Why describing DNA as “software” doesn’t really work

_{Denyse O'Leary

June 18, 2019

Genetics, Intelligent Design, Origin Of Life}

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Check out Science Uprising 3. In contemporary culture, we are asked to believe – in an impressive break with observed reality – that the code of life wrote itself:

… mainstream studies are funded, some perhaps with tax money, on why so many people don’t “believe in” evolution (as the creation story of materialism). The fact that their doubt is treated as a puzzling public problem should apprise any thoughtful person as to the level of credulity contemporary culture demands in this matter.
So we are left with a dilemma: The film argues that there is a mind underlying the universe. If there is no such mind, there must at least be something that can do everything that a cosmic mind could do to bring the universe and life into existence. And that entity cannot, logically, simply be one of the many features of the universe.
Yet, surprisingly, one doesn’t hear much about mainstream studies that investigate why anyone would believe an account of the history of life that is so obviously untrue to reason and evidence.Denyse O’Leary, “There is a glitch in the description of DNA as software” at Mind Matters News

Maybe a little uprising wouldn’t hurt.

Here at UD News, we didn’t realize that anyone else had a sense of the ridiculous. Maybe the kids do?

See also: Episode One: Reality: Real vs. material

and

Episode Two: No, You’re Not Robot made of Meat

Notes on previous episodes

Seven minutes to goosebumps (Robert J. Marks) A new short film series takes on materialism in science, including that of AI’s pop prophets

Science Uprising: Stop ignoring evidence for the existence of the human mind Materialism enables irrational ideas about ourselves to compete with rational ones on an equal basis. It won’t work (Denyse O’Leary)

and

Does vivid imagination help “explain” consciousness? A popular science magazine struggles to make the case. (Denyse O’Leary)

Further reading on DNA as a code: Could DNA be hacked, like software? It’s already been done. As a language, DNA can carry malicious messages

