The Book is not the Ink and Hardware is not the Software

_{Barry Arrington

October 19, 2011

Intelligent Design}

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In this post the UD news desk quotes OOL researcher Jack Szostak: “We think that a primitive cell has to have two parts. First, it has to have a cell membrane that can be a boundary between itself and the rest of the earth. And then there has to be some genetic material, which has to perform some function that’s useful for the cell and get replicated to be inherited.”

He believes they have the “membrane” part figured out, which leads him to suggest that they are about “halfway” to figuring it all out.

Really? Consider a computer in a paper sack. If I figure out how to make a paper sack does that mean I am “halfway” toward figuring out how to make the computer-sack combo?

The other thing that caught my eye was in the comments. Joseph suggest that even if it is true that they are halfway there in figuring out the origin of the “hardware,” they have not even begun to figure out the origin of the “software” (which I take to mean the digital code in DNA).

To this, Dr. Liddle makes the astonishing reply: “The hardware is the software.”

No, Dr. Liddle. The medium is not the message. Your statement is akin to saying of a book, “The paper and ink are the novel.” This is obviously not so for the book. Why do you think it is so for the cell?

Comments

“OR you can change teh sequence and have the ribosome reject it.”
No idea what you mean here.
The ribosome is a genetic compiler!
The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist.
Think about it- What happens to a newly written or modified computer code that has an error? All new and modified codes have to go through a compiler. A compiler is nothing if not an editorial perfectionist! I bet if we were to watch we would see the compiler doing its thing right up to the point the error occurs and then spits it out much faster than if the code was OK, ie error free. Biologists need to be introduced to and experience computer science. Then this sort of discovery wouldn’t be so “shocking”. Compiler- source code in, object code out. Ribosome- mRNA in (string of nucleotides), polypeptide out (string of amino acids).Joseph_{October 21, 2011
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kellyholmes:
It seems you use you blog as a forum to threaten others with violence, abuse them in the most disgusting ways and generally act in quite a different manner to which you comport yourself here.
It seems you have reading issues as I treat people as they treat me and other IDists. IOW kelley it appears that you condone the nastiness of evotards.Joseph_{October 21, 2011
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Clive, Is that what happened here: https://uncommondescent.com/intelligent-design/a-word-about-our-moderation-policy/comment-page-11/#comment-309228paragwinn_{October 21, 2011
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Compiler- source code in, object code out. Ribosome- mRNA in (string of nucleotides), polypeptide out (string of amino acids).
Water, sugar and yeast in, alcohol out! (Although today I prefer going to the liquor store.) The point is, we may use language to create different views of the same thing but essentially, it is all chemistry, nature at work.Cabal_{October 21, 2011
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DrRec: I agree that a change in information is always accompanied by a physical change in the physical medium where information is stored. But that in no way makes the separation between information and its physical medium difficult or ambiguous. Information is about the meaning conveyed to a conscious observer ny the form imparted to the physical medium. It is essentially a consciousness related concept, implying the fundamental consciousness related concepts of meaning and purpose. I don't find at all surprising or confounding that a conscious content can be represented in the form imparted to a physical medium. Humans have been doing that for millennia, through books, works of art, and so on. What has become of human cognition, that now people find so difficult to grasp a concept that has been so constantly in our experience for millennia?gpuccio_{October 21, 2011
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Putting information inside a RAM does not change the RAM.
Yes it does. In Dynamic RAM writing data would alter the charge state of capacitors.
Putting information on a piece of paper does not change the molecular structure of the paper.
No, it doesn't, and the paper doesn't contain the information. The information is represented in the pattern of ink that lies on the papers surface. To create the information you have to add material.DrBot_{October 21, 2011
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kellyhomes,
Previously Clive has banned people here for things they have said on other sites, unrelated to this one. I guess double standards are only OK if they help your supporters…
Only if they were outed as a sock puppet on another site and banned previously.Clive Hayden_{October 20, 2011
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Petrushka, Your certainty about the relationship between energy and information processing is only founded in a presupposition of materialism and completely ignore the points made by Deutsch in his talk. If you can show insight into Deutsch's position on materialism highlighted in his talk then you will have to admit that there are no known physical barrier for information processing. There is nothing that preclude information processing to happen before it instantiate in a physical form. This non-material aspect seems to be required to instantiate things like creativity, love etc. How stupid does Reductionism look when it tries to explain the artifacts of intelligence... Another thought... How about the modern notions of information escaping from black holes?mullerpr_{October 20, 2011
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Alternatively it wasn't so much an insight as a bit of a muddle :) Referring to "information" as an agent is fraught with problems.Elizabeth Liddle_{October 20, 2011
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Physical things that "process information" are changing their physical state while doing so. Every instance of information is also an instance of a physical entity. Talk about defying entropy. Try processing information without expending energy.Petrushka_{October 20, 2011
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I tried, but it is clear that you are sufficiently obtuse not to grasp the insight that was presented to you. All the best...mullerpr_{October 20, 2011
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My point here, from post 1, is that the hardware/software analogy is tortuous, and leads to misunderstandings. Your link doesn't do much to suggest otherwise, or convince me the physical state of a processor is unchanged as information is passed to it, as JoeG suggests.DrREC_{October 20, 2011
