29. The real tree of life
(continued) Chapter 3. Long Evolution: Life Emerging
The Tree of Life graphic above nicely conveys much of evolution’s background context that I’ve been so carefully emphasizing in this chapter. It nicely shows that first molecule that became alive – our common ancestor – down there at the root of the tree where it belongs. It nicely shows how all subsequent life grew out of the common ancestor, gradually branching off via limbs and twigs into different families, different species, ever more and different kinds of living things. Out of one, millions. And, especially nice, everything proceeds “upward” just as you intuitively knew, from lower simplicity to higher complexity. So the higher you go the more complex the life forms become, the more conscious they are, the less unlearned instinct they depend on. As an abbreviated depiction of the millions of different life forms and species that make up life on earth, it’s a very nice tree of life.
The trouble is, it’s all wrong.
Symbolically, the tree does usefully convey the concept that creatures evolve up, out of other creatures, and the most recently evolved – the most complex – are way up there on the topmost twigs. (For all his genius, Darwin said it backwards when he spoke of The “Descent” of Man. In truth, Man ascended – up.). Sadly, this page-size tree must omit the millions of creatures that evolved between the bottom of the trunk and the outer branch tips, but it does symbolize the concept of evolution. Even so, it’s wrong in how it classifies these creatures – it’s based on their apparent shapes rather than the facts.
In recent times our knowledge has grown, and with it has come understanding that an accurate depiction of life’s evolution over the ages doesn’t look much like the tree above. The old way of classifying life groups according to their observed shape is obsolete. The new way classifies according to the DNA each (apparent) plant and (apparent) animal carries around inside its cells, way down at the level of complex molecules. To get it right, we must squash the tree of life flat as a flitter, reshape it with only three main branches, and then add branches and outer twigs – this time based on genetic information.
The new look looks a bit odd, and viewing it this way presents some surprises. For example, a reasonable person might reasonably think a porcupine and a hedgehog, both bristling with spines, are probably related to each other, and so rank them based on “shape.” But the newer phylogenetic classification based on DNA proves these two mammals not only are unrelated, they are in fact far apart in the genetic evolution of species. Their similarity in surrounding themselves with spines is mere coincidence. Assumptions based on shapes can produce other sticky situations – such as the two species of freshwater worms which look identical but are genetically twice as different from each other as humans are from chimps. Since the two had for years been thought one species and used interchangeably in research laboratories, discovery of their great genetic separateness has raised some distress about all that research based on a shape-based logical assumption which turns out to be flat wrong.
Nature abounds with thousands of comparable examples. Abetted by contrary scientific mindsets, confusion and error have resulted. Though the giant panda is shaped like and looks like a bear, for decades the conventional scientific mindset perversely said no, the panda is not a bear, it is a large member of the raccoon family that just happens to look bearlike. DNA analysis has now proved conclusively that the panda is, indeed, a bear, just as its shape proclaimed all along. How many other mindsets await correction?
Convergent evolution
Many are the old and established shape-based conclusions that have fallen before modern DNA analysis which cannot be denied. Widespread examples arise from convergent evolution whereby, through random chance mutations at the level of molecular DNA, unrelated life forms have slowly evolved into similar ways to handle similar functions. For example, convergent evolution has endowed quite a number of species with long sticky tongues and strong foreclaws which enable their survival urge to raid and consume ants and termites, their favorite tasty prey. Such long-tongued sharp-clawed comrades-in-function include anteaters, the African aardvark, the oddly-named aardwolf, armadillos, pangolins, the Australian numbat (a marsupial) and possibly the south Asian sloth bear – not one of which has any genetic relationship to any of the others in its DNA.
In an example perhaps closer to home, anyone who has eaten frog legs may have noticed (for how could they not?) that frogs have very human-looking legs which serve them well for hopping, a function they use quite a lot to catch bugs and escape snakes. Humans’ legs, which also serve quite well for hopping as well as walking and running, clearly look quite a bit like frogs’ legs. But nobody claims frogs and people are closely related just because they sport similarly-shaped legs. We can all agree the look-alike legs just happened, naturally and coincidentally, by chance mutations along two completely separate genetic paths of convergent shape evolution according to function.
Phylogenetic (DNA-based) classification
We now have ample proof that phylogenetic classification is more accurate by far than the shape-based approach which seemed so logical over the nearly three centuries since Swedish botanist Carl Linnaeus created the original classification scheme in the 1730s. This new system’s depiction looks a bit weird compared to the old traditional tree, but your web search on “phylogenetic tree of life” will quickly convey understanding of the new tree’s substantial differences. You probably will quickly find a website presenting several dozen symbolically different depictions of DNA-based classification, and the basic three-branch separation will be evident in all of them. How did this change happen?
