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11 September 2007

Acquiring Genomes

Acquiring Genomes. A theory of the Origins of Species.
Lyn Margulis & Dorion Sagan ©2002
LM and her son by Carl Sagan , their most notorious book yet, wherein they attempt to overthrow the neo-Darwinian 'modern synthesis' orthodoxy. LM bravely allows a forward by the eminent Ernst Mayr who says "there is no evidence that any of the 10000 species of birds or the 4,500 species of mammals originated by symbiogenesis" - which undercuts the central message of the book. LM repeatedly decries mutations as the source of species, perhaps giving succor to creationists, of which she is vociferously not a member.
Opening shot: Darwin's The Origin of Species ironically never explains where new species come from.
LM posits a new definition of species: "composed of the same set of integrated genomes" which merely begs the question what is "same". Integrated genomes are terrific, LM is the queen of symbiogenesis, the matriarch of mitochondria, but in this book she and her son get a little silly. But it's an important read withal.
P11 "random mutation is wildly overemphasized." … "Mutation accumulation does not lead to new species"
P12 "The important … novelty comes from the acquisition of genomes"
Examples: green slugs with algae, lichen, cows with gut microbes…
LM dislikes lots of words in biology; cooperation, competition, mutualism… forced on science from politics… ANW "the fallacy of misplaced concreteness" other deficient terms: altruism, mutualism, higher organism…

"no evidence… shows unambiguous evidence that random mutation… leads to speciation. [I don't know what LM says about Lake Tanganyika, which is 14,000 years old and had 20 unique species of fish, for one familiar with billion year timespans, she seems impatient to await a dozen millennia to see new species]
"speciation … has never been directly traced"
P39 (microbes) play the major creative role in the genesis of new species

"Complex systems… reduce the gradients around them… an atmospheric pressure gradient, will take longer to reach the state of randomized chaos without.. a tornado…" - I will have to ponder this. If a tropical forest is cooler than desert sands, I suppose this has 'reduced' the gradient from the 6000° solar surface to the 3° of intergalactic space. Right now all I can see is that it has moved the temperature, so the gradient is less at the cold end, but surely the gradient is thereby steeper at the hot end? Meanders, which LM doesn't mention, perhaps provide a clearer example: steep river flow scours alternate banks, eventually the river is less steep and longer. Somehow this idea must be in LMs mind re climax systems…

LM famously has 5 kingdoms: (billions of years ago (ybp))
Bacteria 3.5, Protoctists 2.0, Fungi 0.45, Plants 0.45, Animals 0.6
She is annoyed with the current 3 kingdom model of Bacteria, Archaea, Eukaryotes. Because archaea are bacteria in her book. I hate that word 'protoctist', wish she'd picked a better term for all those nucleated single celled bugs that thrive in dirt and termites guts. nb not all are single-celled, 100 meter-long kelp are protoctists.

Lists of associations: Lichens, corals, ardisia's fluted leaves don't prove her case to me, but they are fascinating. A new example: the hundreds of 'bumps' on the ciliate protoctist Euplotidium, are actually bacteria. Each bacterium has an apical dome containing DNA and protein and tubules. The tubules are long hollow and 24nm in diameter, "surprisingly similar to the typical microtubules of eukaryotes." Sensitive to colchicines and antitubulin antibodies. "They are unquestionably microtubules… The presence of such structures in bacterial cells is rare, almost unknown". LM has been pushing the bacterial origin of microtubules for years, hampered by the absence of tubulin in bacteria. (bacterial flagella have a different protein) so these Euplotidium, passengers, with their protective harpoons, are a godsend to her theory. (not literally folks, LM and I share a distaste for the Miraculous Interventionist designer) Because in the wild, Euplotidium without its harpooners is rapidly eaten, LM calls the associates a new species.
"The natural selector is Gaia" - one of those statements so large as to be content-less.
LM introduces terms "friend, ally, kindness" which are apparently OK, perhaps because they don't come from economics ( see deficient terms above)

P72 "random mutations are important aspects of the evolutionary process… mutations do not create new species." Can LM have a bet both ways?

