In order for evolution to occur it must happen at the molecular level?

Question

My molecular biology of the cell book says that genomes have evolved through mistakes and accidents. With DNA polymerase having a high fidelity (I believe one mistake in 20,000 base pairs), how do you explain evolution from a common ancestor (I.e. an ape-like creature)? Is this the best it gets? Accidents and mistakes in DNA replication and DNA repair have created intelligent human beings. How so?

Answer 1

One in 20,000 might seem like a low rate of errors (I actually think it's *much* lower) ...

... but do the math!

Remember that a single strand of DNA contains hundreds of thousands to billions of base pairs. (A bacterium has about 600,000 base pairs, and human DNA has 3 billion base pairs.)

So in a bacterium with 600,000 base pairs, that's 30 errors in *every single new individual*. (That's why I think the number is *much* lower.)

But even if the rate is much lower than what you said ... say only 1 error every 20,000 *individuals* (not base pairs) ... in a population of trillions of bacteria, that is still *millions* of bacteria born every second with a new mutation. That is why even the population of bacteria in a human can develop resistance to antibiotics in a matter or weeks or months. Now imagine all the bacteria in all the oceans of the world, mutating for 3 *billion* years of time!

With larger organisms like mammals the genome is *much* larger (in the billions of base pairs), but so is the error correction (because diploid organisms have additional error correction), and the populations are much smaller. But they have the additional advantage of sexual reproduction, which dramatically increases the number of new combinations beyond what simple mutations can do.

The point is that evolution does not depend on a high rate of mutation.

It isn't just "accidents and mistakes in DNA replication" that drive evolution ... it's the fact that NATURE SELECTS ONLY THE *GOOD* MISTAKES (hence the term "natural selection"). In other words, nature is a relentless weeding out of bad mistakes, and replication of good ones.

So even if beneficial mutations are rare ... given enough individuals and enough time, those beneficial mutations will propagate ... and the cumulative effect is plenty to explain evolution from bacteria to intelligent human beings.

Answer 2

When people attack evolution on the basis that humans cannot simply have arisen by "accident", they miss the point. According to the theory of evolution, human beings exist in their present form due to a series of mutations that better enabled us for survival. If one of our genes mutates and gives us, say, a greater resistance to some environmental toxin, then that gene will be selected for, since any individual carrying it has a greater probability of survival than those that don't. What you don't hear about are all the millions of individuals who were born with UNHELPFUL mutations: for example, suppose that a child were born with a mutation that made them MORE susceptible to the toxin. Why don't you hear about them? Because they usually die before they can reproduce. The harmful mutation dies with them. It's not merely an accident that we're the way we are, it's the result of many, many, many, many random mutations, the most beneficial of which survived.

It is true that DNA polymerase has an outstanding accuracy record, but it's not 100%, and cells divide a lot. Even if it only makes one mistake every 20,000 base pairs, there are more than 3 billion base pairs in a single cell, and they all have to be copied every time the cell divides. Mistakes can and frequently do happen. Most of those mistakes are harmful, but all it takes is one beneficial mistake to the genome every couple of generations (and remember...out of trillions of mistakes, one of them is likely to be beneficial), and evolution doesn't seem so unlikely.

Answer 3

I believe mutation rate is even lower than that. Let say for types of mutation combined (base changes, deletions, etc) it is 1 in 10 million per base. A single set of chromosomes is 3 billion bases. This would make 300 random changes. There are various checkpoints and correction mechanisms that may reduce the number even further. Let say it is 100. There are many cell divisions and rounds of replication between the times a sperm fertilizes an egg and a new grown-up organism produces its own sperm (let say its male). If there are 20 cell divisions in-between, the new sperm will have about 2000 new mutations. If the time between the generations is 10 years and there is absolutely no selection (that is, no mutations are eliminated or enriched), 1500 generations or 150000 years would create a genome that is 10% different from the ancestral one. This is about as much as our genome is different from that of the apes. In the evolution of species we are often talking about millions of years and are comparing the separate evolutionary branches not to the ancestor, but among themselves, which further increases the differences. As you see, even with the mutation rates that looked too low to you, we could have been much further away from the apes that we currently are be it not for stabilizing selection and drift.
We can assign some significance to about 20% of our DNA. This is a low-end estimate that still assumes that most of the DNA is non-functional “junk”. That would mean about 400 potentially functional changes between the generations. As I mentioned before, this would include both small and big changes. If these calculations are accurate and there are 40000 functional regions in the genome (“genes”), which is the highest estimate, every individual gamete presents to the forces of evolution new variants for 1% of a genome. Think how many individuals exist simultaneously and you will realize how much material there is for evolution. Moreover, every time a diploid organism produces a gamete it reshuffles the genome: some of the chromosomes, or even fragments of individual chromosomes, in the gamete come from the mother, while others – from the father. This creates additional combinations of gene variants, which may make them function in new ways. In fact, it is sometimes more difficult to explain why the genome appears relatively stable. So there is no shortage of the material on which selection or random drift may act. Of cause, most mutations would be predicted to ruin something. That is why many gametes are non-functional and many zygotes would never develop into organisms. Even this loss-of-function may be evolutionary beneficial, e.g. loss of pigmentation for someone migrating up North. A large portion of the mutations, even in the general vicinity of functional areas, will be essentially neutral. Some would increase the function or gain a new function. Importantly, there are many ways how the same function could be achieved. For example, there are countless ways to alter two proteins to make them bind each other. If they are on a cell surface, there would be many ways how a random mutation would force a tighter association of two neighboring cells. So, over sufficient time the changes of a potentially big significance (e.g. bringing two neurons together) are not that unlikely.

