The Placental mammals, whose cladings are shown here, are one of the descendant nodes on the next chart.
In old age I enjoy learning new science. Putting my learnings into my own words is a good way to practice my learning and challenge myself. Most of what I show on this page comes from the marvelous books by Nick Lane.
Let's start with a "family tree" (or clading diagram) of the Eukaryotes. Nothing in these four charts really matters to our story here, but they were fun to draw. And I wanted to make sure the notion of Clading was clear. None of these diagrams is complete, but I do try to show representatives of the major groups.
Except for dinosaurs, these diagrams show only creatures that still exist. This makes the charts very misleading. In fact, the tree of life is very VERY bushy. Lots and LOTS of experiments, almost all of which have gone extinct. Paleontologists have uncovered dozens of fossils of extinct horses, just to give one example; these fit into a detailed and complicated tree. But we don't show anything like that in these simplified diagrams.
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| The first diagram shows the placental mammals.
See that deer, cattle, and giraffe are so closely related that
I lump them together. That may not be surprising (they're all ruminants),
but wolf, bear and seal are also lumped together!
The close relationship between wolf/dog and bear may not be a surprise
-- they look similar -- but inclusion of seal in the group may be a surprise.
Another surprise may be the close relationship between whale-dolphin
and hippo! This came as a surprise to scientists also; many of the
relationships shown in these diagrams were discovered only recently
with detailed studies of creatures' biochemistry.
In hindsight, perhaps the close relationship between hippos and whales
shouldn't be a surprise. Hippos are so large that their legs barely support
them: they mostly stay in water and don't walk much.
Perhaps it's logical that some very ancient hippos would end up adapting
their legs to be swimming fins!
The Placental mammals, whose cladings are shown here, are one of the descendant nodes on the next chart. |
| The second diagram shows how the placental mammals
fit into the terrestrial vertebrates,
The mammals are adjacent to the frogs, as listed at the left,
but this does NOT mean they are closely related. It is the connecting lines
that show relationships: the frogs and mammals are just two different groups
that split off before the reptiles and crocodiles split.
You may also see that the tyrannosaurs and brontosaurs -- both dinosaurs
are separated, at the left, by the birds!
Again, it is the lines that you need to follow: positioning the clades
on the page is somewhat arbitrary.
The Terrestrial vertebrates, whose cladings are shown here, are one of the descendant nodes on the next chart. | 
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| The third diagram shows the animals.
I've left off a variety of primitive animals.
Note that sponges are paraphyletic -- If you follow the lines
to find the common ancestor of sponges, you will see that it is also
the ancestor of all multi-cellular animals as well!
The Animals, whose cladings are shown here, are one of the descendant nodes on the next chart. |
| The fourth diagram shows eukaryotes.
Many of the little-known small groups have been omitted.
Note that the group containing red algae, flowering plants, etc.
is shown with TWO parents: a Eukaryote and a Blue-green algae.
Somehow, long long ago, a lucky Eukaryote engulfed that
alga (a type of bacteria) and used it to supply energy.
All plants today depend on chloroplasts to do photosynthesis;
these are chloroplasts that descend from that engulfing,
probably a SINGLE event in life's exotic history.
(The brown algae had an engulfing of their own, but we needn't go
into that much detail.)
The Eukaryotes, whose cladings are shown here, all descend from LCAE shown on the next chart. | 
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I hope you didn't waste too much time studying these four clading diagrams (unless you thought it was fun). The details shown in the diagrams are NOT part of our story.
In fact, when looking at "the big picture" the most remarkable thing about the eukaryotes is how similar they are to each other! Obviously there's a huge gulf between a giraffe and an oak tree. And seaweed (brown algae) is different still. And yet when you look at the detailed apparatus inside the cells in a giraffe's kidney, or the cells in an oak leaf or piece of seaweed, that machinery is very VERY similar in all eukaryote cells.
| Finally, here is the Tree of Life I want to present.
The Eukaryotes, shown in the previous section, are just one of the Three Great
Domains of Life.
This chart shows ALL the domains of life.