"Predatory bacteria penetrate their prey" - so we remain safe with Cavalier-Smith, "phagocytosis is the defining feature that sets the eukaryotes apart from bacteria"

250 or more human genes have come directly from bacteria. - cf Nick Lane (NL) 350 presumed to come from mitochondria

LM brings up punc-eq, discontinuities in the fossil record … "At least in easily recognized animals the species borders did not blur" - this sounds remarkably circular to me. There must be several dozen fossil variants in the horse evolution, how many hundreds would be required for LM to say 'no gaps' ?

LM apparently ascribed free choice to bacteria, she admits that Christian de Duve has called this 'biomysticism'
Bacteria have 20 metabolic modes - so they are more complex than us, from a biochemical viewpoint.

Wolbachia-like bacterial symbionts in rice weevils promote reproductive isolation. One of the key elements of speciation. (mixed matings of infected and uninfected are infertile)

"All photosynthetic organisms, either bacteria … or descendants of bacteria, leak organic compounds" - note that Nick Lane (NL) was keen to suggest that bacteria do not leak.
Clover root nodules have bacteria converted to oversized hole-ridden "bacteroids" . The pinkish color is from a hemoglobin… a chimera the protein part (globin) is made by the plant, the heme is made by the bacteria. So far only bacteria, or bacterial symbionts can fix N2 (the hemoglobin ferries toxic O2 away from the sensitive Nitrogenase. There are only a few tons of Nitrogenase on the planet, these days 2/3 of the Nitrogen in a Chinese boy's flesh comes from Natural Gas via the Industrial Haber-Bosch process (V Smil))

Early termites have guts full of microbes to digest wood. 'Higher' termites grow fungus in gardens, so they don't need the big gut. Macrotermes natalensis colonies: 1-2 million termites, 3m high, 9.5litre Oxygen per hour, 8l for fungal respiration. Heat generation 55W, 47W from the fungus. Since 80mybp??

Vernadsky 1926 The Biosphere saw life as a complex mineral… Locust swarms as flying mountains (I recall reading that V greatly over-estimated the mass of Locust swarms)..
"Living matter is the strongest geological force" … "without water as a lubricant the movement of crustal plates might have ground to a halt" - If Gaia has kept the place wet, she might be that important
How did she recover from "Snowball Earth" 600 mybp when glaciers were at the equator? Reduced photosynthesis? Did volcanoes assist? "Within 100my the earth was teeming with larger, more diverse, and more stunning forms of life"

Origin of the nucleus: "a peculiar story … detail not yet verified"
2000 mybp Thiodendron latens - still around. Actually a consortia of 2 bacteria; a rod that produced hydrogen sulfide and a filament forming spirochete that thrived in H2S. Something similar the origin of us all.

Dennis Searcy U. Massachusetts argued all nucleated cells evolved from a free-living wall-less microbe like Thermoplasma acidophilum. No flagella, no cell wall. Makes 'motility' proteins. Lives in hot acid fresh water. Produces H2S belongs to archaebacterial subkingdom (ie NL would call it Archaea)
…unlike nearly all other bacteria, produces histone-like proteins that surround its DNA
[but cf. NL "eukaryote histones resemble methanogen histones… the original host in the eukaryote merger was a methanogen."
-so we have a fundamental disagreement …]
Histones protect the DNA from hot acid?
LM proposes that a Thermoplasma-like archaebacterium formed an alliance with an eubacterium… "very much like today's Spirochaeta that craved the hydrogen sulfide to protect itself from oxygen." but they lived under "anoxic conditions" so the alliance benefit is unclear. The rise of oxygen around 2byp, presumed to be due to cyanobacteria seems central to all eukaryote origin stories. Searcy actually found that his own red blood cells generate "copious quantities of hydrogen sulfide when supplied with elemental sulfur" if the poisonous sulfide was removed as it was made… "they still 'remember' their origins" - a weird experiment, and its usually believed that cells lose chemical pathways that they don't use, efficiency and all that.
R H Gupta looked at amino-acid sequences in nucleated cells that lack mitochondria … "We believe that some of these protists descended from ancestors that never had them" - NL reckons that all a-mitochondrial protists once had mitochondria. He says that every one examined so far has traces of mitochondrial proteins in their nuclei. But recall the promiscuous swapping of bacterial DNA, and just maybe, those mitochondrial remnant genes just floated in. Gupta says that all nucleated cells have some protein sequences that resemble archaebacteria, and some that resemble eubacteria (like spirochetes). But nb Gupta is not claiming spirochetes. LM believes it was spirochetes in the original alliance, and that the spirochetes brought with them the nucleus and a motility organelle that evolved to become the undulipodium, the 9(2)+2 cilium and sperm tail, and the 9(3)+0 centriole. The big problem here is that modern spirochetes have a flagellum that is a different protein, not the tubulin in the undulipodium [check this] hence the significance of the bacterium (above) that had tubulin - 'rare' in bacteria. Part of the confusion is that eukaryotic cilia are sometimes called flagellae, but bacterial flagellae are a different protein [??]

