Sapere Aude
Tag: dna
those event horizons are coming on fast these days.
If it works as promised, the MinIon is so vastly better than existing machines that the comparison is hard to make. biological technologies are improving at exceptional paces, leaving Moore’s Law behind. In fact, we should expect biology to move much faster than semiconductors.
say hi to your daddy LUCA, the last common universal ancestor.
ONCE upon a time, 3 ga BP, there lived a single organism called LUCA. It was enormous, a mega-organism like none seen since, it filled the planet’s oceans before splitting into 3 and giving birth to the ancestors of all living things on Earth today.
by comparing their sequence of DNA letters, genes can be arranged in evolutionary family trees, a property that enabled Dr. Martin and his colleagues to assign the 6m genes to a much smaller number of gene families. Of these, only 355 met their criteria for having probably originated in Luca, the joint ancestor of bacteria and archaea. The 355 genes pointed quite precisely to an organism that lived in the conditions found in deep sea vents, the gassy, metal-laden, intensely hot plumes caused by seawater interacting with magma erupting through the ocean floor. Dr. Sutherland too gave little credence to the argument that Luca might lie in some gray transition zone between nonlife and life just because it depended on its environment for some essential components. “It’s like saying I’m 50% alive because I depend on my local supermarket.”
2024-07-23: Molecular Adam and Eve
These 2 proteins, emerging as mirror images from the same gene, form the foundation of all subsequent encoded proteins. Given their central role in the inception of the genetic code—perhaps the most critical moment in the origin of life—Carter named them Αδάμ and Εωε (Adam and Eve, in Greek characters). Their existence underscores a fundamental principle: a code can only arise when there are at least two options to choose from.
Through the pioneering biochemical experiments conducted by the Carter laboratory, it was revealed that molecular Adam and Eve exhibited distinct specificities towards different groups of amino acids. This specialization allowed them to carry out an initial, albeit rudimentary, production of proteins (themselves), marking a significant advance over random synthesis. Over millions of years of evolution, these 2 proteins each diversified into 10 distinct forms. The fact that the symmetry was maintained between the two classes suggests that they were still part of bidirectional genes as they coevolved. The diversification process mirrored the complexity of the genetic code itself: the incorporation of new amino acids led to the addition of new codons, and at the same time allowed the synthetases to become more accurate at decoding genetic information. This cycle of coevolution between the code and its interpreters elegantly exemplifies how a code can be refined by the very entities it generates.
perhaps i am taking this “to the cloud” thing too far.
Of course, in the future we also have dna matching as an option for finding contacts. The etiquette of dna networking is hilarious to watch develop:
hi, i believe we are 6th cousins!!! OMG!
Yes, you and 100k other people.
The researchers analyzed metagenomic data and used them to search the Global Ocean Sampling (GOS) Expedition dataset for novel lineages in 3 gene families commonly used in phylogenetic studies: trees that use small subunit ribosomal RNA, recA, and rpoB genes — highly conserved genes that appear in nearly all organisms, including the domains of prokaryotes, the bacteria, and archaea. They found some deep branches in the recA and rpoB phylogenetic trees that might represent viral genes. However, they acknowledge that the novel sequences possibly come from a new 4th major branch of cellular organisms on the tree of life.
not found in a petri dish or in nature but by trawling dna. there’s also
viruses make up the majority of the genetic information on the planet, more than the genetic information of all other species of life combined.
40% of the DNA in your gut is from an unknown domain of life. the notion of biological dark matter means there might be a 4th4th-domain-of-life domain of life.
faster progress than moore’s law. and here’s a bit more background:
The technology that enables reading DNA is changing very quickly. I’ve chronicled how price and productivity are each improving in a previous post; here I want to try to get at how the diversity of companies and technologies is contributing to that improvement.
