Man-made codes are usually first conceived as abstractions before someone goes and built devices that use them in physical communication. But even though that is how man-made codes begin, that doesn’t make abstraction a necessary attribute of a code. It seems to me a code really can be nothing more than the fact that one system of information (whether symbols on a monitor or piece of paper, or in your mind) is used to represent another, whether physically or in the abstract.
Of course, the genetic code can be conceived of abstractly anyway despite how it is physically implemented in the translation system. And any of it’s currently known variants could in principle be changed so a different assignment existed between codon and amino acid. And yes those would likely have physical effects that would make some genetic codes more deleterious, or less conducive to evolution than others, but they’d still be codes.
We can conceive of alternative genetic codes, and before we build devices that use them should we then consider them true codes up until the point where someone constructs a translation system for them? That is absurd.
The genetic code is a real code by a perfectly sensible understanding of the concept.
The subject here would be that of hermeneutics and I’m sure you’ll get as wide a variety of opinions on it as of any other topic discussed in these forums.
The issue for me at least is one of what is called “Authorial Intent”. What did the author mean by what he wrote? The process is not always straightforward. At other times it can be.
So what I was trying to get at in my post is that once we’ve determined that intent, how does it correspond to what we find in the world around us? At times (like a fixed earth) science has helped theologians understand that they had misunderstood a text. We may be facing a similar revolution here and it represents a much greater paradigm shift than that of a fixed or moving planet.
It is also much greater (and the stakes much higher) than the planetary question because Genesis 1-11 does not stand in isolation. Can we reconcile it with our current scientific understanding by allegory, metaphor and other literary devices? Sure, but there are many moving pieces and any changes must maintain the coherence of the whole. It also needs to respect the authorial intent.
For my part authorial intent trumps what I might prefer to be true. If the Bible is in fact wrong on some of these issues, then let it be wrong. Let the author say what they meant. I think we owe any author that privilege. Conversely they also are owed the privilege of being rightly understood.
I may not understand your question but the goal of my original post was to outline my approach to these difficult questions. I would prefer it to be true but here we are discussing some of the grounds by which we try to determine its veracity. So in a spirit of scientific inquiry (where things may be falsified) I don’t want to beg the question of the truth of the Bible in favor of my own position.
So in this case I’m willing to consider that maybe the Bible is actually wrong on some points. What that would say for the rest of the text is then its own large and complex discussion.
I’m not sure that any a-priori assumptions hold here in terms of what I tried to mention concerning the empirical claims of the Bible. I’m not ruling out God or claiming that nature is all there is. I’m just asking that when the Bible (or any religious or secular work - doesn’t matter) makes a claim, do we find evidence for it? At a minimum what we do find must not contradict the claim in question.
I don’t think it is fair to exempt the Bible (or anything else being argued for) when it makes claims in the realm of a discipline that has the ability to evaluate those claims.
However, that is entirely dependent on the physical structure of the chemicals involved. You can’t just change some abstract rules in someone’s mind and suddenly have three thymine bases produce valine.
I think we may be in danger of going around in circles here. It seems to me that at various points the Bible makes claims about the external world. Whether that be creation or more recent historical events.
Since it exposes itself to evaluation by making such claims it seems fair to test them using the tools at our disposal. I would apply the same techniques to any other religious work.
Perhaps you can explain why portions of the Bible are either exempt from critique or are subject to critique by some other means? Help me understand.
True, but nothing in that is contrary to my original point, which was that while humans may analyze biology in abstract terms, molecular biology is “essentially physical, which is opposite of abstract, and cannot be a layer of independent abstraction such as would fit the OSI communication model.” A change in a biomolecule is inescapably a change in the physical world. It cannot be independent of the physical strata.
DNA is a code, in the same limited sense that a series of round holes and square holes is a mapping for round sticks and square sticks. That is not to belittle the Rube Goldberg machine complexity involved, but progress in biochemistry generally involves better understanding of how these electrostatic shapes interact with each other. The mutations we have witnessed for the COVID causing virus spike protein involve alterations which affect the affinity for human ACE2 receptors in various tissues. They fit better. The feedback from the better fit is positive selection. The allele frequency shifts. That is an evolutionary change in prevalent code. The end result is a functioning gene encoding a better fitting protein. This all takes place in a physical world with no programming necessary, and has been for hundreds of millions of years before the advent of human language and abstractions.
Just because something is a code does not mean it possesses the attributes of a program. Codon based DNA is perhaps similar to ASCII - a basic mapping. As found in nature, DNA is not set up to run on a Turing machine.
