Evolution Science and Naturalism

[Aedes]

Originally Posted by NeitherExtreme

IWhat I find unnatural about evolution (or life in general) is that it exists in a natural universe only capable of entropy

Every single chemical reaction in a human body, a human cell, in cellular metabolism, in DNA transcription and replication, etc, loses energy. ALL chemical reactions lose energy. THAT is entropy. All of the processes through human evolution that apparently seem ordered (by virtue of resulting in us) are still completely consistent with entropy, because all of the processes lost energy at every step of the way. That's all there is to it. This is one of the oldest arguments against evolution in the books, and all it is has been a theological appropriation of a thermodynamic 'law'.

and life is extremely complex- to the point of needing foresight and intellegence for it to come about.

No one has ever been able to show that foresight or intelligence is necessary. Many people believe that to be the case, but there is no logical necessity, no evidence, and given all the crap and inefficiency and garbage in our genome, if something designed us they were not very intelligent.

In particular, I see this in the fact that nothing new or of increased complexity could ever be added to the genetic code (DNA) of an animal by chance.

Again, an egregious misunderstanding of both genetics and evolution.

1. Mutations don't happen by chance. They happen because of DNA damage from various causes (UV light, toxins, etc), or because of recombination events, and they are not corrected by our DNA polymerases. Some regions of DNA (telomeres) and some sequences (A-T rich) are more likely to have mutations.

2. Fundamental genes do not vary much from our very distant ancestors. Why? Because they're fundamental and mutations will not persist. That's why everything from humans and plants down to yeast, amoebas, and bacteria have the genes for glycolysis, and cytochromes, and for producing membrane phospholipids. They are so fundamental to the life of the cell that there is a lot of homology even between humans and bacteria.

3. Mutations don't persist by chance. They persist because they are advantageous under the existing conditions. They are extinguished if they are deleterious under the existing conditions. The preservation of mutations within a population has mostly to do with selective factors, though it also has to do with non-random mating and founder effects.

4. Selective pressure, when strong enough, can cause us to evolve protective genes that are harmful in other ways. This is hardly the work of an 'intelligent' guiding force. In the last 10,000 years, malaria has exerted such a strong selective pressure in African populations that many new alleles have arisen. Most famously, sickle cell disease (which is caused by a single mutation) has independently arisen 4 times within Africa. How do we know it's arisen 4 separate times? Because the mutation for sickle cell segregates in meiosis with genes that are nearby on the chromosome -- and by looking at these "linkage" relationships, it's clear that there are 4 separate linkage patterns. In addition to sickle cell, malaria has also selected for G6PD-deficiency (in the Mediterranean), Hemoglobin C (in Mali), Hemoglobin E (in southeast Asia), a glycophorin C mutation (in Papua New Guinea), hereditary ovalocytosis, hereditary spherocytosis, beta thalassemia, and alpha thalassemia. All of these protective mutations cause significant medical illness, especially sickle cell. An intelligent creator would be pretty dumb to give us sickle cell disease to protect us from malaria. But it turns out that this terribly harmful mutation is extremely advantageous where malaria is common, which is why it's arisen and then swept through populations 4 separate times.

5. New things ARE added to genomes. Our genome is filled with all of this crap, like introns, which may well be dead viruses that have integrated into the genome, are no longer functional, and just sit there doing nothing. Staphylococcus aureus duplicated its transpeptidase gene just to produce an enzyme called beta-lactamase that digests penicillin. Plasmodium falciparum has duplicated its EBA and PfRh genes in order to invade a more diverse repertoire of target cells. Gram negative bacteria of different species can pass genes to each other on plasmids to spread drug resistance (that is selectively favored by the pressure we put on them with antibiotics).

6. Genetic complexity IS added through evolution -- that's how a relatively simple organism, green algae, gave rise to every terrestrial plant from mosses to ferns to spinach to giant sequoias. That's how Pseudomonas aeruginosa has picked up resistance genes to 5 or 6 classes of antibiotics solely since these antibiotics have been invented.

[NeitherExtreme]

Didymos Thomas: Yeah, after I your other reply, I realized I had completely missed your argument about apeal to authority. Your point it valid, and certainly something I must take seriously and not simply throw out without thought given to it. At the same time, authorities on any given subject have at times throughout history been wrong, even when they are nearly unanimous in their beliefs. That fact obviously doesn't prove evoultion sicentists wrong, but IMO it certainly leaves the door open- and if everyone throughout history had apealed to authority I don't think science itself would really exist...

Aedes: I hear your arguments, and I thank you for your well thought out post. I have heard most of them and considered them before in some form or another before I ever started this thread. And thats not to say that they are invalid, we just disagree on a lot of the finer points, and I don't think I'll touch on all of them right now... Entropy seems like an important one to me though. And first, I realize that the second law of thermodynamics does not directly apply to evolution or earth in general. Entropy as a general principle (not the technical 2nd law version) seems to be observable in nearly everything that we can observe. This may be logic rather than science, or something else, but I think that anyone can understand what I'm talking about- even if they don't agree with my conclusions. More on that in a bit...

Not to be nitpicky, but one thing that you both have done, whether intential or not, is base some of your arguments supporting natural evolution on the assumtion that natural evolution is already true.

"Genetic complexity IS added through evolution -- that's how a relatively simple organism, green algae, gave rise to every terrestrial plant from mosses to ferns to spinach to giant sequoias. "

"What do you mean by new, then? Even new physical qualities are just reorganizations of what has already been."

Both of those statements hang on the already assumed belief in natural evolution... If you take away that assumtion, there is nothing left of the argument. So, even if you are right in your conclusions, those arguments don't seem good IMO. The assumtion of natural evolution shouldn't be the only example that someone can give to prove itself. Honestly, wether through laziness or acutally being wrong, I feel like I've seen that kind of reasoning running all throughout evolution science. Of course, these actually are good arguments, but only from a pre-assumed naturalistic world-view. In my last post I said that trust was an important difference between us, but I think world-view is just as important, or maybe more-so, and is really where my point is: That Natural Evolution Science is a science based on world-view rather than observable fact. I've said something similar to that a few times now, but I think I've done a terrible job of making myself clear on that point...

(Please forgive yet another long post Hopefully you will find it interesting, and maybe it will explain a bit better where I'm coming from.)