There are six nodes that are specially marked.
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Let's now look in detail at LUCA, the Last Universal Common Ancestor of All Life. It may not even have been a complete cell as we know them today, but it was still amazingly complicated. I read a magazine article that said something like "Then there was LUCA and evolution could begin." NONSENSE! There was a HUGE amount of evolution needed just to get to LUCA. LUCA is already an elaborate creature with powerful and complex machines.
The two most complicated machines in LUCA were ATP synthase and the Ribosome. Although each of these machines are much too small to be seen with a microscope, scientists have been able to deduce what they look like and how they operate. In the next sections I show animated gifs of their operations. Wow! These amazing pictures is one reason why I wrote this webpage at all.
Scientists cannot work directly with LUCA itself -- it disappeared many billions of years ago. But they can deduce what proteins it MUST have had: They just look for mechanisms common to ALL living creatures. So they know LUCA had ribosomes and ATP synthase. LUCA's version was slightly more primitive than the versions today: There has been improvement through evolution. But the changes have been slight; machines not unlike the animated gifs here must have been present in LUCA. (One of the Gifs mentions "Mitochondrial ATP synthase." Prokaryotes, including LUCA, do not have mitochondria. But the ATP synthase in mitochondria and the ATP synthase in prokaryotes are VERY similar.)
I've pulled two animations off the 'Net that depict the operation of ATP Synthase. Never mind the details (although it is impressive how scientists have figured this out: ATP synthase is much too small to see with microscopes). The animations do not do a good job of showing exactly what's happening. Watch this YouTube for more details. Viewed from the inside, the rotating part seems to move counter-clockwise in the animation on the left, but clockwise in the animation on the right. I don't know which one is correct. We can be pretty sure the spin is in only one direction and that it is is the same direction in ALL living creatures, Handedness is built into even fairly simple organic molecules, and life would need to start from scratch to develop a mirror-image version. ATP Synthase can rotate as fast as a whopping 130 revolutions per second! During each rotation, three ATP molecules are produced and about twelve protons pass through to do the cranking. With very few exceptions, bacteria and archaeotes mount their ATP synthase on their cell membranes. If the size of the cell doubles, the cell's volume increases by a factor of eight, but the area of the membrane increases by a factor of four. This puts a limit on how big a bacterium can be. Eukaryotes, on the other hand, have lots of internal membranes on which to mount as much ATP synthase as they choose! This is one of the many many big differences between prokaryotes and eukaryotes. The human body contains about 50 grams of ATP, but it cycles ATP-->ADP-->ATP about 1200 times per day, so each human manufactures about his own body-weight of ATP every day. ATP (Adenosine triphosphate) weighs about 507 Daltons (grams per mole) so there are 6x1022 (0.1 Mole) molecules in the body, or 1026 produced per day, or 1021 (1 sextillion) per second. The human body contains about a trillion cells; the average cell therefore needs 10 million ATP synthase complexes if each turns out 100 ATPs per second. (This ignores other ways the cell has of producing ATP. Anyway I'll guess the ATP machine, on average, is much less active than that.) In fact Google tells us there are 100,000 to 600,000 mitochondria per human cell, each with 100 to 5000 ATPases. Back of the envelope calculated about right! There is no "Free Lunch" of course. The protons are supplying the energy, but where do those protons come from? We'll look into that later. | 
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| Here are two diagrams comparing mitochondrial and bacterial ATP synthase, suggesting that this machine has retained the same basic form over billions of years. |
These three animated gifs I pulled off the 'Net should give an idea of what a magnificent machine this is! And it was already present in LUCA.
The three gifs all show exactly the same thing, but the depictions are at different scales and different speeds. The gif in the middle shows the interior of the ribosome, where there is room for three tRNA molecules: As a 4th tRNA arrives, one is pushed out. You can see a tiny white blob at the tip of each tRNA which gets added to a growing chain. Each tRNA arrives in its "activated" form, with that amino acid in its tip, and leaves "unactivated": without the amino acid. That gif starts over before you can see that chain grow to great length.
