Biological organisms are [i]primarily[/i] Software Defined Lifeforms.

@Leadfoot,

No. An affirmative answer implies the existence of a programmer or 'creator'.

There are recent claims for abiogenesis involving the (automatic) principle of 'dynamic kinetic equilibrium', which if valid, would render computer analogies inappropriate except perhaps for subsystems of lifeforms such as neural structures.

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That is exactly LF's intention, to imply a creator, or to use the entirely dishonest and evasive term, intelligent designer. If one were to accept the premise, moreover, it would completely deny any form of evolution, because "software" cannot change itself (unless programmed to do so). Another religionist here has been banging on about algorithms for months now, and this is just a variation on that theme.

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@fresco,

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No. An affirmative answer implies the existence of a programmer or 'creator'.

I must thank you. That is such a beautiful example of classic philosophical error and non scientific approach!

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@Setanta,

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If one were to accept the premise, moreover, it would completely deny any form of evolution, because "software" cannot change itself (unless programmed to do so).

Entirely wrong. Software can be altered unintentionally by some of the very same things that alter DNA. X-Rays, alpha particles, cosmic rays, environmental conditions and copying errors are some. Computers sent into space have to use radiation tolerant components and shielding for this very reason.

Evolution theory is completely compatible with the DNA/software analogy. Actually, there is no need to call it an analogy. They are directly comparable. The only question is whether the mechanism of random errors (with natural selection) could account for what we see in the fossil record.

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@Leadfoot,

No, it is not compatible. As Fresco pointed out, the implication is that there is a "programmer," which is to say, a creator. Computer components on space craft a shielded precisely because software ceases to function properly if subjected to the effects of radiation. To attempt to continue this silly analogy would certain imply that evolution can't take place, because software only functions properly when undisturbed.

Fresco sometimes indulges philosophical foolishness--those are the times when I call him on it. This is not one of those occasions.

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@Setanta,

Again, this beautifully illustrates the disconnect in this type of discussion.

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No, it is not compatible. As Fresco pointed out, the implication is that there is a "programmer," which is to say, a creator.

I’m talking about agreed upon science here. The central dogma of modern molecular biology is about information flow. The comparison to computers and information flow is undeniable by anyone knowledgeable about it. Yes, I’ve asked real scientists.

Phenomena are the subjects of science. They occur independently, regardless of reasoning. Once you or Fresco declares phenomena unreal it is no longer science.

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Computer components on space craft a shielded precisely because software ceases to function properly if subjected to the effects of radiation.

Exactly! But DNA also ceases to function properly when changed by radiation, why do you think that pretty X-Ray technician is wearing a lead apron?

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To attempt to continue this silly analogy would certain imply that evolution can't take place, because software only functions properly when undisturbed.

Are you trying to convince me that biologists don’t all know and agree that the vast majority of DNA mutations (which is a corruption of the original) are negative? They are the cause of cancers, birth defects, etc. The theory of evolution just says that once in awhile one of those mutations will result in an advantage. The very same thing is theoretically true of computer software, unless you are saying that software can never be improved, but that would be silly.

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@Leadfoot,

It is hilarious for you to speak as though with authority about what is or is not science, given your track record here. This is Wikipedia's definition of software:

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Computer software, or simply software, is a generic term that refers to a collection of data or computer instructions that tell the computer how to work, in contrast to the physical hardware from which the system is built, that actually performs the work. In computer science and software engineering, computer software is all information processed by computer systems, programs and data. Computer software includes computer programs, libraries and related non-executable data, such as online documentation or digital media. Computer hardware and software require each other and neither can be realistically used on its own.

This is a definition from Technopedia:

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Definition - What does Software mean?
Software, in its most general sense, is a set of instructions or programs instructing a computer to do specific tasks. Software is a generic term used to describe computer programs. Scripts, applications, programs and a set of instructions are all terms often used to describe software.

The theory of software was first proposed by Alan Turing in 1935 in his essay "Computable numbers with an application to the Entscheidungsproblem." However, the word software was coined by mathematician and statistician John Tukey in a 1958 issue of American Mathematical Monthly in which he discussed electronic calculators' programs.