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DrREC, It might stand you in good stead to consider the insight of David Deutsch presented in this post. Information is not defined by physics, it is as far as we know simply instantiated in physical things. The greatest wonder of it is that it can change the state of physical things profoundly. Going against this observed reality has no support in nature or consciousness.mullerpr_{October 20, 2011
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Could you give an example of where “software is loaded” in biology? As per comment 10. If software and hardware exist in biology then can you give a couple of examples of what specific biological structures represent hardware and software? Also how much ram does the hardware have? What programming language is the software in?
I think that is what the biologist and "allied sciences" researcher within the ID "movement" is attempting to discern at present, is it not? Specifically, things like "How much RAM does the hardware have?" or even more fundamentally "Does it (system) have RAM at all or is it all ROM?".
One of the features of language is that it can be translated into other languages.
I assume you mean "programming" languages? If so, then the "feature" you call out only exists because each "high level" language serves as an abstraction from the hardware's logic circuits. Logic circuits which are designed to produce certain "states" (i.e. on or off) given external stimulation (current of a particular voltage). Interestingly enough, the arrangement of the logic gates in a CPU's arithmetic logic unit (ALU) has a significant impact on the performance (usually measured in time) of the CPU at performing addition, subtraction, and basic logic operations such as AND/OR. Similarly, in the "genome" world, the arrangement of proteins in a DNA have a significant impact on the processing of that DNA does it not? Perhaps, as in the case of ALU design, there are "optimizations" of the arrangements that exist to achieve a desired outcome more quickly or efficiently? The CPU (general purpose processors) translation of the results of the execution of logic gates (i.e. voltage manipulations of transistors)in a particular arrangement into "0" and "1" produces machine code (0s and 1s in a particular sequence). My understanding of cellular hardware is that its execution of DNA (i.e. transcription, loosely) produces RNA which is proteins in an ordered sequence is it not?
Would you be able to translate some of the “biological software” into, say, Pascal? Or Forth? Or Python?
The languages (Pascal, Forth, and Python) you mentioned are all fairly abstracted from the hardware. They are high level languages in that respect. I speculate that the "language" represented by DNA is more akin to a machine language. I think once we understand the base "logic" (i.e. AND, OR, XOR, etc...) of the machine language being used then we can begin creating abstractions from the hardware. I think, in the biology world, we are still trying to decipher what logic is being applied and how the hardware creates an environment for the execution of that logic. Perhaps when we understand "enough", we can talk about creating language abstractions. There are researchers that are attempting to utilize the biological hardware to solve problems using our developed logic (AND, OR, aritmetic, etc...). Specifically, with respect to using DNA to input the "problem" and having cell systems "solve" for that problem. See this reference: Computing with DNA However, note that this would be co-opting the biological hardware and its native machine language to solve some of our logic problems. Though, this sort of research does bode well for identifying the sorts of "logic" capable of the biologic hardware.
If not, is “software” really the right name for it? Presuming that you can actually come up with some examples of “biological software” in the first place, of course.
I think it depends. If by "software" you really mean an application program, most (if not all) software is "written" in a high level language. It is always executed in machine language. Language with facilities specific to that platform (i.e. Complex Instruction Set Computer [CISC], Reduced Instruction Set Computer [RISC], and Exclusively Parallel Instruction set Computers [EPIC]). If you are referring to the DNA then I would probably say the metaphor to use is a machine language. If you are referring to the functionality provided for by the cellular and organ systems, then I would say the metaphor to use most likely would be assembly language (a singular abstraction). If you are referring to the complex functionality that occurs in both conscious and unconscious thought, then most definitely you could use software as a metaphor.ciphertext_{October 20, 2011
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You can't load software onto a molecule? Maybe, if you're just talking about one molecule. But I hope you're not suggesting that you can't load software onto a sequence of molecules? How do you think software is represented in a physical medium -- surely through an arrangement of particles, whether on a hard disk, magnetic disk, DNA or otherwise.Eric Anderson_{October 20, 2011
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"Putting information inside a RAM does not change the RAM. " Of course it does! Digital information isn't magical, or disembodied from the physical. For example, the capacitors of an integrated circuit represent bits 0 or 1 based on the state of their charge-charged or discharged. That is a physical change.DrREC_{October 20, 2011
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Unfortunately your "evidence" and "reasoning" leave much to be desired. Putting information inside a RAM does not change the RAM. Putting information on a piece of paper does not change the molecular structure of the paper.Joseph_{October 20, 2011
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It's true that sometimes I simply state what I think to be true, Joseph. But I will always cite evidence or provide reasoning if asked, and have done so, repeatedly, in this case. However, thank you for addressing my question:
How do you program a molecule without altering it? Well again information is neither matter nor energy, so why would putting it on/ in a molecule change it?
But I find your answer very odd! How would you put information on/in a molecule without changing it? Can you give me an example?Elizabeth Liddle_{October 20, 2011
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Elizabeth- you always baldly assert and that is why I always respond with TINAE. If you can't grasp that then you have a problem. How do you program a molecule without altering it? Well again information is neither matter nor energy, so why would putting it on/ in a molecule change it?Joseph_{October 20, 2011
