It’s time to admit that genes are not the blueprint for life
It’s time to admit that genes are not the blueprint for life
Review of 2023 book: How Life Works: A User’s Guide to the New Biology Philip Ball. ISBN9781529095999
Theoretical biologist here. This is an incredibly important book. I just bought it a few minutes ago and so I’m only partway through the beginning, but it’s summarizing everything people from my school of thought (complex adaptive systems theory, multilevel selection models, and so on) have been arguing for two or three decades. It’s a very fast read so far (probably less so if you’re less familiar with the points the author is making), but I really hope that this book has an impact that’s reflective of the timeliness and cohesiveness (as I am reading into what the author is preparing to argue) deserves.
Maybe finish the book before you decide?
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.
Yeh! Good to see the rusty machine (and self-deprecating) model fading away and being replaced by real appreciation of the true marvels that have emerged over millions of years. (Science's mechanical models were all so ... 18th century!)
(Not so familiar with biology but did enjoy hearing about the tack Lee Cronin's taken.)
What’s the name of the theory the says cells use the genome like a library of tools?
What a dishonest bs. It's not the scientists who communicate these dumbed down "theories", it's journalists and trivial science books and shows.
Makes me loose all respect for the author.
At the university where I studied professors were constantly talking about what we don't know. Formulated every theory extremely carefully, there was no "it is like that". What kind of scientists is he talking about?
Yeah, I graduated with my BS in zoology over 20yrs ago and my professors wouldn’t have talked about genetics as a blueprint even back then. My focus was evolutionary biology and the one sentence in the article on the topic made me cringe. I would guess that people who focused in molecular bio probably cringed through the rest of it.
Craig Venter, the infamous head of the Human Genome Project and who created the first "synthetic" cell, has been saying this stuff for years. It's remarkable how ahead of the times he is, perhaps because he's not beholden to an academic institution.
He claims that a "tree of life" is fallacious, that there is no junk DNA, and that the bare minimum genes necessary for a living cell still can't be determined even after decades of research.
I hope that the authors of the new Extended Evolutionary Synthesis will admit the deficiency of outdated assumptions and reject dogmatic approaches to the theory, as implied by the author of the book reviewed in this article.
How could there be no junk DNA? There are plenty of inserted regions of repeating codons, between regions that are read (outside of replication). DNA replicators are very simple machines, they copy until they're told to stop, I agree that any junk DNA in the human genome has been there for a very long time, but it's not difficult to find single cell organisms that have introduced previously non-self DNA in their genome. If that DNA isn't used besides replication then it's junk is it not?
Also telomeres are pretty synonymous with junk DNA, until they aren't, or is every shortening of the telomere removing information vital to a cells function?
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.
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.
Which theory exactly are we rejecting dogmatic approaches to?
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
Another metaphor that Ball criticizes is that of a protein with a fixed shape binding to its target being similar to how a key fits into a lock. Many proteins, he points out, have disordered domains — sections whose shape is not fixed, but changes constantly.
I dunno, kinda sounds to me like a good educational metaphor. Yea, not 100% accurate but good enough for high school biology. You need to make some simplifications for the sake of education. Not everyone can care about the complex intricacies of genes and proteins.
Good enough for high school biology. But not when you're doing influential cancer research. The following is from Subanima's article on the same subject:
One of the most influential papers in cancer biology published in 2000 was the "Hallmarks of cancer" by Douglas Hanahan and Robert Weinberg. It outlined six of the main capabilities of cancer and laid out a rough program for studying the disease ointo the 21st century. To date, it has over 39,000 citations which, in academia, is officially known as a shitton.
It was so successful that they released a sequel in 2011 which has over 62,000 citations - also known as a metric shitton.
But at the heart of both papers is the machine metaphor and the idea that if we just map out all the functions of proteins in one ginormous map, we'll just have to run some maths and we'll know everything we need to know to cure cancer. In 2000 they wrote:
Two decades from now, having fully charted the wiring diagrams of every cellular signalling pathway, it will be possible to lay out the complete ‘integrated circuit of the cell.’
He also notes the same thing you noted, that it's a good metaphor for high schoolers.