Software is often divided into three categories:

System software serves as a base for application software. System software includes device drivers, operating systems (OSs), compilers, disk formatters, text editors and utilities helping the computer to operate more efficiently. It is also responsible for managing hardware components and providing basic non-task-specific functions. The system software is usually written in C programming language.
Programming software is a set of tools to aid developers in writing programs. The various tools available are compilers, linkers, debuggers, interpreters and text editors.
Application software is intended to perform certain tasks. Examples of application software include office suites, gaming applications, database systems and educational software. Application software can be a single program or a collection of small programs. This type of software is what consumers most typically think of as "software."

In either case, you are conflating hardware with software, and software is definitely programmed by an intelligence, just as hardware is constructed by an intelligence. Neither Fresco nor I have denied any phenomenon, we have just pointed out the inferences from describing biochemical reactions as "software." Whether or not you like it, the implication is clear, even though you may want to evade it.

DNA, MtDNA and RNA all can continue to function after exposure to radiation, and can continue to replicate, sometimes even correcting errors in the chemical chains. Neither the hardware nor the software of computers can do that. (That was a snotty and creepy comment about "that pretty X-ray technician"--try to act like an adult.)

Have the courtesy to provide an indisputable example of software having been corrupted by radiation which resulted in the improvement of said software.

This is a simplistic and simple-minded analogy, and one which fails.

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@Leadfoot,

Your 'science' is limited and out of date.

'Information theory' is a anthropcentric concept involving 'choice between alternatives'. Biologists such as Maturana have developed non informational evolutionary models with reference to 'systems chemistry' results such as Prigogine's demonstration of the spontaneous emergence of dynamic dissipative structures.

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@Leadfoot,

Leadfoot wrote:

Biological organisms are primarily Software Defined Lifeforms. - Yes or No?

No. Unless you are redefining "software" to apply to biology in some way instead of computers. If you are redefining "software" then I would need to know your new definition before I could address the question.

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Humans have always compared "life" to the latest human technology.

When humans discovered fire (tens of thousands of years ago)... life was fire.
When humans started weaving... life was a thread being spun.
When humans invented the wheel... life was a wheel.
When humans invented metallurgy... life was forged in a furnace.

Now life is a digital computer.

We humans always just take the newest coolest technology we have as a metaphor for life.

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No because living things are all wet, some, like fish, are really wet. If my computer gets just a little bit wet, let alone well wet, it's fucked.

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@Leadfoot,

dont know. But we do seem to have inndications that earliest life was NOT associated with DNA or even RNA. So, we really dont know how the ribonucleic acids were inserted. We do know (from a great statistical evaluation of aqueous mineralogy and oxy hydroxides in early the neoArchean period) that mineral species also "evolved " from earliest oxide and sulfitic states to branch, chain, and more complex mineralogy.
Siderite and Marcasite and Hematites were seen to be following a helical and multihelical state as they grew crystals.
I would really like to know how the initial information was programmed so that life could replicate beyond its earliest forms(remember all complex life, if viewed on a clockface would be less than the last 3 minutes of the clock face.

pre biotic and biotic chemicals really arent that different, so when ammonias led to amines and were availablein abundance, the story of life had a full toolkit.

Is it possible that the"RNA world" hypothesis kicked in only after cyanobacter (or cyano archeobacters ) instituted magnesian /calcian transfer of oxygen that the RNA actually developed .(Sugars and water (requiring ample O2) could have stimulated many kinds of nucleic acids (simple to complex).

I dont know and neither do you.
HOWEVER, in my mind, theres really NO means where DNA (in the Ediacara and post Ediacaran " complex life eras" ) that requires any kind of "Planning or bar coding instruction" to ccomplish any of the gen addition, duplication, or gene abandonment techniques other than changes in environment or mere mistake. Im more inclined to see the evidence that supports such genomic events because in present dqy living forms, we see many genic adaptations and mutations as a result of environmental changes. (Arctic Stickelbacks have modified heolysis genes from the same pile of genes that control blood clotting, and these genes have modified to become a sort of haem "antifreeze" with the only cost a significant drop in haemoglobin so that the stickleback blood is actually clear--This arose when populations of arctic stickelbacks were "trapped" in the high arctic and evolved. The High arctic expanded after onset of the Illinoian/Mindell (I think the date is right). Connecticut River Cichlids (crappie bass) have been trapped behind colonial era dams and have evolved new structures and lifestyles that have been seen in ther genomes.
Today we hve some of the same events occuring in reverse, with Ursus maritimus apparently re-evolving to favor and "turn-on" the pseudogenes that were turned off in the dim past.
All these above were environmental responses.