Trichomonas vaginalis (annoying itch) tended to have 4 kinetosome centrioles, divide to become 8… with a thin fiber that formed between the old and the new… called a paradesmose.. acts to segregate nuclei during cell division.

Here LM has an annoying erratum that adds to the confusion. "the paradesmose is composed of standard 24 Angstrom-diameter microtubules (twenty-four nanometers (sic) in diameter) just like the spindle" Now an Angstrom is not the same as a nanometer, and in this area precise terminology helps. I don't have text-books to hand to tell the actual microtubule diameter, I believe its 24 nm, 24 Å is a bit small for a tube of proteins. I also lack a text to determine if spirochetes have tubulin, I'm fairly sure they don't, in the 90's I was watching the research to see if any tubulin-containing bacteria turned up. Very rare?]

Chap 10 has a delightful suggestion from Donald I Williamson U. Liverpool & Port Erin Lab. Isle of Man.
It is clear that "Extremely different adults (sea urchins, brittle stars) enjoy nearly identical larvae… whereas closely related adults (another urchin, or a starfish) develop from entirely different larvae. Williamson did some weird cross-phyla hybridization… Chordata hanky panky
…all echinoderms… lacked larvae until just after the Permo-Triassic mass extinction 225 million ybp… echinoderm survivors of several different classes acquired and retained adults with which they had illegitimately mated". Now Williamson reckons that all species that produce larvae, even caterpillars, acquired foreign genomes. He reckons that adult Peripatus look suspiciously like caterpillars. Perhaps they provided the larval genomes for several different insect genomes. I love this idea, its always been a mystery to me how insects form from tiny 'imaginal discs' in a larva - looks too much like parasitism. Not sure about Peripatus (which I once saw in a rotten log in a Manawatu paddock) - its rather possible that the 'caterpillar' shape is merely a convergent convenient form in which to crawl about.

Nudibranches that incorporate nematocyst stingers, and Luminous squid that incorporate glowing bacteria, are wonderful things, but don't really convince that symbiogenesis makes animal species mainly.

In the glossary:
Gunnera The only angiosperm group that forms regular symbiotic relationships with cyanobacteria. 45 species in the genus Gunnera all associated with Nostoc cyanobacteria. The largest species G. manicata is called "poor man's umbrella"

But in the text: "…Nostoc infects stem glands, leaf stalks… Gunnera is by no means the only sedentary land dweller thus fertilized by a cyanobacterium. Such odd couplings abound." - [??]

Azolla (water ferns, hence not angiosperm?) have special cells to hold Anabaena (a filamentous cyanobacteria)
All cycads are symbiotic with cyanobacteria.
Leguminoseas … soil rhizobial bacteria and root hair invasion is at least 100 million years old
[note the fungal association with roots is much older, perhaps to the first land plants, and at least 80% of plants connect with the "inland sea" of fungal hyphae. Cyanobacteria have only 'recently' (70-100mybp) noticed plants and jumped into bed with them].

Chap12. Another jumping gene story: Asian deer of the genus Munjiacus have between 3 and 23 chromosome pairs. Obviously a rapid way to genetic isolation and speciation. The "Karyotypic Fission theory" may apply to bats, rodents, other mammals and even to birds and reptiles.

So jumping chromosomes, duplicating genes, and jumping genomes are all around, but LM hasn't demolished mutations as the bedrock origin of novelty. The wonder is that DNA replication is so good that we are here at all, with just 500my before the seas get too hot for protein enzymes as we know them.

… … … …… … … …… … … …… … … …… … … …… … … …… … … …… … … …… … … …… … … …… … … …… … … …… … … …… …
11 Aug 07