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Archaeal ribosomes are like eukaryotic not bacterial forms

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Celebaelin
1378603.  Tue Apr 06, 2021 8:40 am Reply with quote

The thing is justification for the 'endocytosed bacteria' explanation of both mitochondria and chloroplasts (and the nucleus) has taken occasional hits from mere trifling details like 'mitochondria are not usually present as distinct units but rather as a network' and 'the mitochondrial network is contiguous with the endoplasmic reticulum'. Not only that but we continue to amass ever more experimental data that undermines any confidence we might retain in the concept of symbiogenesis.

However when investigations provide evidence which does not support the proposition, like this negative result from 2018, there is an overwhelming tendency to ignore it and merely re-iterate the same stale and increasingly unlikely doctrine.

Quote:
Mitochondria’s Bacterial Origins Upended

Contrary to some hypotheses, the organelles did not descend from any known lineage of Alphaproteobacteria, researchers find.

https://www.the-scientist.com/daily-news/mitochondrias-bacterial-origins-upended-33345

Deep mitochondrial origin outside the sampled alphaproteobacteria
Joran Martijn, Julian Vosseberg, Lionel Guy, Pierre Offre & Thijs J. G. Ettema
Nature volume 557, pages101–105(2018)

It's getting a bit embarrassing frankly.

Just to be clear I'm not saying that a good deal of the DNA of eukatyotes isn't bacterial in origin (there is some strong evidence to suggest it is) but I am saying that DNA molecules bearing bacterial or archaeal genes could enter a proto-eukaryote from any/multiple sources by tranformation/transfection and become incorporated into the host's functional genome and expressed without the necessity of being carried in an endosymbiote.


Last edited by Celebaelin on Tue Apr 06, 2021 9:08 am; edited 1 time in total

 
ali
1378604.  Tue Apr 06, 2021 8:54 am Reply with quote

When I was at school, we were taught that living things divided into animals and plants - full stop. Even in those dim-and-distant days of the early '70s, this was out of date: Whiitaker's 5-kingdom model was devised in the late 60s. While things have moved on, I find it rather shocking that even now, a version of Whittaker's classification is still being taught at A level. Under this classification, Bacteria and Archaea (both in Kingdom Prokaryotae) are considered less disparate than plants (Kingdom Plantae) and fungi (Kingdom Fungi).

That some biologists are failing to engage with the latest ideas on the origin of Eukaryota, seems unsurprising in this light.

 
Celebaelin
1378609.  Tue Apr 06, 2021 9:42 am Reply with quote

I've just read a 2010 article from Genome Biology which is a prime example of what I'm talking about.

It ties itself in knots over the problems of reconciling endosymbiosis of an α-proteobacteria alongside the essentially known* archaeal origins of certain mechanisms

Quote:
Strikingly, this archaeal heritage seems to be patchy with respect to the specific origins, with apparent evolutionary affinities to different groups of archaea (Table 1 and Figure 4). For instance, comparative analysis of the translation system components tends to suggest an affinity between eukaryotes and Crenarchaeota. Similarly, the core transcription machinery of eukaryotes shares some important proteins with Crenarchaeota, Thaumarchaeota and Korarchaeota, to the exclusion of Euryarchaeota.

but doesn't stop to consider that the origins of the bacterially inherited portions of the genome might be similarly disparate. The paper predates the 2018 work discounting all known α-proteobacterial lineages but it is still a touch short-sighted in terms of its search for the truth regarding the LECA (Last Eukaryote Common Ancestor).

You might find the mixed origins of certain highly important eukaryotic enzymes rather interesting.



Yep, some of our DNA is borrowed from bacteriophages - they're viruses that feed on bacteria.

* ie statistically highly likely

The origin and early evolution of eukaryotes in the light of phylogenomics
Eugene V Koonin
Genome Biology volume 11, Article number: 209 (2010)


Last edited by Celebaelin on Tue Apr 06, 2021 1:24 pm; edited 1 time in total

 
suze
1378623.  Tue Apr 06, 2021 11:24 am Reply with quote

ali wrote:
When I was at school, we were taught that living things divided into animals and plants - full stop.