Worldview: "the framework of ideas and beliefs through which an individual interprets the world and interacts in it." (Wikipedia) A person's world view in many cases come "before" the facts that the person percieves, and is the grid through which a person understands them. Many times the person is unaware of the influence of their world-view on their interpretation of facts, and sometimes is even completely unaware of their world view at all- they simply take it for granted. Because of this, the same facts can be presented to any number of different people, and to each of those people the facts can have different meanings. And most often, each one assumes that their interpretation is "right" and that everyone who sees it differently must be wrong. This is in large part why people from different world view can have a very unproductive discussion if they never acknowledge their own world view and that of the other person- they argue over the conclusions but never realize that they aren't starting with the same understanding of the facts. World views are also in large part not provable of falsifiable: they simply are, though they can be shaped and changed. IMO world views (especially those that aren't acknowledged) have the ability to "blind" people to some facts and their implications, since they are the very thing thtrough which the person sees the facts. (And this can happen to me too, just like anyone else ) And in that way, any world view, once accepted, has a certain amount of irrationality built into it. Also, People often become defensive and/or irrational when they feel like their world view is being attacked, especially if they are not used to it. I think this is partly because of the insecurity that comes from having their whole life's framework become vulnerable. But whatever the reason, we don't like to have our world views questioned or disregarded.

A quick example from another thread (or two) that doesn't directly relate: I read (and posted a few times) about the "free will or not" topic. After a few posts (and the replies) I realized that the debate was not going to get anywhere (from my standpoint anyway) because the differences were on the level of world views. Even though free will seemed so obvious to me, I quickly realized from the well thought out responses that the "causality" folks were not dumb, but that I simply didn't understand them because we were coming from such different world views. I still haven't changed my mind on the subject, but I decided not to debate any more on the topic until I felt that I could say that I understand their world view. There was no benefit in further debate because any presentation of "facts" by me would not be interpreted to mean the same things to them. Logic to one side was nonsense to the other, and vice-versa; with no way to prove one world view right or wrong. (Though that's not to say that no one is right or wrong, it's simply not provable. And of course, I could be the one thats wrong... )

And now back to the topic at hand: Personally I didn't want to start an ID vs Evolution debate; I wanted to simply examine natural evolution on it's own merrits rather than put forth a replacement. But, I'm not sure that can happen without adressing some other world-views, since from a naturalist world view natural evolution appears to make sense. (Even if IMO it means being "blind" to a few facts or ideas.)

First, I think everyone would agree that the naturalist world view is not "provable", though many people would argue that they don't see any good proof otherwise, and that science has steadily replaced supertitious ideas with real understanding. Based on those ideas it is then assumed that all things must be governed by the natural laws. And in large part, I can understand and appreciate where they're coming from, and I don't think that I have the right to expect them to change their views for my sake...

The basic "supernaturalist" world view: This world view instinctively assumes that there is "something else" beyond the natural universe, which in turn can affect the universe. While this basic premise might seem silly to those who have grown up surrounded by naturlism, it has been an instinctive belief across all of humanity, and IMO is the basic premise behind our desire for meaning- which even the most atheistic have a hard time shaking off, even though meaning appears to them nonexistant(at least in the traditional sense). I realize that there are arguments that explain away this world view as a evolutionary response to curriosity, but they have never seemed good enough to me. And anyway, they are based on the assumtion of natural evolution, which is a part of the naturalist world-view, so the to the supernaturalist they don't "prove" anything.

Now lets look at a few cases of interpreting "facts": (obviously from my perspective to some degree I'll be the supernaturalist... )

(1) Non-Entropy (technical definition) exists in the Universe.
-Naturalist: This proves that nature is capable of non entropy. This follows logically (and necessarily) from it's world view, but is not supported by observable examples. (and naturalist evolution doesn't work- we can not observe it happening or make conclusive tests about it's methods.)
-Supernaturalist: This proves that something other than nature is involved here. This is based on the uncountable observations of entropy that are witnessed everywhere. Still not provable, but based on observation and scientific law none the less.
(If you want more explanation of this one, the first part of my first post goes into that argument a bit more)

(2) Complex life exists:
-Naturalist: Nature must be capable of naturally producing complex life. This again follows logically (and necessarily) from it's world view. Again the evidence apears self-evident, and the figuring out of "how" is simply details. Natural selection is the best guess under the naturalist world view, so it must be the best guess that exists. Any seeming problems are simply new areas of discover left for us to uncover, never woul their be a problem big enough to rule it out as a viable method- unless of course some other natural method could be found.
-Supernaturalist: Something other than nature must be involved. This is based on the observations that entropy (general) appears to be always working, while increasing complexity always (in our experiences) means that there was intellegence involved. The complexity of DNA, as well as other logical issues are "proof" that natural selection is not a viable method. Although life appears to only way in nature where entropy is "defeated", even then it is only for a time, and seems to be the lone example in a universe and earth filled with increasing entropy. Logic would say that the universe did not create it.

(3) Miracles: I don't want to make a big point or argument out of this one... But I think there have been experiences in people's lives (including some who are close to me and very trusted) that would be very difficult to "explain away", espescially when they are closely related to prayer- The odds of everything happening by chance get pretty slim in some of the cases that I'm thinking of. To the supernaturalist, these are further "proof". To the naturalist, they by definition can not happen, so they are not even considered seriously. However, if you don't believe me, or have never had a credible example of such an event (and many people get exited and call anything a miracle), then I in no way expect you to give any credit to this argument... But I would be ignorant to not seriously deal with what I have personally know about. (If you want to hear more about my stories, you may ask- but I don't just expect you to take my word, so I'll stop here.) The point of this paragraph is not to make anyone believe in miracles, the point is to show that any world-view (even a seemingly logical naturalist one) has it's "blind spots". If the supernatural exists, and miracles occur, the naturalist would be almost blind to them unless they came in the exact way that would "prove" something to them from their world view.