In the first gif, you can see the growing chain (the protein being constructed) slowly lengthen. In this case there is a special code in that protein which causes a different machine to hook up and excrete the growing protein through the cell membrane. (the protein being constructed) slowly lengthen. In this case there is a special code in that protein which causes a different machine to hook up and excrete the growing protein through the cell membrane.
The third gif shows that the ribosome is reading one long string (the mRNA, or "messenger RNA") while writing a new long string (the protein encoded by that mRNA). This gif is fun because it shows the protein synthesis operating at high speed. However that is not realistic. A ribosome will typically add about three amino acids per second to the growing protein chain. A large protein may take a quarter-hour or so to produce. Thus it is the first two gifs that have the speed in the right ballpark (though too slow by a factor of about three). Unlike the ATP synthase machine which is built from proteins (all of which had to be produced by ribosomes), the ribosome machinery is assembled from BOTH proteins and RNA molecules, with the specially shaped RNAs playing key roles.
Something important NOT shown in these animations, is that for every tRNA that successfully enters the ribosome and contributes its amino acid to the growing protein chain, there will be several tRNAs that attempt to enter, but are unable to gain a foothold, and therefore drift off. Only a tRNA with the exact anti-codon corresponding to the RNA codon will be permitted in. As the tRNA passes through the ribosome, the mRNA advances by one codon to get ready for the next amino acid in its encoding.
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Before moving on, note that the several molecules that make up the ATP synthase complex are ALL proteins. Each one is a linear chain of amino acids which, due to the specifics of their amino acid varieties, fold into the elaborate shape required for the ATP-producing motor. The Ribosome, and the machinery that serves it, are all made from TWO chemical types: Protein and RNA. But both these machines also incorporate one or more Magnesium ions to serve as catalysts. The structures fold into just the right shape for a Magnesium ion to nestle into permanently when it happens by.
The elaborate machines we just saw -- ATP Synthase and Ribosome -- seem amazing. Such complex machines operate with ordinary chemistry, with molecular building-blocks hooked together like Lego blocks or TinkerToys. Erwin Schrodinger wrote a very long essay on Life way back in the 1940's. Here is a copy of that book, with some other essays by Schrodinger, along with a Preface by the brilliant Roger Penrose. People sometimes ask: Could there be another form of life in our universe, perhaps with long silicon-based chains instead of carbon chains? I think it's doubtful: What is amazing is that even one particular combination of chemistry allows the sort of impressive machines we just saw.
So we'll assume OUR universe, and that we already know such stupendous chemical machinery is possible. This still leaves the mystery: How did Life arise? Even granting that VERY special molecules COULD become such machinery, how did those complex molecules arise?
That proteins (peptide chains) could come into being isn't so very remarkable. Amino acids arise readily, and have even been detected on lifeless meteorites. Two amino acids have a natural point of connection: Spit off a water molecule and a peptide bond is formed -- two amino acids connect together, Merge with another amino acid and do it again and again: a long protein is the eventual result.
Nucleic acids are rather more difficult. The nucleotides themselves arise readily, just like amino acids, but in RNA and DNA they attach to ribose, a sugar relatively difficult to synthesize. And the nucleosides (Nucleotide plus Ribose) connect to each other via Phosphate, relatively rare in seawater. For this reason, some scientists suspect that the earliest proto-life used PNA instead of RNA, or some other easier-to-synthesize nucleic acid. (But for brevity we'll just assume that proto-life started with RNA.)
The "A" in "DNA" and "RNA" stand for "Acid"; the acidity arises from the phosphate backbone: Each phosphate is ready to give up a proton and take on a negative charge. This charged backbone may be essential to the functionality of DNA: it keeps the linear molecule from folding and ensures that two strands will interact only at their "Watson-Crick edges."
The early ocean contained copious amounts of the simple gases CO2, N2, H2, as well as H2O. These precursors are all that is needed to produce amino acids, nucleotides and sugars if conditions are right. From these are produced peptide chains and nucleic acid chains of increasing complexity. With trillions upon quadrillions of different chains forming by chance, eventually this "proto-life" will stumble on a combination that catalyzes the rapid production of more chains, and eventually some combination that can reproduce itself will arise by chance!
