GP 25 Web Book

Day 9
Real Correlations and False Coincidences

Is the Earth created for the benefit of mankind? This is the premise of Judaism and most of the religions derived from it. (The view is not universal. Hindus view life as an opportunity to do good works amongst suffering. The Greek Gods toyed with mankind.) Divine providence was a given in 1800 England despite the fact that the universe had grown beyond that of the time of Bruno.  To this point, the worst fears of Galileo’s inquisitors had proved unfounded. The evidence seemed irrefutable. Wasn’t the Earth a very suitable place for humans? Aren’t humans very well suited to live on the Earth?

1800. The resurgence of anatomy and biology shows that the human body is very complex. William Paley documents complex structures in animals and plants that fit them for their environments. All this can not be a coincidence. Paley’s argument is that if we find a watch, there must be a watchmaker. A watch is just too complex to form on its own. Life is obviously very complex. Thus the Creator must exist. Buckland follows Paley’s lead, supplying more careful observations including those of fossil organisms in the 1830’s. All this will change before the century is up after careful attention to the meanings of “coincidence” and “chance” by nonmathematical men.

At the time, Paley’s work had the positive effect of encouraging people to look at nature. Recently Creationists resurrected his ideas as “Intelligent Design.” Debased forms of his Natural Theology appear in K-12 science books, like animals having assigned roles in the environment, such as predators being here to weed out sick prey.

Coincidences come up every day especially if we look for them. Some are real correlations from cause and effect. Stella Brown most likely had the recipe out that she was cooking. The fraction of women over six feet in Tall Girl or on a basketball team is likely to be higher than in a grocery store. Few commercial fishermen toil at their trade in the middle of a desert.

Others come after the fact. Any person can say they are 1 in 6 billion. The chance of getting any bridge hand from a fairly shuffled desk is the same as getting all 13 spades. One can easily create astronomically small probabilities in this way. Take for example the census list of a tiny village in China. There are 10 names listed in order. The chance of any one name occurring from the 1 billion population of China is 1 out of 1 billion (1 with nine zeros). The chance of the whole list in order is 1 in 10⁹⁰ (1 with 90 zeros). There are about this many atoms in the visible universe. However, we can say this about any list of 10 people from China.

Some coincidences, like flies having wings, come after the fact from the human endeavor of giving names. Lou Gehrig died of the disease named after him. Bookworms eat books. Fruit bats eat fruit  Flycatchers catch flies. Ad nauseam.

Yet the type of coincidence orchestrated by Paley remains. House flies are obviously well suited to find their food sources like open garbage cans.

Begetting.  Like begets like. No farmer, even in the Dark Ages, waited for chickens, sheep, cows, pigs, and goats to spontaneously generate in his farmyard. Christians regarded their purported virgin birth as a divine miracle, not a mundane event. Yet Izaak Walton (1593-1683) discussed spontaneous generation with only a whiff of skepticism.

When Walton published in 1653, biology was just becoming a new science. Both the people and the learned believed that complex organisms generated spontaneously from lifeless matter. Walton acknowledged that some pike beget pike in the ordinary manner, by generations of spawning. Yet some formed spontaneously from weeds. Geese formed from barnacles, mice from sacks of grain, and maggots from rotting meat. These ideas were not totally absurd. Strange transformations do occur, like butterflies from caterpillars.

1668. An Italian anatomist wants to see for himself. He is familiar with the work of the Englishman, William Harvey, that mammals grow from small fetuses and presumably from even tinier “seeds.” Francesco Redi (1626-1679) does a simple experiment in the hot Italian sun.  He leaves some meat to rot in open jars and some in jars covered with gauze. The powerful stench soon attracts swarms of flies that cover the open meat. Frustrated flies cannot get through the gauze.  Soon maggots swarm over the exposed meat. Further work confirms that maggots hatch from tiny fly eggs and grow up to become more flies. (You have already done part of this experiment when you put a lid on your garbage can.) It is less clear whether decay microbes come in and reproduce or spontaneously generate. Spontaneous generation of microbes festers until 1859 when Louis Pasteur does careful experiments analogous to Redi’s experiments.

However, the idea of cleansing with heat predates the knowledge of microbes, rot, and disease. The Roman physician Galen treated his surgical instruments in fire. Jews cleansed pots by boiling them over hot coals. Pasteur deserves credit for cauterizing spontaneous generation. Unfortunately his later dogmatism (to self-promote pasteurization) delayed the discovery of spores that can briefly survive boiling and “thermophile” (heat-loving) organisms.  By convention the term thermophile is anything that grows above 60°C and hyperthermophile is anything that grows above 80°C, the usual temperature of pasteurization. The distinction is a vestige of dogmatism that nothing could live above 80°C. It is not useful in most astrobiology discussions. I use thermophile to include anything living above 60°C.

The plan of nature. 1700s. Explorers continue to discover (for Europeans) the great diversity of plant and animal life. It is evident that “apting” a pond for pike outside their normal range involves stocking them, just like King Charles II (1630-1685) had to stock his parks with Canada geese. Biologists designate the origin of higher organisms as species to the Creator. They set out to deduce his plan.  Carl Linnaeus (1707-1778) goes about classifying animals, plants, and fungi into a natural order.  He is a good enough observer to start the basis of modern taxonomy (the science of classifying organisms). At first, he considers species to be God-given forms dating from Creation. Later, he recognizes hybrids and that introduced species may change with acclimation. He willingly accepts some change over time, but not wholesale evolution. The geologist Hutton shared this view.

The Linnaean classification works for macroscopic organisms. At one end, plants, animals, and (later) fungi are natural kingdoms. At the other, species are a natural, but fuzzy concept. Intermediate taxa group various species. Many, like birds and fish, date from antiquity.  All Linnaeus did was to assign their Greek or Latin names. (Politically dead languages do not invoke the wrath of nationalism.)  Parts of the classification required careful study. For example, vertebrates have backbones and share numerous other characteristics. Dicots have two seed leaves (like peas) and a common flower structure. Humans fit well into the classification. (Omitting several intermediate groups)  Our species, Homo sapiens (man wise), is part of the great apes. The apes in turn are part of the primates, which includes monkeys and lemurs. The primates are mammals.  Mammals are vertebrates and the vertebrates are chordates (vertebrates and animals including sea squirts with a notochord, which is analogous to a backbone).

Fossils fit well into the classification, especially the more recent Cenozoic ones. Many recent fossils tend to resemble living organisms. It is obvious that a mammoth is a type of extinct elephant.  There are numerous extinct groupings, some ancient, like trilobites. There are, however, intermediates between modern taxa, like mammal-like reptiles.

