Midichlorians, midichloria, and mitochondria

Nathan Lo is an evolutionary biologist interested in creepy crawlies, i.e. arthropods. Well, he’s Australian, so I guess that comes with the territory (see what I did there?). While postdoc’ing, he and his colleagues published a paper (Sassera et al., 2006) that would seem boring for anybody without an interest in taxonomy, a truly under-appreciated field.

The paper describes a bacterium that is a parasite for the mitochondria of a tick species called Ixodes ricinus, the nasty bugger responsible for Lyme disease. The authors obtained a female tick from Berlin, Germany and let it feed on a hamster until it laid eggs. By using genetic sequencing (you can use kits these days to extract the DNA, do PCR, gels and cloning, pretty much everything), electron microscopy (real powerful microscopes) and phylogenetic analysis (using computer softwares to see how closely related some species are) the authors came to the conclusion that this parasite they were working on is a new species. So they named it. And below is the full account of the naming, from the horse’s mouth, as it were:

“In accordance with the guidelines of the International Committee of Systematic Bacteriology, unculturable bacteria should be classified as Candidatus (Murray & Stackebrandt, 1995). Thus we propose the name ‘Candidatus Midichloria mitochondrii’ for the novel bacterium. The genus name Midichloria (mi.di.chlo′ria. N.L. fem. n.) is derived from the midichlorians, organisms within the fictional Star Wars universe. Midichlorians are microscopic symbionts that reside within the cells of living things and ‘‘communicate with the Force’’. Star Wars creator George Lucas stated that the idea of the midichlorians is based on endosymbiotic theory. The word ‘midichlorian’ appears to be a blend of the words mitochondrion and chloroplast. The specific epithet, mitochondrii (mi.to′chon.drii. N.L. n. mitochondrium -i a mitochondrion; N.L. gen. n. mitochondrii of a mitochondrion), refers to the unique intramitochondrial lifestyle of this bacterium. ‘Candidatus M. mitochondrii’ belongs to the phylum Proteobacteria, to the class Alphaproteobacteria and to the order Rickettsiales. ‘Candidatus M. mitochondrii’ is assigned on the basis of the 16S rRNA (AJ566640) and gyrB gene sequences (AM159536)” (p. 2539).

George Lucas gave his blessing to the Christening (of course he did).

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Acknowledgements: Thanks go to Ms. BBD who prevented me from making a fool of myself – this time – on the social media by pointing out to me that midichloria are real and that they are a mitochondrial parasite.

REFERENCE: Sassera D, Beninati T, Bandi C, Bouman EA, Sacchi L, Fabbi M, Lo N. (Nov. 2006). ‘Candidatus Midichloria mitochondrii’, an endosymbiont of the tick Ixodes ricinus with a unique intramitochondrial lifestyle. International Journal of Systematic and Evolutionary Microbiology, 56(Pt 11): 2535-2540. PMID: 17082386, DOI: 10.1099/ijs.0.64386-0. ABSTRACT | FREE FULLTEXT PDF 

By Neuronicus, 29 July 2017

The oldest known anatomically modern humans in Europe

A couple of days ago, on December 1st, was the National Day of Romania, a small country in the South-East of Europe. In its honor, I dug out a paper that shows that some of the earliest known modern humans in Europe were also… dug out there.

Trinkaus et al. (2003) investigated the mandible of an individual found in 2002 by a Romanian speological expedition in Peștera cu Oase (the Cave with Bones), one of the caves in the SouthWest of the country, not far from where Danube meets the Carpathians.

First the authors did a lot of very fine measurement of various aspects of the jaw, including the five teeth, and then compared them with those found in other early humans and Neanderthals. The morphological features place the Oase 1 individual as an early modern human with some Neanderthal features. The accelerator mass spectrometry radiocarbon (14C) direct dating makes him the oldest early modern human discovered to that date in Europe; he’s 34,000–36,000 year old. I’m assuming is a he for no particular reason; the paper doesn’t specify anywhere whether they know the jaw owner’s gender and age. A later paper (Fu et al., 2015) says Oase 1 is even older: 37,000–42,000-year-old.

