Field of Science

Two new books on evolution


Here are two new books on evolution. I wrote chapters for both :o

Predicting Evolution and Visualizing High-Dimensional Fitness Landscapes

Effects of Epistasis and Pleiotropy on Fitness Landscapes

You can download the chapters via those links at least for a while. After that they can always be downloaded from the arXiv.

Both chapters are about fitness landscapes. The first one explains that fitness landscapes is the third "parameter" that is needed to make predictions in evolution. The first two are the population size and the mutation rate. If all the known effects of mutations are known (which implies the fitness landscape), then it is possible to statistically say which direction an evolving population will go and where it will end up. Stochasticity is still important, but one can still make sensible predictions.

Admittedly, both population size and mutation rates can change over time, and so can (and does) the fitness landscape. But we have to start somewhere if we want evolutionary theory to make predictions about the future. Simplify the problem to one that can be solved, rather than including every factor that contributes to the real-world problem.

In the second chapter I argue that ruggedness of fitness landscapes (think of many hills and valleys, rather than a single peak to ascend) is created solely by epistatic interactions between mutations or genes or traits. No other mechanism creates ruggedness, and epistasis always creates ruggedness.

For more about fitness landscapes and epistasis, see
Smooth and rugged fitness landscapes
Can we predict evolution?
Epistasis in evolution
Crossing valleys in fitness landscapes

Life was not created

This brochure from The Watchtower was sent to me by a reddit user, who in turn received it from a friend who believes God chose this place for us and directed evolution. You can download it here.

Here are a few comments on the section that attempts to refute evolution.
Myth 1. Mutations provide the raw materials needed to create new species.
Mutant fruit flies, though malformed, are still fruit flies
This is a stupid semantic argument. Does calling them fruit flies make them the same species? Suppose I choose to call one of these differently looking organisms something else, like "Østman fly", then have we learned anything at all, or are we just playing a semantic game?

The Drosophila fruit flies (there are other fruit flies, btw), such as the famous Drosophila melanogaster, are species members of the genus Drosophila. Thus, if we observe speciation (which we have) within Drosophila, it would be most appropriate to classify that new species within the same genus, thereby still making it a fruit fly. For actual, observed speciation in Drosophila, see this article in the TalkOrigins Archive (e.g., 5.3.5 Sympatric Speciation in Drosophila melanogaster).

Are Great Danes and Chihuahuas the same species? They are still dogs, right? But no matter what we do, we can always just say "they are still dogs". The point is that in a relative short period of time (insanely short, actually), both flies and dogs have evolved enough variation to argue that we have observed speciation. Just imagine what could happen to them if the different variants or flies and dogs were separated and allowed to evolve independently for another 100,000 years or more. If 200 years of changes in dogs can produce such differently looking dogs, imagine what 500 times more of that could produce.

