From the website:
Utilizing over 300 scanned documents, photographs, audio clips and video excerpts, this website narrates the breathless details of the pursuit of the discovery of the double helix structure of DNA. Scattered throughout the project are images of a number of very important and extremely rare items, most of which are held within the Oregon State University Libraries' Ava Helen and Linus Pauling Papers, and many of which have not been previously displayed. It is expected that this website will serve as a primary reference point for individuals interested in the history of DNA.Vital Question: Energy, Evolution, and the Origins of Complex Life, Nick Lane.
I'm not sure why I posted these two items (the Linus Pauling website linked above and the book by Nick Lane on this page.
Introduction: Why is life the way it is?
A common ancestor 4 billion years ago; was this a freak accident or did other "experiments" fail?
That ancestral cell was complex, and already looked a lot like cells that exist today; all complex living cells appear very, very similar.
Timeline:
- life arose about one-half billion years after the earth's formation
- got stuck at the bacterial level of complexity for more than 2 billion years; half the age of our planet
- that singular ancestor arose 1.5 to 2 billion years ago
- that singular ancestor was recognizably a "modern" cell; no surviving intermediaries, no "missing links"
Part of the reason: biologists afraid of issues of creationism and intelligent design: to admit we don't know, opens the door to naysayers, who deny we have any meaningful knowledge of evolution.
Three major revolutions that wrecked our view of life in the past half century:
- Lynn Margulis, 1967; endosymbiosis (mitochondria and chloroplasts)
- Carl Woese, phylogenetic revolution; protein taxonomy; a single gene tracked; bacteria, archaea, and eukaryotes are genuinely distinct groups; Woese's revolution was real
- how do the first two revolutions relate; this revolution is on-going
Radical proposition: that complex life arose from a singular endosymbiosis between an archaeon host cell and the bacteria that became mitochondria: predicted by the brilliantly intuitive and free-thinking evolutionary biologist Bill Martin, 1998; based on a "mosaic," a mosaic he pretty much uncovered himself.
The example: fermentation --
- archaea do it one way
- bacteria do it another way
- but get this: eukaryotes have a few genes from bacteria, a few from archaea; they fuse them together and do fermentation their own way, a third way. This mosaic applies to almost all biochemical processes in complex cells.
The reason Martin's hypothesis is not well known/well understood/taught is because it is confounded with the serial endosymbiosis theory (Margulis).
Again, the long paragraph on page 11: the acquisition of the bacterial cell (that became mitochondrium) is the origin of complex life.
We'll have to see how that differs from Margulis' theory.
Why did this happen? Why did archaea and bacteria not evolve; why did they remain so separate in their genetic makeup?
The author then gets to his thesis, p. 13: "I believe the clue lies in the bizarre mechanism of biological energy generation of cells....proticity...the use of cross-membrane proton gradients to power cells was utterly unanticipated. First proposed in 1961 and developed over the next three decades ... by Peter Mitchell ... has been called the most counterintuitive idea in biology since Darwin, and the only one that compares with the ideas of Einstein, Heisenberg, and Schrodinger in physics."
Proton power is as much an integral part of all life as the universal genetic code. Two questions:
- why did life evolve in this perplexing way, and
- why are cells powered in such a peculiar fashion
In the next paragraph, he does say the two questions are closely intertwined. The author:
- "hopes to persuade you that energy is central to evolution
- that we can only understand the properties of life if we bring energy into the equation."
- this relationship between energy and life goes right back to the beginning
- that the fundamental properties of life necessarily emerged from the disequilibrium of a restless planet
- that the origin of life was driven by energy flux
- that proton gradients were central to the emergence of cells
- that proton gradients constrained the structure of both bacteria and archaea
The author wants to prove that a rare event, an endosymbiosis in which one bacterium got inside an archaeon, broke those constrants, enabling the evolution of vastly more complex cells.
And much, much more -- top of page 14.
He wants to show that this was incredibly difficult and thus that is why it happened only once.