This special mixture of complex molecules reproduces itself over and over, but with "errors." The unreliable nature of the reproduction will mean that many different "experiments" can operate, gradually honing in on configurations that reproduced themselves better and better. Self-reproduction was "success" -- those configurations multiplied in number. Evolution through natural selection!
During the earliest proto-life the mutation rate was probably very rapid: It needed to be in order to explore the space of configurations very rapidly. When a configuration well-tuned enough to be "life" finally emerged, stability became important: That may be when RNA -- with its phosphate backbone providing stability -- replaced PNA. Finally, life became VERY well-tuned, and a very tiny mutation rate was best. That's when the stability of DNA became necessary, rather than the more flexible but less stable RNA.
LUCA and all creatures descending from LUCA use both RNA and DNA. The RNA strands are flexible which make them capable of folding into the special Ribosome and tRNA shapes and easier to process as mRNA. But the valuable genome is maintained as DNA -- with a transcription error rate of just one in 100 million -- and only called upon when needed to transcribe new RNA.
So, it all seems very simple, no? Not so fast! Complex chemicals will not be created by chance, especially if they're just jostling around in the vast ocean. And even if a few dozen proteins and nucleic acids did arise by chance, that wouldn't ignite Life. Quadrillions upon quadrillions of complex molecules must arise and interact to provide the opportunity for evolution. Try to imagine how much random experimentation would be needed to come up with the ATP synthase machine by chance. There must have been a HUGE amount of experimentation by the earliest proto-Life before LUCA could arise. That LUCA could arise at all might seem more unbelievable than the fact that LUCA eventually evolved into humans!
In addition to raw chemicals like water and carbon dioxide, here are four necessities for the production of complex chemicals:
Although the generation of nucleotides, sugars and amino acids from inorganic precursors is straightforward, it does require the consumption of energy. And producing complex chains from the building blocks requires more energy. And trillions upon quadrillions of these chains were needed to enable evolution; HUGE amounts of growth and reproduction required HUGE amounts of energy. Where did this energy come from?
(The notion of entropy may help us understand the dilemma. Life has Order, which is negative entropy. But entropy always increases: To obtain negative entropy, a larger amount of positive entropy must be "excreted" to the outside. The earliest proto-life was very inefficient: To produce just one gram of complex proteins or RNA, hundreds of kilograms of waste material might have needed excretion.)
Plants have intricate machinery called photosynthesis to generate energy efficiently from sunlight, but it couldn't be used by early life. The evolution of photosynthesis required huge amounts of growth and reproduction, and that energy couldn't come from photosynthesis -- it hadn't evolved yet. Animals develop energy by eating sugar produced by plants; that energy required plants' energy, which in turn required photosynthesis which wasn't available to the earliest proto-life. Where did the energy come from?
First: What is "free energy"? Imagine a tank of water separated into two halves by an insulating membrane; let the water on one side of the membrane be hot and on the other side, cold. Where is the available energy? The hot water has lots of heat energy, but that energy may be useless. It is at the membrane, the boundary between hot and cold, that energy can be harvested. A battery stores electrical energy at both the anode and the cathode, but to harness that energy, you need to let electrons flow from one pole to the other. Similarly, acid and alkali each have a form of energy, but energy is best harnessed at the boundary between the two states.
We've already seen where much of a cell's energy comes from. It is produced by ATP synthase, which converts the electrical energy of protons into building ATP molecules -- the cell's energy currency. The protons carry positive charges; their crossing the membrane though the ATP synthase machine is like connecting the terminals of a battery through an electric motor. Instead of focusing on the electrical charge, it may be better to think of membrane's sides being acidic and alkaline, but the effect is the same: Energy is harnessed at that boundary. This process is called Chemiosmosis.
But where do the protons come from?