If you can't imagine, let me do it for you: Suppose you had been living in Australia all your life, and suppose no dogs had been seen there for as long as you had lived. Then one day you have the chance to sail to sea with some friends in on a large raft (this is clearly after our present civilization has collapsed), and after getting into a storm, you end up somewhere in Indonesia. There you find two different species of four-legged furry carnivores. One is about a foot in length with really long hair, and the other is tall enough to lick your face without standing on its hind legs. They eat different things, live apart from each other, and do not mate whenever they come into contact with each other. You have absolutely no reason to think that they are the same species, but just to be sure you forcefully mate them with each other, but this never amounts to anything, as they are just too different genetically to impregnate each other, just like humans and chimps. They are different species. However, what you don't know is that only about 115,000 years before they both descended from the same species of wolves.
Mutations can introduce changes in plants—such as this mutant with large flowers—but only within limits
How do they know that it can only produce changes within limits? That is an unverified claim that at most rests on the shallow observation that "plants are still plants". In fact, speciation has been observed numerous times in plants. The "only within limits" argument is pulled out of a creationist's hat. The reason why we observe that evolution only produces new species "within limits" is that the time we are here to observe these events is limited. We simply do not expect that a dog or a hibiscus evolves into something that we would never recognize as dog or hibiscus in our comparatively short lifespans. Mechanistically there is absolutely nothing to prevent organisms to evolve beyond their "kind", except in the minds of humans. The only border between microevolution and macroevolution is time, which is what we as humans do not have enough of.
    So, can mutations cause one species to evolve into a completely new kind of creature? The evidence answers no! Lönnig’s research has led him to the conclusion that “properly defined species have real boundaries that cannot be abolished or transgressed by accidental mutations.”
    Consider the implications of the above facts. If highly trained scientists are unable to produce new species by artificially inducing and selecting favorable mutations, is it likely that an unintelligent process would do a better job? If research shows that mutations cannot transform an original species into an entirely new one, then how, exactly, was macroevolution supposed to have taken place?
Lönnig is saying this without any evidence whatsoever - contrary to evidence, actually. The reason why he is saying it simply that creationists do not want evolution to work because it contradicts the Biblical account of creation. The real lesson to take from the quote above is that the unintelligent processes are actually better at producing new species than humans. Neglecting those processes is not learning, but ignorance.
Myth 2. Natural selection led to the creation of new species.
Indeed, Darwin’s finches are not becoming “anything new.” They are still finches.
And you are still using the same fallacious semantic argument. The point is that natural selection can drive organisms in different directions, and with sustained environmentally driven divergence they can become different species. So in the case of the finches, that selection pressure reversed back, but this again ignores that these processes can take a long time. However, they don't always. One group of a lizard in Crotia, Podarcis sicula, underwent amazing changes in just 30 generations on an isolated island, adapting to a new environment (i.e., different selective pressure). More examples of speciation.
Myth 3. The fossil record documents macroevolutionary changes.
To date, scientists worldwide have unearthed and cataloged some 200 million large fossils and billions of small fossils. Many researchers agree that this vast and detailed record shows that all the major groups of animals appeared suddenly and remained virtually unchanged, with many species disappearing as suddenly as they arrived.
Eeerh, no... Not very many researchers agree that the fossil record shows that all the major clades appeared suddenly. The Cambrian explosion took 70-80 million years! It may well be that species sometimes do change abruptly on geological time-scales, but the more fossils are analyzed, the clearer it becomes that evolution is a gradual process.
Many scientists refuse even to consider the possibility of an intelligent Designer because, as Lewontin writes, “we cannot allow a Divine Foot in the door.”
Lewontin can speak for himself. There are many scientists who can consider the possibility of a designer, myself included, but there is just no evidence for it. None. It is the difference between a conclusion from the evidence vs. a foregone conclusion that comes from a book that some people cannot allow being wrong.
In this regard, sociologist Rodney Stark is quoted in Scientific American as saying: “There’s been 200 years of marketing that if you want to be a scientific person you’ve got to keep your mind free of the fetters of religion.” He further notes that in research universities, “the religious people keep their mouths shut.”
No, the religious do not keep their mouthes shut. The religious do great science, but they do not mix science and religion, because religion has no say in the matter. Ask Kenneth Miller.
Really, belief in evolution is an act of “faith.”
Really, it isn't. Belief in evolution is based solely on the available evidence. Nothing more. Empty your mind of any preconceived notion about the natural world, and just look at the evidence, and the best minds have nearly unanimously come to the conclusion that life evolved. Life appeared and evolves by natural processes, and there is no need to hypothesize that any intelligent being ever interfered. Even scientists who are religious believe in evolution (of course). Just take a look at the Clergy Letter Project.

★  ★  ★ 

I know, I know, I know that the reason creationists can't allow themselves to accept evolution is that it directly contradicts what scripture teaches about our origins. But you cannot refute evolutionary theory if you do not understand it. You cannot refute evolutionary theory by quote-mining scientists. Evolutionary theory is one of the very best supported scientific theories - comparable to the theory of relativity - based on fossil evidence, field observations, laboratory experiments, computer experiments, and a thorough theoretical understanding. And the evidence keeps coming in with new scientific papers published every week. A person can either read scripture and believe it is the infallible word of God, or they can join the rest of the growing amount of people who understand that religion has no place in science.

Smooth and rugged fitness landscapes

ResearchBlogging.orgHere are a couple of maps of different landscapes I just made today. The top landscapes are "smooth" and the bottom ones is "rugged". Smooth means that if you start anywhere on the map, there is a route to the highest point on the map that only goes up. Rugged means that there are multiple peaks. The bottom right is more rugged than the bottom left. Update 11/15/13: the smooth landscape depicted on the top is not un-epistatic. There is epistasis (interaction between gene or mutations), as can be seen if you imagine moving from the bottom left corner to either neighboring corner: fitness doesn't change. However, if you start in the middle of one of the axes and move parallel to the side, then you will cross the hill: fitness does change. In other words, what value one trait is when the other is changed can result in different changes in fitness, which is exactly what epistatic interactions mean.

