14 DAY TRIAL // One of the most striking aspects of the theory of evolution by natural selection is its simplicity - it is capable of explaining so much using such a simple mechanism. Nonetheless, the Darwinian theory does have its subtleties and its simplicity is often misleading. Moreover, as biologists have learned more about the inner workings of living beings, the Darwinian theory itself has evolved and we can now identify four major scientific revolutions inside the evolution theory itself. The last such revolution happened very recently, in the last 10 or 15 years, as biologists figured out how the living creatures are actually constructed as a result of the interaction between the inherited DNA and the environment.
The four major events in the history of the Darwinian theory are these: the first is the appearance of Darwin's theory that described the basic outline of the theory of evolution, but lacked a proper description of how inheritance works. The Modern Synthesis happened as a result of the advances in genetics and solved the problem of heredity. The Modern Synthesis lacked however a proper account of altruistic behaviors and it was very unclear at which "level" (the genes' level, the individual's level, the species' level?) natural selection happens. What exactly is selected? The "selfish" gene theory showed how altruistic behavior at the individual's level can be understood when one thinks in terms of genes. It's not that natural selection happens at the gene's level, but that - in order for some traits to be preserved in a population - certain genes have to be passed from generation to generation. The question about the level at which natural selection happens is not answered, but rather dismissed as a bad question: it's not that something is being selected, but that something (the genes) are being replicated and inherited for a very large variety of possible reasons. The selfish gene theory raised a number of wrong questions itself, most importantly the question of whether some traits are genetically inherited or the result of education (the nature vs. nurture dispute). Finally, the evo-devo revolution showed that the genotype (the DNA) does not uniquely determine a certain phenotype (how the living being looks and behaves) but it rather makes possible a fairly large number of potential phenotypes and the environment "chooses" one of these (or more precisely: the actual phenotype is the result of the interaction between genotype and environment). Thus, the nature vs. nurture dispute is also rendered obsolete.
The birth of Darwinian theory
Darwin and Wallace described evolution as the outcome of a simple algorithm that gets repeated again and again over the course of a very large number of generations in an environment of scarce resources. This algorithm states that at each generation there is variation, the inheritance of variation, and natural selection. This means that the offspring inherit much of their parents' traits but not perfectly, they're slightly different from their parents.
All the living creatures that need roughly the same kind of resources in order to survive and reproduce are said to belong to a certain biological (or ecological) niche. (The concept of biological niche is obviously a fuzzy one - there are no clear cut borders between one niche and another.) The creatures inside one biological niche compete with each other for the scarce resources. Only some of these creatures actually manage to survive and reproduce - this is the natural selection. The survivors' offspring carry with them the traits that have proved successful in that given environment. The competition among the closest related creatures is the fiercest as they need the same resources (but there is a catch: see the selfish gene below).
How different species form. The algorithm described above leads to a larger and larger diversity of creatures - it is like a continuous cone of living creatures each slightly different form one another. But, as it happens, not all these creatures manage to have descendents - and this creates gaps in this continuous cone and leaves behind a tree-like structure: the tree of life. If creature A resembles creature B, which in turn resembles C (A and C may not resemble each other very much), and A and C have descendents but B does not, then we get a fork-like situation: the parent of A, B and C gives birth to two different - separate - evolutionary lineages. On a sufficiently long term, this separation can get amplified until the descendents of A and C are so different from one another that we call them different species (and often they are so different that they cannot interbreed anymore). But this separation is not a creative result but a consequence of the destruction of the intermediate, "unfit", creature B.
Moreover, the appearance of a new species is not an event that can be observed as it happens. The descendents you and your brother have might diverge into different species a million years from now, but it's impossible for us to see this now. Thus, the appearance of a new species can only be inferred long after it has happened.
