The fruit of evolution model ?

[lucaspa]

Would you introduce me one of these studies and summarize how did the study use evolution to discover?

Read them. They are all easily available either online or in your public library.

What I will do is introduce you to one of my studies and how evolution is used to discover. Juvenissun, what is not usually understood about science is that hypotheses are not tested singly. Instead, they are tested in huge bundles. All except one of the hypotheses -- the "favored" hypothesis or the one lay people think we are testing singly -- are assumed to be true. If, however, they are not true, then the favored hypothesis is not going to "work".

I study fracture repair. Specifically, I study the use of adult stem cells to regenerate bone where so much bone has been lost that repair will not happen -- non-unions. Obviously, I am interested in human fracture repair. But I can't do the experiments on humans for a multitude of ethical and practical reasons. So I need to choose an animal model. Now comes the crucial question: Which animal(s) do I choose as models? Evolution states that certain animals are similar because they share a common ancestor. Because of inheritance, they will share characteristics of that ancestor. As the relationship moves farther apart, they will share fewer characteristics. OK, the original determination of similarity is based on (usually) static characteristics visible to the naked eye: shape of bones, shape of limbs, warm vs. cold blood, fur vs. scales or feathers, etc. More recently, genetics has come into play.

No one ever looked at fracture repair as a basis for deciding similarity or relationship. However, at this stage we make a prediction based upon evolution: since the animals descended from a common ancestor, then the unknown characteristics (fracture repair) will also have to be similar as well as the known characteristics.

So what are the closest relatives to humans? The great apes, especially chimps. They would make good models, but they are too expensive to use in large numbers. From there we go to monkeys, but the same objection applies. The next step would be other mammals, then reptiles, then amphibians, then fish. Mammals are the closest relatives of that list to humans, which brings us to the humble rat, rabbit, and dog as experimental models. As it turns out, the prediction is correct, and it is possible to study fracture repair in those animals and have the results be applicable to humans.

So a current study I have going is to isolate multipotent adult stem cells (MASCs) from an adult rat. I have shown that MASCs are present in humans (as predicted by evolution). The MASCs are expanded in culture (to get a huge number cells, into the hundreds of millions) and seeded into a matrix where they attach. Then I make a non-union defect by cutting out 7 mm from the center of adult rats. This is what is called a "critical sized" defect and will not heal on its own. There is a size in humans where defects will not heal (as predicted by evolution). I place the matrix + MASCs into the defect for 8 weeks and then assay to see whether the defects regenerate the bone. They do.

At this point, because of evolution, I (and the FDA) are ready to try this treatment in humans.

Please note that creationism does not permit this prediction. There is no reason fracture repair HAS to be similar between rats and humans. It MAY be, if the Creator so chose, but you can't predict that. Instead, you would have to test all species to see which one had fracture repair closest to human. Maybe the best model would be fish. Evolution allows a shortcut to choosing animal models. I don't have to check each and every species.

I also want to check the ability of MASCs to regenerate a skin wound. There's no reason a Creator would have to make BOTH wound healing and fracture repair similar. Under creationism, perhaps the best animal model for skin wound healing would be a toad.

But under evolution, both skin wound healing and fracture repair should be similar to that of humans, because of that common ancestry relationship. So I can skip all the time and expense looking at all species to see which one the Creator decided to make skin wound healing similar to humans and use rats again. Because of evolution.

 

[lucaspa]

That statement wasn't from me. I don't even agree with it.

My sincere apologies. Both to you and to Sihya, who actually stated it.

You should seriously think about changing your mind.

 

[lucaspa]

And the reason that scientists bother judging the usefulness of theoretical models to the classification and explanation of available data is because they want to know how the world works.

Science does more than look at "usefulness". When you say "how the world works", that leads you to which theories are "true" in that they really do explain how the world works.