As we have said, ALL living creatures use this proton gradient through the ATP synthase to generate energy. Plants get their energy from sunlight and use part of that energy to pump protons across a membrane, where they then flow back through the ATP synthase machine. Animals produce energy in an opposite way -- Burning sugar -- but they use some of this energy to pump protons across a membrane, again getting ATP energy from the ATP synthase machine. Does that seem peculiar? Completely different sources of energy, but both using the roundabout method of spending energy to pump protons across a membrane, only to have them release the pumped energy as they flow back in? What gives?
The answer is simple: Progeny recapitulates ontogeny. All living creatures evolved from LUCA and LUCA didn't need to harness energy to pump protons across a membrane: It was getting proton flow for free!
In other words, a unique creation in the evolution of proto-life invented the way to utilize a natural source of free energy in the form of a proton flux. That creature developed ATP synthase, the magnificent machine that converts proton's electrical energy into the useful currency ATP. ALL living creatures on the planet use that same machinery, but without a free source of protons they had to generate their own protons and pump them across the membrane, just so they could flow back in through the ATP synthase machine!
So where did the earliest life, probably including LUCA itself, get the proton flux they needed for their free source of energy?
In 1977, scientists discovered hydrothermal vents on the ocean floor near the Galapagos Islands. Water was being heated by the Earth's magma and came gushing out, bringing minerals with it which precipitated into rocky vents, mostly iron pyrite. These vents are called "black smokers," after the color of the sulfide gasses emitted. Although the water gushing out is extremely hot -- about 850 degrees F -- a wide variety of life abounds near these vents; all species specially adapted to such extreme heat.
Could these black smokers have been the venue for the earliest life? NO: the hot water was just TOO hot for fragile early proto-life. But it got theorists thinking. What if the water was significantly cooler? Perhaps water could be heated by the Earth's mantle, much cooler than magma. And with iron and other metals being stripped of their electrons and ionized, the water in these vents would be alkaline. The ocean was only slightly acidic in the early Earth (and is even less acidic today), but it is relative acidity that matters, and compared with the alkaline water in the hypothetical vents, the ocean is very acidic: the boundary between the ocean and the water in these hypothetical vents would provide the pH gradient exactly as needed for the Chemiosmosis on which early life depended. In 1993, Michael Russell from JPL wrote a paper discussing how such alkaline vents, cooler than the "black smokers" would be an ideal venue for early life. Too bad they didn't exist.
Then in 2000, "white smoker" vents were discovered exactly as Russell had hoped! Heated in the mantle instead of the magma core, their water is less than 300 degrees F -- much cooler than the "black smokers." Today's white smoker vents are mainly composed of minerals like limestone but in the very early Earth, iron was plentiful in sea water and the vents might have been primarily iron pyrite, just like the black smoker vents.
The boundary between the alkaline water of the vent and acidic seawater provided the free energy needed for early life. What about containment, catalysis and waste disposal?
Within the vents are tiny pores, often separated by thin inorganic membranes. If you look at a micrograph of a cross-section taken from such a vent, you will see a fractal-like shape, with pores and membranes of various sizes. Could there be pores of just the right configuration to contain a proto-cell with evolving proto-life? Sure! In fact, the fractal-like structure almost guarantees that there will be pores with just the right "Goldilocks" size. Happenings in the inside of such a pore might be relatively tranquil, while seawater flows past on one side of the pore, supplying the protons needed as the energy source, and alkaline water flows past on the other side, providing waste disposal.
And iron pyrite, a mineral conjectured to be present in the early such vents, has pairs of iron and sulfur atoms that can serve as a good catalyst for synthesizing amino acids and other simple organics. And -- guess what? Progeny recapitulates ontogeny -- that exact same iron-sulfur pair, with the same inter-atom distance as in the mineral, is present in some key proteins found in LUCA!
The Ribosome implements the genetic code. The genetic code is central to all life: it is the recipe by which RNA is translated into Protein. A thorough account of the Origin of Life would need to spend some time explaining the Genetic Code but we'll lower our goal, and just mention that a very large portion of LUCA's genome was spent implementing that Code, several dozen proteins needed for the Ribosome and tRNAs to do their jobs.