Adaptation and exaptation. One of the most subtle aspects of the Darwinian theory is that the traits do not develop for a certain purpose: natural selection does not positively select the traits that are "useful for something that it wants", it doesn't aim at anything, it negatively selects against the traits that prove sufficiently deleterious to the organism's survival and reproductive capacity. Living beings are indeed beautiful and amazing, but they are anything but perfect. Natural selection does not mean "survival of the fittest" (this was an expression coined by Herbert Spencer and reluctantly accepted by Darwin), it means the survival of everything just remotely fit to reproduce. Nature doesn't promote only the best of the best, it "just" destroys the underdogs.
On the short term, this process of selecting against the unfit (and not in favor of the "fittest") leads to gradual improvements of certain traits - and we say the animal is adapting, i.e. after a number of generations the surviving offspring are better at coping with the environment than their ancestors were. But on the long term, the environment itself changes, partly because of the physical factors and partly because the environment is made of other living and evolving creatures, and there remains nothing to adapt to. What often happens on the long term is that certain traits that had been useful stop being useful anymore. Such traits (organs, behaviors etc.) either wither and eventually disappear or get hijacked by other purposes. This hijacking process is called exaptation. Thus, adaptation is prevalent on the short term and exaptation on the long term.
"Throughout nature almost every part of each living thing has probably served, in a slightly modified condition, for diverse purposes, and has acted in the living machinery of many ancient and distinct specific forms," wrote Darwin in 1862 edition of the Origin of Species.
For example, legs first developed in lung fish - surprisingly from our point of view - were used by these creatures for keeping their heads above the water - the climate became very warm back then in the Devonian and - as warm water retains less oxygen than cold water - the fairly large animals had to either breathe air directly or die. The original function of legs and fingers was thus that of a floating device. The legs were later on exapted by walking and jumping. Once they ended up on land, the creatures didn't need to struggle to keep their heads above the water anymore - instead, the legs were either put to a new use or abandoned. In case of snakes they withered away. But other animals invented walking, jumping and running and retained their legs. Of course, that wasn't the end of the story, this story is never-ending: later on, the front limbs of some tetrapods transformed into wings in case of birds or later on bats, or in hands in case of, say, monkeys. In other cases, the legs even turned back into fins in case of whales and dolphins! Thus, legs obviously have no general, long term, purpose or function. What is true for legs is true for all the other biological devices.
Sexual competition. Animals in the same species obviously belong to the same biological niche (they need the same resources). They compete for resources but, in case of sexual beings, also for sexual partners. In the same way as resources are scarce, sexual partners are also scarce. And high quality sexual partners, capable of guaranteeing offspring with high survival rates, are even scarcer. Sexual reproduction fuels the appearance of seemingly absurd (i.e. not useful for dealing with the environment outside of one's species) but beautiful (i.e. useful for getting sexual partners) traits such as the peacock's tail. Such apparently absurd traits are the means by which an animal (usually a male) advertises its high survival capability to its potential sexual mates - if a moose for example can survive in spite of that crazy construction on its head it must be really apt for surviving. (Why do we have sex: see article.)
The problem of heredity. How are the traits being transmitted from generation to generation and how is it possible for a certain novel trait not to be swamped by mediocrity? For example if all the proto-giraffes had short necks and one random mutant proto-giraffe happened to had a slightly longer neck than usual, wouldn't all the descendents of this longer-necked proto-giraffe also have short necks? (Because the longer-necked proto-giraffe would have to mingle with a short-necked proto-giraffe.) How could a bunch of horses turn into giraffes?
Mendel and the Modern Synthesis
The key to this dilemma is offered by genetics. What gets inherited from one generation to the next is not the actual set of traits, but the recipe for constructing these traits. The code for a particular trait might include only a very small number of genes (for example the eye color) or a large number of genes (e.g. the skin color). To make things more complicated, a particular gene can get involved in a number (even a large number) of different traits.
To use a computer metaphor, the genome is like the set of .dll files in Windows: it is a database of tools or subroutines. A particular living being is a certain combination of genes that get activated in a certain sequence. In the same way, as the same subroutine (e.g. create a button or draw a line) is used in many programs, the living beings share many genes. In the same way, as the same subroutine can be accessed in many places in the same program, a gene can get involved in many traits of the same living being. But unlike the world of software where we have more than one operating system, all living beings on Earth are coded on the same operating system (the DNA). This operating system (the set of basic genes) has evolved itself as the number of genes has grown.
