Baseball or Genetics?


(system) #1
If you’ve wondered how geneticists come to the conclusions they do, this video is a good place to start.
This is a companion discussion topic for the original entry at https://biologos.org/blogs/jim-stump-faith-and-science-seeking-understanding/baseball-or-genetics

(Roger A. Sawtelle) #2

@jstump

“1. Populations change genetically from generation to generation.”

That statement is true, but we cannot start a discussion of evolution with this statement, because it is circular. Evolution does not take place because populations change, evolution is population change.

We might say that we have evolution because of genetic change, but that is not true either. Genetic change is not automatic. Genetic change can be negated by natural selection if it does not increase or maintain the fitness of the plant or animal.

Therefore it would seem that populations change genetically when these changes increase fitness. In other words populations change genetically when these changes enable them to better adapt to their environmental niches. We can also say that the environmental niches are constantly in flux so populations change from generation to generation as they adapt to these changes.

This is most evident when environmental niches disappear and the existence of whole populations are threatened with extinction.


(Steve Schaffner) #3

I’m not sure exactly what you’re objecting to here. “Populations change genetically from generation to generation” is just a fact about the world, a fact that lots of people don’t know. It seems to me a good place to start a discussion of evolution, because lots of people don’t know it. It’s not circular, since it’s not a tautology and doesn’t even mention evolution.

Now it’s true that some genetic change is driven by natural selection, and that some is inhibited by natural selection; it’s also true that most genetic change (at least for organisms like humans) happens independently of natural selection. None of that seems to me as important to understand as the basic fact: populations are changing all the time.


(Roger A. Sawtelle) #4

@glipsnort

We seem to disagree as to how natural selection works as part of evolution. I did not hear you specifically mention natural selection in your presentation, but the example that you mention, skin color is based primarily on natural selection as you indicate indirectly. Dark skin is an adaption against the harmful rays of the sun. White fur is an adaption to help the polar bear and arctic fox to hunt in the ice and snow. They do not happen independently of natural selection.

What important adaptions take place independent of natural selection? How about bipedalism? How about opposing thumbs? How about the human brain?

I understand that you are a geneticist, which is good reason why you would emphasize the role of genetics in evolution, but that is the problem that I find with the science of evolution. It has become the specialty of geneticists, who overlook the ecological and historical aspects of evolution and natural history.

Mammals and the yet to be produced humans received a break when the climate of the earth changed and the dinosaurs died out with the exception of the birds. All of these changes were primarily the result of natural selection and adaption to the environment as I understand it and science indicates.


(Steve Schaffner) #5

I don’t see any sign we disagree about anything. I’m well aware of the importance of natural selection to adaptation, and in fact have spent a fair bit of time studying (and publishing about) the history of natural selection in humans. What I think you’re missing, however, is that the talk wasn’t a general introduction to evolution: it was an introduction to evidence that humans are related to other animals. For that purpose, the mechanisms of evolution really aren’t very important. What’s important is the genetic traces left by common descent.

I think I mentioned in passing why certain pigmentation-related mutations stuck in some populations without using the words “natural selection”, but I really didn’t want people to focus on that aspect, since it had little to do with the evidence for common descent later in the talk.


#6

Evolution is a change in allele frequencies in a population.


(Roger A. Sawtelle) #7

@glipsnort

Steve,
I apologize for taking what you said out of context. In my defense it was not clear what the context was.

However the real issue for me is that no one on BioLogos has addressed the important issue of the role of natural selection in adaptation.

I really wish that you would. If you are not able to do so, please tell me to where I can read your findings. You can send a private message if you wish.

Thank you,

Roger


(Steve Schaffner) #8

What I’ve worked on(*) is detecting places in the genome which have recently been affected by positive natural selection; that’s mostly been in humans, but also in malaria and other pathogens. The basic idea is to find places where genetic variation has been altered by the rapid rise of a favored allele. The kinds of approach are laid out in this review paper (now rather out of date). If you’re willing to listen to another talk by me, this talk is from last year and covers more recent developments. (That talk assumes some knowledge of genetics lingo. I also see that I’m wearing the same shirt as in the other talk.)

Really brief summary: we have good evidence for recent selection in humans for a number of traits: resistance to infectious disease (lots of cases); skin pigmentation (a couple of dozen genes, at least); diet (the exact selective force varies with local conditions); high altitude hypoxia; stature (selection for taller people in northern Europe, probably for shorter people in southern Europe. That last case involves lots and lots of genetics variants, thousands if I remember correctly, all individually of small effect.

(*) Mostly in the past – I spend most of my time on other things currently. I tend to work on things that people will pay me to work on.


(Roger A. Sawtelle) #9

@glipsnort

“In the case of humans, these beneficial traits likely included bipedalism, speech, resistance to infectious diseases, and other adaptations to new and diverse environments.”

