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.