In evolutionary theory, a fitness landscape is a map where fitness is a function of either the genotype or the phenotype. The genotype is some description of the genetic make-up of an organism. This can be the DNA or a list of the mutations/alleles, and are discrete variables. The phenotype is the complete set of physical and biological features of the organism (e.g., weight, height, wing-span, hair color, number of limbs, blood-type, probability of courting a female, temperature tolerance, etc., etc.). A phenotype component can be either discrete (number of limbs) or continuous (weight). Both the genotype and the phenotype of real organisms are multidimensional, having very many different axes describing each component of the type.


Fitness - aka reproductive success - is then a function of the genotype or phenotype, and is represented by the height in the maps above. An evolving population will seek the highest point it can. In the smooth landscape it will not have trouble finding the highest point on the map (the global peak), because there is only the one. However, when the landscape is rugged, the population may initially ascend a peak that isn't very high, and it can potentially get stuck there. The problem in evolutionary dynamics is then how populations cross the fitness-valleys between peaks in order to ascend adjacent peaks that are higher. Several papers in recent years have addressed this problem (e.g., Weissman et al, 2009; Østman et al., 2012).

Here is the fitness graph of Aspergillus niger, a filamentous fungus. 


The data is taken from Franke et al. (2011). Here the data is fitness as a function of genotype. The data is displayed such that an arbitrary genotype is on the left at zero mutation (call it the wild-type), and every other genotype is displayed a distance away on the x-axis equal to the number of mutations away from the wild-type. Lines between genotypes indicate that the two genotypes differ by only one mutation. Peaks are genotypes whose neighbors (genotypes one mutation away) all have lower fitness, and are displayed in red.

The structure of fitness landscapes is informative about evolutionary dynamics, i.e., how populations behave as they evolve. Just a quick glance at the Aspergillus niger landscape make it apparent that a population could potentially get stuck on one of the lower peaks if it started out way over on the right of the landscape. Whether the population can cross the valleys to the global peak depends on both the population size and the mutation rate. The more mutations in the population (given by the mutation-supply rate, the product of population size and mutation rate), the higher the chance of crossing valleys. See Østman and Adami (2013) for more on how these three parameters enable prediction of evolutionary dynamics, or this post with some more details and a video: Can we predict evolution?

References:

Jasper Franke, Alexander Klözer, J. Arjan G. M. de Visser, Joachim Krug (2011). Evolutionary accessibility of mutational pathways PLoS Computational Biology 7 (8) e1002134 (2011) arXiv: 1103.2479v2

Weissman DB, Desai MM, Fisher DS, Feldman MW (2009). The rate at which asexual populations cross fitness valleys. Theoretical population biology, 75 (4), 286-300 PMID: 19285994.

Østman B, Hintze A, Adami C (2012). Impact of epistasis and pleiotropy on evolutionary adaptation. Proceedings. Biological sciences / The Royal Society, 279 (1727), 247-56 PMID: 21697174.


Østman B, Adami C (2013). Predicting evolution and visualizing high-dimensional fitness landscapesTo appear in "Recent Advances in the Theory and Application of Fitness Landscapes" (A. Engelbrecht and H. Richter, eds.). Springer Series in Emergence, Complexity, and Computation, 2013.




Reddit AMA FAQ

I did a Reddit/r/IAmA AMA yesterday and got a huge amount of questions. Some of them were repeats, so I post them here with answers. I'm planning to do another AMA perhaps next month, so this can serve as a reference.

Update 11/12/13: Randy's interview about this AMA is featured on BEACON's blog.




Q. What came first the chicken or the egg?


A. The egg. All chicken start out as eggs, but eggs evolved long before birds. Lots of animals start life as hard shelled eggs, including of course dinosaurs and reptiles, which birds evolved from. So when the first chicken was born to non-chicken parents (though it is hard to say when that would be, even if we know every chicken ancestor) it came from an egg, just like its parents did. The egg is also the earliest developmental stage, so therefore comes first in that sense as well.


Q. Are you religious?


A. No. I am not religious and I have no faith. I am atheist with respect to any gods that I have heard of. I have been non-religious since I started to think about it as a child. My parents did not raise me with religious beliefs.