Steve,

Thank you very much for your response. The paper and the talk are helpful, but I am not really satisfied.

You continually indicate that natural selection is environmentally driven, but you never come out and say that it is ecologically driven. For instance the quote above from the beginning of the paper indicate that natural selection results in “beneficial traits (which) likely included … and other adaptations to new and diverse environments.” In slightly other words bipedalism, speech, resistance to infectious disease, a highly developed brain are most likely adaptations to new and diverse environments.

In the video you constantly infer that genetic change is a defense against disease, but never say that it is an adaption to protect against disease.

You indicate that balancing selection is different from positive selection, while at the same time indicating how balancing selection creates diversity which is a important ecological principle. Purification is negative selection which prevents from harm from the environment. Positive selection is positive adaption to one’s environment.

A genetic change that meets an adaptive ecological need results in a changed life form that is naturally selected in. That is what the evidence indicates. Don’t you agree? So, why isn’t anyone saying that, unless they are biased against the theoretical implications of this fact…


(Roger A. Sawtelle) #10

@glipsnort

Steve,

I know that you are a busy person and I have no right to expect a response from you, but I am still hoping that you will respond. Brad is supposed to close the blog if the comments stop coming.

I know also that your work on evolution is based on math, which is far different from my ecological point of view. However I understand that it was a think tank like yours, very possibly yours that convinced E. O. Wilson to split from Dawkins over kin selection. If it was yours, I want to thank your group for this service to science and humanity. Now we need to go farther to alter Darwinian natural selection to show that it is based on the ecology, rather than on conflict.


(Steve Schaffner) #11

Sorry – I haven’t responded because I’ve had trouble thinking of anything intelligent to say. I agree that ending the story at “natural selection happened” is completely unsatisfactory. That tells you almost nothing interesting about what’s going on. Why a trait was selected for is where the interesting stuff is, and to understand that you have to go beyond genetics to ecology, to developmental biology, to biochemistry and biophysics. How the various constraints and opportunities offered by those areas is a huge puzzle that’s only beginning to be unraveled.

My problem is that, as you pointed out, I’m a geneticist. With good data and a little luck, I may be able to tell you where in the genome selection has been active, or what the genetic basis of a beneficial trait is. With a whole lot of work, some of my colleagues may be able to tell you what trait is associated with a beneficial variant. So those things I can talk about. Beyond that, though, I don’t know enough to comment.


(Roger A. Sawtelle) #12

@glipsnort

Steve,
Thank you for your honest response.

I think the problem is not that the ending of the story is natural selection as Darwin would have it, but “natural selection” takes place at the beginning of the story.

Let us take the example of sickle cell anemia. We know that it makes no sense without the threat of malaria, and your studies bear this out. So what can we deduce from this situation. That people in Africa were threatened by the serious disease of malaria, which of course is the result of a mutation. Somehow the body same up with the sickle cell mutation which protected carriers from malaria, which was why it was selected in. Unfortunately as you point out, when someone received a double potion of sickle cell genes, they inherit sickle cell anemia. Thus the sickle cell gene protects in many circumstances, but in others causes problems.

Now I know it is difficult to admit that a scientific theory is not correct, esp. Darwin’s Theory which has been so hotly debated, even though that is what we are supposed to do as scientists. Let me refer you to a new book, A New History of Life by Peter Ward and Joe Kirschvink who seem to get it basically right. Also I can send you my book, Darwin’s Myth, which explores the theoretical basis for this position.

Steve, I am not looking for you to be the Answer Man. I would like your support in saying that the need for adaptation is the basis for genetic change and evolution, rather than random genetic change creates evolution and adaptation. Did sickle cells create malaria, or did malaria give rise to sickle cells?


(Steve Schaffner) #13

The body doesn’t have to “come up with” a mutation: mutations just happen, all the time.

There are lots of things wrong with Darwin’s theory, but what exactly are we supposed to be admitting is wrong here?

Neither. A mutation (along with all of the existing human biology) created sickle cells, and malaria made them thrive.


#14

This is an important fact that many people can’t seem to grasp.


(Roger A. Sawtelle) #15

@glipsnort
@Joao

Steve,

Thank you for your response

No one said that the body had to, meaning by necessity, come up with a mutation. No one said that humans or anything else has to exist, but they do and not by accident, or by magic, but by a rational process.

However, to say that mutations happen all the time raises the question as to why we have this particular gene in parts of Africa and not in other parts of the world, where malaria does not exist.

You say that mutation created sickle cells. Last time I looked mutation was a physical process that occurred in an organic body, and not in rocks. It also takes place in non-human bodies of animals and plants. Therefore I believe that it is reasonable to say that the Variation or mutation was created by the body in the form of sickle cell genes. Then since as you say malaria made this mutation thrive. Malaria then which is part of the ecosystem acted as Natural Selection to select this mutation into existence as part of human genetics.

