Is there a biological mechanism for evolution encoded into our DNA?

Question

Throughout high school, I remember learning about Darwin's theory of evolution as if it were near-fact. But something always seemed wrong about the ideas presented.

• Survival of the fittest
• Random mutation
• Natural Selection

All of these things seem to account for some margin of evolutionary progress, but I always remained skeptical that the extremely complex features of life could have formed from these methods alone, even after hundreds of millions of years.

Here's what I notice:

Any time a species has needed the development of a specific feature to survive, it has developed that feature, and that feature precisely.

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I'm going to use this example:

Turtles on an island where shrubbery grew higher up developed longer necks, to reach the leaves.

I imagine that turtle looking up at that food, and sub-consciously wishing to get to it, constantly straining, for its entire lifetime.

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It seems plausible to me that we (advanced life) could have a biological mechanism to "write" needed alterations into either our own DNA or our reproductive DNA over time, triggering the very specific evolutionary developments necessary to our survival without relying on random mutation.

My question:

Is this possible? Does any similar mechanism exist that we know of? If not, how can so many specific (advanced) evolutionary leaps be otherwise explained?

Answer 1

This entire answer will be long, so read the short part first, then read the rest if you (or anyone else) is curious. Citations are included in the long section. I can include additional citations in the short section if needed.

Long Story Short

Your question touches on some common misconceptions about how the evolutionary process. Organisms don't "want" to evolve traits. Traits evolve through the biological processes of random mutation and natural selection.

Organisms do not "want" to evolve traits. (Well, OK, I'd love to evolve an extra pair of hands but that is not possible.) Natural selection works by modifying existing traits. Your turtle can stare all she wants at food out of reach but she will not evolve a longer neck. Instead, natural variation exists among neck lengths of the turtles because of variation of the genes that determine features related to overall boxy size. Those individuals with longer necks may be able to get a bit more food, live a little longer, and reproduce a little more. They will pass along their genes to their offspring, so perhaps more of their offspring will also have longer necks. Over many generations, the turtles may have somewhat longer necks.

A common misconception is that the traits of organisms are precisely adapted for a specific need. They are not, for a few reasons. First, natural selection occurs relative to the current environment. Adaptations that work well in one environment may not be so useful in another environment. Environments are rarely stable over evolutionary time so traits are subject to constant change.

Next, as mentioned above, natural selection can only work on what traits are present. While an extra set of arms would be handy, I am a tetrapod. My four appendages, along with the appendages of all other tetrapods, trace back to our common ancestor. The appendages of all tetrapods are modifications of that ancestral trait.

Finally, organisms haven't "sampled" the entire realm of possible mutations and combinations of mutations. In other words, a certain mutation or set of mutations might actually be able to adaptively improve a particular trait in the current environment but, if the mutations never occur, then the improvement can never happen.

We only need to look at ourselves to realize how imperfectly adapted we are. We get bad backs and knees because our bodies weren't designed to walk upright. We evolved from quadrupedal organisms. This has happened so recently that changes in the structure of our knees and backs haven't yet evolved (and may never). Search the internet for the "blind spot" eye test. We have a mass of blood vessels in front of the retina of our eyes, which reduces our visual accuity. We often have to have teeth pulled from our jaws because the flattening of our face (relative to our australopithicine ancestors) has shorted our jaws. We don't have as much room for our teeth but we have not evolved a reduced number of teeth.

As for human technology being able to make direct changes to our DNA to improve our adaptability, I would say no. While I do not have the ability to see into the future, the complexity of our genome, and more specifically how genes are regulated, suggests to me this would be a very daunting if not impossible task. See the long answer below for more on regulatory genes but the gist is that a small set of regulatory genes control most of the other genes (including other regulatory genes). The interactions are extremely complex and we have a detailed understanding of very few of these interactions. I speculate that affecting one such gene in a "positive" way is very likely to have many unintended negative consequences.

Below are some simple math and other ideas to show you how mutations can lead to the many adaptive traits that you see among the diversity of life on earth.

Long Story

how can so many specific (advanced) evolutionary leaps be otherwise explained?

Mutations occur at random throughout the genome. Most mutations will be neutral. That is, they are neither bad or good from an evolutionary viewpoint. The mutations are neutral because the genome for most organisms is non-functional. Mutations that occur in the functional regions of DNA (i.e., protein-encoding and related regions) are more likely to be detrimental (bad) because the mutation may negatively affect the function of the protein or even the ability to produce the protein. However, some mutations are beneficial. The mutation may actually enhance the functionality of the protein or even produce new proteins.

