3d printer as analog of DNA translation

In the somewhat misnamed “Is DNA computer language source code?” We established a couple of things:
1 - There seems to be an agreement that a good way to get generic definitions of terms is to search for the term on google. Having to dig past the first page sounds a bit stretchy.
2 - There seems to be tentative agreement that a 3d printer qualifies as a “computing device”

Two things are interesting about the 3d printer’s operating language:
1 - It can be incredibly simple.
2 - It can evolve parts.

(We will be examining the popular budget 3d printer – the kind that lays down molten plastic filament.)

First the operations. There are 8 whole operations:
1 - Turn filament feed on. (Start printing.)
2 - Turn filament feed off. (Stop printing.)
3 - Increment Z axis. (Raise printhead 1 notch.)
4 - Decrement Z axis. (Lower printhead 1 notch.)
5 - Increment X axis.
6 - Decrement X axis.
7 - Increment Y axis.
8 - Decrement Y axis.

(A real 3d printer may also have an initialization, and conclusion command.)

Note: A notch is defined by the resolution of the machine. It most usually involves one step of a stepping motor.

The next thing we need is a language. This requires an abstraction layer. The choice of memory for this implementation will be DNA. DNA naturally contains a 4 value word, (A,T,G & C). As we have 4 letters per nucleotide but need 8 letters to implement our language, we will read the letters in pairs. This, of course, is analogous to how organisms read DNA in triplets. Now we get, well, arbitrary. With 2 “words”, we have 16 available values. Which value attaches to which command is totally up to us. We can start a random number generator, or roll a dice, to decide.

We will make our truth table as follows:
AA = Turn filament on
AT = Turn filament off
AG = Increment Z
AC = Decrement Z
TA = Increment X
TT = Decrement X
TG = Increment Y
TC = Decrement Y

We will leave the remaining 8 values as “no action”.

There, we now are using DNA as the software (Though DNA is “hardware” the fact that its very structure is the digital code causes me to believe that we can call it hardware (a touchable thing) and software (the information.))

Ah, we decide that 8 “no actions” is kinda dumb, so we do what is done in the codon table, we assign values for each of the remaining 8 commands. We now consider efficiency for a moment. Moving on the horizontal plane (X/Y) will dominate the code for virtually anything we print. So rather than making more filament on/off or Z axis moves, we will make more X and Y axis moves. (We see that though the relationship between codes and action is arbitrary, there still can be room for a non-random “optimization” component.

We extend our table with:
GA = Increment X
GT = Decrement X
GG = Increment Y
GC = Decrement Y
CA = Increment X
CT = Decrement X
CG = Increment Y
CC = Decrement Y

Or we could go a little obtuse, it doesn’t matter, its arbitrary. How 'bout:
GA = Increment X
GT = Decrement Y
GG = Increment X
GC = Decrement Y
CA = Increment X
CT = Decrement Y
CG = Increment Y
CC = Decrement X

Now let’s evolve something. In this case, we will take a table knife and turn it into a screwdriver. Our situation is that we have software that defines a table knife. Often enough we have been using the knife as a simple slot screwdriver. It works, but not well. So what we’ll do is mutate the software (DNA) a little bit, and see what we get. If we like it better as a screwdriver, we’ll start using the “improved” software. If we don’t think its better, we won’t.

Hey, what do we do with a printed table knife that is, well, different; it’s neither particularly better or worse? Well, let’s copy it off. We’ll now mutate and print knife 1, then mutate and print knife 2 etc. Same game, look for better, look for different but neither better nor worse. By keeping neither better nor worse, and trying both the old and the new, we have reasonably analogized neutral drift.

Even though filament printers are notoriously slow, and we only have one, it shouldn’t take forever for the result to be more like a screwdriver than a knife. This should qualify as reasonable analogy to cooption.

On “computing device”, we need to broaden our thinking. We have this idea of a general purpose computer, something that can realistically implement the Turing machine. Such general purpose CPUs are available now at under $1, so we tend to throw them into everything – like 3d printers, for instance. However, it is ABSOLUTELY ROUTINE to not use most of the capacity of the 99 cent processor when implementing robotics. Robotics routinely live with an extremely narrow subset of the Turing. This very simple “computer language” is, in fact, a computer language.

You’re wasting an awful lot of time and energy on this exercise. Does it or you have any sort of point?

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@Bfast I’m lost on where you are going with this. You’ve told us what you are NOT doing, but not what you are doing. Is this an argument for design?

It’s interesting that you evolution theorists cannot see that big challenges start with small steps. I am working on making one small step, to demonstrate compellingly that a living organism (most especially a single-celled organism) is (ie, not a metaphor ) a self-replicating software driven robot by the standard definition of the terms.

Why care?