and

How a computer programmer looks at DNA And finds it to be “amazing” code

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Comments

Brother Brian:
Are you seriously suggesting that we could put a man on the moon without a standard unit of mass?
Unbelievable. TRY to stay focused. We could easily put a man on the moon without an INTERNATIONAL standard. So you are parroting the nonsense here, Brian. And you have once again avoided the question. That is very tellingET_{June 21, 2019
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DaveS, I would be interested in you opinion on my statement that the standard kilogram artifact that was used for over a century had functional information. It was critical for a century's worth of advances in industry, technology and commerce. Every country maintained their own kilogram artifact that was traceable to the prototype kilogram housed in France, and these artifacts were critical in the design and manufacture of everything from bicycles to airplanes to space craft. As well, it was used in commerce in the sale of anything that was based on weight. However, in 2019 this artifact was replaced. Does this mean that the functional information that this artifact contained for well over a century cease to exist?Brother Brian_{June 21, 2019
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ET
How do you know?
Are you seriously suggesting that we could put a man on the moon without a standard unit of mass? Newton begs to differ. If you are just going to keep parroting back this nonsense I am going to take my earlier advice and continue to ignore your comments.Brother Brian_{June 21, 2019
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ET,
We do NOT use functional information for everything to determine whether or not it was the product of intelligent design.
If that's directed toward me, then of course no one said otherwise. gpuccio says that "any possible function will do", which I understand as implying that we should be able to calculate the functional information required to implement the paperweight function I described.daveS_{June 21, 2019
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Brother Brian:
Without an internationally recognized standard for the kilogram (or an equivalent standard for mass) we would not have been able to put people on the moon.
How do you know?
Surely that means that the kilogram has functional information.
It functions as a standard. But that is all moot. YOU made a claim and I asked you to back it up. Can you?ET_{June 21, 2019
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ET
Let’s see your math. Or are you just fishing?
Without an internationally recognized standard for the kilogram (or an equivalent standard for mass) we would not have been able to put people on the moon. Surely that means that the kilogram has functional information.Brother Brian_{June 21, 2019
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We do NOT use functional information for everything to determine whether or not it was the product of intelligent design. But we do have Measuring the functional sequence complexity of proteinsET_{June 21, 2019
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ET,
I would be curious as to why anyone would want to.
To show it's possible, of course.daveS_{June 21, 2019
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I would be curious as to why anyone would want to.ET_{June 21, 2019
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ET,
Hold down paper- how many bits is that? It isn’t CSI, that’s for sure.
One would hope not. Now to be fair, gpuccio would likely respond by asking for the more information about the specific function. For example, perhaps this paperweight needs to be able to hold down a stack of twenty A4 sheets of paper (say 80 gsm) in a 10 km/hr breeze. I would be curious to see if anyone can come up with a number in bits.daveS_{June 21, 2019
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Brother Brian:
For example, the artifact that was used as the standard kilogram for over a century surely has a tremendous amount of functional information.
Let's see your math. Or are you just fishing? We do NOT use functional information for everything to determine whether or not it was the product of intelligent design.ET_{June 21, 2019
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Hold down paper- how many bits is that? It isn't CSI, that's for sure.ET_{June 21, 2019
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GP@57, you mention that the same object can have different functions, but does that mean that it has more than one measure of functional information. For example, the artifact that was used as the standard kilogram for over a century surely has a tremendous amount of functional information. But as of a few months ago, it is little more than a paper weight. Has it lost its functional information?Brother Brian_{June 21, 2019
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ET, But it shouldn't "all" depend on a specific paperweight. According to our definition, we take a minimum over all functional paperweights.daveS_{June 21, 2019
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daves- While you are awaiting gpuccio: We should investigate everything we observe to get to the root cause of it and understand it. So it would all depend on the specific paperweight.ET_{June 21, 2019
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gpuccio, A couple of random questions: Should any nontriviality conditions be imposed on the concept of "function"? For example, I could ask how much functional information is necessary to implement a paperweight. How about "a solid object which displaces 1 liter of air"? These functions are obviously uninteresting, but it would seem under your definition, they should each possess (or specify?) a well-defined amount of functional information. A slightly more interesting question, perhaps: How much functional information is required to construct a mechanism which rotates a small metal shaft at a rate of 1 rotation per hour (i.e., a very simple clock)? I'm not expecting you to calculate this, mind you, it's more food for thought.daveS_{June 21, 2019
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EricMH:
But, what is the mathematical definition of functional?
It's rather simple. "Functional" just mean that some object can be used to implement some explicitly define function. Any possible function will do. Of course, the same object will be functional for some functions, and not for others. The mathematical definition of functional information, instead, is: the least number of specific bits necessary to implement the defined function. Again, it's as simple as that.gpuccio_{June 21, 2019
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DaveS at #55: I am intrigued too, of course. And that kind of events certainly deserves to be investigated with an open mind. However, I am afraid that at present there is no chance that they are accepted as facts by most scientists, and so it would be difficult to use them in some general scientific theory. So, for the moment, I am perfectly happy to stick to the billions of amazing miracles that everybody can observe daily in living beings. :)gpuccio_{June 21, 2019
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Nonlin.Org: Here we go again... Yes. Definitely, I have not changed my mind! And neither have you, it seems... :)gpuccio_{June 21, 2019
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gpuccio,
