Because I’m a statistician and that’s the way I think?
Also, a lot of ID argument hinge of abuse on Information Theory, especially when they want to portray DNA as a sort of computer code/program.
Here we pretty much agreed, but I would include enzymes and transcription along with the mechanical works of the printer. The “sender” is the population genome (in Shannon Information, a probability distribution) sending a messages to the next generation (receiver), or sending bits of itself to the printer for routine tasks.
Using Kolmogorov Information is this context is a not meaningful at all, but William Dembski goes there anyway with CSI (Dembski 2006).
Where did you get the idea that DNA or RNA is made of amino acids?
It isn’t true.
The message in DNA is decoded according to the base pairing of the mRNA codon with the anti-codon of the tRNA. But the relationship of codon to amino acid is abstract. There is no chemical law that requires a particular codon to map to a particular amino acid.
We are surrounded by human designed devices that send and receive and process human designed coded information without the slightest understanding of the information that it is processing. The “understanding” is purely mechanical and built into the device.
Computers, smart phones, DVD players, Smart devices, printers, etc. The list is long.
It’s true that analogies can be problematic at times, but they can also be very useful if they are reasonable and accurate.
I hope you watched the video. It goes a long way to make the process of expression understandable and you can see how DNA is simply being read as a storage medium. DNA doesn’t do anything beyond that.
Lastly, when you reply to a post, there is a row of buttons at the top of the reply box. The first one on the left will bring the text of the post that you are replying to into the box. You don’t have to use it, but it makes it easier to understand the context of your response.
DNA does not store coded information. According to Collin’s Dictionary, coded messages have words or symbols which represent other words, so that the message is secret unless you know the system behind the code. That certainly doesn’t describe information in DNA, which can be translated by any ribosome as long as base pairing and other factors match a codon to a complementary anticodon.
This is wrong. Certain chemical principles ensure that a particular amino acid gets esterified to the acceptor stem of a tRNA molecule with a particular anticodon. Don’t you know aminoacyl-tRNA synthetases have this proofreading ability?
Wrong. Humans program these machines to receive or send specific types of messages.
I think "arbitrary* suits the purpose of this discussion. The details of how the encoding operates are not necessary to discuss a code.
[quote=“Michael_Okoko, post:47, topic:14274”]
Lets not get off track - human codes are sent and received by humans, everything else is just busy work between sender and receiver. In this discussion we have a tacit assumption to send and receive messages in written English, from which we interpret meaning. For DNA the meaning of the encoded protein is interpreted by chemistry and physics in the cell environment.
If we want to get formal about (Shannon) Information, this applies only as a description of the population (population variability). We can estimate the information in the population genome by measuring the variability in a sample from the population. We cant look at DNA from a single cell and say anything about how much information it contains.
That’s not what he is getting at. In fact, we know that we can reassign the relationship between amino acids and codons by using different tRNAs. That’s what he means that by no chemical law. It is the tRNAs that determine the mapping, and their is little to no chemical constraints on how that mapping is determined.
There are historically contingent constraints though. It’s hard for an organism to remap their code.
There are functional constraints. Some mappings are more efficient and more error tolerant than others.
Codon reassignment or even recoding doesn’t affect my point one bit. Codon reassignment is typically done by altering or removing a release factor protein via mutation accumulation. We do this relying on the chemical constraints offered by tRNAs and aa-tRNA synthetases.
tRNA’s don’t determine the mapping alone. aa-tRNA synthetases are also involved. Incorrect amino acids can esterify to a tRNA molecule and it takes two filters [affinity for aa-tRNA synthetase active site (based on physicochemical principles) and structure-based exclusion of the appropriate amino acid from the editing pocket of the synthetase] provided by aa-tRNA synthetases to remove them. There are important chemical constraints here.
There are chemical constraints as well. Chemical principles dictate which particular amino acid maps to a particular codon through the interactions of that amino acid, tRNA and aa-tRNA synthetase.
There is so many category errors here it is just about impossible to sort out. At least it is impossible for me to do so now with any brief response, and that’s all I have for now.
Sure there is. Try it without the properties of carbon. Nature operates within the constraints imposed by physics, which ultimately restricts the range of possibilities. We do not know what other arrangements might be possible and efficient, but they too would follow chemical principles. As the philosopher Madonna stated, we are material and live in a material world. DNA can exist as an abstraction in our minds, but not so in physical reality.
That does not mean that a full description of the behavior of DNA can be restricted to laws we use to describe chemistry. Phenomena which depends on more basic laws, but is not fully explicable in terms of those laws, is emergent. DNA is emergent from chemistry. Evolution and ecology are emergent from DNA. If a lion brings down prey, that can be both an outcome of genetic code, and a input to genetic code. The kill did not violate any laws of chemistry, and would have involved a lot of ATP, adrenaline, and stimulus-response on the part of both hunter and hunted, but there is also a layer of complexity not fully explicable in terms of strictly chemical law like ionic bonding. Emergence does not negate underlying physical reality but is coherent with and builds upon those laws.
I’m talking about the chemistry of the three bases of the codon not requiring any particular amino acid be mapped to it. Chemistry doesn’t even require any mapping at all.
You are talking about how the code is translated, which depends on the function of the various parts of the process, like the aminoacyl-tRNA synthetase. These functions derive from their respective sequence of amino acids and the fold that it takes.
So, if a functional sequence exists and is expressed, it will perform its function through chemistry, but, chemistry doesn’t require that any particular sequence exist.
How is this wrong? You simply paraphrased what I said.
I’m not sure how to answer this. I’m not denying that the components that carry out expression work according to the rules of chemistry. I’m saying that the rules of chemistry don’t require that those components exist in the first place.
I agree that this is a category error, but I’m primarily looking at the chemistry of the codon bases and the mapped amino acid. I’m not really looking at any of the components of the expression process. The components work according to the rules of chemistry, but the rules of chemistry don’t require the existence of the genetic sequence produces the component.
Yes. The code itself has to be arbitrary. In the case of the Genetic code, the mapping of the codon to the amino acid is arbitrary.
The use of the code, however, does not have to arbitrary. The human designed devices that I mentioned process information in a non-arbitrary manner, and I believe the same is true for processing of the coded information carried by DNA.
We might be discussing thing in written English, but you are missing what is happening inside of your device. Every time you press a key on the keyboard, the character is saved in memory as a grouping of 8 ones or zeros (a byte). The grouping that maps to the character is determined by the codeset (like ASCII) that the software is using. When the character is sent to the screen, it is converted back to the character that you typed.
It isn’t just what you type, either. When you buy a device like a laptop, it already has a great deal of coded information stored on it. All stored as ones and zeros. And, yes, that are not literal ones or zeros (I know someone will bring that up).
This is the comparison that I’m making between human coded information and the coded information that DNA carries.
The information carried by DNA is translated by chemical devices according to the mapping of the Genetic code.
Shannon doesn’t deal with the functionality of information. It is only concerned with transmitting a string of bits no matter if they carry information or not.
I do agree, though, that you can’t determine the functionality of a string of bits using
math or statistical analysis (I think that’s what you were getting at).
I think I see our disconnect. Human devices carry messages from one human to another. Humans are sending and receiving messages, the devices are the medium/mechanics/code.
DNA is not sending or receiving messages, it is the medium for carrying the message, which is interpreted by the laws of chemistry. A very particular sort of chemistry though - biochemical life.
