Papers of the Week: 22.04 – 29.04.2013

Papers from the past week. [OA] are open access. Feel free to request a detailed discussion on any of these.

General Interest, Important:

• Special Issue: Vivisection

Vivisection, the practice of dissecting living organisms for scientific study, is nowadays mostly frowned upon for bioethical reasons. We can study anatomy when the animal is dead, and there are many technologies available to allow us to non-invasively study physiological systems, so there is no major reason to do vivisections anymore. These technologies haven’t always been here though, and a lot of the early biological sciences were filled with accounts of vivisections, which did bring about a wealth of knowledge, so they weren’t wasted (or for fun, as animal rights terrorists would have you believe). This special issue has several papers on the growth of vivisections during the early times of this period, the 16^th and 17^th century.

• Gene similarity networks provide tools for understanding eukaryote origins and evolution. [OA]

There are two interesting and important aspects to this paper. The first is the insights into the endosymbiosis that led to the eukaryotes. The second is the one I am more interested in, and that’s the power of phylogenetic networks over phylogenetic trees. We have many phylogenetic trees of eukaryotes, but it was only with this paper and their employment of a network that we could clearly see the presence of the endosymbiosis, since a tree can only show one set of relationships – detecting things like endosymbioses and organismal fusions is simply beyond the scope of a phylogenetic tree, since a tree portrays hierarchical relationships where genes are passed vertically from parent to offspring, whereas an endosymbiosis is a relationship where genes are passed horizontally between unrelated organisms. Networks have no problem with such things, and can portray hybridisations, endosymbioses, reticulations, and other such phenomena that don’t fit into the standard basal-to-derived branching scheme of a phylogenetic tree. This paper is an example of this.

• A global assessment of the effects of climate policy on the impacts of climate change.

It’s well-accepted that science needs to play a dominant role when deciding how to deal with issues such as climate, not only because meteorology is a scientific discipline, but also because the scientific method has built-in mechanisms to check up on the effect of such policies and modify them as needed. Case in point: this paper, which examines how current climate policies are faring in the overall picture, if they are really working towards keeping the damage to a minimum or whether they’re just useless. We will not see the results of our work until at least the 2030s, according to the paper, and the conclusion is a rather obvious “the sooner the policies get to work, the better”, since a constant result is that the sooner emissions peak, the fewer the damages will be in the long run.

• From incipient to substantial: evolution of placentotrophy in a phylum of aquatic colonial invertebrates. [OA]

I recently wrote a tiny bit on bryozoan placentas, so here’s a paper with much more information.

• The G4 Genome. [OA]

G-quadruplexex are structure formed at the end of telomeres. Telomeres are repetitive DNA sequences at the end of chromosomes that get eaten away through the cell’s lifespan, acting as decoys so that the useful chromosomal DNA doesn’t get damaged. When you have four of them next to each other, they will fold with each other and form the G-quadruplex (G4). The G4 acts to stabilise the telomeres, and so have been actively researched over the past few years because telomere degradation is heavily implicated in cancer and ageing. It was also recently found that G4 complexes are found in other regions of the DNA molecule, not just at the bookends of it. If any of this stuff sounds interesting, this paper has a great summary of it all, and it also delves into a pretty cool discussion of how the genome ought to be viewed as a complex landscape rather than just a string of ATGCs. This biochemical stuff isn’t my cup of tea, but it’s interesting stuff anyway.

Papers of the Week: 25.02 – 03.03.2013

Papers from the past week. [OA] indicates open access. Feel free to request a detailed look at any of these.

General Interest, Important (unsorted):

• Special Issue: Fostering Advances in Interdisciplinary Climate Science.

The papers of this special issue showcase how multifaceted the modern study of climate change is, incorporating atmospheric science to geology to ecology to social sciences, and more. I consider this important to realise and take notice of, as it stresses just how much of a concerted effort is needed to achieve the results that the IPCC presents in its Assessment Reports, for example – and also underlines the unlikelihood that the entire field is a scam, which is an idea brought forth by dangerously delusional quacks.

• Detection and attribution of anthropogenic climate change impacts.

Continuing with the theme of climate change, this review paper summarises how we really can pinpoint the causes of current climate changes to human influence. If you have doubts about anthropogenic global warming, then this is the paper for you.