A couple of factors have to be considered regarding mutations. The mutation rate is very low. For example, Kumar and Subramanian (2002) compared the DNA sequences of 5669 protein-encoding genes from 326 species of mammals. Their results suggested that the average mutation rate among mammals is 2.2 x 10$^{-9}$ per base pair (bp) per year. This means that, on average, a point mutation has changed each DNA nucleotide position in the mammalian genome slightly more than twice (2.2 times) every billion (10$^9$) years. That's a lot of time!

However, this same rate occurs in every individual in the population, so you have to consider the population sizes of the organisms. So, let's do a simple exercise. Consider a species like the rock pocket mouse or another small mammal that has a very short generation time. For this simple example, let's assume the generation time is one year. That means that the mutation rate of 2.2 x 10$^{-9}$ per bp per year would then correspond to 2.2 x 10$^{-9}$ mutations per bp per generation. Generation time is important because new mutations are inherited only through reproduction.

Assume the average mammalian diploid genome is about 6 billion (6 x 10$^9$) nucleotides in size. The number of heritable mutations that occur in a single offspring is

$$(6 \times 10^9) \times (2.2 \times 10^{-9}) = 13.2.$$

Next, assume that about 2.5% of the mammalian genome is composed of functional, transcribed sequences that may affect the phenotype (the traits of the organism). That means that, of all the mutations that occur in every offspring every generation, about 2.5% could potentially affect the phenotype. That is,

$$13.2 \times 0.025 = 0.33.$$

Still a small number. But, now we have to account for population size. Small mammals, like mice and voles, generally have large population sizes. Assume that the population of rock pocket mice contains 100,000 reproducing individuals. If so, then

$$0.33 \times 100,000 = 33,000,$$

which is the number of new heritable mutations that could occur in the population. Most of these mutations will be detrimental and removed from the population by natural selection but, if even a small fraction of these new mutations are beneficial, then natural selection can cause these beneficial mutations to increase rapidly in frequency in the population during future generations.

In humans, Nachman and Crowell (2000) estimated that the average mutation rate was 2.5 x 10$^{-8}$ mutations per bp per generation (not year), by comparing the genomes of humans and chimps. If we assume the same genome size and effective human population size of 500,000 individuals, then applying the same math suggests that 1,875,000 new mutations that potentially affect phenotype occur in the human population every generation. Again, only some of these will be beneficial but that is still the possibility of a number of new beneficial mutations. In evolutionary terms, a mouse or human generation is the blink of an eye.

How long would it take for a beneficial mutation to spread through a population? That depends on two things. How beneficial is the mutation (called the strength of selection, s) and the population size? To estimate how long it would take for a beneficial mutation to spread through a population, we can use the formula,

$$t = \frac{2}{s}\mathrm{ln}(2N_e),$$

where $t$ is time in generations, $s$ is the strength of selection, and $N_e$ is the effective population size (number of reproducing individuals). For the strength of selection, let's assume $s=0.01$, which is weak but positive natural selection. Going back to our rock pocket mice with $N_e = 100,000$, then the beneficial mutation would be spread throughout the population in only 2441 generations (remember, we're talking evolutionary time so 2000 years is nothing). If $N_e = 10,000$, the mutation spreads in only 1981 generations. If we increase the strength of selection t 0.2, then the times are 122 and 99 years for population sizes of 100,000 and 10,000 years, respectively.

These "back of the napkin" calculations show just how quickly even weakly beneficial mutations can appear and spread throughout a population. Yet, this doesn't include other types of mutations like gene duplications that can also allow new proteins to evolve. For example, human ability to see red colors is due to a simple gene duplication (Nathans et al. 1996 and references therein). This duplication also explains the common form of red-green colorblindness.

Whew!

There's yet more to our mutational story. Consider humans and chimps, which are nearly identical from a genetic standpoint (between 96-99% depending on how you calculate it) yet they appear very different. If humans and chimps diverged from their common ancestor within the past five million years, how could they differ so much? This question was initially posted by [King and Wilson (1975)]. They argued that mutations to structural proteins (like those that compose bones and muscles) would not be enough to explain the phenotype differences between humans and chimps. The proposed that regulatory genes are the key to understanding the big differences. Regulatory genes are those that control other genes, by turning them on or off and other important functions. Changes to the regulatory genes can cause fairly rapid changes to the phenotype.

