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.

Moloch

Dominic Cummings on the Sisyphean struggle of getting things done quickly within a government bureaucracy:

Various media organizations have been leaked an email from me, sent at the height of the covid disaster last year, regarding getting cash urgently to Our World in Data. Tellingly, a ‘Whitehall source’ says this is ‘so damaging’ for Cummings because he ‘is just being very blatant that due process, and procedures, are being thrown out the window’. I do not regard it as ‘damaging’ that I tried to throw ‘due process’ out the window. Sticking with ‘due process’ was killing people. I was right to send this email, I sent many other similar messages on PPE, testing, the Vaccine Task Force (see below), and my interventions saved lives / reduced suffering / speeded vital projects like vaccines. I think that if I had NOT acted like this, it would been unprofessional and unethical.

2022-03-06:

Operation Warp Speed was perhaps the most successful government program in more than 50 years but it was funded only because the Trump administration and then the Biden administration finagled the rules, almost certainly breaking some laws in the process. But that is sometimes the only way to get things done today, especially at speed.

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.

Sophia

unclear how staged this is, but impressive either way.

Little Sophia can walk, talk, sing, play games and, like her big sister, tell jokes. With Little Sophia’s software, and included tutorials through Hanson’s AI Academy, she is a unique programmable, educational companion for kids, inspiring children to learn through a safe, interactive, human-robot experience

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.

Switched Reluctance Motors

The switched reluctance motor (SRM) is an electric motor that runs by reluctance torque. Unlike common brushed DC motor types, power is delivered to windings in the stator (case) rather than the rotor. This greatly simplifies mechanical design as power does not have to be delivered to a moving part, but it complicates the electrical design as some sort of switching system needs to be used to deliver power to the different windings. They are 50% more efficient, and if deployed in the US, would save enough carbon to equal 1 Amazon forrest

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.”