So what's my point? The job of science is to look for answers about how nature works, and to verify the theories and facts that it can, and to skeptically examine anything that is not verifiable by observation and logic. And to the best of it's ability, it should do this without any pre-assumed world-views. Science (finding natural answers) and Naturalism seem to go hand in hand in this way- But naturalism is not verifiable by observation and logic. Therefore it is not the job of science to prove or defend any theories based on the fact that they are the best naturalistic explanation. If the theory is verifiable without this world view, then it is good science. If it depends on this world view, or can logically (and maybe more logically) be interpreted by another world view, then it is not science, it is merealy opinion and conjecture until such a time as someone can verify it. (And IMO, since the facts are sparce enough, and since problems exist for every theory, and intellegent and alternate theories abound, much of Natural History should be placed in the heading of "speculative science"- without scientific "authority" being given to anyone for the time being)

And being this self-aware is not an easy thing to do- like I said at the begining, it is easy for a person to be unaware of their own world view and how it affects their interpretation of fact. IMO, this has been the problem with Naturalist evolution science from the begining, and very often a problem plagueing science throughout all of our history. "Science" ends up defending a world view. And if you don't think that science is "defending" anything, I'd like to give you a scenerio. Pretend that you are a well qualified scientist, in biology, paleontology, or some related field. And during your research, pretend that you found or realized something that made it impossible to believe in natural evolution. You re-examined the issue, and came away even more convinced: it just couldn't be natural evolution... What would you do? Do you think the scientific community would examine and then accept your findings, and congratulate you for your important discovery? Do you think the Smithsonean would take down their natural history plaques, National Geographic would run a cover story "Science Had It All Wrong", old science textooks would be tossed, and scientists would say "We don't know how we came to exist... Think hard and make up your own minds."? (Please exuse the over-drama ) Maybe I'm just being a crazy skeptic, but I just don't see it happeing. I would guess you're "problem" would get shelved with all the others that are awaiting answers, and if you clung to it you'd end up with your credibility taken away.

This is not to say that creationists and IDists don't have similar problems of perspective. In fact, they frustrate me to no end by simply debating the facts- which they have already interpreted through their own strongly influencing world view (and of course get nowhere), rather than try to bring science back to it's unbiased best.

Thanks for reading.

[Aedes]

Thanks for the reply! I'm short on time so I'll read it in more detail later, but here are some thoughts of mine.

Originally Posted by NeitherExtreme

Entropy as a general principle (not the technical 2nd law version) seems to be observable in nearly everything that we can observe. This may be logic rather than science, or something else, but I think that anyone can understand what I'm talking about- even if they don't agree with my conclusions.

I think it's quite arbitrary that one would choose to believe entropy and choose to disbelieve evolution (if one were so inclined to see them as inconsistent with each other). I haven't heard a creationist posit "The Second Law of Thermodynamics is disproven by Evolution." Only the other way around.

Be that as it may, if you're going to call evolution inconsistent with entropy, then you also have to call folding your laundry or setting the table inconsistent with entropy because those are also processes that are grossly more ordered. Furthermore, it's an inherently theistic belief that evolution posits advancement or progress. That's not evolutionary theory. Evolutionary theory describes change, it does not describe progress. And because every ultrastructural change in biology is determined at a molecular level, these reactions are no less subject to entropy than dissolving sugar in a cup of water.

I understand that you're using logic here and not science -- but therein lies the problem. I know from my own line of work (clinical medicine and medical research) that intuition doesn't help you very much in the world of science. If you've got a dispute with something in science, you cannot argue from principle -- you have to argue based on the quality of the evidence, and the evidence itself is the opus of scientific literature. If you want to take down evolution on scientific grounds, then you've got to do it on scientific and not logical grounds. But that means taking the data and putting together a story that does not make presumptions about God and creation -- because if you do it that way, then you're biased from the start and it will immediately cease to be science. Does that make sense just methodologically?

Not to be nitpicky, but one thing that you both have done, whether intential or not, is base some of your arguments supporting natural evolution on the assumtion that natural evolution is already true.

That's a funny way of putting it -- you're kind of reversing the God argument, where one might accuse a creationist of seeing everything through a theistic point of view.

The thing is, I'm very familiar with the science of evolutionary biology. This isn't some blind faith on my part, it's based on an overwhelming amount of scientific data. It's as true as any type of retrospective research can be true.

Both of those statements hang on the already assumed belief in natural evolution... If you take away that assumtion, there is nothing left of the argument.

In order to take away that assumption, you have to take away the science. Because that is what the assumption is based on.

This argument of yours doesn't go very far. I mean I can tell you that you eat breakfast every morning because you hang on the already assumed belief that you have a stomach, even though you've never taken it out to make sure it's there.

The assumtion of natural evolution shouldn't be the only example that someone can give to prove itself.

I gave you many examples within science itself that demonstrate evolution -- and don't require the assumption of it.

So here you go: these statements are based on a lot of science and do not require an a priori assumption about evolution:

1. Falciparum malaria is the leading cause of death in African children, accounting for around 20%.

2. The sickle cell gene is caused by a point mutation in the beta chain of hemoglobin. There is only one genotype that leads to sickle cell anemia. It's clearly hereditary, because it follows basic Mendelian genetics for a recessive gene.

3. Carrying one copy of the gene for sickle cell disease has been unambiguously shown to protect children against death from malaria.

4. Carrying two copies of the sickle cell gene will cause sickle cell anemia that is lethal in childhood (except with modern medicine now).

5. Sickle cell anemia and carriage of the sickle cell gene is the most common genetic disease in Africa, and its distribution perfectly overlaps the distribution of malarious areas. Thus, this highly lethal disease (sickle cell) is rare where malaria is rare, and it's common where malaria is common.

From this you can draw a couple conclusions:
a) God decided to create malaria, decided to give humans in malarious areas a protective gene against it, but decided to give children a fatal genetic disease that's caused by that protective gene.

-OR-

b) Malaria is a highly lethal disease (true) that kills children before reproductive age (true), so the disease will preferentially kill off genetically susceptible humans (true). Because 95% of all malaria deaths occur in African children younger than 5 (true), the children who are genetically protected against malaria are more likely to survive to reproduction (true). Therefore, a protective gene is more likely to be preserved in a population in which the vulnerable gene is killed off before the age of reproduction (true).

However, this gene causes sickle cell anemia in people who have two copies of it (true), and sickle cell anemia is nearly always fatal before reproductive age (true). Thus, carriers of the sickle cell gene are less likely to have children survive to adulthood because there is a higher probability of having a child with sickle cell anemia (true). So in areas where there is no malaria, the sickle cell gene has no advantage, and there is no selective pressure that kills off children who lack this gene (true).

When I write (true) here, I am referring to something that is overwhelmingly documented by scientific observation, and for most of these subjects I could give you citations in the scientific literature.