Q. Are humans still evolving?


A. We are not done evolving. We still evolve biologically, though there are some aspects of humans life that have been taken over by cultural evolution. Just to mention one prominent aspect: medicine has alleviated many selection pressures. For much of our history a large factor in how we evolved was diseases. Diseases is a very strong selection pressure for evolving resistance. We are now resistant to many diseases that previously killed us, and yet when new ones arise today, we can fight back with medicine. For example, we don't need to succumb to HIV/AIDS, such that only the few that by chance are lucky to be resistant will survive, while everyone else dies (which incidentally is an excellent example of how selection works). As a result in part of medicine (particularly improvements in hygiene), the human population is now as large as it is. However, most people who argue that humans have stopped evolving seem to not have understood 1) that the increase in our population size leads to an increase in genetic diversity, which is the fuel for evolution, and 2) that evolution takes time, and there will come a time (perhaps in hundreds of thousands of years, but I am not so optimistic) when things will change, and the environment will again favor some human subpopulation over others. You can read more about this from my colleague Madhusudan Katti in reply to the sad claim from David Attenborough's that humans are no longer evolving. http://www.thehindu.com/sci-tech/sorry-attenborough-humans-still-evolve-by-natural-selection/article5141928.ece


Q. What do you think of the Aquatic Ape theory?


A. The aquatic ape theory is not plausible. I do not think humans need to have been semi-aquatic for a while in order to look the way we do (little hair, bipedal, and I forget what else they claim is evidence of it). Tim White once in 2009 told me and Daniel Dennett (who at the time liked the theory) that if it was true, then certain isotopes should be detectable in our bones, which they are not. I don't know the details of this, but can say that it is not a theory that many evolutionary biologists take seriously.


Q. How do you deal with creationists?


A. I start by being as rational as possible, answering their questions and focusing on the biology rather than their religion (which I don't really care about). As long as they try to listen, and acknowledge that I probably know more about it than they do, then we can have a conversation. If and when they start lecturing me, then I quit, as I have no patience for that. I focus on explaining that there is overwhelming empirical evidence for evolution, and give example of what some of it is. I don't have the most patience with people who think one book is all you need to read to learn about the world, though.


Q. Why did you become an evolutionary biologist?


A. I was looking around for a programming job in Santa Barbara, and one professor, Todd Oakley, said that he needed one, but that I should become a graduate student instead. So I accepted. This was extremely lucky, as I had been interested in evolutionary biology for a few years before that. I had even purchased Douglas Futuyma's textbook Evolutionary Biology to read in my spare time.


Q. How much money do you make as a scientist?


A. Not enough. I am a postdoc, which is the job you take after you get your PhD and before you become a professor. Postdocs make between $35 and $55 per year (in the United States), typically between $40k and $50k. Professors make more, up to somewhere between one and two hundred thousand per year.


Q. Have we found the missing link?


A. It's called "transitional fossils", and we have found a plethora of those: http://en.wikipedia.org/wiki/List_of_transitional_fossils


Q. Any advice for an aspiring biologist?


A. Go to college. Read as much as you can muster. Read widely rather than deeply, at least in the first few years. Go to seminars even if you don't think that the talk is about something you are very interested in. You may still learn something, and you may find new interests. And don't be afraid of not understanding everything. No one does, even professors. Discuss everything with your peers. Enjoy it - it's going to be so much fun, intellectually and socially.


Q. Do you find it difficult to get funding for your research?


A. I am a postdoc, so at this stage in my career I don't have to worry too much about applying for funding myself. But yes, generally it is very difficult, as a lot of researchers compete for very little money. The situation is quite bad these years, and applying for grants is the thing I worry the most about for my future. I think the most important contribution from evolutionary biology is simply that it explains our origins, which I think is very important for our curious species. But evolution is also becoming more and more important in medicine and engineering, where evolution explains antibiotic and antiviral resistance , and allow engineers to build better cars, antennae, and other things.


Q. What authors would you recommend for a non-scientist interested in evolutionary biology?


A. Stephen J Gould (mostly his essays from the Natural History magazine, which have been collected in a number of books).

Richard Dawkins (The Selfish Gene, Th Extended Phenotype, Climbing Mount Improbable, and more).
Carl Zimmer (he writes a column for The New York Times, and is the best journalist writing about evolution, in my opinion - and many evolutionary biologists I know would agree. He also wrote a highly acclaimed textbook for undergrads: The Tangled Bank).
Neil Shubin (Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body).
Jerry Coyne (Why Evolution is True).
EO Wilson (Naturalist).
Donald Prothero (Evolution: What the Fossils Say and Why It Matters).