This understanding has led to the broad (and fascinating) field of evolutionary developmental biology. This field focuses on how mutations in regulatory genes associated with development (from embryo to adult) have had a long-term evolutionary impact. The field is rich with examples, but one cool one is associated with duck feet and bat wings. Let's begin with the embryo. Most vertebrate embryos have membranes between the digits (fingers and toes) during an early stage of development. For most vertebrates, the membranes are lost later in development. The small flaps of skin you have between your fingers are the remnants of your embryonic membranes.

A set of regulatory genes called BMPs (and a couple of others) are responsible for causing the loss of the membrane in vertebrates. However, through different sets of mutations, the BMPs are not able to function in duck feet and bat hands. Thus, they both end up with membranes between their digits (Weatherbee et al. 2006). Thus, two different mutations block the same set of developmental genes, leading to novel adaptations in two very different types of vertebrates. One final example is the evolution of bird feathers from scales. As you may know, birds are evolved from dinosaurs. It turns out that bird feathers and alligator scales (alligators are birds closest living relative) use the same regulatory genes to develop. The genes are BMP2 and SHH (sonic hedgehog for fans of the old computer game) (Harris et al. 2002). Other regulatory genes underlie the different types of feathers, like downy feathers and flight feathers (Harris et al. 2002).

Literature Cited

Harris, M.P. et al. 2002. Shh-Bmp2 Signaling module and the evolutionary origin and diversification of feathers. Journal of Experimental Biology 294: 160-178.

King, M.-C. and A.C. Wilson. 1975. Evolution at two levels in humans and chimpanzees. Science 188: 107-116.

Kumar, S. and S. Subramanian. 2002. Mutation rates in mammalian genomes. Proceedings of the National Academy of Sciences USA 99: 803-808.

Nachman, M.W. and S.L. Crowell. 2000. Estimate fo the mutation rate per nucleotide in humans. Genetics 156: 297-304.

Weatherbee, S.D. et al. 2006. Interdigital webbing retention in bat wings illustrates genetic changes underlying amniote limb diversification. Proceedings of the National Academy of Sciences USA 103: 15103-15107,

Answer 2

About your question

This kind of very basic question has the drawback to need a very long answer. In consequence, your question might get some close vote. I'll do my best to help but you might want to look at some source of information as an introduction to evolutionary biology. A book eventually or Khan academy maybe.

Darwin's evolution theory

The expression "Darwinian evolution theory" easily yield to misunderstanding because Darwin was probably the most important scientist (and one of the first if not the first) to develop evolution theory but not the only one. Evolution theory is not anymore Darwin's evolution theory.

What is Natural Selection? Lewontin Recipe

You list:

- Survival of the fittest
- Random mutation
- Natural Selection

It is a list of different concepts that might be present in evolutionary biology but its nothing like a recipe for evolution to occur. This list I think already shows some point you misunderstood about evolution. The Lewontin recipe is a good way in order to understand what is natural selection and when it occurs. The Lewontin recipe says that natural selection occurs whenever:

1. Individuals in a population vary in terms of a given trait
2. This trait has some (additive) heritability. Here is one of the several posts that explain the concept of heritability. It might be slightly a post that is a bit advanced for you though but shortly speaking it means that offspring are more similar to their parents more than they are to other non-kin individuals in the population.
3. The fitness varies (not necessarily linearly) as the trait varies.

Simple example:

1. In a population, there are blue pens and red pens
2. Reproduction is asexual and blue pens create other blue pens while red pens create other red pens.
3. blue pens make more offspring than red pens.

In such a situation, natural selection occurs yielding the frequency of the blue pens to increase in the population while the frequency of red pens will decrease.

What is evolution?

Evolution is not only natural selection. It is for example very important to consider random events. One of them is mutation, another is genetic drift (I am not trying to list every parameter that influence evolution but only to give you a sense of why natural selection is different than evolution with a goal of explaining why a trait that is needed do not necessarily appear). Both mutations and genetic drift explain why a species will not necessarily be perfectly adapted to its environment.