After this paper it seemed to be a race to see what country can boast to have the oldest human remains on its territory. Italy and UK successfully reassessed their own previous findings thusly: UK has a human maxilla that was incorrectly dated in 1989 but new dating makes it 44,200–39,000 year old, carefully titling their paper “The earliest evidence for anatomically modern humans in northwestern Europe” (Higham et al., 2011) while Italy’s remains that they thought for decades to be Neanderthal turned out to be 45,000-43,000 years old humans, making “the Cavallo human remains […] the oldest known European anatomically modern humans” (Benmazzi et al., 2011).

I wonder what prompted the sudden rush in reassessing the old untouched-for-decades fossils… Probably good old fashioned national pride. Fair enough. Surely it cannot have anything to do with the disdain publicly expressed by some Western Europe towards Eastern Europe, can it? Surely scientists are more open minded than some petty xenophobes, right?

Well, the above thought wouldn’t have even crossed my mind, nor would I have noticed that the Romanians’ discovery has been published in PNAS and the others in Nature, had it not been for the Fu et al. (2015) paper, also published in Nature. This paper does a genetic analysis of the Oase 1 individual and through some statistical inferences that I will not pretend to fully understand they arrive to two conclusions. First, Oase 1 had a “Neanderthal ancestor as recently as four to six generations back”. OK. Proof of interbreeding, nothing new here. But the second conclusion I will quote in full: “However, the Oase individual does not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe.”

Now you don’t need to know much about statistics or about basic logic either to know that from 1 (one) instance alone you cannot generalize to a whole population. That particular individual from the Oase population hasn’t contributed to later humans in Europe, NOT the entire population. Of course it is possible that that is the case, but you cannot scientifically draw that conclusion from one instance alone! This is in the abstract, so everybody can see this, but I got access to the whole paper, which I have read in the hopes against hope that maybe I’m missing something. Nope. The authors did not investigate any additional DNA and they reiterate that the Oase population did not contribute to modern-day Europeans. So it’s not a type-O. From the many questions that are crowding to get out like ‘How did it get past reviewers?’, ‘Why was it published in Nature (interesting paper, but not that interesting, we knew about interbreeding so what makes it so new and exciting)?’, the one that begs to be asked the most is: ‘Why would they say this, when stating the same thing about the Oase 1 individual instead about the Oase population wouldn’t have diminished their paper in any way?’ .

I must admit that I am getting a little paranoid in my older age. But with all the hate that seems to come out and about these days EVERYWHERE towards everything that is “not like me” and “I don’t want it to be like me”, one cannot but wonder… Who knows, maybe it is really just as simple as an overlooked mistake or some harmless national pride so all is good and life goes on, especially since the authors of all four papers discussed above are from various countries and institutions all across the Globe. Should that be the case, I offer my general apologies for suspecting darker motives behind these papers, but I’m not holding my breath.

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References:

1) Trinkaus E, Moldovan O, Milota S, Bîlgăr A, Sarcina L, Athreya S, Bailey SE, Rodrigo R, Mircea G, Higham T, Ramsey CB, & van der Plicht J. (30 Sep 2003, Epub 22 Sep 2003). An early modern human from the Peştera cu Oase, Romania. Proceedings of the National Academy of Sciences U S A,  100(20):11231-11236. PMID: 14504393, PMCID: PMC208740, DOI: 10.1073/pnas.2035108100. ARTICLE  | FREE FULLTEXT PDF

 2) Higham T, Compton T, Stringer C, Jacobi R, Shapiro B, Trinkaus E, Chandler B, Gröning F, Collins C, Hillson S, O’Higgins P, FitzGerald C, & Fagan M. (2 Nov 2011). The earliest evidence for anatomically modern humans in northwestern Europe. Nature. 479(7374):521-4. PMID: 22048314, DOI: 10.1038/nature10484. ARTICLE | FULLTEXT PDF via ResearchGate