"I've used metaphors like the idea of alien beings from outer space who wish to travel to a distant galaxy and can't, because they can't travel that fast, so what they do is beam instructions at the speed of light, and those instructions make people on some distant planet build a computer, in which the instructions can be run," wrote Richard Dawkins. "Instructions are all you need in order to re-create the life-form. It's controlling its programming in advance, given that you cannot program the day-to-day running of the thing. The distant galaxy is too far away: you can't send orders, can't say, 'Now do this, now do that,' because every instruction takes millions of years to get there. You send a program that anticipates all possible eventualities so that it doesn't need to have instructions sent to it; the instructions are all there. That's what the genes are. Success in evolution is building programs that don't crash. Programs that crash don't perpetuate themselves. The best way to look at an individual animal is as a robot survival machine carrying around its own building program."
For each particular trait (such as the color of the eyes) an organism gets a set of genes from the mother and another set of genes from the father - but only one set of these genes gets expressed in the actual phenotype. In other words, some kinds of genes are dominant and some kinds are recessive (when recessive genes meet dominant genes they stay silent). For example, the gene for brown eyes is dominant and the gene for blue eyes is recessive: a person that has blue eyes certainly has two blue eyes genes (one from the mother, one from the father); while a person having brown eyes might have either two brown eyes genes or one blue eyes gene and one brown eyes gene.
This makes it much more difficult for a trait to disappear. It may be silent in the next generation, but nevertheless, still get posted to the grandchildren. Moreover, the traits of offspring are not averages of the parents' traits. This is how a bunch of horses can develop into giraffes - the combination between a longer-neck horse and a shorter-neck horse is not necessarily an intermediary-neck horse, it might even be a horse with an even longer neck; it all depends on how the gene for the neck length is expressed during development.
While the Modern Synthesis (between Darwin's theory of evolution and Mendel's theory of genetic inheritance) solved the problem of how novelty can appear and not get swamped by mediocrity, it also raised a number of questions. The most important one was the question regarding the level at which natural selection works: is it the individual, the species, or the gene? "Mostly, the group-selection idea was necessary to the way people were thinking about adaptation," George C. William recalled, "although - and I find this extremely strange - they didn't realize it. They kept talking about things being for the good of the species."
At first, the controversy was between those thinking that natural selection functions at the group level, and those thinking it functions at the individual's level. The idea of group selection seemed to offer an explanation for altruistic phenomena, such as the mother caring for the offspring or the individual ant sacrificing for the colony. On the other hand, the actual concrete mechanism by which this selection could happen was a mystery. All those explanations also looked very arbitrary - anything can be good for some group. The entire theory looked like a set of just-so stories. All the explanations were post-factum, no predictions could be made.
On the other hand, although selection at the individual's level seemed more scientific, it was incapable of explaining all the behavior exhibited by living beings. The solution came from the observation that much of the unconsciousness altruism - such as the one exhibited by ants or bees - was among animals very closely related to each other. In other words, an individual ant doesn't have enough of a brain to be able to think something like "I'll help this fellow because he might help me in the future", its altruism has a different cause: the fact that all the fellow ants have the same genes inside them.
"The only reason why it's important that it's the gene that's the unit of selection is that the gene is what goes on forever," wrote Richard Dawkins. "The gene [understood as information] is what goes on for a very large number of generations. Those units of communication that go on through many generations are the successful ones. They're successful by virtue of their effects upon phenotypes. [...] It's been said that you can easily come up with some Darwinian idea to explain anything. As against that, the proper understanding of Darwinism at the gene level severely limits you to a certain kind of explanation. It's not good enough just to say that if something is vaguely advantageous it will evolve. You have to say that it's good for the genes that made it. That automatically wipes out great swathes of possible facile explanations."