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Dr REC:
Joe, you know changing the DNA or mRNA sequence changes the protein.
Not necessarily.
Are DNA or mRNA elements that code and bind other proteins for regulation hardware of software?
Hardware “programmers program disks without altering the disk- the prom is still a prom.”
And nothing on the disk changes when they do that?
It is still a disc- it's chemical and physical properties are the same. But sure once programmed it is a programmed disc with little deformaties that denote the program.Joseph_{October 20, 2011
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I asserted nothing, Joseph. I asked you tell me something. Asking someone to tell you something is the opposite of asserting something. Let me repeat my request: Tell me how you “program” a molecule, without altering the molecule. And if you do alter the molecule, tell me in what sense that not a hardware change. Thanks.Elizabeth Liddle_{October 20, 2011
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Question 1. Correct! Information exchange is successful only if you have a priori defined common: 1. alphabet. 2. language. 3. semantics.
I did not say that, Eocene. I was answering your question about about "text". I did not generalise to "information". whether it generalises depends on your definition.
Question 2. While these may be of help, they are not critical for inferring design.
Your question was not "was it designed"? It was "can you tell that it was written by a human"? The information I gave is absolutely critical for inferring human authorship. These are not mere nitpicks, Eocene - this kind of equivocation lies at the heart of the ID fallacy (my view is that the ID inference is a fallacy). You might, or might not be able to infer "design" even if the think clearly pre-dated human culture. However, we know there is another alternative to "design" for such patterns, and that is self-replication with heritable variance in reproductive success. So, provided the scroll seemed to have no self-reproductive capacity, I'd infer that it was the artefact of something that did. Otherwise, my inference would not be justified.
Question 3. “It depends…” I define information in the sense of Shannon.
Please give the definition itself. Thanks.
Question 4. The answer is, “No known examples today”. The difference is outlined here.
That answer makes no sense to me. I asked what you mean by "self-organising". Substituting:
Can you give at least one provable example of genuine no known examples today (not to be confused with self-ordering)? Life does not count as such an example simply because we want to prove or disprove the ability of living systems to no known examples today. So again, the question is whether you can give at least one example of no known examples today in the true sense in non-living matter.
:D Please give me your definition of "self-organisation". The paper you cite is useless. Abel goes on and on about how other people are using "sloppy definitions" and how important it is to have a rigorous one - and then does not give one! Just keeps going on about how Chaos doesn't count and "self-ordering" doesn't count, and about his "Cybernetic Cut". No-where is there even an attempt at an operational definition of self-organization. And to answer your question, obviously, we need one. Can you give me yours?Elizabeth Liddle_{October 20, 2011
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I started this thread by stating what a disaster this analogy is for the discussion. Thanks to Joe for demonstrating this. Joe, you know changing the DNA or mRNA sequence changes the protein. Are DNA or mRNA elements that code and bind other proteins for regulation hardware of software? What about a RNA virus, or catalytic RNA. "programmers program disks without altering the disk- the prom is still a prom." And nothing on the disk changes when they do that?DrREC_{October 20, 2011
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The finetuning is still obvious. Its precision is O(nanometer).Eugene S_{October 20, 2011
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Eric, Absolutely! The question is how it was possible that the same physical properties of matter lead to such a difference in behaviour within and without the cell: complexity of organisation vs chaos or order without complexity.Eugene S_{October 20, 2011
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The ribosome is a genetic compiler!
The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist.
Think about it- What happens to a newly written or modified computer code that has an error? All new and modified codes have to go through a compiler. A compiler is nothing if not an editorial perfectionist! I bet if we were to watch we would see the compiler doing its thing right up to the point the error occurs and then spits it out much faster than if the code was OK, ie error free. Biologists need to be introduced to and experience computer science. Then this sort of discovery wouldn’t be so “shocking”. Compiler- source code in, object code out. Ribosome- mRNA in (string of nucleotides), polypeptide out (string of amino acids).Joseph_{October 20, 2011
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Why don't YOU use "I'm going to baldly assert now" And geez Elizabeth programmers program disks without altering the disk- the prom is still a prom. When you download software does the hardware change?Joseph_{October 20, 2011
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"And why do you think all those things are required for first life?" Strange indeed. When one wants to prove something, the burden of the proof is usually on his/her shoulders. It is not enough just to say it may not have been required. I can substantiate this requirement by looking at the cell today. How can you substantiate your claim? For a cell to function as a whole (at the very least, metabolism and replication) a lot is required by definition.Eugene S_{October 20, 2011
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Why don't you use an acronym, Joseph? TINAE. Tell me how you "program" a molecule, without altering the molecule. And if you do alter the molecule, tell me in what sense that not a hardware change.Elizabeth Liddle_{October 20, 2011
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Cell software is whatever is responsible for reading codons in and processing them (the "what" part). Each codon encodes a set of actions. By virtue of this it complies with a certain software interface. Hardware is whatever stores the codons (the genes) and makes sure the information is physically transmitted between senders and receivers (the "how" part).Eugene S_{October 20, 2011
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