3) Benazzi S, Douka K, Fornai C, Bauer CC, Kullmer O, Svoboda J, Pap I, Mallegni F, Bayle P, Coquerelle M, Condemi S, Ronchitelli A, Harvati K, & Weber GW. (2 Nov 2011). Early dispersal of modern humans in Europe and implications for Neanderthal behaviour. Nature, 479(7374):525-8. PMID: 22048311, DOI: 10.1038/nature10617. ARTICLE | FULLTEXT PDF via ResearchGate

4) Fu Q, Hajdinjak M, Moldovan OT, Constantin S, Mallick S, Skoglund P, Patterson N, Rohland N, Lazaridis I, Nickel B, Viola B, Prüfer K, Meyer M, Kelso J, Reich D, & Pääbo S. (13 Aug 2015, Epub 22 Jun 2015). An early modern human from Romania with a recent Neanderthal ancestor. Nature. 524(7564):216-9. PMID: 26098372, PMCID: PMC4537386, DOI:10.1038/nature14558. ARTICLE | FREE FULLTEXT PDF

By Neuronicus, 3 December 2016

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Pic of the Day: Neil on teaching creationism

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Dr. deGrasse Tyson’s picture is from Wikimedia released under PD and the quote is from a “Letter to the Editor” of New York Times retrieved from the Hayden Planetarium website on Nov. 2, 2016.

Lucy’s 9 vertebrae are actually 8

Lucy
Lucy. Left: picture of the real skeleton. Middle and Right: reconstructions. Courtesy of Wikipedia

As Google reminded us, today is 41st anniversary of the finding of Lucy, the first discovered member of the species Australopithecus afarensis. Lucy lived in Ethiopia about 3.2 million years ago and the most extraordinary fact about her is that her fossil represents the first evidence of bipedalism in a hominin (we are also hominins).

Lucy is one “missing link” (not ‘missing’ anymore, obviously) between the common ancestor of humans and chimpanzees and humans because she has ape-like features (jaw, forehead, long arms, small cranium) and human-like features (knee, ankle, lumbar curve, pelvic bones) and walked upright.

Meyer et al. (2015) wanted to do a comprehensive reconstruction of Lucy for display at the American Museum of Natural History in New York. During this work they noticed that one vertebrae of the total of nine found is kindda small compared to the other ones. So they set to measure vertebrae form all sorts of other species, alive and extinct, and after some factor analysis they concluded that out of Lucy’s nine found vertebrae, the little one is not actually hers, but belongs to a different species from the genus Theropithecus (a baboon ancestor).

This finding is functionally uninformative and their “work does not refute previous work on Lucy or its importance for human evolution, but rather highlights the importance of studying original fossils, as well as the efficacy of the scientific method.” In other words, give the poor anthropologists not reconstructions but the original fossils to work with (most people worked with Lucy’s reconstructions which missed some details, thus allowing this pesky vertebra to remain miss-cataloged for 40 years).

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The new alignment from doi: 10.1016/j.jhevol.2015.05.007

This is the first paper of pure anthropology that I have read in full and let me tell you that I found a lot of curious things, unrelated to Lucy. Like, for example, from an anthropologist’s point of view, an adult is someone with the third molar completely erupted. We should then look into the people’s mouths before giving them the keys to the wine cellar, because some 21-year olds are definitely not adults. Also, instead of a medical doctor, get an anthropologist to teach anatomy, because oh boy do these people know their skeletons! Here is an excerpt from the Methods section: “The overall size of the A.L. 288-1am partial vertebra was calculated as the geometric mean of six linear dimensions: lamina superoinferior height and dorsoventral thickness, pars interarticularis width, interarticular facet height, and superior and inferior articular interfacet maximum transverse widths. The pars interarticularis geometric mean includes three variables from the pars interarticularis: lamina superoinferior height and dorsoventral thickness, and pars interarticularis width” (p. 175).

All in all, nice!

Reference: Meyer MR, Williams SA, Smith MP, Sawyer GJ (August 2015, Epub 6 Jun 2015). Lucy’s back: Reassessment of fossils associated with the A.L. 288-1 vertebral column. Journal of Human Evolution, 85:174-80. doi: 10.1016/j.jhevol.2015.05.007. Article | FREE FULLTEXT PDF

By Neuronicus, 24 November 2015

 

Viruses are as alive as crystals

Crystal of ultrapure bismuth. Photo credit: Intangir (public domain)
Crystal of ultrapure bismuth. Credit: Intangir. License: PD

The biology hype of the week is the notion that viruses are alive. Well, the true answer to that is… maybe. But that’s not catchy enough for headlines, is it?