NOW, when I said "I dont know"the only damn thing I hve no real explanation for is the cellular ribosomes (We know that mitochondria (from work by Margulis and Woese) were free living evolving to parasitic forms to take on structures like falciperal "cysts" .
Im willing to listen on how the ribosome evolved because it , to me, is the closest analogy to a biological "let there be light" tool.

I am fairly convinced from all the evidence that COLLECTIVELY explains "non coded " evolution because we can see the environmental relationships for evolution in living forms and no real COLLECTIVE evidence for an ID world

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@maxdancona,

Very astute.

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@farmerman,

If you want to see how bad this metaphor is, you have to understand how Software works.

1. Software is run by a processor. The process is to take an instruction from memory, to process it, and and write any results into memory.

2. This process is deterministic. I can look at the instructions in memory and tell you with complete certainty what the result will be. I can change the instructions in memory and have completely predictable changes.

3. There is deterministic memory. A value can be written into memory at a specific address. The same value can be retrieved later where it is expected. The "state" (all of its properties at a given time) of a software entity can be preserved and read.

4. Software is Turing Complete. This is a mathematical concept, but basically it means that any software program you can conceive can be created using the language.

5. Software is not self-developing. There has been research on this, but as of today it is science fiction. No one has developed software that is able to develop a new kind of software.

6. Software has programmers. There are people who decide what any piece of software should do. They write the software to work according to a plan. When the software doesn't work the way it is supposed, they go and fix it.

This is not a very good metaphor for any aspect of life.

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@Setanta,

First, I agree with the definitions you quoted and FWIW, I was well paid to design and at times program computers for about 30 years so you don’t have to talk down to me on the subject.

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In either case, you are conflating hardware with software, and software is definitely programmed by an intelligence, just as hardware is constructed by an intelligence.

Whoa there, one assertion per sentence please.
I said biological life is a Software Defined Lifeforms, not that it’s only Software.

It's understood that software requires hardware to run on. The MS program 'Word' is a software defined wordprocessor, that is it runs on a piece of general purpose computer hardware in order to do the job.

We are not there yet but of course there is hardware in DNA based Lifeforms. We first have to establish that genetic information is directly analogous to Software. You can’t simply say it can’t be because that’s impossible because it requires a programmer. It is what it is, if it’s software then we look at the implications after. Otherwise, show Why it’s not Software.

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Neither Fresco nor I have denied any phenomenon, we have just pointed out the inferences from describing biochemical reactions as "software." Whether or not you like it, the implication is clear, even though you may want to evade it.

It sure sounds like you are denying the phenomenon of genetic information being Software. Not for any reason other than that you don’t like the implications. Science is supposed to follow the evidence wherever it goes.

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DNA, MtDNA and RNA all can continue to function after exposure to radiation, and can continue to replicate, sometimes even correcting errors in the chemical chains. Neither the hardware nor the software of computers can do that.

Glad you bring this up because it shows the amazing parallels between computers and DNA based Lifeforms. Computers are obviously not your field so I’ll forgive the comment about computers not being able to self correct errors errors. Look up things like 'parity bits' or 'Hamming codes', these are also directly analogous to the DNA error correcting mechanisms. They’re also an impediment to evolution if you think about it.

So of course DNA can tolerate limited damage, but if it can’t be repaired it’s usually death or cancer.

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(That was a snotty and creepy comment about "that pretty X-ray technician"--try to act like an adult.)

Damn, who knew you were that humorless..

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Have the courtesy to provide an indisputable example of software having been corrupted by radiation which resulted in the improvement of said software.

Sometimes you jump five steps ahead and sometimes you're five behind. Don’t you see where I’m going after all these years? My position is that random changes (mutations) do not result in improvements. It is you who are asking us to believe that they can. I don’t know of one example of that happening in computers in my 30+ years of designing and programming them. I don’t think that happens in Software Defined Lifeforms either.

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This is a simplistic and simple-minded analogy, and one which fails.

So far you have failed to show where or how it fails. But thanks for the support in bring up error correcting DNA/computer data. That was coming up later if anyone was interested.

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@maxdancona,

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If you want to see how bad this metaphor is, you have to understand how Software works.

