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I hold to the truth of Evolution, but I've encountered several problems with it, that I can't answer, and I can't find an answer for, despite much research. If would be great if anyone can answer these supposedly fatal problems for Biological Evolution, since I find it troubling that there appears to be no answer for these.

Problem/Question #1:

The first one is called the mutation protection paradox. Simply put, Evolution has evolved mechanisms to protect itself from mutations, that if left unchecked, would build up and wreck the biological system, yet the mutation repair and protection mechanisms guard and stop the very changes that allow Evolution to occur, which is mutation.

Is there an answer to this paradox?

Problem/Question #2:

The problem of genetic entropy. John Sanford has supposedly shown in his book Genetic Entropy and the mystery of the genome, that the human genome is degrading so quickly, that we could not have evolved from ape like creatures over millions of years.

The problem is supposedly that we have 100-300 more mutations than either of our parents. This is supposed to mean that 100-300 new mutations accumulate in every person, in every single generation. Then it's said that these mutations are so small they cannot be gotten rid of by natural selection, and that the vast majority are harmful to the human genotype.

Because the mutations are unselectable, they are left to build up in all people until the entire human race becomes extinct, and it is estimated that this should have occurred in less than 80,000 years. So if Evolution were true, we wouldn't be here to talk about it.

The person presenting this problem gave answers to two responses. He gave a response to the Evolutionist retort that most mutations are not harmful but neutral by saying "most mutations are neutral from the perspective of the organism’s physical fitness (phenotype), but all mutations must have effect on the genetic content (genotype). In no way are mutations truly neutral – they all must have effect on the genotype, even if they only affect the efficiency of transferRNA production. And as pointed out above, most are harmful."

Then he gave a response to the Evolutionist retort that -almost all of the unselectable mutations will occur in non-coding regions of the DNA (the so-called, Junk DNA), and therefore have no effect. Thus, the individual will not die and the population will not become extinct- by saying quote:

"Non-coding DNA does not code for proteins and scientists have previously thought it is largely useless. But mutations in the non-coding DNA won’t make them without effect since non-coding DNA helps during embryonic development and can be a part of many diseases. The idea that non-coding DNA absorbs mutations, thereby making them neutral, is false and is merely an argument from ignorance."

Is there an answer to this?

Problem/Question #3:

This can be called the meta-informaton paradox. How it goes is that you have two types of dynamics. Primary DNA which tells what proteins to make, and meta-information which tells the cell how to maintain the primary DNA. So it is said that primary DNA and meta-information are completely dependent on one another. If they become unrelated to each other, both become unusable and the animal would die.

The problem is that mutations are random, and thus completely independent events, and this means primary DNA and meta-information would evolve by completely random and independent events and thus would not be able to stay relevant and related to one another, which then creates a barrier stopping microbes to man evolution from taking place.

Problem/Question #4:

The person claims his calculations show that there is 1 chance in 10 to the 150 billion, that all species have evolved, each from a previous species. Here's how his calculation works.

He says he is being as generous as possible with Evolution, and has five assumptions:

Assumption 1: Evolution must occur by a net gain in new information. However, this is completely disregarded. We will simply assume that all beneficial mutations produce evolutionary change (including so called 'neutral mutations' which become beneficial later on).

Assumption 2: The rate of beneficial mutations is widely thought to be 1 for every million mutations. Indeed, scientists have observed millions more harmful or 'neutral' mutations than beneficial mutations. But we will assume that the frequency of occurrence is 1 beneficial mutation per 1,000 mutations.

Assumption 3: It will be assumed that 5,000 mutations are needed to make a species 'evolve' into another species (where the two species cannot interbreed). Although the number needed for new single-celled species to arise is probably less, other higher animals require millions more beneficial mutations than accounted for here (40 million mutational differences exist between chimpanzees and humans[1], though different genus).

Assumption 4: We will assume that the total amount of species that have lived in the past is 10 million. In fact, this is the upper end of the estimate for species living today. If 99% of all species have become extinct as many Darwinists claim, then our assumption is extremely generous.