Q. If we found life on another planet similar to earth, do you think the animals would be recognizable? 

A. I think they would be similar to something here on Earth, which has an incredible variety of species.

Q. What is your favorite animal?


A. Cheetah. And corvids, because they are so intelligent and creative (which is largely the same thing). Prehistoric: Argentinosaurus. For evolution: A croatian lizard, Podarcis sicula. Read more about the lizard in this paper: Rapid large-scale evolutionary divergence in morphology and performance associated with exploitation of a different dietary resource.


Q. What is the definition of a species?


A. The most common definition used for sexual species is the Biological Species Concept, coined by Ernst Mayr. It says that two populations are different species if they are reproductively isolated from each other. There are other definitions, but this is the most widely used one when we aren't talking about species that are mostly asexual, such as bacteria, in which case I prefer to use the Ecological Species Concept by Van Valen (1976), which states that a species is a group that occupies a distinct nice (i.e., a unique way of life): "A species is a lineage (or a closely related set of lineages) which occupies an adaptive zone minimally different from that of any other lineage in its range and which evolves separately from all lineages outside its range." The paper is titled Ecological Species, Multispecies, and Oaks. Best title ever.


When house cat and bobcat split from each other, reproductive isolation probably took a while to occur. So for some period of time and evolutionary biologist would have a hard time figuring out if and when they became different species, if they only use the BSC.


Q. Is there a gene for homosexuality?


A. There is no evidence of such a gene, and also only little evidence that homosexuality is heritable in a significant way (e.g., most homosexuals being born from heterosexuals, but see comment by uyedaj below). That doesn't mean that homosexuality is a choice, any more than heterosexuality is ("when did you choose to become heterosexual?"), but it is not likely tied to any specific gene. That said, we don't know what determines our sexuality.


Q. How come there are no other species as intelligent as we are?

A. Why would you expect other species as intelligent as we are? I have been thinking about this for a while, and one answer has to do with competition between species who share similar niches, which is conceivable when they are both intelligent humanoids. Neanderthals were probably pretty intelligent, more so than any other non-human animal (had slightly bigger brains than we do, though that doesn't imply higher intelligence).

Another answer may be that someone has to be the most intelligent. You could equally well ask why there are no animals as fast as the cheetah, or why no other animals has trunks as long as those of the African elephant. You would perhaps be somewhat amazed if there were two different species who were equally fast and faster than all others. That would be some coincidence, no?

Yet another reason could be that it may be really difficult to evolve to our level of intelligence. Perhaps it is short of a miracle that any species are as intelligent as we are. Maybe there is life on many other planets, but it is super rare that any of those species are more intelligent than a pig. I don't think is a likely answer, but we don't know.

Creationist implosion


Since the middle of last week I have been having an email conversation with a creationist. He emailed me after we had a conversation several years ago, now asking various questions about evolution, including stuff that really isn't evolution, but cosmology, geology, and chemistry. I replied that I don't really want to talk about things that I am not an expert in, to which he agreed. Following that the conversation narrowed to something I do know more than a bit about, and out of courtesy I asked if he would be okay with me posting the conversation to my blog. His reply was this:

"As long as you post my responses in their entirety, and give me opportunity to respond to your post, that would be fine."

So I proceeded because I am a nice guy/dumb ass who apparently can't resist getting sucked into time-sinks, but at least with the idea in my mind that I would share with a few readers. Let it at the very least serve as a reminder to myself not to waste my time talking about evolution with creationists - it really leads nowhere. I believe that more and more people will be less dogmatic, but mainly because young people have access to better information, and are therefore less likely to get sucked into the vortex of creationism.

Below I list a few of the email exchanges. Some emails in between are not listed, but these emails are shown in their entirety. My answers in smaller font follow his emails. I have highlighted all that was said about posting to my blog in red.