Now, this doesn't prove all of human evolution, and it doesn't prove that what I posited about God is incorrect. But if you were to set aside God's guiding hand and any presupposition about creation, for just a moment, and you tried to come up with a LOGICAL way to string all these observations together, your LOGICAL conclusion would lead you to natural selection.

It's not worth the effort, but I could go through this series of (truths) in even more detail. I could show you that there is a known mutation rate in the human genome, and that linkage studies have shown that the sickle cell gene has arisen in Africa 4 separate times during the last 10,000 years. And interestingly, a former mentor of mine has shown that Plasmodium falciparum (the parasite that causes falciparum malaria) diverged from its closest ancestor in Africa about 10,000 years ago. This dating is based on known genetic divergence rates that are prospectively observable over the short term and are extrapolated backwards.

[NeitherExtreme]

Thanks for your reply. I also am in a hurry, and will be gone for the weekend, but I'll give a quick initial response:

Yes, I am in a way reversing the "God argument", I am suggesting that naturalism is an assumed world view- not a scientific fact. You mentioned that you were in a hurry, and maybe you didn't have time to read my rather lengthy post, but addressing that issue was the main point of the post. IMO, natural selection as a means for producing life only makes sense after that world view is assumed.

And about the 2nd law- I understand what it's technical implications are, and what they aren't. IMO though, entropy exists in a more general form: If you build a house it will fall down over time. If you find the word "HELLO" writen somewhere, you assume someone wrote it there- nature couldn't put it there. And defying this general idea of entropy is IMO a defining characteristic of life. But that does not mean life had the ability to defy entropy to create itself- as life is still subject to entropy.

And about adaptation: I see that adaptation occurs. But never in a way that makes something any more complex, or contain anything wholely new. I'm sure you disagree with me there though...

About evolution being science: one of my main points is that what you are calling science, I would call a world-view affected interpretation of fact (please see my previous post...).

And if you want to talk about the nature of God, and my view of Him, I'd be glad to do so... but my only logical point so far is that something outside of the natural laws is IMO the best guess we have of explaining the current universe.

Sorry, but I got to go... But I'll be glad to respond to any comments or objections later on.

[Aedes]

Originally Posted by NeitherExtreme

I am suggesting that naturalism is an assumed world view- not a scientific fact.

There is no such thing as a scientific fact, including the laws of thermodynamics. That's problem number one. From an epistemological point of view, scientific assertions are based solely on the strength of the underlying empirical evidence.

So anyone who has naturalism as an assumed world view is NOT a scientist.

What I, as someone steeped in science, will say about my world view, is that physical things are subject to observation, and scientific inferences are based upon the observation and not an a priori world view. This doesn't have anything to do with an assumption about naturalism. For example, I know that men don't live as long as women (on average) because of repeated demographic studies that demonstrate that -- not because of any assumption about male fitness or female superiority.

So if you're going to propose that I have a naturalistic bias, you're in actuality accusing me of not being a scientist. I'm perfectly willing to accept anything written in Genesis as soon as there is a demonstration of it that meets a reasonable standard of scientific evidence. THAT is how science differs from religion -- I'm willing to allow ANYTHING in science to be proven wrong if that's what the data show. So nothing is assumed to be true except for the method.

IMO, natural selection as a means for producing life only makes sense after that world view is assumed.

Then how did humanity come up with that concept to begin with? We didn't always have assumptions about evolution. It was just the story that made the most sense (and in variations continues to make the most sense) based on the preponderance of data.

And about the 2nd law- I understand what it's technical implications are, and what they aren't. IMO though, entropy exists in a more general form: If you build a house it will fall down over time. If you find the word "HELLO" writen somewhere, you assume someone wrote it there- nature couldn't put it there. And defying this general idea of entropy is IMO a defining characteristic of life. But that does not mean life had the ability to defy entropy to create itself- as life is still subject to entropy.

Whoa -- that is absolutely NOT in ANY way part of the 2nd law of thermodynamics. In fact what you're describing has nothing to do with the entire discipline of thermodynamics in general.

Second law of thermodynamics - Wikipedia, the free encyclopedia

Entropy is NOT an observation about life. It's a law about heat transfer during chemical reactions and during interaction between different materials. A house crumbling to the ground cannot be used as an example of any thermodynamic principle, including entropy.

And there are so many palpable examples of order that develops in nature, think of the following common occurences in which "order" is formed out of "disorder":
1. crystal formation
2. frost circles
3. wave patterns (like in dunes and in the ocean)
4. fractal formations (in everything from river drainage systems to veins on a leaf)
5. interference patterns with light waves (i.e. the dual slit experiment)
6. slime molds, in which free living cells come together to form a multicellular organism (kind of like a fungal version of Voltron)
7. snowflakes (forming from suspended water vapor)
8. and in embryogenesis of ALL multicellular organisms, pattern formation

And about adaptation: I see that adaptation occurs.

So you're acknowledging, then, that the genetic predominance of the sickle cell trait is a population-level adaptation to pressure from malaria.

Guess what -- that IS natural selection. Welcome to the club!

But never in a way that makes something any more complex, or contain anything wholely new. I'm sure you disagree with me there though...

Absolutely -- and there are probably hundreds of thousands of actual examples. Just from my sickle cell example, this point mutation introduces a new allele into the population, it increases genetic complexity in individuals by creating sickle cell heterozygosity, and it increases genetic complexity in the population by introducing subpopulations with different genotypes.

I can give you an example from my own research. There is a group of proteins on the malaria parasite called PfEMP1 -- it's a protein that is exported to the surface of red blood cells (which the parasite lives inside of). In ancestral species of malaria (i.e. less differentiated) there is only one copy of this gene. In Plasmodium falciparum there are about 60 copies of this gene -- it's been duplicated again and again and again, and each duplicate has new sequence variations, and each version has a different gene promoter that the cell can use to silence 59 of them and express 1 of them. This is a critical (and frankly amazing) development that allows this one species to evade the immune system by varying which antigens it expresses -- and it's the main reason people don't get lifelong immunity to malaria and why vaccines haven't worked very well. So this is more complex (60 genes instead of 1, with a ridiculously complex regulation system), and it's new.

About evolution being science: one of my main points is that what you are calling science, I would call a world-view affected interpretation of fact (please see my previous post...).