I say rarely because I think events like Guadalupe, the miracle of the sun at Fatima, the shroud of turin, stigmatic or incorrupted saints, for example, are very bold statements of ID, with a designer’s “signature” all over them, so to speak. But since all of those have a theological component, people do not like to investigate them.
Oddly enough, I'm very intrigued by these sorts of events. I think I would find this evidence most convincing, if I could witness it myself.daveS_{June 20, 2019
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Here we go again with 'information' misuse (abuse) and tree rings (very much dependent on the sampling rate) and "specified complexity" nonsense and DNA as information (when 1 GB can't even hold your phone OS). And let's not forget the "Shakespeare sonnet" and "functional information". Here's some help: http://nonlin.org/dna-not-essence-of-life/ http://nonlin.org/biological-information/ http://nonlin.org/intelligent-design/Nonlin.org_{June 20, 2019
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EricMH: While I have nothing against the concept of "detachability", I don't think it is absolutely necessary. Functional specification can be well defined empirically without any problem. I have done that many times here. In brief, the procedure is as follows: a) An observer defines a function that can be implemented by some specific material object. The important point is: any observer can define any function. However, the definition of the function must be objective, and it must include some level that defines the function as present or absent, and an objective way to measure it. b) After we have defined the function, we can verify that the object can implement it, and we can measure the minimal complexity needed to implement that function as defined. IOWs, the number of specific bits of configuration that are necessary to implement the function as defined. That is the functional complexity linked to that defined function, and observed in the object in relation to the defined function. That functional complexity can usually be computed as the ratio between all possible forms (or sequences, for digital information) that can implement the function as defined, and the total number of possible configurations. So, functional information is always relative to some defined function. The same object can have different functional information for different functions. The point is: if an object exhibits more than 500 bits of functional information, for any possible function, we can infer design for it. Of course, any function we define must be defined independently from the observed configuration: this is the only important rule. Maybe this is w, and hat you mean by "detachability": if that is the case, you are perfectly right. IOWs, we cannot define the function using the specific configuration observed. Just to be clear, if we observe a sequence of 100 digits, we cannot use that sequence to set it as the key to a safe, and then define the function as the ability to open that safe. That would be cheating. You say:
E.g. take a Kolmogorov random bitstring, copy it, and now each incompressible bitstring has a perfect, external specification in its twin.
No. You cannot define any function for string B. It is the same as string A because you have copied it. And so? That is no functional specification. And copying simply means to duplicate already existing information. If I copy a Shakespeare sonnet, I am creating no new functional information, no new meaning. The procedure of copying is only a necessity procedure where object A determines the form of object B according to laws operating in the system (the copying system). There is no design here, except maybe the design of the copying system (which has nothing to do with the design of the sonnet). So, when the information for a protein in a protein coding gene is trancribed and translated, and it generates, say, 1000 copies of the protein, no new information about the protein sequence is generated: the necessay information is already in the gene. The gene already has in itself the bits necessary to implement the function of the protein. So, if by detachability you only mean that the function cannot be defined ad hoc for the specific bits observed, then I agree. But that has always been an obvious requirement of the definition of functional information. That said, it is extremely easy to define functional information and a way to measure it. And in all cases, more than 500 bits of functional information imply design, whatever the defined function may be. One of my first OPs here has been about defining functional information objectively: https://uncommondescent.com/intelligent-design/functional-information-defined/gpuccio_{June 20, 2019
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EricMH:
But, what is the mathematical definition of functional?
Does it require one? We observe something doing some work of some type and we call it a function. Functionality is a specification of sorts. Then we attempt to discover how it all came to be the way it is, in part by using our knowledge of cause and effect relationships. We could apply Wm. Dembski's mathematics with respect to discrete combinatorial objects to help us.ET_{June 20, 2019
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John_a_designer:
In my opinion, prokaryote DNA replication is a far more daunting problem for the Darwinist.
All you had to do was ask: Peering into Darwin's Black Box: The cell division processes required for bacterial life Evolutionists just handwave it all away or they will attack the author.ET_{June 20, 2019
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@GP, I agree compression is orthogonal to whether something is meaningful. Functional is some kind of external definition, and perhaps is obvious from a practical standpoint. But, what is the mathematical definition of functional? While a comprehensive definition is probably not possible, at least a necessary component is that it is a detachable specification, per Dembski. Otherwise, we cannot say the function did not itself arise from the chance hypothesis. E.g. take a Kolmogorov random bitstring, copy it, and now each incompressible bitstring has a perfect, external specification in its twin. If we do not require 'detachability' in our specification, then both incompressible bitstrings have maximal CSI. Additionally, this operation can be done entirely through a natural process and does not indicate design. So, in this example, by removing the detachability requirement high CSI clearly does not indicate design.EricMH_{June 20, 2019