Assumption 5: It will be assumed that every single beneficial mutation is fixed in the population after occurrence. This is very unrealistic (in favour of evolution, of course). Beneficial mutations can be lost from a population in a variety of ways; sexual reproduction and death being just a few causes.

Calculating the chance that 50 million species have evolved from a common ancestor:

Chance of 1 beneficial occurring: 1 in 1,000.

Chance of 2 beneficials occurring: 1 in 1,0002.

Chance of 5,000 beneficials occurring (needed to make one species evolve into another): 1 in 1015,000 (i.e. 1 in 1,0005,000).

Chance that 10 million species evolved: 1 in 1015,00010 million.

Therefore: 1 in 10150 billion.

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closed as too broad by Damien, Amory, Michael Kuhn, Oreotrephes, dd3 Aug 2 '13 at 17:40

There are either too many possible answers, or good answers would be too long for this format. Please add details to narrow the answer set or to isolate an issue that can be answered in a few paragraphs.If this question can be reworded to fit the rules in the help center, please edit the question.

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Welcome to Biology.SE! Each one of these points really should be a separate question. Please read through the Help Center, particularly the "How to ask a good question" section. It should help you focus your question down to something that can theoretically be answered in several paragraphs. If you can imagine an entire book being written about your topic, then it's probably too broad. –  MattDMo Aug 2 '13 at 13:38
    
Do John Sanford and the person who has done the calculation described in problem 4, have proposed any other mechanism to explain how organisms arise ? –  biogirl Aug 2 '13 at 15:47
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@biogirl of course they have. It is a very elegant and parsimonious theory that posits the existence of a beneficial old potter in a beard who spends his time creating animals from clay. –  terdon Aug 2 '13 at 16:05
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I don't think this should be closed. Yes it is broad since it is many questions rolled into one but it is the kind of question that often turns up when people have been confused by pseudo-science and we may as well have a good answer to it. I would actually recommend reopening, and even turning this into a community faq post. There are a couple of quite detailed answers both of which answer the question quite well (if I do say so myself). –  terdon Aug 2 '13 at 17:52
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Responding to questions about how biology and evolution works is probably one of the more useful things this site does. –  shigeta Aug 2 '13 at 23:36
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3 Answers 3

OK, I'll have a go although you really shouldn't combine so many questions into one.

1 The mutation protection "paradox"

As already mentioned while many mutations are caught and corrected, not all of them are. You have to consider that a body (the human one, for example) contains several trillion cells, each of which contains 3 billion nucleotides each of which can be mutated. So, if the human body has, say, 50 trillion cells (a relatively conservative estimate), that means that a mutation could occur at any of

                              $3e10^9 * 5e10^{13} = 15e10^{22}$ = 150000000000000000000000

different sites. So even though the cell is pretty good at catching and correcting errors, some are bound to get through from pure statistical chance. In any case, you know that not all errors are corrected, diseases such as cancer are often the direct result of such mutations and errors.

I should also point out that in sexually reproducing species (such as humans) mutations are passed on to offspring only if they occur in one of the cells that become gametes (sperm or eggs) so this does not accurately represent the number of available sites that can give rise to mutations that can directly affect evolution for sexual species. Other species however, do not reproduce sexually. For example, cutting a worm like C. elegans in half will result in two worms so a mutation in any of its cells could be passed on to its offspring.

Anyway, point mutations are not the only way that diversity is generated. Even in the absence of mutations, processes such as chromosomal cross-over during gamete cell division (this is what makes you into a mixture of your Mom and Dad) would still produce differences that selection can act upon.

2 Genetic entropy

This one is a bit harder to answer, largely because it is complete poppycock. I'll try though. Let's see, we do not have "more mutations than our parents", what an absurd idea! The silent assumption here is that there was a "perfect" genome and each mutation is carrying us further from it. Therefore, since my parents were closer to this platonic ideal of the perfect DNA, each mutation that occurs in my cells takes their genomes a further step from that perfection.

