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Let me explain... A friend and I read some articles, part of a Biology book, and watched a video on evolution. We then tried to explain what Evolution is to each other.

My friend said that Natural Selection is a mechanism inside the organism that mutates the DNA to make its offspring survive in an environment; that natural selection mutates the DNA beneficially and that random mutations are not useful (like blue eyes). But I disagree and think that it is closer to Lamarkian theory.

I told him that DNA from male and female recombines and randomly mutates making a new "recipe" for the offspring (adding a new characteristic(s)). If the offspring is well suited for the environment, then it survives and passes on its characteristics to its offspring. If it does not have fitness for its environment, it dies. So, Natural Selection is were nature "selects" who survives and reproduces a lot.

So is the DNA mutation process random or is mutation directed to make an organism that is suited to survive its environment?

None of my friends are Biology students, so I can't ask then which explanation is correct (or at least more valid).

I'd prefer you don't answer: "None of these explanations are correct," but to say which one is more valid and correct misconceptions or add more that is missing (of course these are only summaries of our discussion). But of course, you can answer that neither of our explanations is correct...

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    $\begingroup$ Mutations and evolution are both complete random processes which are undirected. $\endgroup$ – Chris Nov 1 '15 at 11:37
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    $\begingroup$ Well evolution as i understand is not random because of natural selection but mutation is.But even if evolution is not random i think is undirected too .What do you think ? $\endgroup$ – PRO META X Nov 1 '15 at 11:49
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    $\begingroup$ @Chris It's not really accurate to call evolution 'random' (depending in part on how you define 'random'), but either way, the randomness in mutation and evolution are very different. Mutation is (mostly) a random process while evolution can be driven by different processes (natural selection, sexual selection, genetic drift etc). Evolution by natural selection is certainly stochastic but natural selection is also injecting alot of information into that process, and it cannot be seen as "undirected" (rather the opposite). $\endgroup$ – fileunderwater Nov 3 '15 at 8:15
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I accidentally wrote a lot!

I first discuss the term Darwinian evolution. I then describe the main evolutionary processes insisting on the two elements of interest in your question, that is mutations and natural selection. In the end, I directly address your two statements and bring a few more complications into the subjects.

Did you say Darwinian evolution?

Evolution is more than Darwinian evolution

The expression "Darwinian evolution" easily yield to misunderstandings. Darwin was probably the most important scientist and one of the first (if not the first) to develop the theory of evolution but evolutionary biology today is so much more than Darwin's theory of evolution.

Examples of very basic things Darwin did not know

  • We discovered the structure of DNA in the 1950s-1960s only with Miesher, Chargaff and most renowned Watson and Crick (history of the discovery). Darwin had no idea of the existence of DNA and had not even hypothesized about the existence of such a molecule (which came first by Erwin Schrödinger).

  • Darwin was not aware either that inheritance was through the transmission of "particles/atomic" and not through the inheritance of some kind of "fluid/continuum". In other words, Darwin did not know the Law of Segregation by Gregor Mendel (even if they lived in the same epoch).

  • Darwin had no idea about Evo-Devo, that is he had no idea about the similitudes in developmental processes among related (even distantly related) organisms.

  • Globally speaking, while Darwin managed to touch a little bit about many of the subjects of modern evolutionary biology (which is very impressive), he only manages to mention them and failed to provide any prediction. This is a large part because no one had no concept in genetics at that time.

Evolution is more than natural selection and mutations

Evolution is not only about natural selection. Even C. Darwin knew that evolution is way more than 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 process 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. Evolutionary biology is a big field of knowledge and there is a lot to know about evolutionary processes.

Natural Selection and Mutations explained by the Lewontin Recipe

The Lewontin's recipe is a good way in order to understand what is natural selection and when it occurs. The Lewontin's 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.

Natural Selection

Natural Selection is the process by which variants of genes called alleles are selected and therefore increase in frequency. This selection result from a differential reproductive success.

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 wrong. Note that most mutations 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 deterministically. An intuitive explanation of what is genetic drift can be found on this post. It will also allow you to understand why small population undergo a more random change in frequency of their genes than are big population.


Considering your opposing statements

Hopefully, the following is clear from the above discussion but I would like to directly address your statements.

My friend said that Natural Selection is a mechanism inside the organism that mutates the DNA to make its offspring survive in an environment; that natural selection mutates the DNA beneficially and that random mutations are not useful (like blue eyes). But I disagree and think that it is closer to Lamarkian theory.

You are right that your friend is wrong!

It indeed sounds more or less Lamarkian. In any case, it is very wrong, as you said. Mutations are not caused deterministically under the pressure of natural selection to do specific things.

Are mutations completely random?

See Are mutations random?.