• Xenoturbella bocki exhibits direct development with similarities to Acoelomorpha. [OA]

I’ve outlined Xenoturbella in this post, including the important kerfuffle over its phylogenetic placement. This study finds that the development of Xenoturbella is very similar to that of an acoel, providing further support – and, significantly, from a source other than molecular phylogenetics – for the Xenacoelomorpha taxon. However, the position of the Xenacoelomorpha within the general tree of animals is still up in the air – is it a basal bilaterian taxon, or is it nested somewhere within the Deuterostomia as phylogenomic results suggest?

• A Precambrian microcontinent in the Indian Ocean.

I place this paper here because it shows how quickly our knowledge in geology can change. I notice a lot of general ignorance about how geological advances are made. Many people don’t realise that geological maps are still drawn by hand during fieldwork, and that that’s how significant findings are made, for example. Anyway, this is far more sophisticated – geophysics and geochemistry hinting that Mauritius lie on an ancient, Precambrian microcontinent that split off from Madagascar in the early Tertiary.

• Embryos, polyps and medusae of the Early Cambrian scyphozoan Olivooides.

Olivooides has long been known as one of the more spectacular examples of fossil preservation, showing a nearly-complete developmental sequence from embryonal stages (Bengtson & Zhao, 1997). The specimens have always pointed to a scyphozoan affinity, and this paper reinforces that by examining even more awesomely-preserved specimens where the internal anatomy is visible.

• Disposable penis and its replenishment in a simultaneous hermaphrodite.

Placing here only because of the juvenile comedy value of “disposable penis”. And yes, it’s exactly what it sounds like: a sea slug that throws away its penis after mating, then grows another one again. My zoologist subconscious does have an idea for future research: is this mechanism somehow related to the evolution of the “love darts” of gastropods? It’s most likely a crazy idea, but who knows.

• Rapid evolution of troglomorphic characters suggests selection rather than neutral mutation as a driver of eye reduction in cave crabs.

Besides having a great methodology, I find this paper a neat demonstration of natural selection in action and will be incorporating it into my relevant lectures.

• Jaws for a spiral-tooth whorl: CT images reveal novel adaptation and phylogeny in fossil Helicoprion.

Edestid sharks were, back in the Permian, the dominant predators. Nowadays, they serve as a laughing stock for first year palaeontology students, who tend to find the coiled teeth that they sported menacing but ultimately ridiculous. This paper advances our knowledge of Helicoprion, the most famous of these weirdos, including details on how the tooth whorl fit into the jaw. Very interesting stuff; if you need an example of a cool and exotic-looking fossil, I recommend this paper.

• Specialized appendages in fuxianhuiids and the head organization of early euarthropods.

The only taboo subject on this blog is the evolution of the arthropod head, so I will not comment on this unless requested. Suffice it to say that it’s an important paper, although it won’t go down lightly.

• Mapping the Global Emergence of Batrachochytrium dendrobatidis, the Amphibian Chytrid Fungus. [OA]

Batrachochytrium dendrobatidis is a fungal pathogen of amphibians, causing the lethal disease chitridiomycosis. The pathogen and disease are so harmful that they’re single-handedly responsible for the decline in amphibian populations and species worldwide – the spread of the disease is currently being thought of as the primary factor causing the currently ongoing global amphibian extinction. Hence, studying it is of utmost conservation importance, and this paper is an important step forward, amassing geographical and epidemiological data in order to map out the global extent of the disease and its taxonomic reach, identifying which regions and taxa are most at risk.

• Enigmatic Liaisons in Lepidoptera: A Review of Same-Sex Courtship and Copulation in Butterflies and Moths. [OA]

I deal with deeply-ignorant homophobes all the time, especially when I see them claim that homosexuality is “unnatural” and “against evolution”. My usual response is a dump of papers showing rampant homosexuality in the animal kingdom. It puts things into perspective. Here’s a review of homosexuality in lepidopterans, a good addition to the anti-idiotic-homophobe literature.

Climate: The very basics

I know, this is a biology blog. But, well, all organisms live on Earth and have always been influenced by climate (how do you think humans managed to spread across the Earth?). In this series, we will look at the history of Recent climate (since 1 Ma ago) and its future (and perhaps later, I’ll do the entire history – I’ve already done the Neoproterozoic anyway). In this post, I just want to introduce the very basics of climate science, the prerequisites that you need to know to understand the rest of the series; chances are you already know all the info in this post.