Hesitation.  I have already mentioned Darwin and natural selection with regard to the geological time scale. The story of the voyage of the Beagle is quite well known and I will be brief.  When the ship left port, Darwin had trained to be a naturalist.  He had also trained for the day job of a country parson. By the time the ship reached the Galapagos Islands, he had recovered numerous fossil specimens from Patagonia and visited tropical, steppe, subarctic, and mountain climates. He was well aware of the great diversity of life on the South American mainland and the wide ranges of many mainland organisms.

On the Galapagos, Darwin gets right to work collecting.  At first, he just labels specimens “Galapagos”, as he does not expect to find differences between nearby islands. A local then points out the differences between similar species on adjacent islands. Darwin quickly finds numerous other examples of endemic (local) species on the island group. In fact most of the land birds are endemic to one or more of the islands.

The finches play a large part in the legend and a part in Darwin’s thinking after he got back to England.  They resemble the native finches of the South American mainland.  Darwin does not realize they were all finches while he is on the island. They are different from the finches he is familiar with and have somewhat different habits. Strikingly, one functions as a woodpecker eating insects from the tree bark. There are no native woodpeckers on the island.

Darwin’s thoughts turn to evolution and he starts a notebook soon after the ship reaches England. The finch example is straightforward enough (though complex when examined closely) to get to a result.  A wayward flock of finches ended up on an island in the Galapagos and some did not fly back.  Initially they found things to their liking.  There were plenty of insects and seeds to eat and few other land birds eating them.  The finches multiplied and settled various islands and various environments. There was some inheritable variation within the finches.  The “fitter” finches survived to multiply. However, different variations proved beneficial in different environments and finches specialized for one environment did better than generalists. Eventually the isolated populations became separate distinct species.  In general, biologists call this adaptive radiation.

The woodpecker finch evolved because no real woodpeckers existed to compete with it. (On the mainland, a finch that tried to act like a woodpecker would find very slim pickings.) There were plenty of insects on or just under the bark. As the finch acquired the habit and eventually the instinct to act like a woodpecker, traits that made it more suited for the task became selected.

The finch argument is not far beyond what Hutton, or even Linnaeus, would have accepted. Limited natural selection is a common heresy dating from Aristotle that Paley attempted to refute. Darwin continues much further to having all life evolve from one or at most a few common ancestors. He is not comfortable with this concept and realizes that it needs to be fully documented. After reading a book by Thomas Malthus (1766-1834) on the impending human population explosion, Darwin realizes that all organisms produce far more offspring than can survive. They need not breed like rabbits to do this. Slowly reproducing species, like humans and elephants, would overrun the Earth before 1,000 years was up if all offspring survived. The death of some of Darwin’s own children drives in the point that survival is not guaranteed

Darwin continues to amass data and think.  He discusses the issues with his friend Charles Lyell (1797-1875), by now the most noted geologist in the world, and with the botanist Joseph Dalton Hooker (1817-1911). Both are initially skeptical but supportive.  Later they urge Darwin to publish on evolution.  However, Darwin does ordinary science, like explaining corral reefs and studying barnacles and orchids, to get a better hold on the larger issue. He avidly associates with plant and animal breeders.

All this changes in 1858 when a museum collector catches malaria in what is now Indonesia. Alfred Wallace is already a proponent of limited evolution.   In the delirium of his fever, he grasps the real power of evolution by natural selection.  He communicates his result as a paper to Darwin.  Darwin is unwilling to betray Wallace, but does not wish to be scooped. He communicates his predicament to Hooker and Lyell.  They arrange for Wallace and Darwin to publish companion papers. Darwin publishes The Origin of Species in November 1859.  Any educated person should read some edition of this book.

I summarize some Darwin’s arguments with some simplification and modern hindsight

(1) Organisms share common characteristics because they descend from common ancestors.  Species groups with recent common ancestors, like the Galapagos finches, share many obvious traits. The similarities between distantly related species, like sharks and insects, are subtle.  The Linnaean classification is really an attempt at constructing a family tree. Modern taxonomists group organisms in this way. The fossil record provides valuable information on descent with modification. The geographic distribution of organisms also makes sense in this regard. There is an inherent tension between keeping the classification stable for communication purposes and having it reflect descent as more is learned.  The fact of evolution as opposed to its mechanism raised the least controversy at the time.

(2) The primary mechanism of evolution is natural selection. There are far more individuals in any generation than can survive. All organisms thus face a struggle for existence. There are heritable variations in natural populations. The individuals with variations that make them more suited for their mode of life have a greater tendency to survive and breed. The “fit” variations built up in the populations through time. Darwin used artificial selection of domestic plants and animals to show both that variations really exist and that they can be selected for. Darwin had little idea how heredity actually works. He did recognize linked genetic variations and heritable instincts.

(3) Rudimentary organs, like the wings of flightless insects, played a large part in Darwin’s arguments as the result of descent. Such structures were once useful to an ancestor of the organism but later proved useless or harmful. Darwin was familiar enough with shipwrecks to know the disadvantage of being able to swim halfway to shore. It is best to be a very strong swimmer or to stay with the boat. Similarly weak-of-flight insects on windswept islands risk being blown out to sea if they take off. Selection reduces both the instinct and the ability to take off. Once rendered useless and harmless by natural selection, rudimentary wings are highly variable.  Natural selection cannot act to check or enhance variations that do not affect the fate of the organism.

(4) Chance plays some part.  For example, the Galapagos finch ancestor may have been blown off course. Darwin emphasized the chance nature of colonization of isolated islands. On a larger scale, selection is statistical. A single organism with “good adult” genes may never make it beyond being a larva. However, a large number of individuals with the good gene will have a larger tendency to survive.

(5) Species are fuzzy entities from the ongoing process of evolution.  It is a matter of semantics when the variation and breeding isolation of two populations are enough to elevate them to species. Organisms often continuously vary over their ranges so the individuals at each end appear different enough to regard as species. The process of continual species formation is particularly evident in the tropics where both Darwin and Wallace worked.  It is less evident in recently glaciated areas, like England, which were colonized by a limited number of wide-ranging species after the ice melted.

(6) Geological time is vast.  The slight amount of variation in each generation can built up over time to vast differences like between birds and lice. The geological record is incomplete. Paleontologists have found lots of fossils since Darwin including those of early man. Each missing link closes one larger gap and creates two smaller ones. Still there seemed to be sudden changes in the fossil record that Darwin had trouble attributing to an incomplete record. I will return to the issue of mass extinctions in the next chapter.