In the early 1950s James Watson and Francis Crick famously figured out the chemical structure of deoxyribonucleic acid, DNA, the chemical template that our bodies – and all other animal and plant bodies – use to reproduce more bodies in each new generation. Their discovery, as basic as those of Galileo, Newton and Einstein, changed everything about the way we classify living things on earth. In a nutshell, bacteria and other microscopic thingies take up a lot more space on the new tree, whereas much smaller groups – such as the vertebrates – use up only a few outer twigs on one of the three main branches. Complex life, you see, arrived much later than all those one-celled lives that filled up the first three billion years of life on earth. But then came the “Cambrian explosion” of life. And since then, for 500 million years now, more complex critters have really taken off – right down to the current century when, suddenly, more species are being driven extinct than are coming into being. (There have been five previous large extinction events in life’s history, but the speed of this sixth extinction is staggering.)
The three branches of life
Now armed with our improved understanding, it’s time to have a look at life’s true branches – bacteria, archaea, and eukariotes. Something new – we must pause and examine it, for it’s more personal to us than some may realize.
Perception of life as two main kingdoms – plants and animals – was recognized in Genesis, as we have noted, and stood unchallenged for millennia until the twentieth century. After all, since ancient times the plant-and-animal distinction lay clearly right before our eyes – it was obvious, as they say. But – by the 1950s scientists were realizing this two-part classification, regardless how obvious, was inadequate to handle the accumulating knowledge of life’s fantastic diversity. Among several proposed changes, one divided life into two great domains called “prokaryotes” (mostly bacteria) and “eukaryotes” (everything else). This new distinction was based on the distinctly different nature of their cellular structures – i.e., eukaryote cells have a nucleus with a membrane, while prokaryote cells don’t.
Subsequent research showed eukaryotes can be subdivided into four broad kingdoms: plants, animals, fungi and “protists” (i.e., mostly one-celled organisms such as protozoans, algae, and slime molds). When in the late 1970s prokaryotes also were found to be more diverse than realized, they were subdivided into two whole new groups: 1) “bacteria” and 2) an entirely new group of one-celled life called “archaea.” Genetically, these two groups turned out to be as different from each other as both are from eukaryotes.
Thus were lately arrived at the three domains for genetics-based classification of life: 1) bacteria, 2) archaea, and 3) eukariotes – which latter, happily, includes us. Though all are alive and hence share in common the usual life urges to survive and reproduce, none of the three can possibly be an ancestor of the other two. This tells us, therefore, that they all three originated w-a-a-y back, somewhere not too far after that original first life – maybe, say, during the first billion of those three billion pre-Cambrian years. In our bit-out-of-the-ordinary quest to understand Long Evolution from the moment of the big bang to the present moment, let’s now consider each of life’s three great (true) groups in turn.
- Bacteria
Germs – biota – bugs (which they certainly are not)… Whatever they may be called, the microscopic organisms known as bacteria are found ubiquitously everywhere from miles underground to the edge of space. They outnumber hands down (they don’t have hands) all other forms of life combined. Mostly (but not entirely) single-celled, they can be spherical, spiral, rod-shaped or just odd-shaped, and can exist singly, in colonies, or linked in chains. Some bacteria have little propellers (called flagella) on their tails which they rotate to swim around quite well in liquid environments such as your bloodstream and lymph ducts. They easily thrive independently, in helpful symbiotic relationships, and as deadly parasites. Bacteria quite simply are everywhere, including on and inside all other living creatures bigger than they are. The oldest fossils known, three and a half billion years old, are fossils of bacteria-like organisms – vast eons older than we humans who evolved only in the most recent eye blink of earth history.
Considering all that, bacteria by and large don’t get the respect they deserve. Bacteria can be useful or vitally necessary, and in many earth environments they make up the base of the food chain. It is bacteria living on the roots of plants that convert nitrogen into usable form, enriching the soil so it can grow more plants. They put the tang in yogurt, the sour in sourdough, and are the basis of fermentation which so delights when we sip a glass of wine or beer. When the fermentation they cause is unwanted, we call it “rotting.”
A single spoonful of soil may contain ten thousand species of bacteria. The total number of bacterial species – obviously unknown – almost certainly numbers in the millions. On top of all that they mutate constantly, diverging by the hour into ever new and different species. Copious numbers live on and in our skin, mouth, eyes, sinuses, mother’s milk and genitalia, and infants birthed by cesarean section miss out on protective perinatal bacteria that are picked up by babies birthing naturally through the vaginal canal. About five hundred to a thousand species live symbiotically each in human’s intestines where they number tens of trillions of individuals, exceeding the number of cells in our bodies and weighing four to five pounds. There in our guts they break down the food we eat, produce vitamins B and K which our cells relish, stimulate the digestive process, and aid the absorption of nutrients. It should be understood that we could not sustain human life without the bacteria which live within us from our births to our deaths, at which time they routinely switch to processing the decomposition of our dead bodies, after a while returning them as molecules to the earth from whence their earth-fed bodies derived.