It's somewhat wistful to protest against science based on this contention. But the thing is, this contention has no traction whatsoever until you go to the data itself and demonstrate its error. Science isn't a world view. It's a procedure used to learn things. If you disagree with the conclusions, then you need to go back to the data and the methods and see where the procedure went wrong. And if you find the methods and data sound, then you need to go to the results and find some other interpretation . And if you feel you understand science better than evolutionary biologists, then no one is stopping you from hypothesizing that God created the earth and attempting to demonstrate it scientifically. I'd be eager to see your method, though.

And if you want to talk about the nature of God, and my view of Him, I'd be glad to do so... but my only logical point so far is that something outside of the natural laws is IMO the best guess we have of explaining the current universe.

Perhaps worthy of a different thread.

But I think what this comes down to is where one is intellectually satisfied. A pure scientist doesn't need there to be an ultimate explanation. I'm not quite a pure scientist (because I'm a physician, so my approach to all this is far more multidisciplinary), but I'm, for one, completely satisfied with the idea that we don't need to fully "explain the current universe". It's good enough to just look at it and try to make sense out of what we see. But some people really do need an ultimate truth, and while untestable, this is where metaphysics and religion serve their roles.

[NeitherExtreme]

Hi again,
Sorry for the long delay- I've been busy with friends & family... Hope you've been having a good end of '07 as well.

Well, back to work... :

Originally Posted by Aedes

So if you're going to propose that I have a naturalistic bias, you're in actuality accusing me of not being a scientist.

I would in no way accuse you of not being a scientist... Unless you are biased, know it, don't care that you are, and then try to hide that fact from others. But from our discussion already, I can firmly say that this is not a description of you. If only people without any bias (world view) were considered scientist, there would be no one worthy of the title... Everyone has a world view (they must), and to some degree that will always affect their interpretation of the world around them. The challange for you, me, and everone else interested in "objective science" is to recognize our own world views and how they affect our understandings, and then to approach the evidence as nuetrally as possible. And in instances where a strong world view must be accepted before the facts "interperate themselves", the scientist should be honest about it. It appears to me that we would have this value in common, and that we are trying to work out what a nuetral, scientific, observation of the evidence would say...

Originally Posted by Aedes

Then how did humanity come up with that concept to begin with? We didn't always have assumptions about evolution. It was just the story that made the most sense (and in variations continues to make the most sense) based on the preponderance of data.

Interesting question... First, a world view can be accepted (or desired) before any formal explanation or "defense" of it exists. Indeed, some people go through their whole lives whithout defining why the believe what they believe. Second, at the time evolution came around (circa Darwin), Deism was a popular world view, but it had many inconsistancies. IMO, Deism was for the most part just naturalism waiting for a method or "defence", which Darwin graciously provided. From that point on, Deism died out as those who would have been it's supporters gladdly embraced evolutionary naturalism. Third, evolution made a lot more sense (and was therefore easier to concieve of) under the idea of pangenesis and before the discovery of DNA.

Originally Posted by Aedes

Whoa -- that is absolutely NOT in ANY way part of the 2nd law of thermodynamics. In fact what you're describing has nothing to do with the entire discipline of thermodynamics in general.

I agree with you. I guess I'm making this more confusing that I have to by using the word entropy to mean too many things. (I tried to keep the ideas seperate, but I don't think I did a good job at it.) There is the technical (scientific) definition of entropy, which must be applied to a closed system, and describes an increasing uniformity of matter over time. This (the 2nd Law) of course has no direct application to natural evolution or the earth specifically . Period.

The other idea that I associate with entropy is the general idea of things moving from order to chaos. You named some natural examples that are used to say that nature can produce order, but they do not fit my definition of order (except for the life examples that you mentioned, but the ability of nature to produce such things is what is being questioned here). I would define order to mean (at least) organization that suggests (or dictates) that something with intellegence organized it. In response, as far as I can tell, most naturalists would argue that that there is no such thing as order. Personally I think they assume this because they have to in order to keep their world view coherent, not because observation would dictate otherwise. Yes, ice can form (crystylization)- but if you happened upon (1) a frozen puddle and (2) an ice sculpture in the shape of the Statue of Liberty, you could assume (and most likely correctly) that the puddle had no intellegence behind it, but that the sculpture did. There is a difference, is there not? We know that nature could not produce the sculpture. Of course drawing a scientific line between what could happen by chance and what could happen only by intellegence might be a very tricky thing, but that is no reason to pretend that there is no difference. There is a degree of order that is simply more highly "ordered" than nature is capable of producing (observably, anyway).

And if the idea of order is accepted (and of course I think it should be), then we can see that everything that is "order" turns back to natural "chaos" over time, unless intelegence acts upon it. This is where my idea of a house falling apart, etc., comes in. It is a general idea of entropy which applies to "order".

With these ideas in mind, I'll re-quote my problem with Natural Selection (from a previous post):

"What I find unnatural about evolution (or life in general) is that it exists in a natural universe only capable of entropy, and life is extremely complex- to the point of needing foresight and intellegence for it to come about. In particular, I see this in the fact that nothing new or of increased complexity could ever be added to the genetic code (DNA) of an animal by chance. Even the simplest "somthing new" that would give a significant advantage to one organism (to the point that it would out-reproduce its competition) would have a DNA coding that is too complex to happen in a single genetic "leap". At the same time, nothing complex can be added over many generations because each tiny mutation, since it is not complex enough to add a very siginificant advantage, would be cycled back into the gene pool along with the much more numerous negative and nuetral mutations. The net result could not be positive, and in fact logic would suggest that the net result would be negative over time due to the fact that mutations are much more often negative than positive. The math simply doesn't add up. As far as I'm concerned, if evolution is natural it is due to some law or something that we have yet to discover- but not because of anything described by current science or logic.

In short form, here's my logical problem:
Natural Selection + Lots of Time = Decay"

And now I would ask, in light of what I just described, what evidence leads you to the objective realization that nature is capable of producing complex life? (Other than simply noting that life exists, which means nothing outside a naturalist world view...) It seems to me that the adaptation you see is the reason that you find evolution believable, with natural selection being the method. (Please correct me if I'm wrong.) But none of the adaptations that you have described (or I have ever heard of) ever create something "new or of increased complexity". Yes, if there are two different color moths, one may be more fit to survive. Yes, we can breed cows to be "different" from wild ones. Yes, finches can be better suited for survival with slightly larger beaks. And so on... But nothing NEW has entered the gentetic code. Take the cows for example: I'll ready to assume that we could breed cows the size of elephants, or down to the size of mice, or with hair that is 10 feet long, or horns that weigh 1,000 lbs., or that can produce 50 gallons of milk a day. (None of which we can do by the way, there are natural limits...) But nothing new was added.