On November 6, 2013 at 10:17 AM [redacted] wrote: 
Hi Bjorn,
When you say: “ some are deleterious, and the least will be beneficial with respect to fitness,” that is a bit confusing.  You say mutations do not cause a net loss of genetic information over evolutionary time, but then say some mutations are deleterious.  It sounds like you are saying both are true.  The confusing part is saying the least will be beneficial, as though that would always be the case.  My understanding is from what I have read that would rarely be the case, and the randomness of mutational change would not always project that way.
Yes, I realize that this is the crucial point where I have not been able to convey the situation adequately.
In any one individual, when they are egg is fertilized/cell duplicates, there are going to be a number of mutations. On average (but not for all), most will have no effect on fitness (neutrals), some will decrease fitness (deleterious), and even fewer will increase fitness (beneficials). However, within the population, there is going to be a lot of variation. Some individuals will carry many deleterious mutations, but some (fewer) will carry enough beneficial mutations that the overall effect of all the mutations they carry is to increase fitness. Those are the ones that are (with luck) selected and become the ancestors of future generations.

About genetic information: Information is always with respect to something. In evolution it is with respect to the environment. If the fitness has increased, then we say that the information content has increased. Crucially, this can be done by any of the known kinds of mutations that I mentioned in an earlier email: insertions, deletions, inversions, point mutations, transposons, duplications (tandem, whole genome), recombination, crossover, and more. All of these kinds of mutations can potentially be either neutral, deleterious, or beneficial. Genetic information does emphatically not equate to the amount of DNA in the genome; lots of the genome is junk and serves no function currently, though it may have in the past, and it may again in the future.
Concerning deletions though, if the protein is 100 amino acids long, and mutational deletions occur so now it is 98 amino acids long, but because of a rearrangement of genetic sequence it ends up being a beneficial change to fit in with its current environment, an increase in fitness takes place which is passed on.  Am I correct so far?  But if other deletions take place over evolutionary time that eventually shortens the gene sequence to 80 amino acids long, is that not still a net loss of genetic information over evolutionary time?  Am I using the right terms?
See above about genetic information. If the deletion of 18 amino acids is deleterious (decreases fitness and thus the information about the environment), then it will be selected against, and individuals with such a mutation will not likely have any ancestors. If it is actually beneficial to get rid of 20 amino acids, then the change is beneficial. And that is all that matters. Strictly speaking, talking about loss of information is not something evolutionary biologists do very much. The key term is fitness. The crux is whether the mutational changes cause the individuals to have more or less offspring that the rest of the individuals in the population.
You also say: “some individuals in the population will by chance have a net increase in fitness.” Here again we are looking to the occurrence of a beneficial mutation which is said to be extremely rare, and sometimes it seems at the expense of a net loss of information.  Should we always look for or expect the best case scenario, which it seems this would be doing?  I know I’m asking a lot of questions but it has to logically make sense to me before I can accept it.  Thanks again for your patience.
I'm not sure what you mean by best case scenario. Selection of course "looks for" the fittest individual, so to speak.

As explained above, for one individual there is no net loss of information if there is a net increase in fitness. The genome may be reduced in size, but that is really neither here nor there. 

I'm not sure what you mean by best case scenario. Selection of course "looks for" the fittest individual, so to speak.
Bjørn

P.S. I hope that the above clarifies some things, and because I think it does, I'd like to post everything above to my blog, with your permission?

On November 6, 2013 at 5:16 PM [redacted] wrote: 
Hi Bjorn,
So then do you believe there is any accuracy to the following statements at all? 
“Mutations are very rare.  They occur only once in every ten million replications. 
Mutation rates vary a lot. It is not clear what "replications" refer to here, but in humans, for example, there are no children born without some mutations compared to their parents. It is estimated to be ~1.1×10−8 per site per generation, which means that there are an average of about 1.1×10−8  x 3×109 = 30 mutations per generation. It can be much higher in some other organisms.
The chance of two related mutations occurring is one in 100 trillion; given the abundance of genes in living organisms, however, mutations can and do occur. 
I'm not sure what you mean by 'related'. If you mean identical, then that would indeed be a very small number, like one in 3 billion (which is the length of the human genome - and here I am assuming they are point mutations, aka SNPs = single nucleotide polymorphisms).
Even so, most mutations are harmful, leading to death of the organism before birth or a loss of a specific function. 
No, most mutations have no effect at all (neutrals). Most of the human genome is DNA that has no function, and there it doesn't matter if you change one nucleotide. Even in the protein-coding sequences, you can change many nucleotides without effect (the genetic code is redundant). And even if a mutation actually changes an amino acid, it need not matter for the protein. And even if it does matter for the protein, it may not matter for fitness. Even among deleterious mutations, many have only slight effects, and are not lethal (to the organisms or to the traits they affect). Lethal mutations are rare compared, but of course the effect is easy to spot. We all carry genomes with at least minor deleterious effects, but as long as they are minor, we can live with them.
Only one in 1000 are not harmful and most of those are neutral, having no effect on the organism. 
No, again, most, most mutations are neutral. Fewer are deleterious. I am not sure where you get the 1 in 1000 number from. Also, which fraction is neutral/deleterious/beneficial varies over time, between environments, and between organisms.
Certainly this is why mutations are to be avoided.  Mutagenic radiation and chemicals should be avoided, not embraced.”
I agree that for the individual human being, it is best to avoid mutations. No biologists would ever say that it would be good for humans to expose themselves to anything that increases the number of mutations. But mutations are nevertheless the stuff that increases variation, which is what selection acts on.