Still other bacteria are the basis of many infectious diseases that take a terrible toll on humans and the livestock we depend on for food, fabrics and work. When we vaccinate children, the desired immunizations are against biotic disease-causing bacteria. Other bacteria are the source of anti-biotics such as streptomycin and nocardicin.
The old way of classifying bacteria by their shapes was generally so difficult it couldn’t be done well. While a few such as cyanobacteria and actinomycetes have sufficiently complex morphology to permit classification by shape, most types are so very small and simply-shaped that they traditionally were identified and classified on the basis of their biochemistry, and sometimes the conditions under which they grow. The modern turn to genetics for classifying life forms – now called molecular biology – has revolutionized the field by linking similar DNA sequences in related species. The new method has revealed eight (or ten, depending on who you ask) broad families of bacteria. In order from what is believed to be “oldest to youngest” as of this writing, these are:
- Thermatogales (they like heat; some thrive up to 90 degrees C. (194 F.))
- Green non-sulfur bactreria (produce energy from light, have green pigment)
- Cyanobacteria (aquatic, named for bluish-green pigment used to capture light and manufacture their own food by photosynthesis; unrelated to blue-green algae)
- Green sulfur bacteria (depend on light for life, perform efficient photosynthesis)
- Purple bacteria (also photosynthetic, mostly aquatic, widely distributed)
- Flavobacteria (widely found in soil and fresh water habitats, cause septicemic diseases of rainbow trout fry)
- Spirochetes (cause syphilis and lyme disease; symbiotic in ruminant stomachs)
- Gram positive bacteria (cause staph infections, strep throat, diphtheria, anthrax)
There might be a couple more but for our purposes close is close enough. Remember, these outnumber all other life forms combined, but they’re all very, very small.
- Archaea
Archaea, the second great branch of life, also are very, very small. Under a microscope most don’t look all that different from bacteria, though genetically and biochemically they are as different from bacteria as we are. The two don’t interbreed, so we deduce that they can tell the difference (though “breeding” is not quite the proper term at the one-celled level of life). Archaea may be remembered by thinking of them as life’s ultimate extremists, flourishing in some of the most outlandish environments on the planet. They can live and thrive in the anoxic mud of marshes and ocean floors, and they seem to really like living in deep underground oil deposits. They flourish in waters that are extremely acid or alkaline, in hot springs associated with volcanic areas, and around those very deep ocean rift vents where temperatures soar above 100 degrees Centigrade (the boiling point).
In addition to extreme earth environments hostile to all other forms of life, Archaea are also found inside the plankton that float near-infinitely in the open sea. They live comfortably in the digestive tracts of fishes and termites. They constantly produce megatons of the global-warming methane so copiously released as cow farts (anyone who has ever worked in a dairy barn knows full well not to stand behind a cow, especially when she coughs). Archaea, our very (very) distant relatives, really like salty environments and do quite well with or without light. They may also be remembered as exceedingly diverse and remarkably successful at surviving and reproducing, the two primary functions which distinguish living things from non-life.
The major branches of archaea go by the following wonderful names, the meanings of which are important to the mere tiniest fraction of one percent of the citizenry:
- Pyroditicum (deep sea vent-dwelling archaeon, thrives in extremely hot water)
- Thermoproteus (heat-loving sulfur-dependent archaeon; yuck)
- T. celer (spherical-shaped otherwise unremarkable archaeon)
- Methanococcus (methane producing archaeon preferring moderate temperatures)
- Methanosarcina (anerobic methane producing archaeon that can form colonies)
- Methanobacterium (yet another methane gas producing archaeon)
- Halophiles (salt loving archaea)
Which are older – bacteria or archaea?
Answer 1. Maybe: Cyanobacteria fossils nearly three and a half billion (yes, Billion) years old have been documented among the oldest fossils known on earth. Archaea evolved later.
Answer 2. Maybe not: Chemical fossils of uniquely archaean lipids found in Greenland rock strata almost three and a half billion (yes, Billion) years old are quite possibly the oldest life form on earth.
Some scientists dispute one of these claims, other dispute them both. The whole matter reminds me of two old-time fiddlers, Luke and Zeke. They were whiling away the afternoon playing old fiddle tunes, taking turns thinking up which tune to play next.
Zeke: It’s your turn Luke.
Luke: Let’s play Bonaparte Crossin’ the Rockies.
Zeke: (pause) Uh… Bonaparte never crossed the Rockies.
Luke: (beat) …Y’know…experts differ on that…
Notwithstanding a great many differences of expert and not-so-expert mindset, we have now reviewed two of the three major groups of living things – bacteria and archaea – together comprising a vast majority of the individual creatures alive on the earth today. Now at last it’s time to turn our attention to the most interesting group of all, eukaryotes – interesting, of course, because it includes, in a very small way, ourselves.
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…to be continued in one week…
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