Tag: biology

Trigger Waves

Biomechanical interactions, rather than neurons, control the movements of one of the simplest animals. The discovery offers a glimpse into how animal behavior worked before neurons evolved.

We show a minimal mechanism — trigger waves — by which these walking cells may work together to achieve organism-scale collaboration, such as coordination of hunting strikes across 100k cells without central control.

The behavior of Trichoplax can be described entirely in the language of physics and dynamical systems. Mechanical interactions that began at the level of a single cilium, and then multiplied over millions of cells and extended to higher levels of structure, fully explained the coordinated locomotion of the entire animal. The organism doesn’t “choose” what to do. Instead, the horde of individual cilia simply moves — and the animal as a whole performs as though it is being directed by a nervous system. The cilia’s dynamics exhibit properties that are commonly seen as distinctive hallmarks of neurons.

2022-03-30: Physical gradients

Much of the research to date on self-generated gradients has looked at chemical signals, but cells can create gradients in other physical attributes, too, including mechanical properties. The recent paper analyzing migrating neural crest cells revealed a self-generated gradient of stiffness.

2022-07-13: Embryogenesis involves the extracellular matrix contracting

Mechanical forces induce embryonic chicken skin to create follicles for growing feathers. Just as surface tension can pull water into spherical beads on a glass surface, so too can the physical tensions within an embryo set up patterns that guide growth and gene activity in developing tissues. As an organism grows and develops, the cells in its tissues pull and push on each other and on the supportive protein scaffolding (extracellular matrix) to which they are intricately linked. Some researchers have suspected that these forces, coupled with changes in the pressure and rigidity of the cells, might direct the formation of complicated patterns. Until now, however, no studies were able to tease apart the effect of these physical forces from the chemical stew in which they simmer.

Multicellular Emergence

Environments favoring clumpy growth are all that’s needed to quickly transform single-celled yeast into complex multicellular organisms.

During the first 100 days, the clusters in all 15 of the tubes 2x in size. Then they mostly plateaued until the 250th day, when the sizes in 2 of the tubes that didn’t use oxygen started to creep upward again. Around day 350, Bozdağ noticed something in 1 of those tubes. There were clusters he could see with the naked eye. “As an evolutionary biologist … you think it’s a chance event. Somehow they got big, but they are going to lose out against the small ones in the long run — that is my thinking. I didn’t really talk about this with Will at the time.” But then clusters showed up in the 2nd tube. And around day 400, the 3 other tubes of mutants that couldn’t use oxygen kicked into gear, and soon all 5 tubes had massive structures in them, topping out at about 20000X their initial size. “I wasn’t honestly sure if this was a system that would saturate at 1000 cells. We have to continue evolving them and see what they can do. We need to see, if we push these guys as far as we can for decades, for 10000s of generations. If we don’t do that, I will always regret not having taken the opportunity. It’s a once-in-a-lifetime opportunity, to try to push a nascent multicellular critter to become more complex and see how far we can take them.”

2022-11-05: Multicellularity has metabolic benefits

the hollow spheres were Vibrio’s solution to the complicated challenge of eating at sea. An individual bacterium can produce only so much enzyme; breaking down alginate goes much more quickly when Vibrio can cluster together. It’s a winning strategy — up to a point. If there are too many Vibrio, the number of bacteria outstrips the available alginate.

The bacteria resolved the conundrum by developing a more complex life cycle. The bacteria live in 3 distinct phases. At first, an individual cell divides repeatedly and the daughter cells huddle in growing clumps. In the second phase, the clumped cells rearrange themselves into a hollow sphere. The outermost cells glue themselves together, forming something rather like a microscopic snow globe. The cells inside become more mobile, swimming about as they consume the trapped alginate. In the third phase, the brittle outer layer ruptures, releasing the well-fed inner cells to start the cycle anew.
By altering their life cycle to include a multicellular stage, the bacteria can digest the alginate efficiently: Their numbers increase, and the hollow shell helps to concentrate the enzymes. Meanwhile, the structure of the community prevents too many cells from being born. The cells in the shell lose the opportunity to reproduce, but their DNA lives on in the next generation anyway, since all the cells in the orb are clones.