Thus without malaria, no sickle cells. This is what the evidence indicates.

Is the sickle gene an evolutionary adaptation of the body to the disease of malaria? Yes or No? You seems to be indicating in your talk that the answer is Yes, but now you say No, because the body has nothing to do with the creation of sickle cell. I say Yes, because that is how ECOLOGY works. If you want to day that evolution has nothing to do with ecology, then that is your problem. Ecology is the science that will determine the future of the earth, not evolution.


#16

I believe that you did precisely that, Roger. Well, precisely only if we hypothesize a spelling error:


#17

[quote=“Relates, post:15, topic:2735”]
Therefore I believe that it is reasonable to say that the Variation or mutation was created by the body in the form of sickle cell genes.[/quote]
I don’t. More trivially, there’s no such thing as “sickle cell genes.” I don’t think that you can carry on a useful conversation unless you focus on the words you are using. [quote]… Malaria then which is part of the ecosystem acted as Natural Selection to select this mutation into existence as part of human genetics.[/quote]
No, nothing can “select a mutation into existence.” You’re missing the important fact that evolution happens to populations. It might help if you dropped terms you routinely misuse, like “mutation,” and try to think more generally about genetic variation.

What evidence? You didn’t cite any evidence.

[quote]Is the sickle gene an evolutionary adaptation of the body to the disease of malaria?
[/quote]No, the selection of a variant allele of the gene encoding hemoglobin (not “the sickle gene”), causing an increase of the frequency of that allele in some populations, represents the adaptation of a population, not “the body.”


(Roger A. Sawtelle) #18

@Joao

It does seem we are talking past each other. I really do not know who you are so that is easy to do.

I was talking to Steve and he gave me a reference to a very interesting talk that he gave on his work on natural selection. I was using that material, none of which was very new as the basis of my example.

I expect that you are aware of the interesting phenomenon of the sickle cell and sickle cell anemia. The sickle red cell appears only in West Africa and basically were malaria is a common disease. This was well established in the talk Steve gave. It is also accepted with good reason practically and statistically that sickle shaped red cells prevents or ameliorates malaria.

However the talk also said that when persons have two copies of this gene that creates sickle shaped red cell, the cells are too distorted to travel through the blood vessels freely and the person suffers from sickle cell anemia, which can be a very debilitating condition.

First you and Steve said that I said that the body “had to” come up with the sickle cell variation as a defense against malaria. If you look again as I did I said that the body did come up with the sickle cell variation as a defense. I did not indicate that it was necessary, but only that it happened.

This does not preclude this variation from being random. Random does not mean it cannot not arise when needed. Maybe you or Steve knows how often this variation appears “naturally” in the human genome. It must be quite rare or it must be selected out when it appears.

The above is your statement. If I may simplify somewhat… The selection of the variant allele, which causes the increase of the allele represents the adaptation. Again does the adaptation cause the increase, or does the selection cause the increase. Generally what this says, Is we know an allele is fit because it is selected, but we do not know why or how it was selected. What I want to say is that it is selected because it is adapted to a specific situation, which is also what this says in a roundabout indirect way.

I am saying that the variant allele red cell condition known to many as sickle cell was selected in by Natural Variation because it is an successful adaptation to the disease malaria. If you have evidence that this is not true please share.

Now you said that I should have said variation, rather than mutation. Of course I know that variation is a broader term than mutation, although I find that some people use the terms interchangeably. I thought that Steve used the term mutation. I thought that a variation this unique was most likely a mutation, but of course variation is a safer and broader term. You I am sure have your reasons for using it.

You also said that that variations take place in populations, rather than individuals. I am sure in your science you study populations rather than individuals, however populations are made up of individuals. When individuals change, populations change. You cannot have sickle shaped red cells variation in individuals without having it in a population. This variation protects individuals from malaria as it does a population. The word body I used originally can be thought of as the body of an individual, or collectively as the bodies of a population which have been similarly changed.

So we have two conditions. We have the deadly tropical disease of malaria and a sickle red cells caused by a genetic variation. Is there a connection? Steve said Yes, because malaria causes people with the sickle cell condition to thrive (because they are protected against malaria.) This being true then malaria acts as an environmental condition which acts as a form of natural selection to select in the genes that create sickle shaped red blood cells.

This is the evidence you asked for. I hope that it is clear.


(Roger A. Sawtelle) #19

How does saying something hppened get translated into meaning that it had to happen?

Yes. I understand that scientists do not want to think that events have a purpose, so that they refuse to say that adaptations have a purpose.

However Darwinism is based on the idea that populations are struggling to survive, thus to follows that they would adopt any allele that would further their survival.


(system) #20

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