He wants to show how this predicted other traits of complex cells:
- the nucleus
- sex
- two sexes
- even the distinction between the immortal germline and the mortal body -- the origins of finite lifespan and genetically predetermined death
The author collaborated with Bill Martin in Dusseldorf and Andrew Pomiankowski, a mathematically minded evolutionary geneticist at University College London.
Part I: The Problem
1: What is life?
... need to go back and pick up the beginning...
Starting on page 45:
The missing steps to complexity:
This is the recurring theme: "evolutionary theory predicts that there should be multiple -- polyphyletic -- origins of traits in which each small step offers a small advantage over the last step. Theoretically that applies to all traits ... so what about sex, or the nucleus, or phagocytosis? The same reasoning ought to apply...."
This is what the book is all about. Eukaryotic cells all "look" alike and all use same ways to generate energy -- monophyletic, not polyphyletic.
It will be interesting to see if there's any way to connect this with Stephen Jay Gould and the Cambrian explosion?
Sex: bacteria have all the genes to practice full sex. However, only eukaryotes practice 'total sex' but bacteria only a pallid half-hearted from of sex.
The same goes for the nucleus and phagocytosis -- andmore or less all eukaryotic traits -- bacteria have the genetic capability but it doesn't happen.
Author makes the case that it is not due to evolutionary competition between bacteria and eukaryotes.
Archezoa: not evolutionary intermediates, but they're real ecological intermediates.They occupy the same niche. An evolutionary intermediate is a missing link. An ecological intermediate is not a true missing link but it proves that a certain niche, a way of life, is viable.
Why archezoa are important: they are ecological intermediates which prove that a certain way of life is viable. Like flying squirrels -- nothing like real flying animals (birds, bats, etc) but flying squirrels show that gliding from tree to tree is a viable way of life.
I have to back and find when the author switched over to a discussion of archezoa vs archaeabacteria -- he did this starting on page 38, but first mentioning the word "archezoa" on page 39. The biologist Cavalier-Smith came up wit the word "archezoa" and advocated a separate kingdom for archezoa but that has fallen out of favor.
From wiki: Archezoa was a kingdom proposed by Thomas Cavalier-Smith[1][2] for eukaryotes that diverged before the origin of mitochondria. At various times, the pelobionts and entamoebids (now Archamoebae), the metamonads, and the Microsporidia were included here. These groups appear near the base of eukaryotic evolution on rRNA trees. However, all these groups are now known to have developed from mitochondriate ancestors, and trees based on other genes do not support their basal placement. The kingdom Archezoa has therefore been abandoned.[3] Archaezoa is composed of two kingdoms of protists, Kingdom Diplomadida and Kingdom Parabasala. These 2 kingdoms are grouped together because they lack mitochondria. The Archaezoa hypothesis suggests that these two kingdoms originally had mitochondria, but lost them before mitochondria became symbionts of protists. This lineage is believed to be the proof of Eukaryotic Endosymbiosis.[by whom?] Molecular evidence indicates that Archaezoa have the genetic marker of mitochondria in their nucleus that suggests they had and then lost mitochondria.[citation needed] Both of these kingdoms are parasites, as they have to acquire ATP from some source. An example of these Archaezoans is Trichomonas vaginalis, a common urinary infection that is transmitted through sexual contact.In his book, Lane states this as fact but I wonder if there is still some discussion. Lane says: the archezoa were once one eukaryotes with mitochondria. But, as parasites, when they found a new niche, they "lost" their mitochondria. They have mitochondria-like structures called mitosomes or hydrogenosomes -- but these are not mitochondria, and archezoa require a source of ATP from their hosts. Giardia and Chlamydia are great examples of archezoa that have lost their mitochondria and depend on their hosts for ATP.
Lane says the combination of molecular and phylogenetic data shows that hydrogenosomes and mitosomes are indeed derived from mitochondria, not some other bacterial endosymbiont.