The selfish gene
"Our genes are like a colony of viruses - socialized viruses, as opposed to anarchic viruses," Dawkins wrote. "They're socialized in the sense that they all work together to produce the body and make the body do what's good for all of them. The only reason they do that is that they all are destined to leave the present body and enter the next generation by the same route, sperms or eggs. If they could break out of that route and get to the next generation by being sneezed out and breathed in by the next victim, that's what they would do.
Those are what we call anarchic viruses. Anarchic viruses, the ones that make us sneeze, are the ones that don't agree with each other. They don't care if we die. All they want to do is make us sneeze, or, in the case of the rabies virus, make the dog salivate and bite. But most of our genes are socialized viruses, socialized replicators. They're disciplined and cooperative precisely because they have only one way out of the present body: by sperm or egg."
Thinking about genes changes the focus in a very interesting way. One starts to understand natural selection differently, as a more passive force. When one thinks in terms of the individual or of the group, one understands natural selection as a sort of challenge that must be faced or as a sort of grim reaper that chooses the lucky ones. But actually, natural selection is an abstraction, it is the name for all the challenges combined. The way natural selection acts on some animal might be very different than the natural selection acting on some other animal. So the question is: what's the thing that is the same in all the cases?
The answer is that, in evolutionary terms, success means that the genes have replicated - the information has been preserved. All the animals that didn't succumb to natural selection have genes with this property. The individual animal ages and dies because random effects gradually overwhelm the correct replication and functioning of the DNA inside its body. But randomness acts on the larger scale as well. The reason why entire species disappear is that random factors overwhelm their genes' ability to cope with them. For example, the climate changes and some species don't manage to adapt or exapt. While others do (read for example more about how tetrapods appeared).
"The selfish-gene idea is the idea that the animal is a survival machine for its genes," Richard Dawkins wrote. "If the animal gets eaten, if it dies, then the blueprint dies as well. The only genes that get through the generations are the ones that have managed to make their robots avoid getting eaten and succeed in living long enough to reproduce".
"Another way of putting it is to say that the world is full of genes that have come down through an unbroken line of successful ancestors, because if they were unsuccessful they wouldn't be ancestors and the genes wouldn't still be here. Every one of our genes has sat successively in our parents, our grandparents, our great-grandparents - every single generation. Every one of our genes, except new mutations, has made it, has been in a successful body. There have been lots of unsuccessful bodies that have never made it, and none of their genes are still with us. The world is full of successful genes, and success means building good survival machines."
This view has been updated recently due to research on the exact mechanism by which genes create the phenotype - how the organism looks and behaves. According to Dawkins' view there is a one way "causal arrow" from the gene to the phenotype (read his entire essay):
"Genes that are successful are the ones that have effects upon bodies. They make bodies have sharp claws for catching prey, for example. If you follow through the logic of what's going on, there's a causal arrow leading from a gene change to a phenotype change. A gene changes, and as a consequence there's a cascade of effects running through embryology. At the end of that cascade of effects, the claws become sharper, and because the claws become sharper, that individual catches more prey. Therefore the genes that made the claws sharper end up in the bodies of more offspring. That's standard Darwinism."
But this standard Darwinism is not entirely correct - there is also another causal arrow going from the environment to the genetic variation.
Evo-devo
Evo-devo stands for evolutionary developmental biology. In the same way the selfish gene theory limited drastically the type of explanations biologists could put forward (thus limiting the arbitrariness of the theory), evo-devo creates even more limits. It isn't sufficient to say that something might be good for the gene, the gene also has to have a specific physical mechanism by which to create that something. In other words, you cannot assume the genes to be anything else, but very dumb engineers capable of doing only minor alterations to the existing design.
By far the most important evo-devo discovery is the discovery that genes can be turned on and off. Some proteins can attach to a gene and prevent the synthesis of the protein coded by that gene. Some other protein or external factor can detach the inhibitor protein and the gene is turned on. The inhibitor protein is constantly synthesized by other parts of the genome so that gene stays on only as long as it's needed.
The first example of this phenomenon was observed by Jacques Monod, Jean-Pierre Changeux and Fran?ois Jacob back in 1961. They observed that E. coli prefers to consume glucose over lactose (if glucose is present it ignores lactose), but that if glucose was absent from the environment they manage to switch to lactose. E. coli started to make the proteins needed for the processing of lactose, proteins that it doesn't normally produce when glucose is available.