Mutations

In the broad sense mutation is any change in the DNA sequence. Some changes are more likely to happen than other but in any case, the likeliness of these changes to happen is not dependent on the consequence they will have on the phenotype (shortly speaking, a phenotype is how an individual looks like) and on the reproductive success. So mutations occur randomly and the specific mutation that would be needed in the population may not occur. Therefore saying, if a trait is needed (in the sense of "if a trait would be beneficial"), then a mutation will occur to make this trait existing is totally wrong. You may be surprised by the level of adaptation of life but this does not mean that what they needed was created with the purpose to help these individuals surviving but it only means that random mutations occur, most of them are deleterious (decrease the reproductive success) while few of them are beneficial (increase the reproductive success) and those that are beneficial are more likely to rise in frequency in the population.

Genetic drift

If the change in frequency of mutations would depend exclusively on natural selection, then I would not have said before that a beneficial mutation is more likely to raise in frequency but I would have said that a beneficial mutation will raise in frequency. An intuitive explanation of what is genetic drift can be found on this post. It will also allow you to understand why a small population undergo a more random change in frequency of their genes that are big population.

Therefore, when you say that you noticed that Any time a species has needed the development of a specific feature to survive, it has developed that feature, and that feature precisely is wrong. You only noticed that species has some level of adaptiveness if I can say so. It is very hard to imagine what new mutation would be beneficial of a given individual in a population but there are in reality many mutations that are beneficial that has never occurred or that has disappeared because of genetic drift. Also, as it is implied in the Lewtontin recipe different individuals have different traits yielding to different reproductive success. If you do not consider mutations that have never occurred but only to sites in the genome that are polymorphic (where different variants exist in the population), then it is worth knowing that any single individual carries quite a lot of deleterious variants. These deleterious mutations explain many genetic diseases. No, we are not perfect.

About your question again

Hope that helps a bit. But I would need days in order to explain further what evolution is. It is a bit field in biology. Your question is a bit too broad and as I said at the beginning you should seek some information by yourself and come back to this site with a question that can be more quickly answered.

Hope that helps!

Answer 3

Short answer version:

It seems plausible to me that we (advanced life) could have a biological mechanism to "write" needed alterations into either our own DNA or our reproductive DNA over time, triggering the very specific evolutionary developments necessary to our survival without relying on random mutation.

No, it's not. Despite what your feelings tell you, despite what you wish the case might be, there is no evidence in molecular biology to suggest that such a mechanism exists, there is no evidence that such a mechanism is required to explain the different phenotypes we see.

Answer 4

Any time a species has needed the development of a specific feature to survive, it has developed that feature, and that feature precisely.

This statement is clearly false. The dinosaurs didn't develop what they needed, did they?

It turned out that on this occasion, the mammals happened to be best adapted to the conditions at the time, just as the fish had managed to get the upper hand over the large arthropods and the ammonites previously.

In hindsight many of nature's solutions seem wonderfully elegant, but they were arrived at by luck under intense pressure to survive. The fact that our eye is designed with blood vessels on the front of the optical surface instead of the back is an example of a design that could have been done better if thought out from scratch. There are many vestigial features from previous generations which persist, even though they are no longer needed. Notice that flatfish hatch with eyes on opposite sides of their head and one eye then migrates to be on the same side as the other, and whale embryos that have teeth which have disappeared by the time they are born, etc.

Natural selection is a combination of lucky mutations which happen to fit in with the prevailing conditions. It's a tough world out there. Even the plants are strangling each other, as can be seen on this video: https://www.youtube.com/watch?v=aNjR4rVA8to

The turtle didn't have much time to stare longingly at the leaves he couldn't reach. Some other turtle with a slightly longer neck came and ate them. And he got bigger and stronger and fought with the first turtle so he got to mate with all the females. And so the next generation of turtles had longer necks than the last.

It's easy to forget, with our comfortable lives, what a struggle nature is. The reason for this is that humans as a species have developed the most devastating weapon of all: cooperation. Compared to most other organisms, we treat other individuals of the same species pretty well (most of the time) and we actually teach each other how to do things. While some other species cooperate among individuals, humans have taken this to a whole new level. As a result, we have been able to eradicate many species which pose a threat to us and bring many other species which are useful to us under control.