(7) Ecology is quite complex and not well understood. Darwin used the example that mice raid bumblebee nests and cats eat mice.  Thus the abundance of cats influences the abundance of flowers pollinated by bumblebees. Here he argued from ignorance but opened an entire field of study.

Backlash. 1859. The strong reaction that Darwin expected occurs. It does not take long for every ideology to find the moral message that it wants to find or wants to fear. Conservatives justify the plight of the poor as beneficial selection. Socialists point out that the poor merely lack opportunity. The practice of finding the moral lessons that one wants is a major tenet of Natural Theology. It was the basis of Nazi racism. It persists today usually in more benign forms.  The Grasshopper and the Ants is a nice children’s story, but one that tells us little about real grasshoppers and ants.  Such reasoning sometimes makes it into K-12 science books. The selective lesson from the spider is typically that hard work in making a web pays off, not that wives should kill and eat husbands.

Darwin stays out of the religious discussions. He has been brought up to believe that it is rude for a gentleman to denigrate another’s religious beliefs.  Tactically, it is not good to insult people you are trying to convince. What one believes on Sunday need not affect what science one does on Monday.

The implication of natural selection to Paley’s watchmaker argument is obvious. There is simple cause and effect.  Organisms are suited for their environments because they have evolved to be fit. Natural selection can refine an organism over generations just like breeders improve horses for speed. The lack of a role for the Creator chafes the religious minded, as had it initially troubled Darwin.  Moralists fear that if men are animals they will behave like animals. Some scientists attack natural selection on mostly scientific grounds.

George Jackson Mivart (1827-1900) and Richard Owen (1804-1892) lead the foray. I have already discussed the purported lack of time for natural selection to work. Mivart, like Paley, focuses on organs of great perfection, like the eye.  Surely it needed the Creator. To boot, half an eye could never form by natural selection because it would be worthless.

Darwin replies politely to Mivart in later editions of his book. First, the human eye is not perfect.  Otherwise there would be no opticians. The half-an-eye argument owes to Mivart’s lack of imagination, analogous to porcupines being unable to mate. Darwin is a geologist. He had already compared oceanic islands in various stages of their evolution from volcanoes to atolls. He does this with the eyes of various organisms.  At one end, night crawlers have a weak sensitivity to light.  If you want to catch one, you need to keep it in the dim edge of your flashlight beam. Other organisms have eyespots connected to their brains by optic nerves that function to tell light from dark. At the other end, cephalopods (for example, squid and octopus) and vertebrates have complex well-developed eyes.  A continuous sequence exists between the worm’s feeble vision and a hawk’s with each step serviceable to the organism. At each step, natural selection may drive further sophistication. To boot, the cephalopod and vertebrate eyes are different. They evolved independently.  This is what the argument was until a few years ago.  We now know from molecular genetics that the squid eye, our eye, and the compound eye of flies all evolved from a very simple eye of a common ancestor.

Scientists and historians sometimes criticize Darwin for telling a just-so story about how some organs evolved.  This is off base.  Mivart contended that no evolutionary path by natural selection is possible.  Darwin needed to only find one such path.  Clearly, the task of finding the actual evolutionary path is more difficult.

Mivart’s perfection argument is the staple of the Intelligent Design movement. The argument now comes from a self-imposed selective lack of imagination. These professional Creationists have mostly shifted away from macroscopic organs where the refutation involves familiar organisms to biochemistry where the function for many substances is still unknown.  Chemical names make the Creationist sound erudite to the congregation. These Creationists have never produced a single positive result.  They have not even produced a criterion for recognizing the product of genetic engineering.

Ironically, the opposite argument gets made that natural selection cannot occur because the change over each generation is minute. I have heard it from professional paleontologists in my youth, but it does not seem to come up much from Creationists. Consider the giraffe, which is popular in K-12 books, but too big and rare to leave a nice fossil record. In fact, there is no useful fossil record, so we have only a thought experiment. The height of giraffes may have increased a meter over (for simplicity) a million generations. The microscopic change (being one-millionth of a meter taller than the other giraffes) over each generation could not affect evolution.

This argument ignores the observation that evolution occurs erratically on a short time scale. This maintains a wide range of variability. For example take Darwin’s finches. A modern visitor would note little change from Darwin’s specimens. However a resident to the island would note rapid change.  Drought-tolerant forms dominate during the dry years. Wet forms dominate during wet years. Overall, the rapid change adds up to very little net change on a historical time scale.

Back to giraffes, the variability in height at any time was far greater than a millionth of a meter as it is today.  Countervailing selective pressures may serve to maintain variability. A tall neck allows grazing high up trees. (We do not know enough about giraffes in the wild to state that reaching high leaves is the main use driving natural selection, so on with the thought experiment.) It is particularly useful during times of dearth to be able to get just above the other giraffes. The tallest giraffes would then dominate.  The added height, however, might be useless or even harmful during subsequent times of bounty.

In addition, the neck of a giraffe is a highly complex structure. One cannot scale up organisms like giant grasshoppers in a 1950s movie. (Galileo began the science of how different parts of an organism scale with its size.) Rather, many different features, like those to get blood to the head, needed to evolve to let the giraffe be taller.  There was selection both for efficient giraffes and tall necks.

Link to my discussion of Mivart-like arguments of Young Earth Creationist site on the giraffe

Contrivances.  As Paley contended, many organisms are very suited for their environments. Complex structures, like the eye, do look like the products of design. It is easier to demonstrate evolution where it has yielded a kludgy but functional organism.  Something that no designer working from scratch would ever produce.

Natural selection acts one generation at a time on the variation actually present.  It cannot produce a line of unfit organisms over many generations with an ultimate goal in mind. This often leads to inelegant adaptations. To give a contra-possibility outside of the supernatural realm, a selective breeder could produce many unfit generations with an ultimate goal in mind, like a winged horse. A genetic engineer could conceivably do that from scratch, but not during a lunch hour.

Natural selection also acts through the conditions that organisms actually experience. It does not anticipate changes. For example, armor-plated deer did not evolve to be ready for the invention of fire arms. The land biota of isolated islands are a striking example. These animals often evolved in the absence of serious threats from land predators. Their traits often proved wanting in the changed environment. Introduced cats, rats, and mongooses made quick work of the native organisms on many islands by Darwin’s time. Island animals appeared ridiculous and contrived to Europeans familiar with their biota that had evolved along with fearsome predators like wolves. The extinct dodo is synonymous with stupidity. It takes great faith to contend that it was the specially designed work of a benevolent Creator for the island of Mauritius.

