Author Archives: beykex

The last common ancestor of animals: a focus on genes, development and ecology (II)

AI-processed picture of the starlet sea anemone Nematostella vectensis. Source: Wildlife Archives

In the previous entry we learned a bit about the “historical” context of the origin of animals, both in the evolutionary and the chronological meaning of the word. We saw how the fossil record was the first resource explored to unraveling the origin of animals, and how it helped to pinpoint the geological period when this lineage emerged. We also learned that comparing the genomes of different animal species has become a new paradigm of research, as it helps to clarify the phylogenetic relationships of animals, as well as it allows to infer the what genetic information needed to build animal bodies was present in the ancestor.

In this entry, we will explore what was the gene content like in the animal LCA in two ways: firstly, by broadly looking at the changes occurred in the genomes of animals during their evolutionary history; secondly, by looking at the genes found scattered across the early branching animals, which together are like pieces of the puzzle that is the animal LCA.

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The last common ancestor of animals: a focus on genes, development and ecology (I)

From Cosmos: A Personal Voyage (1980).

In my most recent publication, together with some formidable colleagues from my previous lab, we describe the origins of animals by compiling the state-of-the-art of current knowledge and methods. What is special about our work is that we do so by reconstructing two ancestors key to understand this evolutionary transition: the last unicellular ancestor of animals and the last common ancestor of all animals. In this entry, I have compiled some notes and paragraphs that were left out or simplified, but that were very informative and illustrative for me during the reading process of describing the last common ancestor of animals (animal LCA). They have been cohesively edited together adding some notions of evolutionary biology and ecology to provide a solid piece of read. Some parts are somewhat similar to what was published, in the end, this is a sub-field of what we did. I did my best to reflow and change those parts to avoid redundancy. I hope you enjoy it as much as I did!

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Tecnicismos y conexiones profundas del Vaporwave: Influencias temáticas y musicales del Ambient

Tomada de VaporWave Wallpapers (app)

Esta entrada es la primera de una serie sobre el Vaporwave, que bien podría ser el género musical que más me ha influido en la veintena. A raíz de haber escuchado cientos de álbumes, otros tantos EPs, y muchos vídeos (y papers!) de análisis, he decidido recopilar de manera más o menos estructurada todo aquello que me fascina de este género y que, a veces, quedan un poco ‘overlooked’ en los análisis. Con esta entrada también nace la primera categoría en casi 10 años en el blog, ‘Música’.

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Generate wordclouds of Gene Ontology GO terms using wordcloud, RColorBrewer and base::abbreviate() in R

I have two different Gene Ontology annotations for the genome annotation I am working with, and I’ve been trying different ways to quickly visualize Gene Ontology information, such as GO enrichment analysis using p-values as a proxy of significance (as per usual in genomic analyses). I thought of adapting this quick tutorial on wordcloud, but soon I noticed that sometimes the GO term human-readable descriptions are excruciatingly long, and the plots can become a total mess.

One option could be to inject a jumpline character after N words in the GO term string, which the R plotting engine seems to work fine with, but my first I thought was to abbreviate the words in the description. Perhaps unsurprised I learned that the foundational knowledge of R base has what I was looking for: the abbreviate() function.

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Manifiesto SolarPunk

SolarPunk album art by Various Artists under global pattern

Interesante las conexiones que pueda tener con el New Age, la estética de ciencia ficción naturalista, el futurismo y el positivismo.

Como dice en la descripción del álbum en Vapor Memory:

“Solarpunk is a dream, is a speculation, a science fiction – yet, it’s a possible future. It’s not retrofuturism, but instead a vision of how can we get there, to a better world. It is in our power to change the way we live, to think different, to abolish any kind of domination between ourselves and above nature. We have all the means to build a new kind of society: compassionate, ecological, inclusive for all cultures and identities, decentralized and free of political manipulation. Hi-tech may and should co-exist with the biosphere and we have the most powerful source of energy for that – our Sun. Let it shine our way as we look into the future! “

Vapor Memory. (2021) Various Artists : Solarpunk : A Possible Future [Video]. Available at: https://www.youtube.com/watch?v=9O55hfyEZ4s (Accessed: 11 March, 2021).

Redistribuido en este blog a través de su licencia original Creative Commons.

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