I made no such statement. I stated that secret codes involve arbitrary assignments.
The definitional part is abstraction.
I did. The most important criterion is abstraction. Arbitrary abstractions are used to produce secret codes.
Is that more clear?
Let’s see if this works better for you.
All codes involve abstractions.
The subset of codes that are secret involve arbitrary abstractions.
“Abstract” is not the antonym of “physical.” Abstractions are routinely implemented physically.
Your response is conflating them. Moreover, if you can’t see that computers involve many layers of abstractions, you are not understanding the concept.
No, I did not. I wrote:
The most important criterion is abstraction.
Using arbitrary abstractions is the way we make a code secret. Not all codes are secret codes; that confuses many people, which is why I added “code, as in “secret code,”” to designate the subset of all codes that are secret.
You are repeatedly conflating abstract with arbitrary, and all codes with the subset of secret codes.
No, because “physical” is not the antonym of “abstract.” Abstractions are frequently implemented physically. You’re writing pages without grasping basic concepts. Please stop.
Nope. It’s about abstraction. Abstract is not the opposite of physical. This is another misunderstanding.
Nope. It is not a code because it does not involve any abstractions in getting from the codon to the residue.
Starting with “…it appears you are arguing…” instead of “What you’re saying…” as you did in the previous paragraph is a vast improvement, btw.
I think that your use of multiple conflations and straw men revealed a fundamental misunderstanding on your part.
We can, because it involves abstraction. Abstractions are often physically implemented, particularly in computing.
Yes, you do; you really don’t; you really have, respectively.
It is different in that it lacks the abstraction that ASCII has.
There seems to be a lot of equivocation in this thread between DNA as a code and the genetic code as a code. Just to be clear: DNA and the genetic code are quite different. The genetic code, of course, applies only to protein-coding sequences, while the whole genome is DNA.
Hi Ron
For arguments sake I will accept your claim that we can modify gene’s successfully from an existing animal population however this does not explain the origin of the population or the origin of the genes in that population.
Hi Neil
Where are the papers that compare special creation to universal common descent as a hypothesis?
There is one I am aware of and that is by Winston Ewert which in its limited form seemed to support special creation as an alternative hypothesis. The Howe diagram also supported special creation as an alternative without intending to.
The point I am trying to convey is evaluating the Bible against scientific standards is difficult. Science can make untested inferences that do not include special creation in their criteria. Methodological naturalism is the standard that allows this.
The consensus is easy here but have they eliminated special creation? Not until they put the evidence up against the possibility that the world was seeded with living populations as vaguely described in Genesis 1.
I’m sorry but it’s just not clear what it is that distinguishes how the physical hardware in a computer translates a sequence of morse code to alphabet letters through some (ultimately electronic, physical in hardware) set of rules, from how the translation system translates nucleotide sequence into amino acid sequences through some other physical/chemical set of rules, in a way that makes the former constitute an abstraction, but not the latter. Please elaborate. What is the distinguishing feature that makes one abstract and the other, not?
Granted. In contrast to anything in biology, the mapping of ASCII is unconstrained, arbitrary, fungible, extrinsic, and incorporates incidental historical artifact tracing back to the vocalizations of ancient language from the Levant.
Methodological naturalism, the exclusion of the supernatural from the natural sciences, has drawn critique from both proponents of Intelligent Design and some philosophical naturalists who argue that the methods of science can also be used to evaluate supernatural claims. One principal objection to methodological naturalism has been what I call the truth seeking objection. In this article I develop an understanding of methodological naturalism capable of answering the truth seeking objection. I further also argue that methodological naturalism as a convention of science can be best defended by abandoning scientism. In this way methodological naturalism can be reconnected to the original theistic context in which it was first developed.
Uhm, abstraction and abstract really can be commonly taken to imply the opposite of concrete physical examples, and thus in some sense imply something non-physical or immaterial. An abstract as opposed to concrete object, for example. It really can mean something like the concept of a game, or a system of government, as opposed to a particular physical example.
I see now what you are getting at. I think perhaps you misunderstood some of what I wrote - though I may also be to blame for not being clear.
I am not arguing that science has eliminated special creation as a possibility but I am saying that we ought to be as honest as possible since the Bible does make certain empirical claims that are subject to evaluation. Can we prove special creation? Probably not. Can we demonstrate that the Bible is compatible with what we currently understand of cosmology and biology? I think so. I hope so. I joined this forum partly because I appreciate what Dr. Swamidass and others have to offer on this topic.
I’ll look up the article you referenced. Thank you for sharing it.