In other words, the phenotype of E. coli changes as a function of the environment. E.coli's DNA can generate numerous phenotypes and the environment is the one that "decides" which one will actually come to being. Thus, there are two causal arrows intersecting: one from the genome to the phenotype and another one from the environment to the phenotype.
But there is more. The orthodox view on Darwinian evolution states that natural selection happens after variation and inheritance. But it can happen before (this is known as the Baldwin effect). The point is that the environment favors certain phenotype (natural selection) and then, there is some genetic mutation (variation) that reinforces or consolidates that particular phenotype excluding the other possible phenotypes. In their book The Plausibility of Life: Resolving Darwin's Dilemma Kirschner and Gerhart have called this process "facilitated variation".
The dilemma is how exactly random variations can produce novelty and evolution. The solution is a combination of the idea of facilitated variability and the discovery of the fact that genes can be turned on and off.
The point is that there are genes that do something (have direct phenotypic effects) and genes that control other genes (that regulate the expression of genes). Thus, the genome has a hierarchical structure.
Kirschner and Gerhart have uncovered in their book that evolution often involved just the reshuffling of existing structures and processes - a mutation can usually be successful or at least unharmful only if it involves genes higher in the hierarchy, the ones that regulate the expression of others. They have found that all the living beings share the same basic processes and that the evolution of life involved only very few revolutionary episodes when new basic processes have come into existence. (Read a review of the book for a description of these revolutionary episodes.)
"From the perspective of facilitated variation, life on this planet is divided into several epochs of cellular innovation, and these epochs do not correspond to known epochs of transforming geological events," Kirschner and Gerhart wrote. "The conserved core processes appear to have been added in stages - in several relatively short episodes separated by long intervals when no major core processes were added. The core processes were maintained from then on."
Each episode of innovation has three stages: the appearance of a new core process, the increasing robustness and adaptability, and the rampant regulatory usage. The last one occurs after the core processes have been established well and the regulatory genes can start to shuffle them safely, thus producing an explosion of phenotypic variability (although the genome does not change so dramatically).
Conclusion
Since the middle of the 19th century - when Darwin's book appeared - evolutionary theory has changed from being just a smart and ingenious idea together with a collection of just-so stories into a "hard science" capable of describing the world of living beings with increasing precision.
The Mendelian genetic approach added an experimentalist side to the field. The Modern Synthesis brought together into a single theory the naturalistic approach of Darwin, concerned with the observation of animals and plants in the wild, with the experimentalist genetic approach. The discovery of DNA by Francis and Crick has uncovered the material support that carries the genetic information. And then, the rethinking of evolution in terms of the selfish gene added a mathematical, quantitative dimension to the theory. Biologists could now test the quantitative effects of their assumptions and compare the importance of various factors. The collection of just-so stories wasn't good enough anymore. And finally the evo-devo research has brought into attention the deep causal biochemical factors that shape life and evolution from behind the scene.
"To understand novelty in evolution, we need to understand organisms down to their individual building blocks, down to the workings of their deepest components, for these are what undergo change," wrote Kirschner and Gerhart in their preface. "Insights into these components have come only in the past few years. A theory of novelty was impossible to devise until the end of the 20th century; experimental evidence was incomplete on how the organism uses its cellular and molecular mechanisms to build the organism from the egg and to integrate the genetic information into functional processes."
Today the Darwinian theory of evolution is no longer just an ingenious idea, but a full fledged scientific theory similar to physics or chemistry. It doesn't just claim to "explain" how the world works, but it actually has acquired such precision and predictive power that it is capable of generating technological innovations that will undoubtedly change our world beyond recognition. In fact, it has already started doing it. If one reviews the Nobel prices for medicine in the last decades, virtually all of them reward successes that were made possible by the use of the theory of evolution. There is only more to come.
Read more: Scientific American's 15 Answers to Creationist Nonsense.