2015 world capacity of dna sequencing means it would take > 4000 years to sequence all living humans. we still have a long way to go.
one line of evidence is that a purely classical analysis of the energy required to hold DNA together does not add up. It is possible that DNA is indeed quantum-efficient.
if Grover-algorithmic processing is some sort of fundamental property of nature, then you might expect the genetic material to be synthesized most efficiently when the machinery has a choice of 4 different nucleotides. And when translating these into proteins, a triplet code (which requires 3 processing steps) would function most efficiently when working with a palette of 20 amino acids. I will admit to being unusually susceptible to ideas like this, but that makes the hair stand up on the back of my neck.
2 specific genetic mutations on the mtDNA of the Indian and aboriginal samples matched perfectly. Not only that, but these particular mutations do not exist elsewhere in the world
Cells from flakes of skin have grown into mice. This confirms that reprogrammed adult cells share the totipotency of embryonic stem cells.
The RNA hypothesis is very popular but doesn’t explain how fragile RNA can survive in hostile environments.
Dr. Joyce has been studying the possible beginning of history by developing RNA molecules with the capacity for replication. RNA, a close cousin of DNA, almost certainly preceded it as the genetic molecule of living cells. Besides carrying information, RNA can also act as an enzyme to promote chemical reactions. Dr. Joyce has developed 2 RNA molecules that can promote each other’s synthesis from the 4 kinds of RNA nucleotides. “We finally have a molecule that’s immortal”
2016-02-21: Talk of RNA-like
Perhaps before biology arose, there was a preliminary stage of proto-life, in which chemical processes alone created a smorgasbord of RNAs or RNA-like molecules. “I think there were a lot of steps before you get to a self-replicating self-sustaining system”. In this scenario, a variety of RNA-like molecules could form spontaneously, helping the chemical pool to simultaneously invent many of the parts needed for life to emerge. Proto-life forms experimented with primitive molecular machinery, sharing their parts. The entire system worked like a giant community swap meet. Only once this system was established could a self-replicating RNA emerge.
2019-06-30: Viroids, survivors from the RNA World?
Because RNA can be a carrier of genetic information and a biocatalyst, there is a consensus that it emerged before DNA and proteins, which eventually assumed these roles and relegated RNA to intermediate functions. If such a scenario–the so-called RNA world–existed, we might hope to find its relics in our present world. The properties of viroids that make them candidates for being survivors of the RNA world include those expected for primitive RNA replicons: (a) small size imposed by error-prone replication, (b) high G + C content to increase replication fidelity, (c) circular structure for assuring complete replication without genomic tags, (d) structural periodicity for modular assembly into enlarged genomes, (e) lack of protein-coding ability consistent with a ribosome-free habitat, and (f) replication mediated in some by ribozymes, the fingerprint of the RNA world. With the advent of DNA and proteins, those protoviroids lost some abilities and became the plant parasites we now know.
2022-05-06: RNA “species”
Over 100s of hours of replication, 1 type of RNA evolved into 5 different molecular “species” or lineages of hosts and parasites that coexisted in harmony and cooperated to survive, like the beginning of a “molecular version of an ecosystem”. Their experiment, which confirmed previous theoretical findings, showed that molecules with the means to replicate could spontaneously develop complexity through Darwinian evolution. Some of these results confirmed the predictions of earlier experimental studies of how complexity can arise in viruses, bacteria and eukaryotes, as well as some theoretical work.
“Without parasites, this level of diversification is probably not possible”. Evolutionary pressures that parasites and their hosts place on each other lead both sides to split into new lineages.
2024-02-01: Obelisks
A new kind of viruslike entity that inhabits bacteria dwelling in the human mouth and gut. These “obelisks” have genomes seemingly composed of loops of RNA and sequences belonging to them have been found around the world. The Stanford search yielded 30k predicted RNA circles, each consisting of ~1000 bases and likely representing a distinct obelisk. They were unlikely to be bona fide viruses because RNA viruses typically have many more bases. But some of the obelisk sequences encoded proteins involved in RNA replication, making them more complex than standard viroids. Like viroids, however, obelisks don’t seem to encode proteins that make up a shell. Because obelisks contain genes that are unlike any discovered so far in other organisms, they “comprise a class of diverse RNAs that have colonized, and gone unnoticed in, human, and global microbiomes”
Gregor J. Rothfuss 