Friday, June 14, 2019

Nick Lane --The Vital Question, Post #4 -- June 12, 2019

Three domains:
  • eukaryotes
  • archaea
  • bacteria
It appears, if I'm following Lane correctly, there are two types of cells: eukaryotes and prokaryotes.

So what happened to the archaea? Archaea are also prokaryotes.

So, we have prokaryotes (archaea and bacteria) and eukaryotes.


Confusing jargon: protists/archezoa/ancient animals -- these are eukaryotes that have lost their mitochondria; archezoa (protists) are found across all five eukaryote supergroups.

So, skip ahead to page 148 when, according to the index, several pages of discussion regarding the archaea.

Page 149: Lane suggests that the last common ancestor of bacteria and archaea, LUCA, may have been the product of selection acting on such populations of simple cells living in the pores of alkaline hydrothermal vents and dependent on natural proton gradients. Selection gave rise to sophisticated proteins, including ribosomes, Ech, and the ATP synthase -- all of which are universally conserved.

An antiporter -- active pumping -- arose independently in two distinct populations, which had diverged from a common ancestral population with the help of an antiporter:
methanogens are archaea
acetogens are bacteria
These two are representatives of the two great domains of prokaryotes, the deepest branches of the "tree of life."

Bacteria and archaea are similar in their DNA transcription and translation, ribosomes, protein synthesis, and so on, but differ in other fundamental respects, including cell membrane composition.

Page 151: two separate populations then invented pumping independently. One population, which ultimately became acetogens, reversed the direction of Ech, now oxidising ferredoxin and using the energy released to pump protons out of the cell ....

Page 153: the second population, which became methanogens, found an alternate way ...

Once each group had active pumps, there was finally an advantage to improving the membrane ... replete with phospholipids .... and the two domains appear to have done so independently, with archaea using one stereoisomer of glycerol, and bacteria using its mirror image.

Bacteria and archaea emerged independently ...

Now back to page 37 -- aha -- this is why I was confused ... I mis-read "archezoa." Archezoa are eukaryotes that lack mitochondria. An example of an archezoate: giardia.

So, the common ancestor to all extant eukaryotes had "everything" extant eukaryotes have except mitochondria (and chloroplasts?). Those came later.

Page 42: the simple "archezoa" are scattered across all five supergroups (that arose from the last common ancestor of the eukaryote; this again demonstrates their independent loss of the same cellular machinery).

So, finally I get it.

Forget about the archezoa. They are a red herring when trying to sort out the evolution.

Methanogens (archaea) and acetogens (bacteria) solved the problem of "pumping" independently and differently.

Now, how did eukaryotes all of a sudden pop up, seemingly out of nowhere? There are no "missing links," intermediate steps because eukaryotes "evolved" from archaea acquiring bacteria (mitochondria).

[Plants: eukaryotes absorbed a cyanobacterium. It then follows that plants have both mitochondria and chloroplasts.]

Both plants and animals need mitochondria to produce ATP.

Plants use chloroplasts to generate oxygen which is necessary for mitochondria. This leads to the next question: do plants need oxygen? Yes, they also need oxygen. Apparently the oxygen produced by chloroplasts is not enough oxygen needed for the plant to live. Apparently, leaves and stems would survive without oxygen because of the sunlight energy and chloroplasts -- chloroplasts generate oxygen -- but the roots that hold a plant in place, do not benefit from light. They get oxygen from the soil or the water. Water has very little free oxygen so "water plants" need to have roots near the surface where there is air and more oxygen.

So, protists/achezoa/ancient animals are eukaryotes that have lost their mitochondria.

"Extremophiles" are predominately prokaryotes (bacteria and archaea) but there are some eukaryote extremophiles.




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