There are some (and I think uncountable) instances where organs, appendages, designs, etc. must have a specific "begining". Abiogenesis, the first organelles, multicellular organisms, developement of sexes, etc. at some point need to begin. Even something like hair can demonstrate this point... When did the first hair appear? An evolutionist (AFAIK) must say that the "first" hair never existed, it simply evolved from something else that resembled a hair (like a flagella or something). But a hair is different from anything that is not a hair, and the coding for a hair must be very different from the coding for something that is not a hair. And the coding could not be added by chance... I must ask, does the idea that nothing is new- that nothing requires a "jump" to be a significant improvement- is that idea based on observation, logic, and science? Or is a necessary assumtion in order to believe the bigger story?

Viruses, etc. to me observably seem to be in a similar situation. While a random mutation can change it enough to go undestroyed by the imune system, the change itself is "lateral"- it is not more "complex" or any closer to being anything other than a virus. And such random changes can never get it any closer. Of course you know more about this than I do, so if what I said was wrong, please correct me. My biggest argument here is that nothing is essentially "vertically" evolved- during the interaction between diseases and humanity, the disease never gets any closer to being anything but a virus, bacteria, etc., and the human never gets any closer to being anything other than a human...

If you want to read more about possible limits to evolution, you could read this page... LImits to Evolvability: The Misuse of Artificial Selection - Apologetics - Apologetics
The ideas that I've writen in my posts are my own, but this site describes similar ideas, and from a more educated background as well, including a bit about bacteria, etc. I would be especially interested to hear your response to the few paragraphs about bacterial adaptation. He seems to be telling me one thing, while you are telling me another. And you're both more educated than me! Of course he has a world view, as do I, as do you, which complicates things... (Note: It is on a Christian website, and I'm not sure what else is on the site... )

Speaking of world views... I'd like to pose a question again that I have been asking the whole way through this thread. It doesn't directly relate to evolution, but I think it gets at the heart of how world view is affecting our interpretations: How do you explain the non-entropy found in the universe? (And now I am talking 2nd Law proper) A "modern scientist" must assume that the universe is capable of producing non-entropy, but isn't this (whether a correct assumtion or not) essentially a belief that, at least for now, contradicts the observable universe- as described in the 2nd Law of Thermodynamics? And wouldn't it be reasonable for the honest scientist to at least acknowledge that this is a problem, even if they still believe it? Honestly, I think that there are, at least on some level, intrinsic difficulties within any world view that is examined, so I don't grudge anyone the right to believe in a natural-only universe, but let's at least acknowledge that it is a belief, not science.

Just to summarize a few beliefs that I think evolutionists cling to out of their (maybe subconscious) commitment to naturalism:
-Non-entropy in the physical universe exists because the universe is capable of producing it, in spite of all of the observations that lead to the 2nd Law.
-Nature is capable of producing complex life because complex life exists.
-There is never anything "new", everything slowly evolves from some previous form.
-Naturalistic science is credible, anything else is psuedo-science.
-A natural explanation for life (and the universe) exists, so the best naturalist guess is indeed the best guess.
-The supernatural does not exist, therefore nothing can point to its existance.

Well... If you've read this far- Thanks! And please let me know what you think. It's too bad I can't discuss bacteria, etc. on your level, but I'm enjoying hearing your insights about it. The sickle cell history is very intersting... And your comment on the slime molds (where single cells produce a multi-cellular organism) was intersting as well. I honestly don't know much about them, and anything you'd like to add on these subjects I'd be happy to read.

PS- I'm assuming the site from the link in your signature show pictures that you've taken? Some very neat photography there IMO!

[Aedes]

Hey Luke,
Welcome back and glad you like my photography -- my other pastime My avatar is a shot I took on 4x5" large format infrared film at a cemetary in Cambridge, MA.

In short form, here's my logical problem:
Natural Selection + Lots of Time = Decay"

Your logical problem here is based on several huge misconceptions.

1. Natural selection is NOT the mechanism of evolution!!!!!
The mechanism of evolution is genetic change!!! Genetic change happens in MANY ways, far more than is worth getting into, but these include novel genotypes (from nonsynonymous mutations), acquisition of new genetic material through gene duplication or conjugation or genetic crossover events, and the MOST IMPORTANT mechanism of genetic change, which quite simply is nonrandom mating -- i.e. breeding!! Even excluding factors like mutations, the mating of two humans who each have two copies of 23 chromosomes, will produce more than 70 trillion possible genetic combinations.

So you are very much in error by starting this process with natural selection. This process starts with generation of genetic diversity, which is naturally generated with every single new offspring. Selection is one of several mechanisms by which novel genotypes become more or less common over time.

Your second misconception regards the nature of time with respect to selection. Time is time. Selective factors change over time, though -- the planet heats up, cools down, populations become isolated or exposed to new diseases, etc. And previously advantageous traits will be selected out if they become disadvantageous under newer conditions. So time doesn't exert some kind of homogeneous force on traits -- this is a constant process of genetically encoded biological adaptation in response to changing ambient conditions.

Your third part of this equation, decay, is based solely on your logical process and neglects evidence. Our DNA is COMPLETELY AND TOTALLY FILLED with evolutionary junk. Only a small minority of our DNA actually has any kind of genetic function. We have dead genes everywhere, genes whose product has a predicted structure and function, but the genes don't even have a functioning promoter.

If that weren't enough, our embryogenesis very closely reflects our genetic lineage. Our embryos are nearly identical to other mammals until they diverge later in embryogenesis -- which is completely consistent with the fact that it's more terminally differentiated phenotypes that are subject to selection. In other words, things like our size and shape and diet are selected, but not whether we use O2 as our terminal electron receptor in aerobic metabolism.

And finally, we DO have biological junk. We have pinky toes, spinous processes, an appendix, a pineal gland, wisdom teeth, and hair on our head whose biological necessity is dubious.

There are some (and I think uncountable) instances where organs, appendages, designs, etc. must have a specific "begining".