So were we, and that was late 70s to early 80s.

Fungi were "plants", seeing as how they live in the ground and don't go anywhere. Bacteria were "animals", and so were viruses - much as modern opinion has it that viruses are not living things at all.

The treatment of viruses didn't go far beyond "They exist, they make you sick, we don't really know much about them", but we were told to consider them as being like bacteria only different. It was hinted that there wouldn't be any questions about viruses in the exam, and no more were there.

 
Celebaelin
1378636.  Tue Apr 06, 2021 1:48 pm Reply with quote

I'm amazed; bacteria have been considered as separate from plants and animals since the 1860's.

Mind you since published classifications usually still lump Bacteria and Archaea together as prokatyotes as opposed to the rest being eukatyotes it could be suggested that taxonomy has a tendency lag behind the science until a new consensus is finally settled on some time after the last of the grandees of the previous classification has passed into extinction. The voyage of discovery that is the gradual unveiling of the role of the Archaea is proving something of a problem to many.

 
suze
1378645.  Tue Apr 06, 2021 4:37 pm Reply with quote

Celebaelin wrote:
I'm amazed; bacteria have been considered as separate from plants and animals since the 1860's.


This is your field, and it really isn't mine - but sadly, it wouldn't surprise me if school science even now were teaching stuff that has been known to be wrong for 150 years.

To draw a parallel with a subject that I know a bit more about, even now school history teaches that Columbus "discovered America", and he just didn't.

For one thing, he never set foot on the mainland American continent. He went to what is now The Bahamas and what is now the Dominican Republic, but never to the mainland. Where he thought he was when he went to those places, God only knows.

OK, that was a minor quibble. But for a much bigger thing, the Norsemen were there five hundred years before him. When I was in school that was treated as fantasy fiction. It gets slightly more coverage by now, but it's still taught very much as a footnote to Columbus - when in fact, it ought to be the story and Columbus the footnote.

But just as with taxonomy, we probably need a whole generation of historians to be dead before it will be taught the right way around.

 
Brock
1378687.  Wed Apr 07, 2021 5:23 am Reply with quote

suze wrote:

To draw a parallel with a subject that I know a bit more about, even now school history teaches that Columbus "discovered America", and he just didn't.


I remember being taught at primary school that the Vikings were in America before Columbus. Maybe I had a very enlightened teacher.

Quote:
For one thing, he never set foot on the mainland American continent. He went to what is now The Bahamas and what is now the Dominican Republic, but never to the mainland. Where he thought he was when he went to those places, God only knows.

OK, that was a minor quibble. But for a much bigger thing, the Norsemen were there five hundred years before him.


Does that mean that he didn't "discover" it, though? He certainly wasn't previously aware of its existence - the Viking settlements weren't known about in the 15th century. He may not have been the first European to set foot on American soil, but I think you can argue that it was a genuine discovery. Maybe "rediscovered" would be a more accurate term.

This "discovery" concept is entirely Euro-centric, anyway. According to this article there were people in the American continent 15,000 years ago, and possibly as far back as 20,000 years ago.

As to why Columbus is the main story rather than a footnote, I suppose the historical significance of Columbus' voyage is that it was the one that led to widespread European colonization of the Americas.

 
Celebaelin
1378697.  Wed Apr 07, 2021 6:30 am Reply with quote

Another one in biochemistry is Michaelis-Menten Enzyme Kinetics.

Not merely out of date but WRONG. So very, very wrong.

This 108 years old hogwash is a modification of the Monod equation and would only apply to 1st order reactions even if it were applicable; which mostly, and perhaps entirely, it isn't.

This manifests as massive problems with reproducibility so for the most part researchers avoid it and use turnover number instead but it's still taught AFAIK. I had to reassure swot about the matter back when she was studying because she couldn't get her head round it and she was greatly relieved to find out that the reason why it's so impenetrably presented is that it's BOLLOCKS.