Bjørn
On November 6, 2013 at 5:54 PM [redacted] wrote: 
Hi Bjorn,
This still isn’t making any sense.  I don’t think you should post yet.  The DNA code is a set of instructions.  If deletions occur that cause a loss of function, as is sometimes the case, how then is it not a loss of information, and not just a loss of fitness?  Talking about a loss of information might not be something that biologists talk about much as you have said, but that doesn’t mean it doesn’t happen.  You made the statement that it doesn’t happen.
If we are to talk more about information, then please first tell me why we can't just talk about what really matters, namely function and fitness. The crux of the matters, I hope you will agree, is how evolution can make new things. Evolution can, as has been shown, by rearranging DNA in all sorts of ways (the different kinds of mutations as described earlier), applied to both protein coding sequences (which code for proteins) and to regulatory sequences (the DNA that controls gene expression = the turning on and off of the genes that make proteins).
No, I said it doesn't happen very much. In fact, my professor is an expert in applying information theory to evolution (his name is Chris Adami). I also note your reluctance to say what this information is about - talking about information doesn't make sense without stating this. Some code may have information in some context, but not in another.
I do agree with you now about the total amount of DNA not being important.  I just read that duplication of a single chromosome is normally harmful, as in Down’s syndrome, and that Insertions often completely destroy the functionality of existing genes.  A loss of function to me means loss of information, even when something is added through duplication or insertion.  So I would agree the total amount of DNA would not be important but whether or not it provides or takes away function, which would again go back to loss of instruction or information, which is really somewhat different than fitness.
Yes, function is different than fitness. However, it is fitness that determines what happens in evolution. If loss of function increases fitness, then loss of function may happen. As in the case of blind cave-fish, which loss vision after living in dark caves for many generations. It was hypothesized that mutations that caused their eyes to stop functioning was beneficial because eyes are generally a liability (to infections, for example). But whether it was beneficial or not to lose the eyes, they lost them because there was no light in the caves anyway.
You also seem to be saying every time an egg is fertilized there will be several mutations.  If the Biology textbooks are accurate, then mutations are rare, plus the enzymes that repair copying errors factor in.  Look at this statement from www.nature.com : “Mutations can have a range of effects. They can often be harmful.  Others have little or no detrimental effect.  And sometimes, although very rarely, the change in DNA sequence may even turn out to be beneficial to the organism.”  Emphasis on “very rarely.”
Actually, to be precise the mutations happen not when the egg is fertilized, but when then egg and sperm are created. Yes, mutations are indeed rare, in part because of the error-correcting machinery.

I read the article by Joel Carlin. I promise you that he did not mean to say that there are generally more deleterious than neutral mutations. And yes, it is even rarer that mutaions are beneficial. But sometimes they are, and that is enough.
Can you give me any examples of beneficial mutations in humans other than sickle cell anemia?
That is a great example, though, isn't it? Another is the gene that enabled humans to metabolize lactose, and thereby drink milk. Very beneficial

Other examples just found by searching: 

From http://sciphi.wikkii.com/wiki/List_of_Beneficial_Mutations_in_Humans"

"Some people carry a mutant allele of the CCR5 gene that results in lack of expression of this protein on the surface of T-cells. Homozygous individuals are resistant to HIV infection and AIDS."

"Atherosclerosis is principally a disease of the modern age, one produced by modern diets and modern life-styles. There is a community in Italy near Milan whose residents don't get atherosclerosis because of a fortunate mutation in one of their forebearers."