This is very simply wrong. There was never a perfect genome, each cell in each individual of each species in the world is constantly undergoing mutations and has always done so. The genome is dynamic, not static and it has never been static, it can't be. DNA is a chemical substance and undergoes chemical reactions (such as mutations) all the time. Like all other chemicals it exists in a thermodynamic equilibrium, but not a static one. The only way that I have "more mutations" than my parents is if you accept as a premise that humanity comes from the perfect genomes of Adam and Eve. Since this is what Mr. Sanford is, presumably, attempting to demonstrate, using it as a premise is, at best, a circular argument.

Unless you assume the existence of a platonic ideal of a genome you cannot say whether I have more or fewer mutations than my parents because how can you compare them? In order to say that I have more mutations than my parents, you would need to quantify the number of mutations that each of us has and that cannot be done. How do you count mutations? You would need a reference genome of the ancestral human and we don't have that.

The rest of the argument is even more nonsensical. Mutations can either be completely neutral and therefore "unselectable" or they can have an effect. By definition, if a mutation has an effect, it can be selected for or against. That's how selection works. So, stating that these tiny mutations (which do exist) cannot be selected for/against and yet are harmful is a direct contradiction. You can only have one or the other. If they are harmful, there will be a selective pressure to change/correct/lose these mutations.

In any case, if these things "are left to build up in all people until the entire human race becomes extinct" all that means is that these things build up in individuals of a species and the species changes. Ummm, well, yes, we have a name for that, it's called evolution.

Just a final point, tRNAs have their own specific genes, a random mutation in an intergenic region will have no effect on them, why should it? This just shows the fundamental ignorance of the author in question.

Oh, and the whole "Junk DNA" is a very complex question. Yes, we now know that a lot of what was termed "Junk DNA" has a function (this was no surprise by the way, "Junk" was never intended to be taken literally). All this means is that mutations in non-coding DNA can also be harmful. OK, fine, then they will be selected against because that is how evolution works.

3 "meta-informaton paradox" (whatever that is)

This idea is often bandied by creationists but is a basic misunderstanding. Mutations are random(ish), evolution is not remotely random. Advantageous mutations that make an individual more likely to reproduce will tend to be selected for and spread across a population while deleterious mutations will tend to be selected against and be removed from the gene pool. This is not a random process at all.

As for the "meta-information", nothing is "independent". The cell is a complex system with extremely complicated interactions and a lot of cross-talk between the different processes. The DNA is not separate from the cell, it is an integral part of it. The Aristotelian idea of reductionist logic where you study complex systems by cutting them into little bits and understanding those bits is all very well as an intellectual tool but that is all it is, a tool. In reality, complex systems should be studied in their entirety, you cannot disassociate DNA from DNA regulation.

4 The pseudo math hypothesis

Let's have a look at these assumptions.

  • Assumption 1: "Evolution must occur by a net gain in new information. " Of course not. Evolution can create a net loss in complexity (information) just as often (indeed, probably more so) as a net gain. The classic example of this are viruses. They have evolved into lean, mean, minimalist killing machines. They have nothing that is not absolutely essential. Hardly a net gain in information.

  • Assumption 2: I don't know where these numbers are coming from, whenever you read a phrase that starts with "scientists have observed", run away. What scientists? How have they observed this? How do they define beneficial? Anyway, let's say these numbers are right (I really really doubt it, but let's say they are for the sake of argument).

  • Assumption 3: Huh? Let's just throw some random numbers and see if they stick. There is no magical number of changes that results in speciation. In mutations as in real estate, it's "location, location, location". The question is not how many mutations but where they have occurred and what effect they have had.

  • Assumption 4: Wow, this one is just completely wrong. To pick just one problem here, if 10 million species is the upper limit of species living today, and 99% of all species have become extinct, how does it follow that 10 million can also be a good estimate of all the species that have come before? If the 10 million of today are only 1% of all the species that have ever lived (99% are extinct right?) then it follows that the number of species that have existed is around one billion.