If you want to know why this didn`t happen before: humans evolved from an ape-like creature that, due to changes in its environment, came down out of the trees and started walking on the ground. This creature then had its hands free to use tools, and by sheer chance this combination of factors made a bigger brain advantageous, so this creature (which was already social, like apes but unlike octopi, one of the few other creatures blessed with the ability to perform complex manipulations) became even more intelligent and began to educate its offspring in how to control its environment.

There is nothing in biology which enables the mutation of genes to be directed. Finally, human technology has developed to the point where it may be possible to modify genes directly. However, there are significant ethical issues regarding the use of this technology. The termination of an "imperfect" human is frowned upon because it is considered that all members of the species should be given the best chance to survive. Besides, it is not at all clear if there is really ever such thing as a "defective" gene. For example carriers of the gene responsible for sickle cell anaemia have increased resistance to malaria.

Anyway, long before humans were able to manipulate genes directly, they were able to produce massive changes in the phenotype of dogs in a remarkably small number of generations. There is a breed of dog adapted to every possible use. An unfortunate consequence is that the gene pool in each breed is rather small, leading to breed-specific illnesses. If these breeds were left alone it would take many generations for mutations to allow their genotypes to diversify again. And who knows what the final animal would look like?

It seems plausible to me that we (advanced life) could have a biological mechanism to "write" needed alterations into either our own DNA or our reproductive DNA over time, triggering the very specific evolutionary developments necessary to our survival without relying on random mutation.

There is no evidence for such a mechanism, and it is very unclear how a mutation could be proved beneficial without being tested in the environment. What there is, is a way of mixing and matching genes, so that the best ones can propagate throughout the population. Unicellular organisms do this by a variety of means. For multicellular organisms the way of doing is sexual reproduction.

The cost of this is enormous. Look at a flowering plant. That flower has evolved exclusively to enable pollination, typically by insects. In some cases, virtually all the plant's energy goes into making that flower and relatively little into making the actual seeds. Plants do have a particular problem exchanging genes because they do not move about. Stationary animals, such as the barnacle, also have similar problems. The barnacle solves this by having a "penis" several times longer than its body length so that it can copulate with its neighbour without moving from its spot. In humans, fully half the population is male and therefore unable to bear offspring.

Asexual reproduction is far more efficient at producing offspring but does not enable the interchange of genes. The offspring are clones of their parent and therefore have the same genetic strengths and weaknesses. Asexual reproduction does exist, even in some animals, but exclusively asexual reproduction would preclude the spread of beneficial mutations. That's why organisms invest so much energy in sex.

Aphids are a good example of an animal that reproduces both sexually and asexually. At the boom times of the year, aphids reproduce asexually and are actually born as already pregnant females! When the availability of food slows down, they switch to the slower, sexual reproduction system with males and females.

In many animals, males must demonstrate their good health in order to be able to mate with the females (who are choosy, because they have to take the cost of bearing the young.) In many large herbivorous mammals, this is done by males fighting. Male birds often display their health by elaborate plumage, the classic example being the peacock. It is debatable whether such a conspicuous waste of resources is really beneficial to the species, but the females have evolved to select males in this way. In some fish, there is only one male in a group, and when something happens to him, the biggest healthiest female actually changes sex to become a male.

So, if an organism were able to program its own genes, why invest so much energy in sexual reproduction?

Answer 5

The answer provided by Mike Taylor is just perfect and complete.

However, I'd like to add some thoughts of my own in a more colloquial style:

• Survival of the fittest is not always true. There is also "survival of the luckiest" (e.g. the fittest is showing off in the beach with the other turtles and is struck by lightning).

• Reproduction is not that simple and many times the female mates with several mates (apart from the fittest one) and a paternal test should be procured.

• Mutation changes are not always gradual (i.e. the turtles might develop a long neck in just one generation).

• Mutations don't always lead to a phenotype change. Sometimes, depending of the environment, the phenotype change doesn't occur. For example, the turtles might only grow a long neck if the live in a sunny island.

• Not all mutations are beneficial and not all beneficial mutations have an impact on survival (e.g. many actors/actresses are not very tall although they reproduce successfully).

In my opinion there are many shades of grays in between the ideas behind evolution.

The features of the "fittest" are sometimes lost by random reasons as the listed above, and the features of the "less fitted" are sometimes transmitted.

And finally, sometimes, an organism develops (or is developing) a mechanism to alter the genes directly (e.g. human beings). Where would that lead? Does evolution mean something anymore?