Just because we don't know all of this doesn't mean it's false. This is observational research, and we cannot know everything.

But for organs you need to look at common embryogenesis. Our nervous system is a tad different than that of, say, eels. And yet we all, in early embryogenesis, form a neural tube out of ectoderm. Our structures -- and that of EVERY other chordate, diverge later in embryonic development.

For organelles, many of them have very traceable origins. It's known beyond any reasonable doubt that some organelles like mitochondria, chloroplasts, and other plastids (like the apicoplasts in malaria and toxoplasma) are the evolutionary successors to endosymbiotic bacteria. Why? Because these organelles have their own DNA and their own ribosomes, and they are structurally and genetically more similar to prokaryotic chromosomes and ribosomes than to eukaryotic ones.

As for others, I don't know the field well enough to cite you evidence verbatim. But does it matter? The whole point of science is that we don't know everything -- we just keep looking until the answers become more clear. So if we don't know when the first histone proteins existed, that doesn't mean they didn't evolve -- it only means we don't know.

When did the first hair appear? An evolutionist (AFAIK) must say that the "first" hair never existed, it simply evolved from something else that resembled a hair (like a flagella or something). But a hair is different from anything that is not a hair

This is a word game. Forget the word hair. All we know (as far as I know) is that hair is common to mammals, and our ability to study both the genetics and soft tissues of fossilized animals is extremely limited. So for some things we may be stuck saying that the first small mammals appeared in fossils from the X period (triassic or cretaceous or whatever) and these are regarded as mammals because of their anatomical and structural similarity to all subsequent mammals. Just like the archaeopteryx. This was the first bird. It was basically a flying lizard with feathers, and it had teeth in its beak -- it's one of evolution's great 'missing link' stories.

I must ask, does the idea that nothing is new- that nothing requires a "jump" to be a significant improvement- is that idea based on observation, logic, and science? Or is a necessary assumtion in order to believe the bigger story?

The idea that nothing is new is something that seems to be your own invention. It's wholly unsupported by science / observation. Whether it's based in logic or not is irrelevant, because logic in science is useless once it's countered by observation. If you study punctuated equilibrium, you'll find that there actually are huge, abrupt genetic changes historically, and they tend to happen during times of extreme selection when populations become numerically limited, isolated, and are under such pressure that genetic sweeps occur.

My biggest argument here is that nothing is essentially "vertically" evolved- during the interaction between diseases and humanity, the disease never gets any closer to being anything but a virus, bacteria, etc., and the human never gets any closer to being anything other than a human...

You're wrong here. You're just looking at a time scale that's far too short. The sickle cell story takes place over about 10,000 years. Humans and chimpanzees shared a common ancestor more than 5 million years ago. When humans acquire new genotypes, like the several that are alone in response to malaria, they become genetically different than their ancestry. They still may fit the classical definition of a species -- but they are constantly changing, and with enough acquired genetic changes over 2 million years our progeny may indeed be something that would not fit our current definition of what constitutes a human.

As for viruses, they are not even alive so it's hard to talk about them in terms of evolving into something else. But they are genetically encoded and they do evolve. Which is why we have 8 human herpesviruses that are uniquely adapted to different tissues in the human body, and human herpesvirus 4 (Epstein-Barr virus) has even picked up the human gene for the IL-6 receptor -- in other words, the virus has picked up the human gene for a receptor that promotes the growth of the very cell it infects. Pretty crafty, huh? So EBV infects B-cells, expresses the IL-6 receptor, so that B-cells proliferate more rapidly in response to IL-6.

How do you explain the non-entropy found in the universe? (And now I am talking 2nd Law proper) A "modern scientist" must assume that the universe is capable of producing non-entropy, but isn't this (whether a correct assumtion or not) essentially a belief that, at least for now, contradicts the observable universe- as described in the 2nd Law of Thermodynamics? And wouldn't it be reasonable for the honest scientist to at least acknowledge that this is a problem, even if they still believe it? Honestly, I think that there are, at least on some level, intrinsic difficulties within any world view that is examined, so I don't grudge anyone the right to believe in a natural-only universe, but let's at least acknowledge that it is a belief, not science.

I don't explain this. I'm a physician. I am not an expert in thermodynamics. But all science is subject to revision; and thermodynamics, which is a very young science, certainly is. Science is based on acquiring new observations and explaining how they most likely fit together. That's why any mechanical inconsistencies must be further researched -- but they don't bring down the whole superstructure. I DON'T acknowledge that it's a belief -- it may be the best explanation for the data we have, or the best explanation produced by the scientists who have taken an interest in it, but that doesn't make it a hollow, unverifiable belief (whereas belief in Ra the sun god, or in the oracle at Delphi are unverifiable in that they won't stand up to any empirical scrutiny).

Just to summarize a few beliefs that I think evolutionists cling to out of their (maybe subconscious) commitment to naturalism:
-Non-entropy in the physical universe exists because the universe is capable of producing it, in spite of all of the observations that lead to the 2nd Law.
-Nature is capable of producing complex life because complex life exists.
-There is never anything "new", everything slowly evolves from some previous form.
-Naturalistic science is credible, anything else is psuedo-science.
-A natural explanation for life (and the universe) exists, so the best naturalist guess is indeed the best guess.
-The supernatural does not exist, therefore nothing can point to its existance.

One by one:
1) Evolutionists don't study entropy. It's not their science. It doesn't confront them. It's a non-issue. The observations generated by evolutionary biology stand firm on their own whatever physicists decide about heat and energy.

2) Complex life exists. Common ancestry is easily observable by many methodologies. Life has gone through many periods of diversification and then contraction. Life became very simple after the Permian extinction, then diversified again. It became comparatively simple after the dinosaurs became extinct, then diversified again. And the farther back we look, the more simple and the more ancestral life is. This just is what it is. And the more you trust the data, the more this leads to the conclusion (NOT assumption) that complex life arose through an evolutionary process.

3)You keep saying this. It just doesn't make any sense. I am new, because I'm a genetically unique being that was one of 70 trillion possible genetic combinations of my parents' chromosomes. Every mutation is new. Every offspring is new. Every generation is new. And each of these instances adds new genetic diversity.

4)You say this out of sensitivity. It's not something that needs to enter into anyone's consciousness. Science is a process. The discipline of history is also a science -- a social science, because it's based on data. The study of religion is also a social science, because it seeks to understand religion in its historical and cultural context.

