Tag: biology

Why Sex?

The pervasiveness of sex would make a lot of sense if the act increases reproduction both directly and indirectly, such as by increasing longevity

2022-02-16:

Research suggests the molecular machinery that makes this part of sexual reproduction possible may have existed 2 ga BP in the simple prokaryotic cells called archaea, perhaps 1 ga before eukaryotes and sex evolved. But the new findings also hint at an explanation for why this kind of cell fusion for sexual reproduction didn’t appear earlier in life’s history, when it seemingly could have. Fusexins that may once have been used for limited genetic transfer between archaeal cells may then have seeded the evolution of sexual reproduction. “The downside of lateral gene transfer is that it becomes less and less good if you have a bigger genome. If you’re just picking a bit of DNA out of the environment, what’s the probability it’s going to match up? It’s a decreasing function of genome size.” Cell fusion — made possible with repurposed ancestral fusexins — may have been instrumental in the transition to eukaryotes by allowing more coordinated, large-scale genetic exchange: sexual reproduction. Such a radical shift may have been more appropriate for maintaining the fledgling eukaryotic genome.

Where Do New Genes Come From?

some “orphan genes” with no obvious ancestors evolve out of junk DNA, contrary to old assumptions.

see also this older article

several genes that were present in only 1 or 2 species and not others, suggesting that these genes weren’t the progeny of existing ancestors. Begun proposed instead that random sequences of junk DNA in the fruit fly genome could mutate into functioning genes.

Extranuclear mRNA

Researchers found that the cephalopod is the only creature that can edit its RNA outside the nucleus.. now that his team knows that the squid has the cellular machinery to do this RNA editing, the next task is to understand why. He suspects it has something to do with allowing the squid to better adapt to changing environmental conditions such as water temperature.

Gauge CNN

going beyond the Euclidean plane would require them to reimagine one of the basic computational procedures that made neural networks so effective at 2D image recognition in the first place. This procedure, called “convolution,” lets a layer of the neural network perform a mathematical operation on small patches of the input data and then pass the results to the next layer in the network. Gauge CNNs can detect patterns not only in 2D arrays of pixels, but also on spheres and asymmetrically curved objects. “This framework is a fairly definitive answer to this problem of deep learning on curved surfaces”

this has been applied to proteins:

Correia’s system, called MaSIF (short for molecular surface interaction fingerprinting), avoids the inherent complexity of a protein’s 3D shape by ignoring the molecules’ internal structure. Instead, the system scans the protein’s 2D surface for what the researchers call interaction fingerprints: features learned by a neural network that indicate that another protein could bind there. “The idea is that when any 2 molecules come together, what they’re essentially presenting to 1 another is that surface. So that’s all you need,. It’s very, very innovative.”

Physics & Biology

13 tips for engaging with physicists, as told by a biologist this is a great, and unfortunately rare, example of interdisciplinary work:

Understand what ‘I do not understand’ means When physicists do not understand something that you have said about biology, it’s possible that you do not understand that topic either. 2. Seek common ground When a physicist does not understand an aspect of biology, they are not requesting a ‘biology 101’ explanation. In my experience, when physicists ask a biology question, they want to apply the thinking of physics to biology; specifically, they are searching for universal, mathematical explanations. 4. Keep in mind the maths shortfall in biology For most biological phenomena, we don’t have precise equations — unlike in physics. This is not to say that we don’t have maths, but our field needs a lot more detailed quantification. This lack is the Achilles heel of biology, and affects even the concepts we use every day.

there’s also a view from the other side: 12 tips for engaging with biologists, as told by a physicist

Get comfortable being uncomfortable I went from being one of the most knowledgeable people in my research field at the end of my PhD to knowing less than most of the first-year PhD students in my new lab. For me, that meant I was doing something right, but you do have to be OK with taking that hit and spending time building a new skill set Do not blindly accept dogma Challenging prevailing ideas in biology using your perspective can bring about revolutions. I greatly admire colleagues who have upturned decades of accepted dogma using quantitative methods that were not even considered by the biological community.

Biodiversity Evolution

Biodiversity alters strategies of bacterial evolution

a paper published in Nature found that when a bacterial species resides in even a very simple ecological community — one that includes just a few other kinds of microbes — it evolves very different defense strategies against a predatory bacteriophage virus than it does when it’s left alone with the phage. The research is expanding these ideas into the context of the microbiome, where bacteria exist alongside loads of other species. The finding not only elevates the value of biodiversity as an evolutionary factor in its own right, but suggests that some earlier conclusions about the behaviors and capabilities of microorganisms, drawn from laboratory studies of species in isolation, may be seriously incomplete. It also sounds a note of caution about some contemplated strategies for beating drug resistance in bacteria.

Life In Our Phage World

The world of phages is more than a little scary. They have been evolving for billions of years, their numbers are so vast every writer in this anthology resorts to scientific notation, and their generation time is as low as minutes, making for dizzying amounts of selection pressure and optimization – phages seem to have explored every possible way of attacking, subverting bacteria, replicating faster, compacting and making themselves more efficient, and won every arms-race bacteria started with them.

2023-01-12: And the reverse

A species of plankton that populate freshwater worldwide is the world’s first known organism that survives and thrives by dining on viruses alone, an advance that sheds new light on the role of viruses in the global food web. This virus-only diet – “virovory” – is enough to fuel the growth and reproduction of a species of Halteria, a single-celled organism known for the minuscule hairs.

2025-09-18: Viable AI-mutated phages

the researchers mixed all 16 AI-generated phages with ΦX174 and then threw them into a tube with E. coli cells. Because the phages were forced to compete for the same host cells, the variants that reproduced fastest would dominate. By sequencing the phages over time, the researchers could track which phages were gaining ground and which were falling behind. Several of the AI phages consistently outperformed wild ΦX174, with one variant (called Evo-Φ69) increasing to 65x its starting level.

Ultimately, these 16 AI-generated phages were not only viable; in many cases, they were more infectious than wildtype ΦX174 despite carrying major genome alterations that a human would be unlikely to rationally design.