Can I get you to please drop the word "model"? It's very vague and actually refers to some graphical or constructed representation of a theory. As an example, Gibbs came up with a theory to explain which chemical reactions were spontaneous. He described a theoretical surface based on enthalpy and entropy and stated that if you place a ball on the surface and it rolls down then the reaction is spontaneous. Maxwell went out and built -- out of wood -- a surface as Gibbs' described. That wooden surface was a "model". The theory is what was evaluated against observation, not the wooden model.

whether they do or not, however, scientists are going to go on accepting some statements as true and some statements as false, based on their conformity to data.

It's possible that that sentence means something, but I remain skeptical.

Of course it means something. You said it yourself. True means "conformity to data". False means "contrary to data".

 

[sfs]

Science does more than look at "usefulness". When you say "how the world works", that leads you to which theories are "true" in that they really do explain how the world works.

Yes. My point, exactly.

Can I get you to please drop the word "model"?

Sorry, no.

It's very vague and actually refers to some graphical or constructed representation of a theory.

That may be your preferred usage, but it's hardly standard. In the fields I've worked in, "model" refers to any representation of an aspect of physical reality -- or indeed of any system, even if it's not actually a physical system -- whether the representation is conceptual, mathematical or otherwise. I've actually never seen it used to refer to a physical embodiment, in fact, but I have seen it used for mathematical models many, many times; see, for example, "demographic model" or "Wright-Fisher model" in population genetics, or the Standard Model in particle physics. It is a more general term than "theory" (which is vague term itself).

Of course it means something. You said it yourself. True means "conformity to data". False means "contrary to data".

I don't see how that tells me what the sentence means. What does it mean for data analysis to operate in the same domain as subjectivity? What domain is it?

 

[sfs]

Thanks. Like others, you gave too many examples. But none of them are specific enough. So I pick this one to explore:

You didn't pick an example: you picked a general statement. Pick one of my specific examples if you want more information.

 

[ebia]

I've skipped some of the thread, but I think part of the problem here is a failure to recognise the difference in predictive power between a coherent theory capable of some mathematical modelling and a collection of ad-hoc explanations.

Unless someone recognises that the conversation is doomed.

 

[ncmnt2]

Modern medicine is based on ambitious exploration, focusing on repeatable, varifyable evidence... not evolution. In response to your question... A clearer understanding of absolute truth! A foundation that is scripturally based vs. faith in man! Your turn...

 

[juvenissun]

You didn't pick an example: you picked a general statement. Pick one of my specific examples if you want more information.

OK.

 

[juvenissun]

Read them. They are all easily available either online or in your public library.

What I will do is introduce you to one of my studies and how evolution is used to discover. Juvenissun, what is not usually understood about science is that hypotheses are not tested singly. Instead, they are tested in huge bundles. All except one of the hypotheses -- the "favored" hypothesis or the one lay people think we are testing singly -- are assumed to be true. If, however, they are not true, then the favored hypothesis is not going to "work".

I study fracture repair. Specifically, I study the use of adult stem cells to regenerate bone where so much bone has been lost that repair will not happen -- non-unions. Obviously, I am interested in human fracture repair. But I can't do the experiments on humans for a multitude of ethical and practical reasons. So I need to choose an animal model. Now comes the crucial question: Which animal(s) do I choose as models? Evolution states that certain animals are similar because they share a common ancestor. Because of inheritance, they will share characteristics of that ancestor. As the relationship moves farther apart, they will share fewer characteristics. OK, the original determination of similarity is based on (usually) static characteristics visible to the naked eye: shape of bones, shape of limbs, warm vs. cold blood, fur vs. scales or feathers, etc. More recently, genetics has come into play.

No one ever looked at fracture repair as a basis for deciding similarity or relationship. However, at this stage we make a prediction based upon evolution: since the animals descended from a common ancestor, then the unknown characteristics (fracture repair) will also have to be similar as well as the known characteristics.