Ribosomes, the Genetic Code, and ATP synthase complexes were not the only enzyme-moderated facilities in LUCA. LUCA also had facilities to transcribe RNA into RNA or DNA, and a facility to transcribe DNA into RNA. (All but the DNA-to-RNA replicase became almost obsolete in LUCA's descendants.) It also had enzymes to facilitate the "Kreb's cycle" synthesis of sugars and other organic building blocks. And it had the "sodium-hydrogen antiporter" which exchanges sodium ions for protons across the membrane.
This almost completes the story I sought to tell. But looking back to the first section, recall that LUCA is defined as the unique proto-cell that divided into TWO children, one of which was ancestral to all archaeotes and the other ancestral to all true bacteria*. (* - It may be best to speak of "true" bacteria, since "bacteria" is often used loosely to refer to eubacteria AND archaeotes.)
By comparing the commonalities to all archaeotes with the commonalities to all true bacteria, one can make deductions about the nature of LUCA. (Bacteria and archaeotes have exchanged lots of DNA with each other, so that some bacteria have archaeote features and vice versa, but certain functions are so central to a living cell that they cannot be replaced.)
The two big differences -- which led scientists to postulate the two domains of Prokaryote in the first place -- are DNA replication and the cell membrane and wall. Both types of prokaryote have enzymes for replicating their DNA, but those systems are completely different. Both types of prokaryote have cell membranes and cell walls but, again, the bacterial membrane and wall are completely different from those of archaeotes.
The conclusion is that DNA replication and the cell membrane were very late developments in LUCA's pre-history. Perhaps LUCA itself lacked a cell membrane and had no way to replicate its DNA.
This isn't as far-fetched as it might seem. We already noted that when life occupied a micro-pore in an underwater vent, it had no need to build its own membrane: the rock in the vent could provide the necessary constriction. (One of the main purposes of a cell membrane is to restrict access to the cell, so that even tiny protons couldn't pass -- they had to roam on the surface until they found an ATP synthase. If permitted to pass through elsewhere, their energy would be wasted. Such waste would be prohibitive if the cell were investing energy to pump the protons to the outside, but the earliest life didn't do that: It had all the protons it wanted from the acidic sea water.)
So much for the cell membrane, but what about DNA replication? Would it make sense for LUCA to have DNA if it couldn't even replicate it? Actually it could make sense; in fact there must have been an intermediate form of life with unreplicable DNA. There was undoubtedly an early form of life with RNA but without DNA. Such a creature could NOT have had any enzymes that operated specially on DNA: It didn't have DNA! Those early creatures had replicases that could replicate RNA from RNA; a mutation came along which started generating DNA in addition to the RNA.
At first that DNA would be useless, but then another mutation allowed that DNA to transcribe into RNA (just as happens in all life today). This intermediate creature, with replicases for RNA-->RNA, RNA-->DNA, DNA-->RNA but NOT for DNA-->DNA would be useful: The DNA would have a purpose: providing long-term storage of the genome for the life of a cell that would be much more reliable than RNA. Whenever the cell divided, it would need to use two replicases (DNA-->RNA followed by RNA-->DNA) to duplicate the DNA genome for the daughter cell, but at least the unwanted mutations to the genome would be dramatically reduced.
LUCA had two daughters; each developed DNA replication and cell membranes; but the details were different.
ATP Synthase is an amazing machine that is key to life. It consists of several
proteins, one of which is free to rotate.
The other proteins hold the
rotating part in place, and interact with it.
(An ATP synthase in humans has 29 protein subunits altogether.)
The machine straddles the cell membrane; hydrogen ions (H+)
enter the machine from outside the membrane
(from the bottom, in these animated pictures),
and as they pass through their electrical energy causes the machine to rotate.
In other words, their electrical energy is converted to rotational energy,
much as in a motor.
That rotational energy, in turn, drives the
reaction ADP + Phosphate --> ATP. ATP is the energy currency used for
all chores in the cell that require energy.
(ATP Synthase is not the only way the cell produces ATP, but it's a main one.)
By the way, "proton" is another word for hydrogen ion -- these particles are
very small because they have no electrons at all.