Combinatorial Cell Signaling

In particular, in systems where ligands bind uniquely to receptors, the number of types of ligands limits how many different cell types or targets can be uniquely addressed. In a combinatorial system, different pairings between a small number of ligands and receptors can specify a much larger number of targets. The differences between the pairings also permit graded effects rather than an all-or-nothing response.

Woke Imperialism

A great example of woke imperialism was a recent foofaraw in which a woke tried to cancel someone for naming a protocol “AAVE”. The idea was that the authors of said protocol were insufficiently diverse because they didn’t know that “AAVE” stood for African American Vernacular English in the US. Now, the thing is that the word Aave is a Finnish word that means ghost, and the authors of the protocol were Finns, and it was a great word for what the protocol actually did (namely flash loans that could disappear in a second).

So, what this actually represented was Woke American chauvinism in the name of tolerance. A citizen of this gigantic global empire, the American empire, was using woke language to assert authority over some poor Finns as insufficiently respectful of the people his fellow Americans had once oppressed. Quite a trick: America’s history of slavery used to justify America’s present of imperialism! And again, this is similar to a Soviet soldier filling the ear of an Estonian civilian with the story of how Russian capitalists had once grievously oppressed Russian workers, a problem which Comrade Lenin solved with their glorious October Revolution…and that’s why they rolled the tanks into Tallinn. A non sequitur logically, but a useful tool ideologically.

and why might organizations adopt self-defeating woke positions?

It seems fair to say that there is a silent constituency, even a majority, within these organizations that does not support the mob and its methods. Why are they allowing the Woke to take over? There’s an increase of generic human capital relative to specific human capital. You don’t need to be trained on your firm’s computer system; you can navigate based on your experience with interfaces that are familiar on the Internet. People are not tied to organizations as closely as they were a couple of decades ago. They are not motivated to put up resistance when a determined minority of Wokesters tries to take over.

2023-07-03: Woke nonsense is destroying biology

Biology faces a grave threat from “progressive” politics that are changing the way our work is done, delimiting areas of biology that are taboo and will not be funded by the government or published in scientific journals, stipulating what words biologists must avoid in their writing, and decreeing how biology is taught to students and communicated to other scientists and the public through the technical and popular press. The science that has brought us so much progress and understanding—from the structure of DNA to the green revolution and the design of COVID-19 vaccines—is endangered by political dogma strangling our essential tradition of open research and scientific communication.
Campaigns were launched to strip scientific jargon of words deemed offensive, to ensure that results that could “harm” people seen as oppressed were removed from research manuscripts, and to tilt the funding of science away from research and toward social reform. The American government even refused to make genetic data—collected with taxpayer dollars—publicly available if analysis of that data could be considered “stigmatizing.” In other words, science—and here we are speaking of all STEM fields (science, technology, engineering, and mathematics)—has become heavily tainted with politics, as “progressive social justice” elbows aside our real job: finding truth.

Cockatoo Culture

Even when residents in these areas weigh down the tops of their bins with bricks or stones, cockatoos have figured out how to knock these heavy objects to the ground. Once that barrier is removed, the hungry birds can crack the lid open with their beak, prop it on their heads and walk it back until it fully flips on its hinges, as the videos show below. This unique skill has now become so widespread in Sydney, researchers think the parrots are imitating and learning from one another – a sign of cultural evolution.

Plant Senses

There’s a vine that grows in South America that adapts to the form of the tree or bush it is climbing on. Its leaves look just like the leaves on the host plant. You might think this is chemically controlled. In that case, the vine might be detecting scent compounds from the bush and changing the shape of its leaves in a way that was genetically predetermined. 3 different leaf shapes had been observed. Then a researcher came up with the idea of creating an artificial plant with plastic leaves and relocating our botanical chameleon to its new home. The vine imitated the artificial leaves, just as it had imitated the leaves in nature. This is clear proof that the vine can see. How else could it get information about a shape it had never encountered before? In this case, the usual suspects—chemical messages released by the host plant or electric signals between both plants—were absent. It is conceivable that all plants might be able to see.