There are of course other examples of inertia in teaching in my field (or one corner of it or another) including enlightening work published in the 1930s which isn't taught yet; it makes me so angry that valuable work (which you can see must be correct when the maths is applicable) is just shunted aside like this without even being given consideration while work that is essentially an incorrect 19th century approach to understanding enzymic function is reproduced and regurgitated by the hapless, clueless or malignant to the detriment of science in general and their pupils in particular.

GAH!


Last edited by Celebaelin on Thu Apr 08, 2021 7:54 am; edited 4 times in total

 
suze
1378703.  Wed Apr 07, 2021 8:20 am Reply with quote

Brock wrote:
I remember being taught at primary school that the Vikings were in America before Columbus. Maybe I had a very enlightened teacher.


That pleases me, but yes you did.

I had the "advantage" of going to school in North America - and at that age we were taught that the Vikings were never there, and anyone who claimed that they were had been reading too many Marvel comics. Or words to that effect.


Brock wrote:
He certainly wasn't previously aware of its existence - the Viking settlements weren't known about in the 15th century. He may not have been the first European to set foot on American soil, but I think you can argue that it was a genuine discovery. Maybe "rediscovered" would be a more accurate term.


I won't go into detail here since it's not the actual topic of this thread, but I disagree. My position is that Columbus decided to go there precisely because he'd heard about the Norse voyages.

Much as the Norsemen could read and write, they didn't do it very much and so not very many people knew about their voyages. Even so, there were references to their voyages in print well before Columbus. Since he didn't spend his days in a monastic library Columbus probably hadn't read them - but he had been to Reykjavík, where knowledge of the Norse voyages was surely more common than it was anywhere else.

I'd quite like to write a book about this one day, and when I'm retired I might even do it!


Brock wrote:
This "discovery" concept is entirely Euro-centric, anyway. According to this article there were people in the American continent 15,000 years ago, and possibly as far back as 20,000 years ago.


Of course. Before about 1950, that was taught as "Yea well, the Indians, scarcely human, couldn't read and write, weren't Christian, don't count", and I fear that it may still be taught a bit like that as regards Australia.

 
Celebaelin
1378719.  Wed Apr 07, 2021 3:06 pm Reply with quote

suze wrote:
Where he thought he was when he went to those places, God only knows.

As you probably know he told Ferdinand and Isabella he was looking for a Western route to China, India and the East Indies and that's what they wanted from him. Whether he knew he wasn't in the Indian Ocean when he landed in the West Indies is another question.

suze wrote:
My position is that Columbus decided to go there precisely because he'd heard about the Norse voyages.

I've not before heard the suggestion that the rediscovery of the Americas was deliberate on Columbus's part. If that is the case his route was a bit Southerly wasn't it since he never sailed North of Lisbon and the Norsemen who 'preceded' him went via Iceland and Greenland something like 3500km further North.

 
suze
1378726.  Wed Apr 07, 2021 5:19 pm Reply with quote

Celebaelin wrote:
As you probably know he told Ferdinand and Isabella he was looking for a Western route to China, India and the East Indies and that's what they wanted from him. Whether he knew he wasn't in the Indian Ocean when he landed in the West Indies is another question.


He couldn't tell Ferdinand and Isabella that he was looking for America, because they wouldn't have believed his claim that it existed and wouldn't have invested in a fairy story. So he said that he wanted to find the back route to India, but he knew even before he left that he wouldn't find it.

That is my contention, anyway. On the other hand, he probably did think he had found the American mainland when in fact he hadn't. Whether he thought he had found the very Vinland that the Norsemen had been to half a millennium earlier is another question entirely.

There is some evidence that he wasn't a particularly good navigator (or alternatively, he was but he deliberately falsified his Captain's Log). He apparently believed Iceland to be a long way north of where it actually is, and we wouldn't necessarily know about it if he had pointed at Vinland but actually ended up rather further south.

Neither can we rule out the possibility that the folk he met while he was in Reykjavík had - whether through ignorance or mischief - given him wrong information as to the way to Vinland. Or perhaps he had reason to believe that America was large, and so the shortest route across the Atlantic would do.