I do not want to go into too many complications. The sentence "mutations are random" is unclear. Does it mean that the mutation rate is random? Does it mean that the effect of a new mutation is random? And also the concept of randomness only make sense if we consider a set of a priori knowledge. So it is a little hard to fully answer this question and the easy, close-enough approximation for a starter in evolutionary biology is just to say that mutations are random (whatever that means). A slightly better approximation of reality is that mutation rate is an adaptive trait and can vary depending on the environment where the individual is found (adaptively or not). However, the effect of new mutations is really not deterministic.

The mutation rate varies with the type of sequence considered. For example, a microsatellite sequence is a sequence or repeated DNA. For example AATAATAATAATAATAATAAT etc.. (note that the genetic code is written with 4 letters, A, T, C and G). Such sequences are highly mutable. So a mutation is more likely to occur in this region than in the middle of a coding region. And it is more likely for a mutation occurring in a coding region to affect fitness than for a mutation occurring in a microsatellite (it is possible that a mutation occurring in a microsatellite will affect fitness).

Depending on the level of stress some organisms (plants mostly to my knowledge) can change their mutation rate. Consider for example an individual that is maladapted to its environment. If it mutates little, then the offspring will likely be as maladapted and in the long run, the lineage will disappear. If the individual is mutating a lot then, most offspring will have a very low fitness but eventually one will receive a beneficial mutation that will make it very strong and by itself, this offspring may save the lineage. This is what is called a bet-hedging strategy. The concept of bet-hedging can be summarized with the expression "Don't put all your eggs in the same basket".

You will note that the mutation rate is an evolving feature of an organism. This yield observation such as what is now called Drake's rule (original paper). Drake's rule indicates that the genome-wide mutation rate is always at the order of 1 (there is quite a bit of variation but it is a good approximation).

I told him that DNA from male and female recombines and randomly mutates making a new "recipe" for the offspring (adding a new characteristic(s)). If the offspring is well suited for the environment, then it survives and passes on its characteristics to its offspring. If it does not have fitness for its environment, it dies. So, Natural Selection is were nature "selects" who survives and reproduces a lot.

Sounds quite right!

You pretty much nailed it. Mutation adds genetic variation and natural selection selects from the available genetic variation. Your wording is a little uncommon though :). For example, an individual, it is incorrect to say that an individual has fitness or not. Each individual has a fitness, that is some value that encompasses both its fertility and survival probability. In a simple model, fitness is simply the expected number of offspring.

Note also, that the majority of mutations that affect the fitness of the individuals are not so much dependent on the details of the environment. Many mutations are just bad wherever you are. Think about a mutation that would reduce the efficiency of energy production (ATP in mitochondria). Such a mutation will be deleterious regardless of whether the weather is hot or cold for example.


Introductory course to evolutionary biology

You probably want to have a look at an introductory course to evolutionary biology such as Understanding Evolution.

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    $\begingroup$ Wow :) 'Accidentally' :P $\endgroup$ – Dexter Nov 8 '15 at 5:38
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    $\begingroup$ @MakotoKato I am not going to be able to address all the unclear questions and bad claims that you are making in comments of my various answers on this website. As I already said, if you have a (well defined and concise) question, just open a new post and ask it. $\endgroup$ – Remi.b Dec 6 '15 at 9:54
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    $\begingroup$ No, it is not taboo! If you have further questions about why your questions have been closed, ask them on meta.biology.SE. $\endgroup$ – Remi.b Dec 6 '15 at 10:13
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    $\begingroup$ @Remi.b. Don't. I read the paper. It is bad science, whether or not it was published on Plos. In their methods, they mention that their strain is AmpR, but they then make no mention of using antibiotics. That is a recipe for contamination. They also do not check to see whether or not any of their strains were LacZ diploids with an F Plasmid. Their controls are bad, their analysis is bad, and their conclusions are based on incorrect assumptions. No one ever said that you cannot have revertants within a species, gene conversion is well documented, but they aren't reverting to an ancestor. $\endgroup$ – AMR Dec 7 '15 at 8:07
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    $\begingroup$ @Remi.b I wasn't telling you to not read it, just that I didn't think that you should edit. The paper is troubling me, because it could be one of those papers that could be pure crap or could actually have something profound to say, but would require several read throughs and needs to be debated many times. I still am heavily leaning towards it being pure crap, but... I still maintain, however that MK is vandalizing posts, even if the paper has something interesting to say. $\endgroup$ – AMR Dec 8 '15 at 4:16
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Your description of Evolution seems more accurate than your friends. DNA cannot mutate with a particular goal in mind, mutations are random. Most mutations have no effect on an organism's survival, but some will be detrimental, and a few will helpful. Helpful mutations will improve an organisms odds of surviving and passing on its DNA, so those traits will eventually spread through a population.