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EricMH at #29: So, let's go on. The sequence of 1000 heads is specified by its order. Maybe it is designed, maybe it is the result of necessity laws operating in the system. We have to check carefully, before reaching a conclusion. But functional information of the kind we observe in language, in proteins, in living system, is not of that kind. Functional information is not specified by its order, even if some order can be detected in it. Indeed, functional information is specified in spite of its order. I will try to be more clear. Let's consider English language, and my Shakespeare sonnet, again. You say, very correctly, that English language has its redundancies, and that it is, in part, compressible. But the point is: the sonnet we are considering is not specified because it is, in part, compressible. It is, indeed, specified beacuse it expresses specific meanings that are not compressible, using specific configurations of partially compressible components. Just as a reminder, the sonnet I have always offered as an example is Sonnet 76: "Why is my verse so barren of new pride?" Now, while the first verse and the whole sonnet, in a wonderful paradox, seem to affirm the repetition in the poet's obsessions, there can be no doubt that the sonnet itself is a masterpiece of creativity and originality of thought and feeling and beauty. Now the simple question is: does its meaning, and creativity, and beauty, derive from its compressible components? Of course not. We could observe some sequence of letters which is equally compressible, from a Shannon perspective, but which means exactly nothing. In that case, we could infer design because of the compressibility (which, in itself, is a form of order), but not from any meaning in the poem. So, in functional information, be it language or software or proteins, the functional specification is linked to what the object means or can do: meaning or function, descriptive information or prescriptive information, as Abel would say. If the switches used to get the configuration are partially compressible or not has no relevance. It's the meaning or the function in the specific, unique configuration that matters. Functional specifiction, if complex enough, is sufficient to infer design. If more than 500 bits are necessary to implement that meaning or function, and if we observe it implemented in some object, we can infer design for that object. It's as simple as that.gpuccio_{June 20, 2019
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EricMH at #29: There is IMO a lot of confusion about compressibility in the ID debate. That's why I would like to add a few thoughts about that. Order and compressibility can be a form of specification. In that case, and only in that case, the configuration we observe is specified because it is ordered, and for no other reason. Consider my example of the sequence of 1000 heads. It is highly ordered, and that's why we distinguish it from a random outcome, which typically is very different. So, we suspect it may be designed because it is specified (by its order and compressibility) and it is complex (1000 bits). However, as explained in my previous post, we have to consider the poibble role of necessity, because soimple necessity laws can generate order. (More in next post, because this one, again, was posted by mistake: something in my typing, I suppose).gpuccio_{June 20, 2019
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DaveS: The previous post was posted while I was writing, by mistake, so I am continuing here:
We could find a message encoded in nature in some obvious and human-readable way (e.g., in tree rings, perhaps in DNA, etc). It appears no one here finds that a realistic possibility.
We could. But we have not, as far as I am aware. Science is done with facts, not with possibilities.
We could find information circuits, or entire information processing systems (which use codes) somewhere in nature. That sort of message is more subtle, in that the designer is not explicitly announcing his existence. It’s not like the constellations suddenly rearranging themselves so as to spell out “John 3:16” or the like.
This sort of message we do observe all the time in biological beings. Maybe it is subtle, but it is very clear and implies design beyond any possible doubt. For the constellations, you can just wait, while you look at the stumps... :)gpuccio_{June 20, 2019
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DaveS at #37 and #41:
Tree rings in themselves are not a code, but a designer could use them to send messages in Morse Code, presumably.
Not so easily. Messages are coded using configurable switches, IOWs switches which, according to the laws of nature operating in the system, can well assume different configurations. IOWs, the configuration of each switch must be "neutral" according to the necessity laws operating in the system (for example it could be 0 or 1, indifferently), and its specific value is set by the designer. This freedom allows the designer to output the meaningful configuration. In the case of tree rings, the configuration is set by the laws of nature and by the biology of the tree. IOWs, it is set by necessity. That would make it really difficult ti use the tree rings themselves to express any meaningful message. In the same way, we can write a message in the sand, but not in the position of the atoms in a crystal.
We could find a message encoded in nature in some obvious and human-readable way (e.g., in tree rings, perhaps in DNA, etc). It appears no one here finds that a realistic possibility.
gpuccio_{June 20, 2019
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DaveS
Anyway, it seems there are at least a couple of different ID arguments having to do with codes here: 1) We could find a message encoded in nature in some obvious and human-readable way (e.g., in tree rings, perhaps in DNA, etc). It appears no one here finds that a realistic possibility.
ID gives the case that some aspects of the universe show evidence of having been designed by an intelligence. Clearly, it would be a pointless task for ID to travel around human culture and identify everything that we already know that humans created and then declare that as evidence. However, if there was a new discovery of caves where images of animals are inscribed on the walls, that is a relevant use for ID, somewhat - in a forensics task inferring that the images could not have been created by random, non-human movements. Yes, you're right that nobody expects to find a quote from the Gospel written out in tree ring codes. I think, actually, such a finding would be dismissed as a radical outlier by most ID researchers, although it would be almost impossible to explain as a random occurrence. I suppose it would be evidence of human interference or better yet, some kind of alien intelligence. As a single instance, it's an outlier. If every tree in a particular forest showed similar results, it's an ID conclusion. There is some intelligence at work there. We could keep looking for such things, or looking at every rock formation, converting it to Morse Code and then reading it -- but ID finds enough positive, repeated and stronger evidence in fine-tuning of the universe and biological systems.
2) We could find information circuits, or entire information processing systems (which use codes) somewhere in nature. That sort of message is more subtle, in that the designer is not explicitly announcing his existence. It’s not like the constellations suddenly rearranging themselves so as to spell out “John 3:16” or the like.
Right, exactly. The designer appears to be hiding the evidence. For centuries, before the birth of micro-biology, we had no way of really seeing those ID messages in the cell. To me, it appears that those ID messages are imbedded into realty and are only slowly revealed over time, and even though the evidence for ID seems blatanly obvious to me, it is only rarely a case where the designer makes a bold, undeniable statement. I say rarely because I think events like Guadalupe, the miracle of the sun at Fatima, the shroud of turin, stigmatic or incorrupted saints, for example, are very bold statements of ID, with a designer's "signature" all over them, so to speak. But since all of those have a theological component, people do not like to investigate them. In the study of the cosmos or biology, the message is always very subtle, in my view. It can always be denied. The human imagination allows for a lot of escape paths and if people do not like the ID evidence, it's relatively easy to invent alternative scenarios.Silver Asiatic_{June 20, 2019
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