Answer 4

Well, first off: mistakes in DNA replication are far from the only mechanism of mutagenesis (for example, chemicals, viruses, and radiation can alter DNA).

Other than that, I'm not sure what it is you are failing to grasp?
The "mistakes" produce variation in a population of ape-like ancestors (ALA). Different groups of these ALA are split off from each other (perhaps they migrate to opposite sides of a continent, and a desert arises between them, maybe an earthquake destroys a land-bridge formerly connecting two land masses, whatever). So, with ongoing "mistakes", the gene pools of these populations are going to gradually drift apart, until they could no longer inter-breed, even if re-introduced to each other.
One lot of ALA happen to dwell in "montaine" rainforest, where it is advantageous to be large and vegetarian - they evolve into gorillas. Another lot of ALA stay in lower-level rainforest, where the ability to climb quickly is advantageous, and they evolve into chimpanzees. Yet another lot move onto the plains, and develop sophisticated tool-use, and they evolve into humans.

Now, I'm not an expert in human evolution, and I don't think anyone has a 100% clear idea of what the evolutionary pressures were on all the ALA populations, but the mechanisms are established, and the results are plain to see.

Answer 5

It's in the title, Evolution by NATURAL SELECTION.

Mutations and recombinations are selected from by Natural Selection. Or, more simply, those traits which give a statistically increased chance of survival / reproduction / survival of kin inevitably increase in frequency in the population and visa-versa. This is extremely solidly established.

One mutation in 20,000 base pairs is a lot of mistakes across the whole genome... But, evolving a larger brain doesn't take huge genetic changes, just small ones to keep the brain growing for longer.

Answer 6

The main DNA polymerase enzyme has an error rate of 1 in 10,000 to 1 in 100,000 which would lead to about 10,000 to 100,000 mistakes in copying the human genome. However, the observed rate of mutation is much lower. Only one base out of 3 billion is copied incorrectly with each cell division. The overall error rate of DNA replication is much lower because of the quality control checks after DNA synthesis. DNA polymerase adds nucleotides depending on the shape of the template. When it adds a mismatching nucleotide, the base-pair has the wrong size which is detected by the enzyme. The enzyme stops and then goes in reverse and chews up some of the newly synthesized DNA before continuing with replication. This built in error detection is capable of catching about 99% of the mistakes. The one percent that gets through would still yield a mutation rate of 100 - 1000 per cell cycle but there is yet another level of proofreading of the newly synthesized DNA. An error correcting enzyme scans for mismatches. When it finds a mistake, it will cut out a section of new DNA around the mismatch and then re-synthesize to fill in the gap. This step is also about 99% accurate leading to an overall rate of about 1 in a billion.

Enough about the fidelity of DNA replication. There are other sources of mutations, both large and small ranging from whole genome duplication to changes in a single base. Transposable elements are still active and with each generation, another copy of an Alu element is copied into the human genome. These repetitive elements can lead to recombination causing loss or duplication of a chunk of DNA.

It would not matter if every fossil on earth were to disappear because fossils are the weakest evidence in support of evolution by common descent. The molecular data practically screams out that we have shared ancestry. Why else would genetic code be universal? There are millions of ways to assign 3-nucleotide codons to 20 amino acids. Why does AUG code for methionine in all organisms? Why not UCC in yeast or GGG in plants? There is synteny. With a score of chromosomes to place 25,000 genes, why are the same genes found together between species? Even the structure of genes are shared. Why do the great majority of genes have the same position and number of exons and introns between even humans and mouse? The position of transposable elements is another smoking gun. Ancient retrotransposons are found in the same relative positions even if you compare humans to fish. Retrotransposons can insert randomly into a chromosome. It would be extremely unlikely for the same transposable element to insert into the same intron of the same gene in human and chimp and mouse and fish. The only way to reconcile sharing not only similar genes but sharing the same junk is either copying from the same template or having a lazy creator.

Yes, mutations are random. But, there is more to natural selection than just mutation. Selection is anything but random. So what if a particular individual suffers from a deleterious mutation? There are plenty more (usually) for new mutations to work on.

Answer 7

in all life, DNA changes. mutations happen, whether they are random, or if some physical mechanism occurs to change them for a reason. maybe this mutation allows for a larger brain (which may lead to more intelligence), maybe this mutation leads to having a redder skin color. lets say for some reason, mates are attracted to this red skin color. the red skin mutation in the DNA will pass itself on more then. evolution is a mixture of genetics and natural selection. it happens over billions of hears. sometimes quickly, sometimes slowly. you can look at the DNA of chimps and compare it to our own, and see a high correlation between us. dont you ever wonder why every living being has DNA? we all come from the same places if you look down the road long enough. but it is hard to grasp, since humans are such finite beings. but if you dont believe in evolution, you might as well never ask a doctor for help, because a doctor has learned from the same science that points to and supports the theory of evolution.

Answer 8

Not all mistakes or accidents are bad mistakes or accidents. One mistake or accident in a bacterial/viral genome leaves it immune to a vaccine/antibiotic. That's how it works.. extrapolate that.. if you can - and you'll see it on a much bigger level. If you're questioning it - you're questioning it for the purpose of disproving it.. if you want to disprove it, you're already doubting it.. none of us can change that for you.