Darwin studied orchids. Their complex flowers trap insects that go on to pollinate other flowers. The trapping and pollinating mechanisms have evolved from other parts of the flower.  They work, but do not resemble anything designed from scratch.

Darwin used rudimentary organs as examples that have no place in design from scratch. The webbed feet of upland geese that rarely if ever alight on water betray their aquatic ancestors. The teeth in embryo birds expose their reptilian ancestry. The gills in the human embryo unmask our fish ancestors.

The human knee is notoriously prone to injury. Our bipedal stance is geologically recent (a few million years). Natural selection from a quadrapedal knee has occurred over that time from individuals breeding success being lowered by a knee injury or a slow gait from an inefficient knee. At the present, it has produced a serviceable but troublesome organ. Minor design problems exist even in the human eye — Mivart’s favorite. Its lens hardens and most adults need reading glasses by age 50.  The optic nerve comes into the retina in a manner to form the blind spot.

If you want to learn more about contrivances read The Panda’s Thumb by Stephen Jay Gould (1941-2002).  The thumb is really a modified wrist bone that aids it in eatting its vegetarian diet of bamboo. The panda is taxonomically a carnivore, a group also including cats and dogs. Its ancestors ate meat and its body structure reveals that fact. It is closely related to bears and raccoons, carnivores that that often stray from their taxonomically assigned diet.

Life at the hot lane. Darwin saw teeming life everywhere he went. However, he focused his studies and discussions on macroscopic organisms. This was an excellent tactic for the evolution debate. Both scientists and the public relate to what they can actually see. Logistics were a more telling constraint.  One can learn that microbes exist in an optical microscope, but not a lot more. The science of biochemistry exposed the great diversity and extent of life on the Earth in the twentieth century.

Yes salamanders do not live in fire, but what are the limits to life? Temperature is clearly one. I have already noted that the use of heat for sterilization predates knowledge that high temperatures kill microbes. Pasteur was correct that it is an effective method to kill pathogens and organisms that foul wine and milk.

We can see why pasteurization works with human pathogens. The pathogenic organisms need to survive temperatures in a person with a fever up to 40°C and if they spread through filth at “room” temperatures. Such organisms rarely experienced (in pre-sanitation times) high temperatures and when they did the temperatures were quite high, like boiling pots and fires. There was no advantage for a microbe in being able to withstand a slightly higher temperature than its relatives.

Conversely, real thermophile organisms, like those in hot springs, are highly adapted to that mode of life.  They rarely get swallowed by animals or end up in wine vats. If they do somehow end up there, they find that these environments are quite different than hot springs and already teeming with well-adapted microbes. It is unlikely that any survive to evolve into pathogens.

Dogmatism following Pasteur delayed the discovery of thermophile organisms, or relegated them to curiosities. Petroleum geologists knew as early as the 1920’s that bacteria inhabit oilfields. Over time the bacteria degrade oil in the ground, at temperatures to at least 80°C. For example, they cause oil to react with sulfate, which produces sulfide and CO₂. The degraded oil contains a smaller fraction of the compounds that are easier to use in making gasoline. The problem becomes more serious when petroleum engineers pump surface water into the oil-bearing rock to drive out the oil. This introduces sulfate (if seawater is used) and dissolved oxygen. Numerous microbes eat the oil, making it react with sulfate and dissolved oxygen. Some corrode the drill pipe. A cottage industry exists to eradicate oilfield microbes before they can do much harm.

Microbes exist on land in hot springs that are hot enough to boil water. Such organisms are valuable to the biotech industry. For example, the enzyme used in criminal DNA analysis came from microbes in a Yellowstone hot spring.  One can produce enzymes in industrial quantities that withstand boiling. One can heat the culture to get rid of unwanted microbes.

Interest in thermophile organisms took off with the discovery of marine hydrothermal vents.  There were initial claims of living organisms at 350°C. None held up, but it is clear that life thrives up to 121°C, the current record.  (The high pressures at the bottom of the ocean keeps water from boiling at this temperature, like in a pressure cooker.) Here we have a real limit to terrestrial life. Temperatures increase gradually with depth away from the vents and rapidly with position within the vents. An organism that could withstand a slightly higher temperature than its relatives would get first crack at the life-giving vent water. Yet this has not happened even though vents have existed since the Earth formed.

Figure 1: Overturned ice block exposes an interesting Antarctic microenvironment.  Photosynthetic microbes, mainly diatoms, live at the base of the sea ice.  Enough light gets through for them to do photosynthesis.  The block is about a meter across. Photo by Kevin Arrigo.

Cold is no barrier to microbial life as long as liquid water is sometimes present (Figure 1). When my oceanographic voyage docked in Mexico, both the scientists and crew warned me of the dangers of tourist disease from ice cubes tainted with pathogens. In fact, we preserve microbes by freezing them. This includes human sperm, a microbe even though it might not quickly come to mind as one.

Microbes can even inhabit very acidic water from mine drainages, alkaline springs, saturated salt brines, and the driest deserts. There are more microbes in a handful of good soil than people on the Earth. To be more specific, at the current level of detection there are more microbes in a 100-m square than the population of Earth. The only generalization is that microbes that we know about require liquid water that is not too hot. Pressure is no serious problem. The deepest ocean teems with animal and microbial life.  However, the pressure at the bottom of the ocean can be lethal to organisms that evolved at the surface.

There are some potential environments on the Saturn moon Titan for which we do not have viable organisms. They include liquid methane-ethane at the surface and a liquid water-ammonia solution in the shallow subsurface at temperatures down to 235 K and even 153 K if methanol is present. Like with armored deer, there has been no selective pressure for terrestrial organisms to evolve the ability to inhabit environments that have never existed on the Earth.

Garden peas. Darwin considered heredity to be a blending of characteristics. This is certainly a valid overall description of the offspring of animals and plants. He was aware that hidden traits could emerge after several generations. He also believed use and disuse affected heredity.

1860s. An Austrian monk experiments on common garden peas. Gregor Mandel (1822-1884) observes simple traits. Seeds may be yellow or green.  Flowers may be purple or white.  Inbred plants for many generations breed true.  White-flowered plants beget white flowered plants.  Like any breeder of his day, he crosses his plants.  A cross between green-pea plants and yellow-pea plants, for example, yields only yellow-pea plants.  There are no yellow-green peas or green peas. When he interbreeds these hybrids, 1/4 of the plants produce green peas and 3/4 produce yellow peas.  Again there are no intermediate plants.  He has discovered that heredity is quantized in what we now call genes.