So what are the closest relatives to humans? The great apes, especially chimps. They would make good models, but they are too expensive to use in large numbers. From there we go to monkeys, but the same objection applies. The next step would be other mammals, then reptiles, then amphibians, then fish. Mammals are the closest relatives of that list to humans, which brings us to the humble rat, rabbit, and dog as experimental models. As it turns out, the prediction is correct, and it is possible to study fracture repair in those animals and have the results be applicable to humans.

So a current study I have going is to isolate multipotent adult stem cells (MASCs) from an adult rat. I have shown that MASCs are present in humans (as predicted by evolution). The MASCs are expanded in culture (to get a huge number cells, into the hundreds of millions) and seeded into a matrix where they attach. Then I make a non-union defect by cutting out 7 mm from the center of adult rats. This is what is called a "critical sized" defect and will not heal on its own. There is a size in humans where defects will not heal (as predicted by evolution). I place the matrix + MASCs into the defect for 8 weeks and then assay to see whether the defects regenerate the bone. They do.

At this point, because of evolution, I (and the FDA) are ready to try this treatment in humans.

Please note that creationism does not permit this prediction. There is no reason fracture repair HAS to be similar between rats and humans. It MAY be, if the Creator so chose, but you can't predict that. Instead, you would have to test all species to see which one had fracture repair closest to human. Maybe the best model would be fish. Evolution allows a shortcut to choosing animal models. I don't have to check each and every species.

I also want to check the ability of MASCs to regenerate a skin wound. There's no reason a Creator would have to make BOTH wound healing and fracture repair similar. Under creationism, perhaps the best animal model for skin wound healing would be a toad.

But under evolution, both skin wound healing and fracture repair should be similar to that of humans, because of that common ancestry relationship. So I can skip all the time and expense looking at all species to see which one the Creator decided to make skin wound healing similar to humans and use rats again. Because of evolution.

I do not recognize evolution. But if I were you, I would make a similar choice as you did. Use chimps, monkeys etc. Practically, I will make a different choice than you did. I will use dogs, or pigs instead of rats.

I make this choice without any reference to anything about evolution. And I believe my choice will be better than your choice. Of course, I understand dog is lovely and pig is hard to keep it clean.

I am not discrediting your work. But I think your choice of rat for the work has nothing to do with the theory of evolution. It is just a zoological common sense based on classification.

Practically, I still think dogs or cats are better samples than rat. I feel it this way without using any knowledge of evolution. Am I making the right choice? And there is one more thing: if you did not test your result on dog, cat, pig or cow, I don't think you should jump it right way to human.

 

[juvenissun]

Using your logic, one could make all kinds of predictions, many of them completely ridiculous. On the one side, we see quadrupedal mammals, and on the other hand, we see bipedal humans. Therefore, even a child could deduce that we should find fossilized quadrupedal humans.

Do you really think this kind of logic is going to be useful in making predictions?

Then why doesn't it? Why don't creationists make valid predictions, if this kind of logic can be applied so usefully? Why is that only biologists, using evolution, seem to be able to do it?

How was the discovery of the fossil fly not a new discovery?

Because we already predicted its existence. It is only a matter to find it.

Well, if we never find it, we just keep it quiet and assume it must exist.

 

[juvenissun]

Fair enough. I would love to give a detailed explanation but I am no scientist and I know I would fail miserably. One of the things that cemented my acceptance of evolution was talking to a petroleum geologist and a medical researcher, both of whom explained in detail how they used evolutionary theory to build models with successful real-world results. From GIGO, I do know that the likelihood of successful results from bad assumptions is very low; therefore there has to be something to it.

I would love to be able to give their examples, but I know I would fail miserably. I'll leave the science to the scientists on this board.

I don't know about the medical researcher. But the assumption made by the petroleum geologist, whatever it was, I am sure I can make the same without using any concept of evolution. If you remember what it was, I can explain it to you.

 

[juvenissun]

Fair enough. I would love to give a detailed explanation but I am no scientist and I know I would fail miserably. One of the things that cemented my acceptance of evolution was talking to a petroleum geologist and a medical researcher, both of whom explained in detail how they used evolutionary theory to build models with successful real-world results. From GIGO, I do know that the likelihood of successful results from bad assumptions is very low; therefore there has to be something to it.