Let’s start, as usual, with the source. Nasir & Caetano-Anollés (2015) published a paper where they did a lot of computer sniffing in existing proteomics databases to find out that viruses express a few dozen unique protein folds and they share several hundred more with cells. In other words, some of the viral proteins are unique. Using this information and some neat math they managed to calculate an evolutionary tree, that is, they classified the viruses via genetic relatedness to themselves and living organisms. That’s the strictu sensu of the term “tree of life”. From this taxonomy exercise, the authors speculate about when and how viruses might have appeared. They concluded that viruses appeared as RNA chunks spat out of cells. To give you a little background, there are two main hypotheses about the origin of viruses: appeared before cells as free floating RNA, or they were pieces of RNA that have been kicked out of a living cell, so after the evolution of cells. All well and good, I’m not going to open that can of worms, which hypothesis is more supported from data and so on.

Now, and this is the contentious part, verbatim: “Here, we put forth the bold conjecture of a universal tree of life (uToL) that describes the evolution of cellular and viral proteomes. […]. Thus, viruses should be considered “living” organisms that simply survive by means of an atypical reproduction method that requires infecting a cell ” (p.18.). It’s their opinion. Not a fact. Not – and this is important – a direct consequence of their awesome taxonomy exercise. For a formal definition, a conjecture is an opinion or conclusion formed on the basis of incomplete information (Oxford Dictionary).

Don’t get me wrong, I think this is a neat paper, and, frankly, I don’t have a horse in this race: I don’t care whether viruses are alive or not. But I do care to distinguish between fact and opinion, an intellectual exercise that seem to have eluded the science websites and science popularization zines and e-zines like EurekaAlert, IFLS, ScienceAlert, Gizmodo, Daily Mail, Wired, Popular Science, R & D Magazine, Laboratory Equipment, and many others, who ran titles saying “Viruses are alive” in just so many words. Note that even the authors themselves put the word “living” between quotes. Know the difference between opinion (that is, we think that because x makes y, maybe x is blue) and a scientific fact (x makes y, y makes z, therefore x must make z and we know that not only because it’s logical, but also because no other wretched letter wants to make z, believe us we tried, we made sure z is where we put it, because we put dye on it, we measured it, chopped it, looked at it with 5 different instruments, and we cannot make z without x though a poor grad students tried and tried in vain, we even modeled z, and yes, it is made by x, otherwise known as we eliminated all other testable bloody possibilities that we could think of. Unless q makes z in humans, but we can’t measure that. Or r makes z under Jovian gravity, but we didn’t get a grant for that…. get my drift what a scientific fact is?).

Now, rant is not over. The authors argue that viruses have a sort of metabolism and they replicate, so they meet the requirements for being classified as alive. I argue that either these two conditions are not enough for something to be considered alive, or we have then to conclude that cave crystals are also alive. Crystals only grow in the appropriate environment of a saturated solution and bits shattered off from them go into an inert mode waiting for appropriate conditions. Crystal growth can even be looked at as a sort of metabolism. So, if they are willing to characterize crystal growth as somewhere on the continuous scale of life, viruses can be there as well. Using their analogy, the living, metabolically active form for crystals is when they are growing in a saturated solution; and bits breaking off or the bulk waiting for solution conditions to change is just an atypical reproductive scheme. It even gets more interesting with some of the more modern more complicated crystal growth theories with preassembly into nanocrystals, editing or incorporating defects, etc. Ok, I’m getting tired and I made my point anyway. Rant over. Happy debating!

Reference: Nasir, A. & Caetano-Anollés, G. (25 September 2015). A phylogenomic data-driven exploration of viral origins and evolution. Science Advances, 1(8): 1-24. DOI: 10.1126/sciadv.1500527. Article | FREE PDF

by Neuronicus, 29 September 2015

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