The explanation is mathematically simple. Each pea plant gets a gene for seed color from each of its parent.  The purebred parents have the genes YY for yellow peas and gg for green peas.  The upper case Y indicates that it dominates over the lower case “recessive” g.  The first generation hybrids all have a gene from each parent (Yg) and are yellow.  The second cross gets a gene at random from each parent.  Putting the mother gene first, the possibilities are Yg, YY, gY, and gg. Only the gg plant yields green peas. It statistically occurs 1/4 of the time.  Mandel does this with numerous traits.  Each trait behaves independently.  Modern science shows that genes join together on chromosomes.  Traits governed by genes that are close together on the same chromosome are linked. The traits studied by Mandel are on different chromosomes or so far apart on one chromosome that little linkage occurs.

Many biology books state Mandel’s published results are too close to the expected theoretical ratios to be true. Mendel reported enough information that recent statistical analyses indicate that outright fraud or self-deception by Mendel or his assistants is unlikely. At the start of his work, he did not have the expected ratios, but clearly became aware of them later on. The statisticians, however, did not find the expected effect of bias, Mendel's later results are no closer to the expected ratio than his early results. In any case, any deviations of Mendel from optimal scientific practice are irrelevant to the scientific issue of the existence of genes. Anyone one can repete his experiments, countless have done so.

Still it is worthwhile to examine sources of bias that crop up with experimental data. First, peas do behave as Mendel reported, so we can exclude complete fabrication. More subtle issues arise once an experimenter knows the expected result.  Mendel was trained in mathematics and simple statistics. He did not, however, have access to modern probability theory on typical deviations of real trials from the expected ratio (1:3 in my example).  For example, he repeated one trial that came out too far from the expected ratio for his taste. Recent analysis indicates that the deviation in his first trial was well within the expected range. Neither did he have a good idea of how many plants he needed to count to get a representative sample. Conceivably he could have stopped counting once the ratio approached the expected one. (He seems to have counted the whole samples.) He might even have failed to report trials on other traits that did not work out to the expected numbers. (He did report the trial that he repeated so this is unlikely.) There was some tendency to unconsciously bias results with traits that could not be determined with 100% accuracy. (We then would find that hard to measure traits are closer to the expected ratio.)

The genes for recessive genetic diseases, like sickle cell anemia and cystic fibrosis provide a tragic example of an evolutionary contrivance, which is impossible to attribute to design. I have never heard of a preacher going to a cystic fibrosis ward to tell the victims that the divine Creator designed the disease for their benefit.

The cystic fibrosis gene f is recessive. (More precisely two independent mutations are involved in the disease.)  The carrier with one normal gene N and one cystic fibrosis gene f appears normal.  Actually having the mixed genes Nf provides some protection against dysentery, a major scourge in medieval squalor. If the f gene is rare in the population, Nf individuals mate only with NN individuals and produce (statistically) equal numbers of Nf and NN children.  More of the Nf children, however, survive dysentery causing the f gene to become more frequent. Eventually some Nf individuals mate producing (statistically) 1 NN, 2 Nf, and 1 ff children.  The ff child dies from cystic fibrosis (or with modern medicine at least does not breed). The frequency of the f gene in the population reaches an equilibrium where the benefit of producing carrier children is negated by the deaths from cystic fibrosis.  It does no good for individuals to recognize carriers at equilibrium since NN and Nf individuals have an equal chance, with all mating possibilities, of continuing their bloodlines.

At the present, dysentery is not a major problem in countries with good sanitation.  The cystic fibrosis gene is thus useless to carriers as well as lethal to those with the disease. A new equilibrium will eventually occur with the gene essentially absent. Its frequency would be determined by the very slow rate that it is produced from the normal gene as a mutation. There have not been enough generations of people dying from cystic fibrosis for this to happen. Actually, any mutation that makes the normal gene ineffective leads to cystic fibrosis.  It is easier for a mutation to break a gene than to fix it. Just like it is easier to sabotage than fix machinery.

Back to history. Mandel published in German, a language that Darwin did not read. Darwin never opened Mandel’s reprint. Legend has it that biologists dismissed his work as extremely complex mathematics or as something that conflicted with Darwin. This is partly true. Yet three independent groups rediscovered Mandel’s results in 1900 and submitted their papers to scientific journals. As customary, the journal editors sent the drafts to qualified scientists for technical review.  The reviewers pointed out Mandel’s paper.  It had never been fully forgotten.

The existence of genes poses complications to natural selection. Some of these involve figuring out how evolution works. Biologists distinguish between genotype (list of genes) of an organism and its phenotype (actual structure).  For example, a starved individual with “good” genes may be sickly. Natural selection, as I have already noted, is statistical. A gene or gene combination has an expected chance of survival, which changes with time as conditions change. Mathematical genetics is a major field of current research.

Both mutations that produce modified genes and sexual reproduction that redistributes genes are important. To get an idea of the power of sex on the genetic variation already in a natural population, you need merely watch a dog show. The vast array of dog breeds comes mostly from genes already present in their wolf ancestors. Show dog breeders do not practice genetic engineering.  It would kill the sport value.

Code breaking.  After World War II, scientists returned to their peacetime day jobs. The war had brought both carnage and improved technology to Britain.  Its end brought a sense of intense competition to some of the scientists. The story of James Watson and Francis Crick’s discovery of the structure of DNA (Deoxyribose Nucleic Acid) is well known. In fact, DNA is one of the most commonly recognized abbreviations.  Watson and Crick received the Nobel Prize for their work in 1962 with Maurice Wilkins. By then, Rosalind Franklin who had done much of the X-ray work and got little of the credit was dead.

To cut to the chase, DNA is a complicated chain of similar molecules.  It has two spiral chains linked by “base pairs.” (The Double Helix.)  The base pairs are the basis of the genetic code. There are four bases, adenine (A), thymine (T), guanine (G), and cytosine (C). C always pairs with G and A with T. To duplicate; the double helix unzips leaving the bases unpaired. The side of the single helix (with say CGAT) forms its matching helix with GCTA.  The complementary side of the helix with GCTA grabs CGAT.  The result is two double helixes that are copies of the original. This nicely explains like begetting like.

When my son Jacob was four, he took a phone message on the pad as he had seen us do many times.  He did not yet know how to read and write. Neither he nor we could decipher his scribbling. The cell needs to read the information coded in the DNA for it to be any use. The mechanism is highly complicated.  I give an overview.