Answer 6

"I imagine that turtle looking up at that food, and sub-consciously wishing to get to it, constantly straining, for its entire lifetime.

It seems plausible to me that we (advanced life) could have a biological mechanism to "write" needed alterations into either our own DNA or our reproductive DNA over time, triggering the very specific evolutionary developments necessary to our survival without relying on random mutation."

That is a pre-Darwin idea of evolution called "inheritance of acquired characteristics" or Lamarckism after it's creator French natural philosopher Jean-Baptiste Lamarck. Lamarck postulated that given the use of tissues altered those tissues e.g. lifting weights makes muscles bigger, then an organisms descendants would benefit if everything the parent's tissues "learned" could be passed on.

There are actually epigenetic factors in cells that selectively turn genes on or off or otherwise modify their use generation to generation. But this is not evolution because the genes are always there, ready to be used if needed and no new information is ever created.

The flaws in Lamarckism are that, even if the mechanism existed to transmit acquired characteristics, how would it know what characteristics led to what outcome? How could it distinguish positive changes from negative ones?

Most fatally, how could an organism evolve a system that was not related to an existing behavior? For the turtle to stretch its neck, it must desire to eat the leaves and exert effort to do so. How did it acquire the behavior of desiring to eat the leave in the first place? Going forward, if the plants it does eat goes away, how would it ever find another food source? It wouldn't desire to eat inedible plants so it would never exert itself to do so and would never pass that exertion on to it's young.

The hiccup in your understanding of Darwinism is that you've got it backwards. Species don't find solutions and evolve. It's not something species do. It's something that happens to species, a force from the outside. It's not analogous to humans setting down to consciously solve a problem.

Darwin was originally going to use the analogy of "wedging" instead of "natural selection." He wanted to emphasize that it was the environment squeezing in on species that formed them. (Today we think of wedges largely for their splitting power but in but in Darwin's day, if you wanted to compress something you used a wedge hammered in from the side. It was a common tool that performed the same jobs as jacks and hydraulics do today.) But he went with the anthropomorphic analogy of nature being an animal breeder selecting for traits for reproductive success and a lot of misunderstandings followed.

Evolution is not random. Only variations themselves are random. The selection of them is not. It's like shooting dice. The fall of the dice is random but only certain values of dice are winning number and are "selected." The same mutation might show up in every generation for millions of years but produce no change until the environment changes to make the mutation useful.

Species have no existence independent from their environment. The environment squeezes them into a specific form, one that best satisfies the demands of the Second Law of thermodynamics. If the environment doesn't change, then the organism won't either. From that perspective, adaptation is about as amazing as a rock rolling downhill. (That would look pretty fantastic if you didn't know about gravity.)

Imagine you had never seen clay and never seen molding. Your walk along a stream bank lined with clay. Walking one way you pass a blank stretch of clay. After you pass, a leaf falls into the claw and creates a near perfect imprint before being blown away. When you return past that spot, it looks like the clay has somehow altered itself, against all probability, into an exact mirror duplicate of a leaf. How you might wonder, could the clay possibly know how to exactly duplicate the shape of a leaf?

But the clay did nothing. The clay did not alter to fit the leaf, the force of the falling leaf altered the clay.

Likewise, species do not evolve themselves, they are evolved by external forces. Species seem to miraculous fit their ecological niches but, just like the clay, did nothing to shape themselves to the niche. Just as the clay will be passively shaped by the pressure of molding, species have no choice but to assume the forms they do.

It's not survival of the fittist but survival of the fitted.

Answer 7

To add to the previous answers that treat specifically of the biological Darwinism, there is also Universal Darwinism which postulates that evolution is a natural phenomenon that appears when a set of conditions and constraints are present. And indeed, it has successfully been applied to a number of fields (see below the quote), which seems to imply that evolution is not a property of the evolving individuals (as you implied) but a property of the system where the individuals evolve (as long as the individuals satisfy a few special properties, namely variation and heredity, see below).

Here's the definition from Wikipedia:

At the most fundamental level, Charles Darwin's theory of evolution states that organisms evolve and adapt to their environment by an iterative process. This process can be conceived as an evolutionary algorithm that searches the space of possible forms (the fitness landscape) for the ones that are best adapted. The process has three components:

• variation of a given form or template. This is usually (but not necessarily) considered to be blind or random, and happens typically by mutation or recombination.
• selection of the fittest variants, i.e. those that are best suited to survive and reproduce in their given environment. The unfit variants are eliminated.
• heredity or retention, meaning that the features of the fit variants are retained and passed on, e.g. in offspring.