I would love to be able to give their examples, but I know I would fail miserably. I'll leave the science to the scientists on this board.

Ha ha ... No wonder you are a computer scientist.

In geology, we made all kinds of wrong assumptions. But the result would still be good. Is it wonderful?

 

[Pete Harcoff]

APPLIED EVOLUTION:

Evolutionary biology is widely perceived as a discipline with relevance that lies purely in academia. Until recently, that perception was largely true, except for the often neglected role of evolutionary biology in the improvement of agricultural crops and animals. In the past two decades, however, evolutionary biology has assumed a broad relevance extending far outside its original bounds. Phylogenetics, the study of Darwin's theory of “descent with modification,” is now the foundation of disease tracking and of the identification of species in medical, pharmacological, or conservation settings. It further underlies bioinformatics approaches to the analysis of genomes. Darwin's “evolution by natural selection” is being used in many contexts, from the design of biotechnology protocols to create new drugs and industrial enzymes, to the avoidance of resistant pests and microbes, to the development of new computer technologies. These examples present opportunities for education of the public and for nontraditional career paths in evolutionary biology. They also provide new research material for people trained in classical approaches.

http://arjournals.annualreviews.org....ecolsys.32.081501.114020?journalCode=ecolsys

Unfortunately for creationists, evolution *is* a useful science. But the common theme from creationists I've noticed when presented with this fact, is that instead of confronting it head on, creationists instead will either ignore it or try to handwave it away. But it's not going away.

 

[Pete Harcoff]

Specific "real life" example:

EVOLUTIONARY GENOMICS DISCOVERS AIDS SUPPRESSION PROTEIN

The underlying genetics/genomics research leading this this discover is directly based on evolution and more specifically, the common descent of primates (that's the phylogenetics tree based approach to their analysis):

The potential significance of adaptive evolution and dimerization in chimpanzee intercellular cell adhesion molecules:

Cell adhesion molecules are involved in a diverse array of cellular processes. Recent data suggests that human immunodeficiency
virus (HIV-1) co-opts their functions, in particular the properties of the intercellular cell adhesion molecules (ICAMs), to enhance
viral infection and transmission. To investigate mechanisms that may underlie the non-progression that occurs in immunodeficiency
virus-infected chimpanzees, we amplified the protein coding regions of multiple non-human primate ICAMs 1–5 and two ICAM
ligands, leukocyte function-associated antigen-1 (LFA-1) and macrophage antigen 1 (Mac-1). We then employed a phylogenetic
tree-based approach to comparative genomics, in order to screen for the presence of adaptive changes. Strong Darwinian positive
selection in chimpanzee ICAMs 1, 2 and 3 was observed, most markedly in domains that are critical for the integrity and
maintenance of ICAM-1 dimerization. As binding of ligands, including the attachment of virions, is influenced by the state of ICAM
1 dimerization, chimpanzee ICAMs may have evolved to modulate their own dimerization. In concert with previous evidence
suggesting an ancient retroviral pandemic as a prominent selective force in chimpanzee evolution, adaptation of chimpanzee ICAMs
may have effected a mechanism that explains the lack of immunosuppression observed following HIV-1 or simian immunodeficiency
virus (SIVcpz) infection.

 

[sfs]

Because we already predicted its existence. It is only a matter to find it.

Well, if we never find it, we just keep it quiet and assume it must exist.

Huh?

 

[juvenissun]

Huh?

Yes, this is the true situation. This is how earth science works.