Thus, all eukaryotes have mitochondria in some form or another. Archezoa (not archaea) are a form of eukaryotes (also a catch-all term is "protists".)
LANE: "The fact that all eukaryotes have mitochondria may seem to be a trivial point, but when combined with the proliferation of genome sequences from across the wider microbial world, this knowledge has turned our understanding of eukaryotic evolution on its head."
LANE: "We now know that eukaryotes all share a common ancestor, which by definition, arose just once in the 4 billion years of life on earth."
LANE: "Let me reiterate this point, as it is crucial. All plants, animals, algae, fungi, and protists share a common ancestor -- the eukaryotes are monophyletic."
Page 40. Read and re-read.
2. What is living?
Discussion of entropy which is always challenging for me.
Page 60: oxidation is the challenge. "Seeds die. But change the atmosphere, keep oxygen at bay, and seeds are stable indefinitely." Think mummies.
In the presence of oxygen, it costs energy to make amino acids and other biological building blocks, such as nucleotides, from simple molecules like carbon dioxide and hydrogen.
Introduces Gibbs free energy equation (page 61).
Bottom line: we can only exist (stay "ordered" / lower entropy if we release more heat into the environment than required to lower the entropy to stay "ordered"). We generate heat into the environment through respiration. "We are continuously burning food in oxygen, releasing heat into the environment. That heat loss is not waste -- it is strictly necessary for life to exist. The great the heat loss, the great the possible complexity." -- page 62.
ATP: every time ATP is split, it releases free energy that powers the conformational change of the protein plus it releases enough heat to keep Gibbs free energy negative -- which is required if the organism is to continue living. Gibbs free energy must remain negative. -- page 63.
ATP is generally split into two unequal pieces: ADP and inorganic phosphate (PO4 3-). This is the same stuff used in fertilizer and is usually depicted as Pi.
The energy of respiration -- the energy released from the reaction of food with oxygen -- is used to make ATP from ADP and Pi.
Author shows how there is huge (endless) amount of energy available to living organisms; they could use it multiple ways.
But then two aspects to the energy of life that are unexpected.
First: all cells derive energy from just one particular type of chemical reaction: a redox reaction.
Oxidation: passing electron to oxygen. Iron rusts when it oxidizes by passing an electron to oxygen.
This connects with the other book I'm reading now, on oxygen.
The substance accepting the electron is said to be "reduced." In this case, oxygen is reduced.
In respiration or a fire, oxygen is reduced to water because each oxygen atom picks up two electrons (to give O 2-) plus two protons, which balance the charges. So, "greedy" oxygen grabs the electrons ,but then because of the negative charge, attracts two protons to balance the charges. The reaction proceeds because it releases energy as heat, increasing entropy.
All chemistry ultimately increases the heat of the surroundings and lowers the energy of the system itself -- I remember this very, very well -- doing a very, very difficult question in biochemistry over Thanksgiving vacation one year while visiting my grandmother in Storm Lake, Iowa.
Respiration conserves some of the energy released from the reaction in the form of ATP, at least for the very short period until ATP is split again. That split releases the remaining energy contained in the ADP-Pi bond of ATP as heat. In the end, respiration and burning are equivalent; the slight delay in the middle is what we know as life.
An aside and we might get to it later: anything that interrupts ATP to ADP-Pi cycle as the same effect as suffocation (lack of oxygen).
What forms of energy were there for "life" to use?
- thermal
- mechanical
- radioactive
- electrical discharges
- UV radiation
As we said earlier:
But then two aspects to the energy of life that are unexpected. Redox was the first.
Now the second unexpected aspect: the detailed mechanism by which energy is conserved in the bonds of ATP. Life doesn't use plain chemistry, but drives the formation of ATP by the intermediary of proton gradients across thin membranes.
Molecular biologist Leslie Orgel said using thin membrane gradients as the intermediary was the most counterintuitive idea in biology since Darwin.