After those fit variants are retained, they can again undergo variation, either directly or in their offspring, starting a new round of the iteration. The overall mechanism is similar to the problem-solving procedures of trial-and-error or generate-and-test: evolution can be seen as searching for the best solution for the problem of how to survive and reproduce by generating new trials, testing how well they perform, eliminating the failures, and retaining the successes.

The generalization made in "universal" Darwinism is to replace "organism" by any recognizable pattern, phenomenon, or system. The first requirement is that the pattern can "survive" (maintain, be retained) long enough or "reproduce" (replicate, be copied) sufficiently frequently so as not to disappear immediately. This is the heredity component: the information in the pattern must be retained or passed on. The second requirement is that during survival and reproduction variation (small changes in the pattern) can occur. The final requirement is that there is a selective "preference" so that certain variants tend to survive or reproduce "better" than others. If these conditions are met, then, by the logic of natural selection, the pattern will evolve towards more adapted forms.

Examples of patterns that have been postulated to undergo variation and selection, and thus adaptation, are genes, ideas (memes), neurons and their connections, words, computer programs, firms, antibodies, institutions, quantum states and even whole universes.

Also, you may be interested in some terminology associated with this theory, for example for John Maynard Smith an individual that can evolve in an evolvable system is called a Unit of evolution [1]. This shows how much abstract and generalizable evolution can be.

[1]: Fernando C, Vasas V, Szathmáry E, Husbands P (2011) Evolvable Neuronal Paths: A Novel Basis for Information and Search in the Brain. PLoS ONE 6(8): e23534. doi: 10.1371/journal.pone.0023534

Answer 8

There are indeed massive evolutionary control systems integrated into DNA. They constitute the major force for efficient change in living beings.

Random DNA mutations are not as beneficial as controlled ones, you can see random single gene mutations at work in medical books: Anemia, cancer, cheese smelling sweat, no sweat glands, skin conditions, scales, brittle bones, lactose tolerance, These are all examples of mutations of single proteins and single growth hormones and so on.

Instead of random DNA mutations, life-forms control their rate of change and types of variations in very efficient ways, changes in color, longer and shorter bones/arms/legs which you can see in humans, physical maturation times, length and quantity of hair, all these things are safe for an animal to have lots of genetic variation with. Changes in bone length vary more than 10 percent in a single generation of humans, but changes like lactose tolerance occur only every 100ds of generations. Therefore there are hundreds of genes for controlling growth hormones as it's selection-important. If color changes become important to an animal, for example, birds, fish, and butterflies, then hundreds of genes are devoted to color. If color is not important, for example, northern and snow animals, then few gene changes are devoted to color, The many Color genes of a tropical animal would go dormant very fast if it were exposed to snowy conditions.

It makes sense for DNA to favor developments that encourage reproduction and survival in variable settings, and indeed DNA is supercharged to deliver mostly useful morphological and chemical changes in large numbers. Plants, conversely, need to change their chemicals alot to attract and repel animals, whereas animals do not need to attract other animals for food, only to defend themselves, that one reason why animals have a lot less chemical variety than plants. Only Chinese use animals for medicine, and there are few aspirins and sedatives derived from animals. Animals cannot produce powerful random chemicals because their nervous system hormones and cell walls are less robust than cellulose cells and plant hormones. Otherwise, animals would have more variable smell and taste, but all mammals taste similar.

It's the same with computer evolution. If you tell a computer program to vary DNA randomly or to create life-forms randomly, it will have epileptic, disorganised animals that flop around, roll around, hit walls, and that is not what animals do to evolve. If you equip a computer evolution program with DNA tool kits copied from nature, you will much faster have meaningful animals... i.e. simple locomotive insects. If you tell the computer to use sinusoidal limb movements like fish fins, millipede legs, insect legs, using nerve impulses, and to create metameric life forms, you will have alot more success than just adding limbs onto random parts of the body, using random pattern nerve impulses and so on.

It's not an easy thing to study, as it is very complex. I would love some statistics and journals regarding types of evolutionary changes that are prevalent in different life-forms.