Come back to me in fifteen years' time when I've written my book!

 
Celebaelin
1378727.  Wed Apr 07, 2021 8:37 pm Reply with quote

Getting back to the Bio stuff people are already studying the evolution of at least one of the proteins responsible for competence i.e. the ability to be transformed by (internalise) free extracellular DNA.

This gets a bit technical (if you didn't think it was so already) but what they're looking at is sequences of DNA which code for domains (sub-sections of the ComEC protein as a whole if you like) and how they have moved around in bacteria.

So far natural competence has been identified in only approximately 80 species but 96% of the roughly 6000 bacterial genomes examined contain a single competence domain. The lack of clarity regarding domains, sub-domains and the absence of any precise distinction between the two requires a clarity of expression which is not always easily attained but it appears that three distinct sub-domains are found within ComEC only one of which is consistently inherited alongside functional competence - the C (for Competence) domain.

Quote:
Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions.

https://www.ebi.ac.uk/interpro/entry/InterPro/IPR004477/

Model of the DNA-uptake machinery of V. cholerae (image too large)

Quote:
In gram-negative bacteria, initiation of outer membrane double-stranded DNA (dsDNA) uptake into the periplasmic space involves proteins related to components of the type IV pilus, the type II secretion system (Chen and Dubnau, 2004), or the type IV secretion system (Hofreuter et al., 2001). The dsDNA then binds to ComEA, which is hypothesized to pull the transforming DNA into the periplasm and is present in both gram-positive and gram-negative species (Bergé et al., 2002; Matthey and Blokesch, 2016). One strand of the dsDNA is then subject to degradation, for example, by the nuclease EndA in Streptococcus pneumoniae (Puyet et al., 1990) or by a putative nuclease domain of the ComEC protein in Bacillus subtilis (Baker et al., 2016). The single-stranded DNA (ssDNA) retained from degradation of its complement strand is then transported by a conserved ComEC protein into the cytosol (Draskovic and Dubnau, 2005; Baker et al., 2016). In a following step, the cytosolic ssDNA is recognized by DprA and recombined into the genomic DNA by RecA (Mortier-Barričre et al., 2007).

The homologous interaction with existing bacterial DNA does not always occur. A cell transformed with plasmid DNA would generate a separate self-replicating double stranded loop by using cellular DNA polymerase to regenerate its complementary strand for example.

DNA-uptake machinery of naturally competent Vibrio cholerae
Patrick Seitz and Melanie Blokesch
PNAS October 29, 2013 110 (44) 17987-17992

Natural Competence and the Evolution of DNA Uptake Specificity
Joshua Chang Mell, Rosemary J. Redfield
Journal of Bacteriology 31 January 2014

Evolution of the Natural Transformation Protein, ComEC, in Bacteria
Zachary T. Pimentel and Ying Zhang
Front. Microbiol., 12 December 2018

 
CB27
1378753.  Thu Apr 08, 2021 6:49 am Reply with quote

suze wrote:
Or perhaps he had reason to believe that America was large, and so the shortest route across the Atlantic would do.

That would suggest to me to be a case of very bad navigation.

His whole argument was that the world was round, so if he thought the part of America that the Norse had found was stretching all the way south, he should have realised that the distance at the latitude he was travelling would have been tremendously greater than the distance at the latitude Iceland was in.

 
crissdee
1379092.  Sun Apr 11, 2021 5:41 am Reply with quote

No one of any consequence doubted that the world was round by that time, AIUI, his effort was aimed at proving that it was possible to carry enough stores to make it across the Atlantic, i.e. that the journey in and of itself was possible.

 
Jenny
1379116.  Sun Apr 11, 2021 9:34 am Reply with quote

Cele I remember that when my first husband went to university in 1966 to study Chemistry, one of the first things he was told was to forget everything he'd learned at A level. Sounds as if it was similar in your field? Or did that happen to be a particularly turbulent time in the world of science studies?

 

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