Explanations of the natural world that are not based on observation are, quite simply, not based on observation -- so why, pray tell, should we believe that life must have been created by an intelligent designer? What if I believe that the earth must have been crapped from the ass of a cosmic elephant, and I provide an intricate explanation of how that explains the complexity of life? How is that any less valid than intelligent design? What they share is their lack of verifiability in observation. And you know what, I like the idea of being crapped from the ass of a giant elephant, because in the real world I tend to see more elephant crap than I do intelligence

5) We learn about the world through observation. We explain our observations. That's it. The "naturalistic explanation" is the one that best fits our empiric observations. The intelligent design, flying spaghetti monster, elephant crap, or anything else don't fit empirical observations because they refuse to change themselves in the face of what we observe!!!!

6) Whether or not the supernatural exists is immaterial to science. There can be witches and ghosts and devils for all I care. But how exactly does that affect the way I interpret genetics? You say God designed our DNA (including all the nonfunctional crap in our DNA and our error-prone DNA polymerase), I say that our DNA is a tiny strand of cellulose from undigested grass in the crap-ball of the great cosmic elephant, may his hairy trunk be forever exalted.

I don't mean to demean religious beliefs. But they are simply not part of explaining things one observes. You want to do good science, then you have to ground yourself in observable data. If you infuse it with supernatural or metaphysical ideas, then it's no longer science. Better or worse? Just depends on your intellectual priorities.

Paul

[NeitherExtreme]

Hi again!

I do like that picture (your avatar), and I found it in its full size version. I also like the B&W inside cathedral pictures. And for whatever reason, I really like the Spare Change picture- even though I hate pennies!

First, I’m not offended or feel that my beliefs have been demeaned. (In fact some of those ideas were rather funny, though I might think that some of them apply better to evolution science…)

Also, thanks for the responses so far, and the obvious time and thought put into your reasoning and examples. That said, your previous post (while interesting) didn’t answer the questions I’ve raised for various reasons IMO. But… Instead of responding to each point (which takes a lot of time for both of us), I’m going to try to just get to the heart of the issue as I see it. (But if you do want to discuss any specifics further, I’ll gladly return to them.) Before I do though, I do want to point out that my logical argument against evolution is not that it didn't happen, but that nature couldn't have made life, and that if life does evolve ("vertically" as I called it), it couldn't have gotten that ability by chance... But I'm digressing already.

My real complaint all along has been that evolution science (and maybe a lot more of modern society and science) is based on an assumed naturalistic world view. And I don’t feel like you’ve understood what I’m saying, though I’ll take some of the blame for that since I don’t think I’ve been as coherent on this point as I could have been. Realizing the biases of our own world view is a tricky thing; and I’ve made too many arguments on this thread based on my theism to pretend it’s all your fault…

Anyhow, whether your fault or mine, your posts have been full of demonstrations of my argument. And yes, the conclusions you come to seem to you (and most of the scientific community) to be self-evident and fully justified, but that is the very nature of unexamined world views... Obviously I can’t say with certainty that your conclusions are wrong, but I do feel confident in saying that a lot of your arguments have been based on naturalism.

I’m not going to go back and try to point out each case but here’s IMO a very telling example:

“Whether or not the supernatural exists is immaterial to science”

If you can’t or won’t see that the premise of this sentence is a naturalist world view, then I’m not sure we have much hope of understanding each other on this subject. If (please remove your all-natural glasses for a moment) the supernatural does exist, and there are things in our universe for with the supernatural is the only good explanation, then we would adopt a certain humility about what we assume is a “good enough guess” to be considered scientific. And if we hold the neutral world view that the supernatural could exist, we should approach science with that same humility, even if it would never be science’s place to use the supernatural as an explanation.

Also, your willingness to simply shrug off the problem I raise about the universe being a closed system (and the 2nd Law), leaves me with very little trust in your neutrality. The problem is as much based on observation and science as anything that you have presented. And its not a little problem either- it’s based on one of the fundamental understandings of science and applying it to the whole structure of the naturalist world view (the physical universe). To be able to disregard such a problem so easily is mind-boggling to me, and I honestly don’t think that I would be able to do the same thing in your position. (And certainly hope that I wouldn’t.) Please don’t take that offensively, and I’ll give a personal example of what I mean (if you want to read through it):

My world view (personally, not scientifically) has at its center has the idea of an all-good, all-powerful, all-knowing God. (The basic premise of Theism) Now, let’s say someone asks me seriously how such a God could create a world that included all of the evil that we see. Let’s say I responded by saying “What do you mean, I don’t see the problem”, “Don’t ask me, I’m not a theologian”, or “That’s your own problem if you’re not intellectually satisfied”, yet still expected them to believe that my premise is true. That would make me feel like a hypocrite... It’s a big problem, and once raised, it ought to be addressed. If I had no answer, and didn’t even show an interest in helping them find an answer, then I don’t think I have any reason to expect them to take my world view seriously. As it is, I spent years (and lost a lot of sleep) fighting with myself over that very question, until I eventually was able to come to grips with it and accept it with peace. And even now I still wouldn’t tell anyone that it isn’t a valid question or even a mind and heart wrenching problem, but I am happy to talk through it with anyone who is interested. (This is not to say that a person needs to have a perfect answer for every possible problem, it is just to say that serious problems should be taken seriously.)

So part of my point is that to openly acknowledge the problems with one’s own world view (or scientific view), and to treat them as serious and important, even to the point of putting their own world view on the line, is to me a sign of self-awareness and of an ability and willingness to examine their own world view (and it’s biases) from a neutral standpoint. (At least as neutral as a person can get…)

It is this neutrality and self-awareness that I find lacking in modern science.

[Aedes]

Luke,

The Spare Change photo was a life-sized macro picture that I took with black and white film; I then printed the picture in the darkroom and toned it with a selenium solution, which turns the silver halide in the printing paper that kind of copper color. I have a photo of how I set up the shot if you're interested.
____________________

I'll try to address what I see as the fundamental problems in this conversation. And while I may seem a bit harsh here, realize that I'm not critiquing you as a person or as a conversationalist, but rather critiquing your general approach to this subject. You've been very patient with me as we've been talking both at and past one another, so I hope you'll read this with the right frame of mind.

We know that you're approaching this subject from the standpoint of theism, but rather than critiquing evolu