Consider this article in which Massimo Pigliucci and Maarten Boudry wrote:

Creationists and their modern heirs of the Intelligent Design movement have been eager to exploit mechanical metaphors for their own purposes. … If we want to keep Intelligent Design out of the classroom, not only do we have to exclude the ‘theory’ from the biology curriculum, but we also have to be weary of using scientific metaphors that bolster design-like misconceptions about living systems.”

They argue that the metaphor is a “misconception”. I argue that the statement is not a metaphor. Which is true? Does truth matter?

The metaphor is a misconception. If the metaphor were accurate, cellular differentiation would not be possible.

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You aren’t any where near this though. That is a very large leap into the void. I don’t think it’s true.

Let’s us suppose against all the evidence that it is true, what then?

First, if I understand cellular differentiation correctly (I may not) some single-celled organisms do it, but most do not.

Second, I am sitting at my computer which currently is a web browser. With the click of a couple of buttons, it differentiates into a word processor or a spreadsheet calculator. I can differentiate it into an effective 3d modeller.
Third, gene regulation technology implements a tight analog of the if statement. Once the if statement is implemented, cellular differentiation is no challenge for software (ie, DNA).

Then you’ve already failed because neither DNA nor biological entities fit the definitions of “software” and “robot” you already agreed upon.

No, they argue the use of metaphors in scientific language is being exploited by ID-Creationists to push the ID-Creationist agenda. I see nothing wrong with the use of metaphors to get sometimes complex concepts across to lay people. The authors suggest taking greater pains to ensure laymen understand the examples are just metaphors and do not represent physical reality. Then we wouldn’t get near as many scientifically untrained computer programmers confusing analogies for the real thing. :slightly_smiling_face:

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I find it intriguing that you avoid the presentation that I have made.

Then the biologist looses his status as high priest of evolution. Then terms like “information” take their proper place at the table. Then proteins become recognized as parts in synergistic machines, which they are.
Now, does it become harder for evolutionary biology to be explained once these terms are invited to the table? Actually, it shouldn’t be. If evolution by chance and necessity is correct, then biology should be willing to accept terminology brought in from other fields.

However, the dialog here shows rejection out of hand, rather than considering the facts. As soon as an honest case is put on the table, everybody gets suspicious that they are going to get into some sort of “gotcha”. Well, I don’t believe that recognising the reality that an organism is a self-replicating, software driven robot is a gotcha. But if it is, then the chance plus necessity position is falsified.

You know what you sound like? You sound like the painfully over-trodden meme, “it’s just a theory”.

You haven’t presented any facts. just your untrained layman’s personal opinions. You really need to learn the difference.

Still flogging your silly strawman and still ignoring actual evolutionary processes which are a combination of chance plus necessity. The only thing your argument is going to do around here is give everyone eyestrain from eye rolling.

If you go to the dentist and he tells you “this painkiller will get you high as a kite” do you run outside to see if you can really fly up in the air on a string? Intelligent people can recognize metaphors as metaphors. Why are you having so much trouble with them?

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My statement: “an organism is a self-replicating, software driven robot.”
Lets falsify this as “real”.

Is an organism self-replicating? I hope we have no nay sayers.

Is an organism software driven?
What is “software”? “Computer software, or simply software, is a collection of data or computer instructions that tell the computer how to work.”

Is the order of the nucleotides in DNA a collection of data? Well, if we implement it into our 3d printer is is.

Does it “tell the computer how to work”? Change it, and how the organism works changes. Change it in the wrong place, and the organism quits working.

Is the organism a “computer” or “computing device”? Computer: “A computer is a machine or device that performs processes, calculations and operations based on instructions provided by a software or hardware program.” The DNA in my example is the software for my 3d printer. The DNA in an organism is, um, some magic other.

Is the organism a device? “a thing made or adapted for a particular purpose.” Love that definition, adapted – simile to evolved. Surely one can find more purpose for an organism than to replicate itself, but it is adapted to replicate itself. Note the nature of the maker is undefined. If the maker is chance and necessity, so be it.

Therefore, according to standard definitions of the terms, an organism is a self-replicating, software driven, robot. Not metaphor, IS.

After you take the painkiller you do.

LOL! If equivocation and word twisting was an Olympic sport you’d sweep the medal podium. :smile:

No, DNA does not provide real time step by step executable instructions to the organism to “tell it how to work” like a software program does to the hardware suite it runs on. DNA is part of the complex chemical reaction which allows the organism to self-replicate with a (relatively) high degree of fidelity. Changing the DNA won’t affect the real time “operation” of the organism until the organism replicates. Even then it will only produce a new, slightly different phenotype. Your analogy fails badly here.

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Thus far, you have not compellingly demonstrated anything of the kind.

You have asserted. But assertion is not the same as compelling demonstration.

You assert. But you have not provided a persuasive argument.

I made a logical case as follows:

Please show me the error in my logic.

Already done. You claimed DNA works like human designed software to control a computer when the the two processes (DNA, software) are almost completely different. Big time fail there BF.

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