis placed fluid) using phrases like 'the water molecules don't like being pushed out of the way and try to get back' was merely a pedagogical device used to communicate with children. Your computer analogy has little more status.

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@maxdancona,

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I believe that your metaphor breaks down with the simple question. Your claiming that biology is software... yet you are unable to explain who the programmer is, nor what the programmer does to arrive at the desired program.

The metaphor doesn't work at all.

It’s not a metaphor, it’s a direct comparison.

This is Bill Gates statement on the subject:
“

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DNA is like a computer program but far, far more advanced than any software ever created.”

There are also thousands of scientists in biology who disagree with you, even though many of them are uncomfortable with the same implications you are. They are able to separate the question of what DNA is, from what seems like abject fear of the implications. It is this illogical resistance to seeing the comparison that interests me as much as the biology.

But I thank you for a good and honest discussion. It was refreshingly free from personal attacks.

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@fresco,

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You used the phrase '...going where science leads..' somewhere above which alludes to the exploration of analogical models

The actual phrase I used was 'Science is supposed to follow the evidence where ever it leads.' When science stops following the evidence because of a philosophical position, it is no longer science. The idea that something can’t be true because someone can’t accept what the clear evidence might suggest is a philosophical error in addition to scientific error.

I understand what you are saying about invalid analogies but as I told Max, I’m not putting the OP forward as an analogy or metaphor, I stated it as literal fact. What I want are factual arguments that show why this is not the case, not personal philosophies that are uncomfortable with the implications.

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@farmerman,

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archaea exit today

No argument but the archaea alive today are DNA based Lifeforms and also fall under the claim made in the OP.

So Can you tell me why that is not true?

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

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