science

If you’re familiar with the subject, you can tell exactly where the author is going to go with it. I’ve been working on and teaching this material for about 20 years, and I’ve applied it against quite a diverse number of areas.

I’m not learning anything new from the book, but simply reading a well-assembled argument as to why it should become a dominant paradigm.

So I think I can make the claim that I am an expert in this, at least compared to 95%+ of biological researchers. My research foci include epigenetic and emergent interactions like the ones discussed in the article, and although I am not going to back this up by identifying myself, please believe me when I say I've written some papers on the topic.

The concept of junk DNA is perhaps the problem here. Obviously there are large swaths of our genome that do not encode anything or have instructions for proteins. However, dismissing all non-coding DNA as "junk" is a critical error.

Your telomeres are a great example. They don't contain vital information so much as they serve a specific function-- providing a buffer region to be consumed during replication in place of DNA that does contain vital information. Your cells would work less well without telomeres, so calling them junk is inaccurate.

Other examples of important non-coding regions are enhancer and promoter regions. Papers describing the philosophical developments of stochasticity in cellular function note how enhancers are vital for increasing the likelihood of transcription by making it more likely that specific proteins floating in the cellular matrix interact with each other. Promoter regions are something most biologists understand already, so I won't describe them here (apologies for anyone who needs to go read about them elsewhere!). Some regions also inform the 3D structure of the genome, creating topological associated domains (TADs) that bring regions of interest closer together.

Even the sequences with less obvious non-coding functions often have some emergent effect on cellular function. Transcription occurs in nonsense regions despite no mRNA being created; instead, tiny, transient non-coding RNAs (ncRNAs) are produced. Because RNA can have functional and catalytic properties like proteins, these small RNAs "do jobs" while they exist. The kinds of things they do before being degraded are less defined than the mechanistic models of proteins, but as we understand more stochastic models, we are beginning to understand how they work.

One last type of DNA that we used to consider junk: binding sites for transcription factors, nucleosome remodelers, and other DNA binding proteins. Proteins are getting stuck to DNA all the time, and then doing things while they're stuck there. Sometimes even just being a place where a nucleosome with a epigenetic flag can camp out and direct other cellular processes is enough to invalidate calling that region "junk".

Anyway I'm done giving my spiel but the take home message here is that all DNA causes stochastic effects and almost all of it (likely all and we haven't figured it out yet) serves some function in-context. Calling all DNA that doesn't encode for a protein "junk" is outdated-- if anything, the protein encoding regions are the boring parts.

I'm not an expert on the subject. I can only repeat what Venter said: "the only junk DNA is in my colleagues brains". He claims that all DNA has function and that it should not be referred to as junk just because we don't know the function yet.

He talks about at intervals in this interview.

Not an expert but it's easy to see that information is not function. Like in computers, a sequence of bytes in memory can encode both operations and data. A single byte can be both. The two also mix up in dna, and adding a new random chunk of data to a mechanism like that will alter the expression, the fInal output. If an action must be repeated on all the elements of a list, and you add three random elements to the list, the result of the program changes. So no, it's perfectly believable that there is no junk dna.

There are several. One is the gene-centric theory of biology, which carries less weight in biology itself than it does in how biological sciences are communicated to laypersons - eg the Selfish Gene, which I could rip on for pages - and others include ideas that are considered contentious within biology, such as multilevel selection theory that extends beyond kin selection. I can’t begin to tell you about the number of arguments I’ve gotten into on that subject alone. I will frequently bring up that there is confusion as to what a “gene” actually is, and how it’s really determined by the context in which we’re using the word. There’s really just so much that needs to be re-evaluated.

i believe the article suggests that the current way of communicating biology - that genes are the code that runs the machinery of life - is dogmatically adhered to by science communicators

it also suggests that when we communicate our new understandings that we are careful not to fall into another dogmatic theory, because it’s complex and we just don’t know

this is language used in the article, i don’t have enough information or understanding to know whether it’s true or not

I still feel like he's nitpicking tbh, wiring diagrams can have devices with variable or probabilistic states and though the maths is very complex it's theoretically possible to similate and map.

Why can't we have both?

Edit: switched what to why.