1. Software is run by a processor. The process is to take an instruction from memory, to process it, and and write any results into memory.

Great post Max. Correct. This is directly analogous to cellular processes. A need for an ATP making protein is sensed. Another protein type is sent to a specific address in the DNA. The instructions for making an ATP making protein are found and copied at that address. The instructions are then transported to yet another specialized organelle that translates the instructions into an amino acid string, which is then folded into a very specific shape where it becomes an ATP making protein. ATP is the source of energy for all cellular activity.

This example was from a higher level, more like a subroutine call than a single instruction fetch but I’m sure you get what I’m saying.

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2. This process is deterministic. I can look at the instructions in memory and tell you with complete certainty what the result will be. I can change the instructions in memory and have completely predictable changes.

Yes, exactly, just as in DNA. We know the results of lots of instructions but only a small percentage. We know a few very specific spots that if damaged give you breast cancer. Perfectly predictable and repeatable. The HOX genes appear to be the axial blueprint for body plans, which order, how many, head, neck, arms, chest, etc. We learned exactly the location to give a fruit fly an extra pair of non functional wings for example. It is deterministic just like a computer program.

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3. There is deterministic memory. A value can be written into memory at a specific address. The same value can be retrieved later where it is expected. The "state" (all of its properties at a given time) of a software entity can be preserved and read.

Yes again, exactly as I explained above. You are making my points for me.

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4. Software is Turing Complete. This is a mathematical concept, but basically it means that any software program you can conceive can be created using the language.

I give up, Max and Set are doing this for me. This is exactly the claims made for evolution, this biological hardware architecture is infinitely variable (programmable). It claims that a small land animal can become a whale by manipulating relatively few genes (program locations), how great an example of Turing Complete can you get? The same architecture works for every single Lifeform we know of. Because it’s programmable.

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5. Software is not self-developing. There has been research on this, but as of today it is science fiction. No one has developed software that is able to develop a new kind of software.

No argument. There are limits to software. I don’t personally believe that true 'AI' exists for that reason. There are also limits to the architecture of biological life but I am amazed all the time by it. Especially it’s software defined nature.

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6. Software has programmers. There are people who decide what any piece of software should do. They write the software to work according to a plan. When the software doesn't work the way it is supposed, they go and fix it.

Yes it does.

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This is not a very good metaphor for any aspect of life.

I'm willing to be shown, but so far you’ve done nothing but give supporting comparisons. Im looking for counter arguments, seriously, I’m not joking or trying to rib you here.

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@Leadfoot,

It looks like we disagree (although I think you for you compliment).

1. Cellular process are not anything like a processor.

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.

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.

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.

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@farmerman,

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dont know. But we do seem to have inndications that earliest life was NOT associated with DNA or even RNA

That is a completely novel claim to me and counter to every expert opinion I’ve ever read so I can’t comment on that. I’m sure there is speculation about pre DNA/RNA Lifeforms just as some entertain the idea of multiverses because it makes their hypothesis more plausible. But there is zero evidence or experimental results for either.

So far, do you agree that I have given reasonable explanations for why biological organisms are software based Lifeforms or at least why the cellular processes are comparable to those in software/hardware environments?

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@Leadfoot,

there was , and perhaps you just need to read up on the concept RNA world literature has many references to a "pre RNA" world.

PS glycolysis , Krebs acid cycle and gluconeogenesis are processes that are carried on and are understood quite well in the living state. Qll this goes back to organic biogeochem and biochem) It is a constant in all eukaryotes and some prokaryotes(Other energy cycles more primitive thn Krebs or AMP/ADP/ATP include Phosphoarginine acetyl phosphate Phos. There are many styles of energy production within all kinds of life groups. phosphocreatine and Phosphopyruvate THESE Are rsponsible for whole other energy deriving chem processes (CTP GTP TTP and UTP) in plants animals archaea etc.(How many phyla do we agree upon now thanks to the " life trees aan clades defined by Margulis and Woese)
I think, if you wish to propose a Puter based world instruction manual, you have a lot more work to do to spell it out besides merely proposing something that gives you comfort. You will need to look at the nutrition, cell structure, respiration etc styles of life in ch of the 5 (or 7) phyla. Jut cause DNA LOOKS like a barcode diesnt men that its a done deal . tarting with the fact that lifes 'ladders of information are tetradecimal not binary.
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.

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

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