Protein concentration in bacteria is regulated primarily at the level of transcription initiation

The amount of a given protein in Escherichia coli depends on a number of factors such as the amount of mRNA and the rate of translation. The standard model of regulation is based on decades of study of individual genes and it reveals that the amount of protein is mostly dependent on the amount of mRNA that was translated. This, in turn, indicates that most regulation occurs at the level of transcription initiation.

It's now possible to look simultaneously at the characteristics of large numbers of protein-coding genes to see whether this generality holds. That's what Balakrishan et al. (2022) reported in a Science paper a few years ago. They looked at the characteristics of 1900 protein-coding genes in E. coli to see how protein concentration was regulated.

Paralogs and LUCA

We're interested in the last universal common ancestor of all life (LUCA). In theory, this is a species that gave rise to both Bacteria and Archaea. The general assumption is that this is a single species with a well-defined set of genes that can now be found in all, or almost all, living species.

There are some scientists who question that assumption because they see massive transfers of genes between "species" during the early history of life. This gives rise to a web of life and not a well-defined tree. [The Three Domain Hypothesis: RIP] [The Web of Life] If that model is correct, then the ancestor of all living species could be a group of species that contributed different genes to a pool of organisms that lived billions of years ago. Early Bacterial and Archaeal ancestors could have independently acquired some genes by horizontal gene transfer.

How intelligent is artificial intelligence?

Over the past few years I've been assessing AI algorithms to see if they can answer difficult questions about junk DNA, alternative splicing, evolution, epigenetics and a number of other topics. As a general rule, these AI algorithms are good at searching the internet and returning a consensus view of what's out there. Unfortunately, the popular view on some of these topics is wrong and most AI algorithms are incapable of sorting the wheat from the chaff.

In most cases, they aren't even capable of recognizing that there's a controversy and that their preferred answer might not be correct. They are quite capable of getting their answer from known kooks and unreliable, non-scientific, websites, [The scary future of AI is revealed by how it deals with junk DNA].

Others have now recognized that there's a problem with AI so they devised a set of expert questions that have definitive, correct, answers but the answers cannot be retrieved by simple internet searches. The idea is to test whether AI algorithms are actually intelligent or just very fast search engines that can summarize the data they retrieve and create an intelligent-sounding output.

Genetics and the human life span

It seems reasonable to assume that there's a genetic component to aging and the human life span. For example, it's clear that if you inherit bad genes (alleles) from your parents then your chances of living a long life will be diminished. It's also clear that a lot of deaths (short life span) are not due to alleles you inherit from your parents but to extrinsic factors such as accident, war or disease. It's true that some diseases, such as cancer, have a heritable component but even people with "good genes" can die of cancer.

What's not clear is how much of the underlying, intrinsic, component of life span is due to alleles you inherit from your parents. If you look at the average life expectancy of men and women in different countries you can see that the average life expectancy of an American is about 80 years but people in Japan can expect to live five years longer. Is that difference due to genetics, or better health care, or something else?

Is epigenetics one of the best ideas of the 21st century?

New Scientist has produced a special issue on the best ideas of the 21st century. Here's the complete list.