The DNA functions as a genetic code to make proteins from chains of amino acids. Groups of 3 bases act as “letters” to code from 1 of 20 amino acids or a stop (analogous to a period in English) to end the chain. There are 4 times 4 times 4 or 64 possible letters.  So more than one letter codes for the same amino acid.  For example TCT, TCC, TCA, TCG, AGT, AGC all code for serine.  Ribosomes composed of Ribonucleic acid (RNA) and proteins do the reading.

The code is almost but not completely universal. To see why evolution locks the code, consider the human genome.  It has around 3 billion base pairs and 35,000 functional genes (that is, genes that make protein). A change in a gene that codes for the reader in the ribosome would cause all these genes to generate different chains of proteins than they did before.  This gross change would be lethal to the cell.  Yet minor differences from the standard code exist, showing that it can and did evolve. For example, humans have a nonstandard (21st) amino acid containing selenium.  It occurs in 25 proteins.

It is useful to consider English as an analogy. It, like DNA, is a code intended to be read, even though first graders have some trouble. We could transmit English with the genetic code.  We would instead have 26 caseless letters (like on an old telegraph or teletype) and a space and a stop.  We would have several combinations code for vowels (in analogy to serine) and only one code for z.

The point is that there is much redundancy in English writing.  There is also considerable redundancy in the genome.  Most changes are not lethal. The simplest mutation changes a single base pair. Often this does nothing, like replacing AGT and AGC. There are large parts of the genome that do not code for proteins. There are other parts of the genome that code for rudimentary or unimportant structures.

Another class of mutations involves omitting part of the genome. One or more complex genes may be lost. Typically, this does not benefit the organism. Yet changes of this type occur, particularly in microbes that live within the cells of other organisms like pathogens. The loss of a gene for an important function need not be lethal as the host may also do that task. Like organisms on oceanic islands, pathogens have many chance colonization events. For example, a strept throat microbe with a missing gene may start an epidemic.  Once a complex gene is lost, it cannot be regenerated by evolution.  A newly evolved gene that performs a similar function will be different, just like the independently evolved squid and human eyes differ.

Reproduction sometimes leaves two independent copies of a gene where one existed before.  Initially the genes do the same thing, but they can evolve to handle specialized purposes to the benefit of the organism.  Gene families originate in this way.  Biologists construct family trees of genes within a single organism.

Immortality.

There are two meanings of immortal. One is like the Greek Gods that can never die. The other is like the elves in the Lord of the Rings or the children in A World Without Time.  They can potentially live forever, but can be killed. Microbes that reproduce by dividing and genes are immortal in the second sense.

Typically the fate of a gene in a mouse is tied to the fate of the mouse. The immortality of genes and the existence of multiple copies give rise to exceptions.

Some genes have evolved to preferentially duplicate themselves and jump between chromosomes.  They are particularly abundant in maize (field, pop, and sweet corn for Americans). Barbara McClintock (1902-1992) began documenting these effects in the 1940’s.  Legend has it that she was universally regarded as a crackpot. She did have difficulties, but the National Academy of Sciences elected her in 1944.  She received the Nobel Prize in 1983.

Self-duplicating genes are a form of parasite, but one whose fate is linked to the host. If they get too out of hand, they cause frequent mutations, in addition to making the genome excessively large. Either the unfit organism dies out with its jumping genes or evolves mechanisms for keeping them in check. It is to the advantage of the jumping genes not to get too greedy.

There are also jumpy genes that are readily carried by viruses between microbes, like one-celled photosynthetic cyanobacteria in the ocean. The exchangeable genes, the "core" genes of the cells that do not exchange, and the viruses are three nonstandard classes of organisms with a complex ecology. An exchangeable gene benefits by being readily picked up by viruses, by having its cell host easily infected by these viruses, and by not having the infection be lethal before the cell as had chance to divide. These traits are not necessary advantageous to its host or to its virus. Natural selection thus acts on the core genes and the viruses, sometimes to the detriment of the exchangeable genes. An exchangeable gene, like many parasites, benefits when it is not a major detriment to its host, here the core genes of the cell, and its vector, here the virus.

Conversely, there are copies of many successful genes in the genomes of many individuals, say a population of butterflies.  As the copies are identical, it is irrelevant to the genes which butterfly actually reproduces.  It is the net increase or decrease of the gene in the population that matters. A gene (or group of genes) that renders the butterfly toxic to birds and recognizable from its nontoxic relatives may spread in the population by group selection. A bird eats a toxic butterfly, killing that copy of the gene. It becomes sick and avoids the toxic butterflies in the future. This benefits the remaining butterflies that carry the gene.

The tree of life.  My aunt recently had her membership in the DAR disqualified because the ancestor had fought on ships, not land, in the American Revolution.  With some effort, she found an ancestor who had served in the army and registered to collect his pension (and hence modern documentation).  This aroused my curiosity and I did some looking on the web.  There are two types of family trees, the ancestors of James Hatfield and the descendents of James Hatfield.  Biologists from the advent of evolution dealt with both types of trees using morphology and the fossil record.

DNA provides a solid method of determining family trees.  It has put an end to contested paternity suits.  It is far more reliable in crime solving than eyewitness accounts of the “morphology” of the suspect. Scientists can sequence the DNA as a long list of AGCT’s, sequence the amino acids in the proteins, or sequence the RNA in the ribosomes.

If we wish to use DNA to deduce the recent family tree, like in a paternity suit, we need to concentrate on parts of the genome that are highly variable. These are partly genes of traits for which there has been much recent natural selection, like skin color with latitude, and unimportant traits (including DNA that does not code for proteins).  If we want to work out our relationships with microbes and plants, we need important DNA that evolves slowly.  The ribosome is ideal.  It occurs in all cellular organisms.  Its failure is lethal in that the genetic code cannot be read. It is also quite complex.  This alone shows that all cellular life has a common ancestor.  It is easier to sequence the RNA in the ribosome than the DNA that codes for it.

For purposes of discussion, I start at the root of the tree, the last universal common ancestor (LUCA). There are three major branches (Figure 2).  The first branching from the trunk is Bacteria. (The public and scientists over 40 tend to use bacteria to mean microbe.  This use needs to be avoided like the plague that is caused by a type of Bacteria.) Bacteria also include Escherichia coli (E. coli) in our guts and Streptococcus in our throats, as well as numerous free-living forms. The second branching is between Eukarya and Archaea.  We belong to Eukarya.  Plants, other animals, and Fungi are our close relatives on the tree.  Single celled Giardia is a more distant relative, a bane to back-backers. The Archaea are small single cell organisms.  The name reflects the hypothesis that they retain ancestral features of early life.  They are quite common on the Earth but escaped detection until scientists discovered forms that live in extreme environments. They are a significant part of the oceanic biomass.