However, if we wanted to talk about "goals" for evolution, then the goal of every piece of DNA is to be copied and passed on. (of course it cannot think about achieving that goal, it's just a chemical.) DNA mutations that make an organism more suited for a particular environment will be selected for, and those that are detrimental will be selected against. This competition between different copies of DNA eventually optimizes the species for that environment.

So at the molecular level, mutation is a totally random process, but if we zoom out to the ecosystem and population levels, then evolution "designs" a species to better survive in its environment. But this design is a result of random mutations and trial and error.

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Great answers have been given already. But one phenomenon that is mostly not explicitly mentioned that can and should be regarded a part of the process of Evolution is symbiosis.

symbiosis

The probably most fundamental example for symbiosis is endosymbiotic theory. This theory in strongly simplified terms says that eukaryotic cells are the result of a symbiotic relationship between prokaryotes and early bacteria: both evolved separately with the prokaryotes probably being predators of some bacterial species. These species then are proposed to have evolved towards mutually beneficial, symbiotic relationship which essentially created a new form of life, eukaryotes.

From a more abstract point of view, symbiosis can be regarded a further mechanism of evolution: while mutation and recombination act on a molecular level, symbiosis acts on a similar level to selection. It is basically a macro-level recombination of not just genes, but whole or partial organisms into new life forms.

Some random examples:

  • eukaryotes: mitochondria from proteobacteria, chloroplasts from cyanobacteria.
  • bioluminescence in "fireflies" by vibrio bacteria
  • microbiome inside "guts" of more complex organisms
  • mycorrhizae (phosphor fixing) at the roots of some plants
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Mutation is a random process that mainly happens when a cell's DNA is replicated (= copied) before the cell's division, because the enzyme responsible for this replication sometimes makes mistakes. It's a rare process, as for eukaryotic cells (the ones with a nucleus, so animals and plant cells), it happens once every $10^9$ nucleotide.

Now, let's say we consider an organism that has sexual reproduction.

To be transmitted to the descendants of the organism, the mutation must appear in a cell of the germline (spermatozoid or ovule for example). If transmitted, this mutation can have several effects :

  • It can be lethal, the organism cannot survive because the mutation makes a vital protein inoperative
  • It can give the organism a disadvantage in his environment (e.g. living in a snowy environment, the pigmentation of the organism's skin becomes glowing red)
  • It can be neutral, something is modified, but it keeps working (e.g. a certain protein has a different amino acid sequence but keeps working)
  • It can give the organism an evolutive advantage, the protein works better, in a way that favorises the organism vs. its fellows' organisms in surviving in their environment (e.g. in the snowy environment, the pigmentation of the organism's skin becomes perfectly white, whereas one of its fellows is greyish)

In the fourth case, this organism has more chances to reproduce (because he is less likely to be killed, or more likely to access a resource), and hence, to transmit this mutation. This is where natural selection applies: the "fitness" of the organism in his environment is greater than the one of the other organisms of his species.

Now, it's important to note that the evolution (= the change in a specie) is driven by the natural selection (= the process of selection), and that those changes, in nature, are random and take a long time and aren't easily noticeable at the scale of a human life.

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Short Answer: As far as we know, it doesn't.

Mutations at Conception

The mutations you describe as occurring during conception which generate new information have never been observed to take place. Instead, we have observed mutations which reduce existing information. In humans, approximately 100 such mutations take place every generation.

Necessarily if information-additive mutations existed, they'd need to produce a lot more information to make up for the loss. Necessarily, descendants would have a larger and more complex genome than their ancestors. The opposite has been observed, where descendants have smaller genomes than their ancestors.

Abiogenesis

Before Darwin had written On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life, Pasteur was disproving the idea of abiogenesis, as the theory had gone around that germs could spontaneously appear. Despite this, Darwin took abiogenesis as part of the theory of evolution, which has consistently proved impossible in tests with no observable data to the contrary.

Genetic information is fragile and is quickly destroyed over time if it doesn't have enzymes to continually maintain it. There is no gradual process of accumulated information that can result in life able to reproduce, as far as we have found from study and observation. The very difficult process of creating amino acids to bond and form the nucleotides (necessary to form DNA chains) is complicated by the chirality problem, where artificial tests have resulted in both left-handed (L) and right-handed (D) optical isomers were created in a racemic mixture. In biological systems, almost all of the compounds are non-racemic, or homochiral, and biological creatures only use left-handed amino acids in the construction of DNA and RNA. All subsequent have tests run into the same problem.

Theory

As for the theory itself, you and Remi.b have described it accurately. As genetics was an unknown field at that time, it was the mistaken idea that natural selection changed a creature through the creation of information, rather than the reformation, sharing, and loss of existing information.

Sources: Genetic Entropy and the Mystery of the Genome by John Sanford. The Miller–Urey experiment.

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