Completed Human Genome

The development of a reference genome was absolutely critical for progress in human genomics, and was of central importance in the sequencing revolution, serving as a foundational tool for sequencing alignment methods as well as genome assembly methods. The initial draft of the human genome and all following patch updates have consisted of the euchromatic regions, which comprises roughly 92% of the genome. Addressing this remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium has finished the first truly complete 3.055b base pair sequence of a human genome, representing the largest improvement to the human reference genome since its initial release. A crucial aspect to realize about making improvements to the reference genome is that it has tremendous downstream impact for research and engineering in genomics. Because it is such a foundational coordinate system, it impacts everything that relies on it. This means that all new sequencing data can be more accurately mapped with a complete reference.

2023-05-13: We keep “completing” the human genome, now with more pangenome.

Reference genomes are crucial coordinate systems for genomic analyses. However, the references that scientists currently work from when studying humans (the draft human genome and its complete, gap-free successor, dubbed T2T-CHM13) are both based mostly on single individual genomes. A linear genome sequence of this type cannot adequately represent genetic diversity within our species. Instead, such diversity is more accurately described using a graph-based system of branching and merging paths, the first human reference pangenome. Using the pangenome for read mapping and variant calling resulted in 34% fewer errors in calling small variants (those shorter than 50 bases) than did using a linear reference. The difference was particularly pronounced in challenging repetitive DNA regions. Impressively, the pangenome identified 2x as many large genomic alterations, called structural variants, per person than is possible using a linear reference. However, challenges remain. Alignment of sequences against highly variable repetitive regions in the pangenome could be improved by more-accurate assemblies or new algorithms. More samples from diverse groups are also needed. Finally, widespread adoption of the pangenome by scientists could take time, because new methods supporting pangenome analysis are continually being developed, and scientists will often require training to use them.

2023-08-31: Even more complete, now with more Y chromosome

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished. Here, the Telomere-to-Telomere (T2T) consortium presents the complete sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30n base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.

Fractals Everywhere

The genes that cause Romanesco, a kind of cauliflower, to grow in a fractal pattern have been identified. “we found that curd self-similarity arises because the meristems fail to form flowers but keep the ‘memory’ of their transient passage in a floral state. Additional mutations affecting meristem growth can induce the production of conical structures reminiscent of the conspicuous fractal Romanesco shape. This study reveals how fractal-like forms may emerge from the combination of key, defined perturbations of floral developmental programs and growth dynamics.”

It’s the fact that this gene appears to function in other plants, though, that is blowing my mind. Give this technique another 10 or 20 years, and the resulting experiments—and the subsequent landscapes—seem endless, from gardens of infinitely self-similar roses and orchids to forests populated by bubbling forms of fractal pines, roiling oaks, and ivies.

Cell Size Regulation

“It’s been a profound mystery for many, many decades in biology, how cells are able to accomplish this task of almost magically knowing what their size is”. Shape and size regulation are important because they are closely tied to how a cell functions: Too large and it can be difficult for the cell to quickly retrieve information contained in its own DNA; too small and the cell doesn’t have enough space to split properly, causing errors in division and growth that could lead to disease. The secret to cell size regulation lies in the concentration of KRP4 in each new cell. Though the daughter cells inherit an equal amount of KRP4, because they might be different sizes, the concentration of this protein in each cell isn’t necessarily the same. Smaller cells started with a higher concentration of KRP4 and spent more time growing. For bigger cells, the concentration was diluted, so they grew less. Overall, this balanced out any asymmetries in cell size.

Mesopelagic Fish

Mesopelagic fish that live 100-1000m below the surface constitute 95% of the world’s fish biomass, 10-30x more than previously thought. “This very large stock of fish that we have just discovered is untouched by fishers.”

2023-02-24: The seafloor is similarly underappreciated

The majority of the bottom of the ocean is covered in morbid ooze, 100m deep. This substance is made of the skeletons of an uncountable number of tiny creatures, raining down from above. The passage of material through this ooze is a substantial part of several biological, chemical, and geological cycles.