Figure 2: All extant organisms descend for the Last Universal Common Ancestor (LUCA).  There are also last common ancestors of the three major branches, Bacterial, Archaea, and Eukarya.  Plants animals, and fungi are closely related.  Red lines indicate thermophile organisms and black lines indicate organisms living at lower temperatures.  The last ancestors will change if organisms with lower branches are found. The truck below LUCA is poorly constrained. FYI: Aquifex, Thermotoga, Thermomicrobium, and Thermus are thermophile bacteria.  Chlorobium is a non oxygen-producing photosynthetic organism.  Tritrichmonas, Giardia, Encephalitozoan, and Trypanosoma are Eukaryotic pathogens.   Euglena and paramecium are feed-living Eukaryotic microbes that can be easily observed in a microscope. Thermofilium, Sulfolobus, Methococcus, Thermococcus, and Methanopyrus are Archaea thermopphiles.  Haloferax is in saturated salt brine and does photosynthesis.  I have pruned the tree to have a manageable number of branches.  I prune a vast number of branches leading to extinct organisms which we cannot sequence.

Biologists can do better in constructing the family tree by taking account of the function of genes.  Take for example a gene that codes for an important protein in primates.  We have copies of the gene and the protein in many primates including lemurs and ourselves. Every change between the ancestral gene and the current one coded for a functional protein.  A lot of mutations in any branch did not all occur in one generation.  With these restrictions on evolution, it is possible to reconstruct and genetically engineer several tens of million year old genes and their proteins.  Linguists do the same thing to reconstruct the Indo-European language. They can deduce the speaker’s lifestyle.  For example, our words “ewe” and “wolf” trace back to the original language.  The speakers raised sheep in a wolf-infected region.

In analogy with languages, borrowings do occur.  Genes jump from one “species” to another.  The process is a major part of genetic engineering. It is frequent among microbes in nature. It creates a problem in constructing the tree of life. Did the gene that we are sequencing jump in from another line? Again the analogy to “word borrowing” is useful. For example, there are no deserts in England or eastern North America.  The British encountered deserts in Arabia.  Their desert words like wadi (dry streambed) come from Arabic.  The Americans reached the desert in the southwest.  “Arroyo” comes from Mexican and Microsoft Word recognizes it as American English. Back to the genome, burrowed genes come into the genome as groups and stay linked. They also tend to do tasks that the organism did not already do well. The west coast settler did not need to borrow the Mexican words for public body parts that were already in English.

Gene transfer can be turned into a signal on the timing of various branches of the tree.  Back to languages, careful examination of regional varieties of English would show that groups of Mexican words came into western English after 1830. With regard to life, the chloroplasts in plant cells are the descendents of cyanobacteria that plant microbial ancestors once trapped with their cells. By examining the chloroplast genome and the genomes of its free-living relatives, we could tell where within the branching of the tree the chloroplasts moved into the ancestor of plant cells.  We can correlate branching events in two limbs by seeing which Eukarya lack chloroplasts as a primary feature.

What was LUCA like? It was obviously a highly complex organism. The genetic code was already in place.  Several gene families predate it.  Biologists construct the family trees of these genes to times predating LUCA.  In addition, genes transferred from extinct lineages probably exist within LUCA and its living descendents.  None have been recognized as such.

Where did LUCA live?  Probably in the dark. Photosynthesis evolved much later well up into the tree, though billions of years ago. It got its “food” from chemical disequilibria as occur now around hydrothermal vents.  LUCA’s resistance to arsenic indicates that it (or its ancestor) hung out around hydrothermal systems. The universal need for elements, like nickel and cobalt, indicates that it lived within rocks erupted from very hot volcanoes (where these are common) on the young planet.

Did it live in hot water? Probably. Both the Bacteria’s and Archaea’s last common ancestors were high temperature organisms.  It is less clear whether Eukarya had a thermophile ancestor.  This provides a hint that LUCA had ancestors that evolved at temperate conditions.

What does this portend for planetary habitability? First we can throw out traditional ecology dependent on primary photosynthetic producers. The early ecology did not depend on sunlight and in fact may have found it lethal. Dark oceans in ice-covered planets like Europa and ground water a kilometer down in Mars are habitable provided that the planet is geologically active enough for hot springs and volcanism to maintain disequilibria, like those LUCA lived around. There is no outer limit to the habitable zone for microbes, provided the planet is large enough to maintain liquid water and some geological activity. It is a matter of logistics that it is hard for us to get at the subsurface of a frozen world.  Fortunately, life-charged water may erupt to the surface.

There is no “ladder” of life on the Earth, like in bad K-12 science books. All organisms have had equal time to evolve from LUCA. Vent Archaea, for example, are quite fit for their environment.

We are quite fit ourselves.  This is to be expected of a common wide-ranging organism. Yet we are not even the most successful organism by many measures. There are a lot more worms than people on your yard after a hard rain. Our body structure is more complex than microbes and I am writing now. But our chemistry is quite similar to microbes. We are really microbes (at the start of our lives) that have evolved to be multicellular.

We call our close relatives “primates” and call animals and plants “higher organisms.” The former is vanity and the latter is, at best, a useful fiction. Modern biologists avoid the word “primitive” especially with extant organisms.  It is best to use "conservative" to imply that the organism has retained ancestral traits. They do not belittle traits, like the external fertilization of eggs by sperm. These traits aptly serve many organisms.  They do not go looking for some gross misadaptation in extinct species, like the popular meaning of dinosaur.  After all, extinct organisms had successfully evolved for billions of years.

There are real evolutionary contrivances. To boot, the first organisms to occupy a niche were likely to be inept at it, like the first land animals, including fish-amphibians. They had no competition at first.  It may be productive to call the first adaptations for land life “primitive” but not the organisms as a whole.

Chicken and egg. My children (at ages 6 and 7) were, as often, fighting in the car. To stop the fight, I asked them, which came first the chicken or the egg?  They stopped to think for a while. Finally some quiet! But it did not last. In a crescendo, Zacky insisted that eggs hatch into chickens and Jacob insisted that chickens lay eggs. Through the din, I realized that the question, as phrased, relates only to Creationism. There is no problem in evolution for an ancestor of chickens to evolve the ability to lay eggs.  There is a more fundamental problem of how life started in the first place. Darwin avoided the problem beyond stating it might have happened in a small pond.

