Tag: images

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.

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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

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.

Robot Sculptors

Carving with pinpoint precision, and at least some of the artistic flair of its more celebrated (and human) predecessors, ABB2, a 4m, zinc-alloy robotic arm, extended its spinning wrist and diamond-coated finger toward a gleaming piece of white marble. “Artists want to perpetuate this idea that they are still chiseling with a hammer,. It makes me laugh.”

The Human Family Tree

Our planet was very different 100 ka ago, and if we could survey that time, we would be astounded by the human diversity across its surface. To enumerate what little we know with certainty, there were at a minimum: modern humans, Neanderthals, at least 3-4 varieties of Denisovans, and 2 pygmy Homo populations in Southeast Asia. Likely there were still remnant Homo erectus in Southeast Asia as well, and other diverged lineages within Africa, and a new Homo in Nesher Ramla, Israel, in the Middle East with affinities to Neanderthals.


2023-02-04: More evidence of a much more distributed situation

“Cognitive revolutions”—such as the widespread shift some 300 ka BP from clunky, handheld stone tools to more refined blades and projectile points—were probably instances of different populations with distinctive cultural and biological features coming together and recombining their genes and ideas.

This mosaic evolution would explain certain seemingly unexplainable findings. For example, researchers found human fossils in the Democratic Republic of Congo that dated to 22 ka BP but physically resembled people living 300 ka BP. In Senegal, scientists uncovered 12 ka BP stone toolkits that could easily be transplanted to a situation 100 ka BP.

These finds probably resulted from periods of isolation where different populations in different parts of the continent each developed distinctive cultural and physical adaptations to their local environments. At the same time, instances of connectivity allowed different populations to acquire beneficial traits, behaviors, and technologies from one another, becoming better adapted and more flexible.

Great Green Wall

The “Great Green Wall”, has helped raise total forest coverage to nearly 25% of China’s total area, up from less than 10% in 1949. In the remote northwest, though, tree planting is not merely about meeting state reforestation targets or protecting Beijing. When it comes to making a living from the most marginal farmland, every tree, bush and blade of grass counts – especially as climate change drives up temperatures and puts water supplies under further pressure.

2022-02-04: Apparently people are really bad at naming, since there’s another Great Green Wall project in Africa:

In the mid-2000s, African leaders envisioned creating a huge swath of green that could help combat desertification and land degradation. The project, called the Great Green Wall, began in 2007 with the aim of planting a 15 km wide belt of trees and shrubs that would extend from the coast of Senegal on the Atlantic to Djibouti on the Horn of Africa. The World Bank has poured over $1b into this endeavor, and the initiative’s scope has grown to include efforts to fight poverty, reduce inequality and build climate-resilient infrastructure. In ecological terms, the program has been a huge success. As of 2020, nearly 4000 km2 of land has been restored to arability in Niger alone.

2023-05-13: As always, projects in developing countries that are declared “huge successes” are not, on closer look

The pace of financing is too slow to achieve this target. As of 2020, 20% of degraded land (200k km2) had been restored and 350k of the promised 10m jobs had been created. That is mainly, although not solely, because just US$2.5b of a required $30b has been spent since the project began. Donors have committed $15b to a pipeline of 150 projects. It’s not clear how much of this is grants, how much is loans and how much is existing funding relabelled as Great Green Wall money. Moreover, coordination between Great Green Wall countries and donors is weak. Trust between the African Union and international donors is in short supply. Donor nations seem to be picking and choosing which countries to invest in, with a preference for those in relatively stable regions.

Restoring The Night Watch

The missing edges of Rembrandt’s painting The Night Watch have been restored using artificial intelligence. The canvas, created in 1642, was trimmed in 1715 to fit between 2 doors at Amsterdam’s city hall.

Rembrandt actually used 4 different colors to paint a miniscule light effect in the eye of one of the many life-sized protagonists featured in this group portrait, which probably wouldn’t be seen by anybody anyway.

Ocean 20% mapped

Modern measurements of the depth and shape of the seabed now encompass 20.6% of the total area under water. When Seabed 2030 was launched in 2017, only 6% of the oceans had been mapped to modern standards. So, it is possible to make swift and meaningful gains. For example, a big jump in coverage would be achieved if all governments, companies, and research institutions released their embargoed data. Seabed 2030 is not seeking 5m resolution of the entire floor (close to something we already have of the Moon’s surface). 1 depth sounding in a 100m grid square down to 1500m will suffice; even less in much deeper waters.