The second aspect: proton gradients. We know the mechanism in astonishing detail but not how this counterintuitive mechanism of biological energy generation evolved. For whatever reason, it seems that life on earth uses a startlingly limited and strange subset of possible energetic mechanims:
a quirk of history; pure serendipity; pure chance
are the systems so much better than any alternative that they came to dominate through Darwinian evolution
or more intriguingly -- could this be the only way.
Proton gradients -- proton power is as much part and parcel of life as DNA itself.
I suppose a biology teacher at the beginning of the year could frame this to the class, the two issues regarding life:
the information technology (IT)
the energy generation
Author then gives great visual of the inside of a mitochondrion, beginning on page 68.
- Electrons flowing down the respiratory complexes: for every two electrons flowing down the complex, ten hydrogen protons extruded to opposite side of the membrane. This sets up two things: voltage differential across the membrane (all those positive protons on one side)
- proton surplus on one side
The protons then flow back in, literally turning a ATP synthase crankshaft. It takes 10 ATP to turn the crankshaft one full turn, and each full turn generates three ATP molecules.
The system is incredible, but get this. Every living organism (save a couple of fermenting bacteria) use this exact synthase system.
Part II: The Origin of Life
This was a very difficult chapter for me. I will come back to it later.
Six fundamental processes of living cells:
- carbon flux
- energy flux
- catalysis
- DNA replication
- compartmentalisation
- excretion
4. The emergence of cells
The tree of life; currently, pretty much based on one RNA gene -- chosen carefully by the pioneer of molecular phylogenetics, Carl Woese: a gene for small subunit ribosomal RNA. Woese argued with some justification that this gene is universal in across life, and is seldom ever transferred by lateral transfer (which is how bacteria transfer genetic material0.
Last universal common ancestor (LUCA).
Fewer than 100 "universal genes" -- a very small number. Paint an unusual picture of LUCA.
What is universal between bacteria and archaea:
What is different between bacteria and archaea -- a huge parade of stuff, remarkable:
Replication
Transcription
Translation
Author's crazy idea: LUCA had everything in place -- translation, transcription, etc, but DID NOT HAVE REPLICATION in the beginning -- page 130.
Jargon: fixing carbon -- converting inorganic molecules such as CO2 into organic molecules, p. 131.
Part III: Complexity
Bacteria and archaea: never evolved; stuck in their tracks, and yet biochemistry of bacteria put eukaryotes to shame.
Two orthodox reasons why bacteria did not evolve:
- cell walls prevented movement and phagocytosis: author shows why not a good explanation
- straight vs circular chromosomes: again, author shows why not a good explanation
- straight chromosomes
- a membrane-bound nucleus
- mitochondria
- various specialized "organelles" and other membrane structures
- a dynamic cytoskeleton
- traits like sex
Orthodox science: eukaryotes closely related to archaea; but no clue how eukaryotes evolved.
There seem to be eukaryotic "signature" genes: unique to eukaryotes; note seen in bacteria, archaea.
This is what is interesting to the author: humans, yeasts, fruit flies, sea urchins, cycads -- about 3/4ths of their genome similar to that of prokaryotes; 1/4th similar to archaea; we are chimeras, it appears
That much is uncontestable. What is means is bitterly contested.
Some suggest eukaryotes were around from the very beginning; the author then asks why it took 2.5 billion years for eukaryotes to "take off," to become large and complex?
Others suggest that the eukaryotic signature genes evolved so much more quickly; again, that makes no sense to the author.
Author's answer, page 164: the first eukaryotes picked up thousands of genes from prokaryotes, but then ceased to ply any trade in prokaryotic genes. The simplest explanation for this picture is not bacterial-style lateral gene transfer, but eukaryotic-style endosymbiosis.
Author's summary, page 167: this is the simplest possible scenario for the origin of eukaryotes: there was a single chimeric event between an archaeal host and a bacterial endosymbiont.
Why would this happen? Complexity relates to energy.
6. Sex and the origins of death
Part IV: Predictions
Epilogue: From the deep
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