"In humans, two cone cell pigment genes are located on the sex X chromosome, the classical type 2 opsin genes OPN1MW and OPN1MW2. It has been suggested that as women have two different X chromosomes in their cells, some of them could be carrying some variant cone cell pigments, thereby being born as full tetrachromats and having four different simultaneously functioning kinds of cone cells, each type with a specific pattern of responsiveness to different wave lengths of light in the range of the visible spectrum. One study suggested that 2–3% of the world's women might have the kind of fourth cone that lies between the standard red and green cones, giving, theoretically, a significant increase in color differentiation. Another study suggests that as many as 50% of women and 8% of men may have four photopigments."

Note that it is not always obvious that these mutations actually increase fitness (i.e., the amount of children people have), but even if they are neutral mutations, they certainly changed function.

Read this blog-post: http://bigthink.com/daylight-atheism/evolution-is-still-happening-beneficial-mutations-in-humans

"Most random genetic changes are neutral, and some are harmful, but a few turn out to be positive improvements. "
"People with the Apo-AIM gene have significantly lower levels of risk than the general population for heart attack and stroke, and pharmaceutical companies are looking into marketing an artificial version of the protein as a cardioprotective drug."

"Mutations which impair the function of LRP5 are known to cause osteoporosis. But a different kind of mutation can amplify its function, causing one of the most unusual human mutations known."
I found this interesting also.  Have you heard about this?  I just read this this afternoon.  It was once believed that flies resistant to DDT were mutants.  However, it was found that a certain population had the genetic material to make them resistant to DDT all along.  Gotta go.
Next time please supply links to these things.


On November 7, 2013 at 3:53 PM [redacted] wrote: 
Question: Do mutations cause a net loss of genetic information over evolutionary time?                            Answer: "Yes", lost protein function can be said to be loss of information with respect to that function, and  "No", mutations do not cause a loss of function over time.  Thanks for clearing that up for me.  Mutations cause lost protein function and do not cause a loss of protein function, as long as they don't reproduce.  Hypothetically, if it produces a fitness and is passed on, or it can just still survive, and the next generation loses more protein function, but not enough to become extinct, has information been lost in regards to that protein function? 
But that doesn't happen. Some/most individuals in the population will not have deleterious mutations, so those with deleterious mutations will mostly be selected against. Hypothetically yes it could be as you said if the mutational load is really large, but it isn't.
Every time a beneficial mutation survives because of fitness, it still loses genetic information in regards to protein function. 
No! If an individual has a beneficial mutation, there is no loss of genetic information with regard to protein function. There is in fact an improvement of protein function and thus an increase in genetic information.
Fitness will eventually lose out in all beneficial mutations because of loss of protein function.  Your theory is on a downward path in spite of all your optimism, and that will never produce an increase in complexity over time.  Look around you.  Life forms are going extinct, not new life forms coming into existence.  That is what is observed.
The theory is fine, and I observe adaptation happening in digital systems and in laboratory experiments, despite your perceived problems with it. You asked me what I was afraid of and this is it. That I spend all this time trying to explain how evolution works, and then you end up not getting it anyway. :( I'm going to post exactly what I want, now.

I do look around me, and while we are in the middle of a mass extinction event where more species are going extinct than new species appear, new species do nonetheless appear by speciation (that is not to say I am at all optimistic about the current mass extinction, which is a sad and horrible affair). Speciation takes many generations to complete, so it is not something we can easily observe in nature. But sometimes we can, like in the case of Podarcis sicula, a lizard in croatia, with stickleback fish, fruit flies, house mice, and in many plants, just to name a few off the top of my head.
On November 7, 2013 at 9:46 PM [redacted] wrote:
Hi Bjorn,
You do understand if you post what you want now you are not only doing so without my permission, I specifically told you you couldn't.  You might want to rethink that.

On November 7, 2013 at 9:48 PM [redacted] wrote:
Hi Bjorn,
After all the forced mutations of fruit flies, aren't the ones then ended up with less fit for just about any environment, and the last I checked they are still fruit flies.
Omg, this is just a creationist talking point!!! "Fruit flies" are not one species - there are many species of fruit flies. 

Yes, I will post some of our conversations on my blog. If you want to talk more, the comments there will be the place to do it. Please do not waste my time by emailing me again.
On November 7, 2013 at 11:16 PM [redacted] wrote:
Since you refuse to heed my request to not post our conversations, you leave me no alternative but to take another course of action regarding this matter.
EOF. 

So now I look forward to finding out what "another course of action" will be...

Here's one of those memes that I keep seeing on Facebook. I add it here for no other reason than I like to have an image in every post I write. It bears absolutely no relation to the topic of this post.