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.
Tag: science
400 ka Knowledge Exchange
Different groups of hominins probably learned from one another much earlier than was previously thought, and that knowledge was also distributed much further. A study on the use of fire shows that 400 ka ago knowledge and skills must already have been exchanged via social networks. The most important question is: what was it that made widespread cultural diffusion possible 400 ka ago? ‘I hope we can change the discussion surrounding fire use by hominins. That we look more at what the use of fire meant for human development and how that related to social change.’
Jurassic Pompeii
The misfortune that struck this place 167 ma BP has delivered to him an extraordinary collection of fossil animals in what is unquestionably one of the most important Jurassic dig sites ever discovered in the UK. The quantities involved are astonishing. 10Ks of these animals that scientists collectively call “the echinoderms”. It’s a great name, derived from the Greek for “hedgehog”, or “spiny”, “skin”. What is a sea urchin, if not an “underwater hedgehog”? But it’s also the quality of the preservation that’s jaw-dropping. Lean in close to a slab of rock that’s just been cleaned up and you’ll observe what, at first sight, reminds you of a plate of noodles. It is in fact a great mass of fossil arms from who knows how many sea lilies. You can clearly discern the individual calcite plates, or ossicles, that made up the skeletal frames of these animals when they were alive. What’s more, the specimens are fully articulated. Everything is captured in 3 dimensions.
2023-05-13: And a similar site also in the UK
Fossils from 462 ma BP recently discovered in a quarry, called Castle Bank in central Wales reveal some Cambrian life forms held on for millions of years longer than paleontologists had thought before going extinct, and certain classes of modern animals got their starts earlier than expected. The quarry also holds strange creatures thought to have arisen and vanished during the Cambrian period, such as opabiniids, which had five eyes and a long proboscis, and scaly slugs called wiwaxiids. Newcomers spotted in the deposits include modern families of glass sponges and a group of crustaceans called horseshoe shrimp, which were thought to have arisen much later. The researchers have found 170 species. “There is every reason to expect that the diversity of the fauna will continue to climb as the authors continue their research”. But even the currently documented diversity emphasizes the underappreciated importance of this time, called the Ordovician, which set the stage for the world’s current biodiversity. The Welsh quarry could definitely be as famous as the Burgess Shale.
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.
see also
Eating a leaf off a plant may not kill it, but that doesn’t mean the plant likes it. The newest study to examine the intelligence (or at least behavior) of plants finds that plants can tell when they’re being eaten — and send out defenses to stop it from happening.
2023-04-03: Plants emit ultrasound under stress
Stressed plants show altered phenotypes, including changes in color, smell, and shape. Yet, airborne sounds emitted by stressed plants have not been investigated before. Here we show that stressed plants emit airborne sounds that can be recorded from a distance and classified. We recorded ultrasonic sounds emitted by tomato and tobacco plants inside an acoustic chamber, and in a greenhouse, while monitoring the plant’s physiological parameters. We developed machine learning models that succeeded in identifying the condition of the plants, including dehydration level and injury, based solely on the emitted sounds. These informative sounds may also be detectable by other organisms. This work opens avenues for understanding plants and their interactions with the environment and may have significant impact on agriculture.
Alignment-free Sequencing
Single-cell RNA sequencing (scRNA-seq) is largely reliant on the existence of a reference genome to which the new sequencing reads can be aligned to. Unfortunately, that rules out 99.9% of organisms! “Single-cell transcriptomics for the 99.9% of species without reference genomes” proposes a new computational pipeline called Kmermaid that relies on the power of k-mers in an attempt to obviate the need for a reference genome when using scRNA-seq. The first step processes the reads into amino acid translation frames, because “protein sequences are more evolutionarily conserved than the underlying DNA.” The last step is to use these k-mer representations to search in a database of expression profiles for common cell types to make the final prediction. This constitutes an exciting new paradigm for alignment-free cross-species prediction of cell types that throws out far less data
Distributed Innovation
contra “innovation only happens in person” beliefs:
- it’s not actually that hard to collaborate productively at a distance in academia, at least once you’ve gotten to know someone.
- innovation requires ever more collaboration among specialists as knowledge accumulates.
- Over time, falling travel and communication costs have increasingly favored building those teams by turning to remote colleagues with the right specialization.
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.
To throw is Human
300 ka ago, H. sapiens might have been very proficient at using thrown weapons. Humans are so good at throwing because our body stores energy in our shoulders. But based on the results of experiments with athletes, as well as studies of fossil and modern skeletal measures, the capacity for high-speed throwing was already present in H. erectus—placing humanity’s particular talent for pitching all the way back to 2 ma ago.
Leaky pipes
Researchers have taken inspiration from trees and developed a system for moving water around that depends on capillary action and surface tension. They 3D printed tiny open-faced cells that can expose a large surface area of water to the surrounding gas – which could be useful for things like cooling or gas exchange systems. Their pipes had 3x better performance.
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.
Gregor J. Rothfuss 