We can start with LUCA and try to work back. LUCA, like modern microbes, is too complex to be a first common ancestor.  No one would repeat Pasteur’s spontaneous generation experiments now except as a demonstration. The most telling issue is that its DNA needed proteins to replicate, but the proteins needed the DNA to form. We are back about 4 billion years to chicken and egg.

We can go back to RNA.  The RNA in the ribosome may be the vestige of an earlier genetic material. RNA can act as its own catalyst in replication. It also has a 4-base system that codes for proteins. Perhaps RNA-based organisms evolved the ability to produce proteins and then DNA to aid their replication.  The DNA proved to be a better genetic material. (It is more stable.) It eventually evolved into that information function, relegating the RNA to the ribosome.

This RNA world has been the subject of much speculation by biologists.  There may be vestiges of the original RNA molecular organisms in repeated sequences in ribosomes. So far, no one has a model for working RNA organisms. In any case, modern RNA is too complex to be the first living thing. Biologists have ideas for simpler self-replicating systems.

There is a wide choice of other bases and compounds similar to RNA and DNA, but the vestiges of them are not evident in living organisms. Overall RNA seems to be the best material that might be generated abiotically. Its "backbone" sugar, ribose, has 5 carbons. It forms spontaneously in alkaline water that occurs naturally within serpentinite, a rock consiting of hydrous magnesium and iron silicates and hydroxides for those with some chemistry. The trace element boron stabilizes ribose from decomposing into tar.

The lack of evidence in extant organisms occurs because evolution tends to wipe out some of its tracks. Some of the early evolutionary lines may have retained pre-RNA and RNA heredity. The DNA life out-competed these organisms, eventually driving them to extinction. We have no fossil record from this early time on the Earth. As we will see in the next chapter, disasters may have helped cull these conservative lineages.

We can start with the conditions on the early Earth and try to work forward. It is easy to generate complex organic molecules, like amino acids, without life. (Organic is royally awkward here but we are stuck with it. The term dates from when scientists believed a vital force is necessary for life. Laboratory chemists have “abiotically” produced organic compounds since the early 1800s. Chemistry and physics inside a cell are the same as chemistry outside but often more complicated.)

The first serious attempt at replicating early Earth conditions comes when a graduate student at the University of Chicago mixes water, ammonia, and methane and hydrogen in a flask. He sends electric sparks to simulate lightning on an early planet. His advisor, Harold Urey, is expecting negative results. To his surprise, Stanley Miller finds complex compounds including amino acids.

Debate continues to the present day on whether these conditions represent the early Earth. The flask material is probably too reducing (has too little oxygen) for a long-lived planetary atmosphere.  It could occur when there was a lot of iron metal around, like after an asteroid hit.  Subsequent work shows that other somewhat more oxygen-rich mixtures generate complex organic compounds and that the bases in the genetic code can form abiotically.

Fortunately, we have natural examples where complex organic matter formed abiotically. A class of meteorites called carbonaceous chondrites frequently falls to the Earth.  Geochemists eagerly analyze samples that have not been fouled by terrestrial organisms, like pissing dogs.  As expected from their name, these meteorites contain complex carbon compounds including amino acids. They formed underground with water circulating through the asteroid-sized body (many kilometer-diameter) from which the meteorite formed.  There was iron metal around.  These are conditions expected on any clement body in the early solar system.

In addition, organic compounds occur in interstellar space, especially the star-forming regions of giant molecular clouds.  These include simple amino acids.

How far did this prebiotic chemistry get toward life?  There are no cellular fossils in any carbonaceous chondrite meteorite yet studied. Life did not form in the hundreds of thousands to a few million years that these objects stayed clement.  We do not know the duration of clement conditions very well. Still there is a hint of autocatalysis, but it is not a smoking gun.

Amino acids have mirror image forms, left (L) and right (D, dextral from Latin). Terrestrial life uses the L forms. An abiotic process produces both forms equally and a biotic sample will eventually decay to equal amounts.  The dry-cold environment of meteorites is sufficient to preserve the L:D ratio for geological time. There is an excess over 50% of L in some samples where terrestrial contamination can be excluded. This would occur if autocatalysis produced an excess of the L forms or if it “ate” more of the D forms. We do not know which. On the Earth, it proved advantageous for life to use only the L forms.  There are plenty of D forms around in degraded organic matter so this did not occur from lack of supply.

Bottom lines.  Life on the Earth is typically well suited for its mode of existence.  Natural selection over geological time produced this illusion of design. With a little thought you can see the effects of evolution. [see Do it Yourself with Acorns] Evolution also produced many contrivances that any conscious designer from scratch would promptly reject.

Evolution gives us, the sole conscious survivors on our planet, an illusion of miracle. With an aura of Darwin's time, consider the analogy of a shipwreck on the Dover coast. (Darwin never sailed again even to France once the Beagle reached port.) The survivors, once ashore, reflect eloquently on the miracle of their fate to the press. The drowned victims cannot partake in the interviews. The miracle of the accident does not impress the families of the victims, nor the owners of the ship and cargo. Survivor bias is well known to salesmen and hence the wary. A new car salesman will point in the lot to used cars of his make that are still running after 12 years and not take the client to visit the junk yard. The majority players remaining around a roulette table at 4 A.M. may be ahead. Families of hedge and mutual funds exist partly for this region. The salesmen notes with pride that both of his company's funds doubled in the past year; never mind that the other 8 went belly up.

We can export to astrobiology that natural selection leads to a vast assortment of life forms if it can act for geological time. It also limits what we can export it detail.  Terrestrial biota have evolved for the conditions on the Earth. Early biochemical innovations have been locked in because too many things in the cell depend on them.  We can at least export that the biological innovations that we see on the Earth are possible.

We can trace evolution back beyond the last common ancestor of extant life and probably back to an RNA world.  An unknown genetic mechanism possibly RNA existed at first.  We do not know when life became cellular.  In fact the building blocks of cell walls form abiotically and the wall material can self-assemble abiotically.  Still the issue is merely finding out how a series of biological innovations and adaptive radiations occurred once we are into descent with modification.

Getting abiotically to complex organic molecules like amino acids is easy even in the laboratory. A poorly understood gap exists between this “Darwin soup” and descent with modification. We will never find this gap preserved in terrestrial rocks. What happened as autocatalysis moved toward life? Biologists just do not know at this stage and it makes the very religious happy. Biologists are stymied, but by the lack of a rock record and the lack of vestiges in extant organisms.  We still do not know whether the origin of life is hard or easy.  We still face the weak anthropic principle that we need to be here to observe.

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