  • Assumption 5: It is most certainly not true that every beneficial mutation is fixed. Many are, others aren't. Also, bear in mind that the same mutation can be both beneficial and harmful in different contexts. For example, a mutation that makes me more resistant to cold would be very useful during an ice age but less so (and could be harmful) during a period of high temperatures. To take a classic example, there is a known mutation in some humans that makes them susceptible to sickle-cell anaemia. However, the same mutation also protects from malaria. So, is this one harmful or beneficial? That depends on whether you are living somewhere where malaria is prevalent or not.

OK, so now the numbers. These wonderful probabilities all assume that evolution happens through "beneficial" mutations. First of all, that is not the only way that genomes change. I mentioned chromosomal crossing over earlier and you also have things like genetic drift (you also have all sorts of other weird things such as horizontal transfer).

In any case, it does not take X beneficial mutations to make a new species. As I said, there is no magic number and evolution is not restricted to beneficial mutations. Just mutations.

However, the most serious problem in this reasoning is that you are not calculating probabilities, you are calculating frequencies. What the argument you are presenting says is that it will take $10^{150billion}$ events for 10 million species to evolve from a common ancestor. It says absolutely nothing about the probability of such events because you are not taking into account the size of the event pool.

Let me explain, if you toss a coin, you have a 50-50 chance of getting either heads or tails. Therefore, getting 5 heads in a row is not very likely if you throw five times. If, however, you throw a few billion coins a few trillion times, you are very very likely to at some point get 5 heads in a row. In order to calculate the probability of something you need to take into account the number of tests performed.

If we keep the arbitrary numbers you have quoted, we have 10 million species, let's say each of them has a genome of 1 million base pairs and each has just 10 cells whose genome is passed on to their offspring (non-sexually reproducing species are actually the vast majority but most of them are unicellular so let's just take 10 as an average). Let us also assume that the creationists are right, the world is about ten thousand years old and let's say that species live for an average of two years (absolutely wrong of course but let's just pick small numbers). Finally, let's say that each species has only 1 million living individuals (again wildly conservative, just think of the number of ants in the world). This means that we are talking about

10 million species * 10 cells each * 1 million individuals * 1 million bases per cell = 100000000000000000000

If the rate of mutations is a tiny (much much smaller than the real value) 1 mutation every 24 hours, this means that there are $10^{20} * 365$ potential mutations a year. And, therefore, there have been $10^{20} * 3650000 = 365*10^{23}$ opportunities for mutation in the last 10000 years, that's 365 followed by 23 zeroes, that's a hell of a lot of chances. So, yes, if one in a thousand of them were beneficial that still makes it really quite likely that such mutations have occurred and have caused speciation events. This becomes even more likely if we take a realistic estimate of the time elapsed (10000 years is extreme for all but the most bullheaded of creationists).

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Excellent answer +1. As an extra for point 3, it may be worth adding support for some mutations being neutral that often a nucleotide in a triplet can be changed with no effect on the protein it codes for (ie synonymous substitution) –  GriffinEvo Aug 2 '13 at 19:09
    
Thanks to everyone who answered, but a special thanks to Terdon. Your answer was excellent, and I appreciate the amount of feedback you gave. These problems were very troubling to my belief in Evolution. Shook it pretty good cause there was no answer for them despite me trying to research it deeply. –  KineticBiology Aug 4 '13 at 16:32
    
Nice answer. However, I do not like how you highlight the large number of cells in an organism in parts 1 and 4. Yes, mutations do occur in somatic cells (and could lead to cancer as you mention), however this is irrelevant to discussions of evolutionary biology. Only mutations present in the gametes have the potential to be passed to the next generation. –  John Blischak Aug 19 '13 at 22:03
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@JohnBlischak fair enough, I have edited my answer to make that clear. The point still stands for non-sexual species but they do tend to have fewer cells. In any case, I have factored in the number of individuals so we a re still in the same ball park. –  terdon Aug 20 '13 at 10:09
    
@terdon: Trying to help out here with the statistics. I think you need to adjust for the fact that you were considering sexually reproductive organisms and you assumed random mutations to get genomes. What you actually need to assume is random mutations that produce two viable partners (unique species) of both male and female within the same generation. Unfortunately, that might add orders of magnitude to the statistical unlikeliness of getting a proper match. Maybe I missed something in your example? –  Jim Oct 24 '13 at 4:16
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Thought I'd try this one too...