 

[juvenissun]

APPLIED EVOLUTION:

Evolutionary biology is widely perceived as a discipline with relevance that lies purely in academia. Until recently, that perception was largely true, except for the often neglected role of evolutionary biology in the improvement of agricultural crops and animals. In the past two decades, however, evolutionary biology has assumed a broad relevance extending far outside its original bounds. Phylogenetics, the study of Darwin's theory of “descent with modification,” is now the foundation of disease tracking and of the identification of species in medical, pharmacological, or conservation settings. It further underlies bioinformatics approaches to the analysis of genomes. Darwin's “evolution by natural selection” is being used in many contexts, from the design of biotechnology protocols to create new drugs and industrial enzymes, to the avoidance of resistant pests and microbes, to the development of new computer technologies. These examples present opportunities for education of the public and for nontraditional career paths in evolutionary biology. They also provide new research material for people trained in classical approaches.

APPLIED EVOLUTION - Annual Review of Ecology and Systematics, 32(1):183 - Abstract

Unfortunately for creationists, evolution *is* a useful science. But the common theme from creationists I've noticed when presented with this fact, is that instead of confronting it head on, creationists instead will either ignore it or try to handwave it away. But it's not going away.

So, please tell me ONE thing about evolution which is applicable to scientific research.

 

[juvenissun]

Specific "real life" example:

EVOLUTIONARY GENOMICS DISCOVERS AIDS SUPPRESSION PROTEIN

The underlying genetics/genomics research leading this this discover is directly based on evolution and more specifically, the common descent of primates (that's the phylogenetics tree based approach to their analysis):

The potential significance of adaptive evolution and dimerization in chimpanzee intercellular cell adhesion molecules:

I am interested. But I do not understand. Please translate.

What is the discovery? And how did the concept of evolution lead to this discovery? Notice that the term "adaptive evolution" does not mean evolution leads to the adaptation. It means that we call the adaptation "evolutional". It is not appropriate to add a big hat (evolution) to a common feature (adaptation). Something adapted to some conditions does not mean it is evolving.

 

[juvenissun]

Some examples coming primarily from the study of humans:

The first evidence for large magnitude changes in recombination rate across the genome (i.e. recombination hot-spots), done by measuring the autocorrelation in genetic diversity. Interpreting the result required an estimate of the variation in mutation rate across the genome, which was obtained by measuring divergence between humans and chimpanzees.

Measurement of the mutation rate in humans, again done by comparing the human and chimpanzee genomes.

Realization that human chromosome 2 represents a relatively recent fusion of two previously existing chromosomes, leading to the subsequent discovery of the vestigial telomeric and centromeric sequences.

Measurement of the difference between mutation rates in males and females, done by comparing divergence within families of transposable elements that had been inserted into the X and Y chromosomes. (Strictly speaking, while this analysis was done in an evolutionary framework, I think it really only relied on the human genome being the result of many millions of years of genetic change.)

Estimation of the ancestral population size of humans and chimps, showing that it was substantially larger than the recent human population.

Determination of the ancestral base at sites that are variant in humans, done by comparing humans to chimps, gorillas and macaques. Knowledge of the ancestral base been very useful both for inferring historical demographic changes in the human population, and for detecting and localizing loci where natural selection has occurred recently in the human lineage.

A more general class of very important discoveries: Evolutionary conservation is used all the time for a range of inferences about human genetics and biology. The essential point is that any part of the genome that is nearly the same between a range of species must have a functional role of some sort. This has been used to identify protein-coding genes, regulatory RNAs, and many kinds of regulatory element.

You want me pick one. So I pick a seemingly simpler one.

How was the measurement of mutation rate guided by the understanding of evolution?

I believe you do know what "guided" mean. Do not get it reversed. If you do not want to talk about this one, then bring up one you like to me.

 

[gluadys]

Notice that the term "adaptive evolution" does not mean evolution leads to the adaptation. It means that we call the adaptation "evolutional". It is not appropriate to add a big hat (evolution) to a common feature (adaptation). Something adapted to some conditions does not mean it is evolving.

Yes, juvie, it does. The adaptation of species is brought about by natural selection. Adaptation cannot be separated from evolution.

(You may be confusing species adaptation with adaptations in individuals.)