1) The DNA repair mechanisms in an organism can be fairly minimal ( bacteria with smaller genomes such as M genetalium do not seem to have DNA repair enzymes at all) or there can be many redundant backup genes for DNA repair (I'm thinking of D radiodurans, a bacterium found growing in the Chernobyl reactor after the disaster). In each of these cases the DNA repair genes do not stop mutations, they only reduce the number of mutations that occur. Its well known that all sorts of living things can die of radiation poisoning and new mutations that have occurred recently are observed in all living things.

2) The argument has been given some detail in Wikipedia. I would just say here that if some mutations has little selective power, but when there are enough of them to show a real disadvantage, then they will be eliminated from the gene pool. They don't just all of a sudden get together and say 'here we are - you are dead!' Selection is pretty good at finding pretty small disadvantages and kicking out the responsible variants. I guess the answer is the system is more robust than is assumed in this statement.

That's not to say that low profile mutations can't combine and kill a living thing - they do. Every generation of people genetic diseases kill thousands of people. There are also lots of others who do not experience such diseases. No family will be exempt from such defects over time, but nearly all families will continue as well. The proportion being predicted here is not realistic.

There are species that go extinct too. So all this does happen, but not in the proportions or degree being speculated. Really mountains are being made of molehills here.

3) There may be some cases where 5000 mutations (or even fewer) might prevent interbreeding between subpopulations to create species of a sort. But in most cases it takes a lot more mutations than that to create a new species.

Bacterial species are entirely different from animals and plants. They don't need to breed to make offspring in the sense eukaryotes do. Often they can't. Bacterial species usually reproduce by single celled fission - they cells just split. occasionally they transfer DNA, but they can do so between species by more than one means. In the link its noted that bacterial speciation has been observed in the lab. Just among the 30 or so E coli strains that are sequenced the number of genes can vary by 50%.

So though there are very few species of bacteria named, its also possible to say that there are many trillions of bacterial species, because they work in such a different way than we are used to seeing among animals and plants.

4) While I can't really verify the numbers here, the idea that we could estimate all the possible species seems difficult. There are definitely more species possible then there are atoms in the universe.

There are many more powerful arguments that there is one common ancestor to all living thing on earth. Each living thing shares exactly the same mechanisms for preserving information - DNA, copying the DNA into RNA and then translating this into protein. The idea that this would evolve in the same way twice seems completely unlikely. Moreover there are genes in bacteria that have the same shape and work in the same way as in human beings and every other animal. In fact the phylogenetic 'tree of life' shows that the more similar two living things are, the closer they resemble each other in terms of their sequence. This is the primary argument for the last universal ancestor (LUA). Most folks would have to have a counterargument that against this evidence. The generation of a ribosome in the laboratory from primordial chemicals might be such an argument, since we think it took nearly a trillion years for it to happen the first time, I would be genuinely astonished to see it happen again.

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1: Not a paradox. Mutations are generally protected against, especially in more complex organisms. Protection mechanisms are not perfect, hence mutations still arise. Plus, diversity can arise through other mechanisms.

2: "...these mutations are so small they cannot be gotten rid of by natural selection, and that the vast majority are harmful..." is a very dumb and self-contradictory statement. If there is an effect it can be selected for or against. Also, 100 mutations compared to 3 billion bases...

3: This is nonsensical.

4: Very confused assumptions and statistics. You previously pointed out that many mutations happen in an individual. Individuals do not evolve, populations do. You don't need a single individual to mutate a lot, you need changes in genotype to accumulate, and millions of years is a very, very long time.

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