Evolution Science and Naturalism

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'.


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.


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.

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 :p ) 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.

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.


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?


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.


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.


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.

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.

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.


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.


Whoa -- that is absolutely NOT[/b] 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


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!


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.


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.


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.

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... :



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...



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.



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! :eek: 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!

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.


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.


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.


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.


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.


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.


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).


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

Whether or not the supernatural exists is immaterial to science"

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.
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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 evolution on the authentic grounds of your faith (something that I could easily accept on your behalf), you're engaging in a great deal of fallacy to try and poke holes in it in all sorts of ways from the outside.

And the problem is you're trapped in blindingly circular arguments. Anything I say that is derived from my career in science, you'll dismiss as biased -- but you do this without taking the initiative to learn science on its own grounds (and with all due respect to your interest in the subject, your scientific understanding of both evolution and thermodynamics is very limited, more or less at a high school or very limited college level, whereas I am in my 8th postdoctoral year in medicine -- so our training in scientific process and vocabulary are extremely different). And you do this without acknowledging your own bias, which is a theistic vantage point that is permanently dubious about evolution and therefore MUST assume that evolution has some kind of fatal flaw.

Your rhetorical skills are excellent. But that's not the crux of the matter. Science isn't won or lost by skills in argument or logic -- it comes down to method and data. And you haven't once in this thread demonstrated that you understand this fundamental fact about what science is.
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1. You want to impose the importance of the supernatural on science, and you accuse scientists of being biased against it. Well, no ****. Science is the domain of the natural. Science has no access to the supernatural, so it doesn't consider it. If science did have access to it it wouldn't be supernatural.

In other words, you're bemoaning science's lack of attention to things that BY DEFINITION it cannot address. It's like bemoaning a blind person for not appreciating paintings.

And that's why the supernatural is entirely and completely immaterial to scientific inquiry and speculation. Is there a God? Maybe, maybe not, but that question is outside the scope of science. Did God have a guiding hand in life as we scientifically observe it? Only if you believe it without scientific evidence, because it cannot be scientifically demonstrated.

This is not to say that all that's important in life boils down to what's scientifically demonstrable -- but science doesn't make that claim either. (Whether or not some individual scientists do is irrelevant). For instance, while in this thread I've been going to bat for science, that doesn't change the fact that art, literature, photography, and spirituality (in a somewhat non-orthodox way) are quite important to me as a human.

Science is how we understand the natural world through observation and experiment -- and the natural world is exceptionally complex and all around us. If theological or (generically) supernatural questions arise, that is the domain of something other than science.

And as for what we consider to be truth or reality, well, that sort of depends on your individual standards. But if you're going to impune science as not giving us access to truth, then you can't be selective -- you need to throw out ALL of science, not just evolution.
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2. You're basing your argument on a specious contention of "naturalistic bias". This is about as ridiculous as accusing the Pope of having a "Catholic bias". Science (natural science, that is, i.e. not social science or economics, etc) is a wholly naturalistic enterprise, so when it operates within itself there is no bias towards natural explanations -- because science is a process that only has access to natural explanations. If science were so dumb as to invoke supernatural things, it would no longer be science. So you cannot have it both ways -- if you want there to be such a thing as science, then it HAS to be the domain of the natural.

Science is based on a methodology, the data it produces, and the conclusions drawn from the data. If you have a problem with that data, then by all means go to it and critique it on its own merits -- there are good papers and bad papers out there. But for you to impune the findings of science for having a "naturalistic bias" does not even remotely address the merits of the findings it generates. Bias needs to be shown, not alleged, and it's usually pretty obvious in the results and methods of a paper when present.

And as for bias in science outside of research communications, like speculative statements about how life began, these are merely hypotheses that both tie together past research and propose new research. If you want to hypothesize in a scientific forum that God created the earth, by all means go and do it -- but you'd best have your study protocol ready to show how you're going to demonstrate it.
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3. You're using logic to criticize a natural science. Sorry, but this has neither logical nor scientific merit. Without going to the scientific arguments themselves, and by this I mean the actual scientific literature, your logic doesn't even have access to what the science is. And by actual scientific literature, I'm not talking about Wikipedia here. I'm talking about scientific journals.

Your incredulity that life can arise from nature does not make that theory any more or less true. But it certainly bespeaks your willingness to accept science solely based on whether or not it conflicts with your faith. And this makes the problem an issue of your vantage point, not of the science itself.
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4. Your problem with entropy has NOTHING, ZERO, ZILCH, NADA to do with evolution. These are SEPARATE areas of research that DO NOT DEPEND ON ONE ANOTHER.

I'm not saying that there are no underlying thermodynamic principles that pertain to evolution like anything else. I'm saying that thermodynamics research is a much less mature, much less practical field that can only be understood in highly simplified terms, it's got gross limitations, and any inconsistencies within the field of thermodynamics bespeak only its immaturity or lack of generalizability as a science. Thermodynamics cannot model evolution-level processes, and therefore it's almost entirely useless outside the tiny microscopic sphere of the individual chemical reaction, or in practical terms large scale but very simple processes like the catalytic converter or a power plant.

Furthermore, with more of an understanding of both thermodynamics and biology, you'd know that a certain amount of energy is lost just from the cleavage of an ATP molecule (the main energy-producing reaction in any metabolically active cell -- from bacteria up to humans), and this is ENTIRELY and COMPLETELY CONSISTENT with entropy. And you'd know that the mechanism of evolution is genetic change, which at the molecular level ALWAYS loses energy, which is part and parcel of entropic theory.

By the way, the issue with entropy in a closed system is because that's the only way it's measurable. How's that for a limited science?

And as for the universe being a closed system, who cares? This is something that can only be theorized, and it's thermodynamic theory that has to accomodate a changing view of the universe, not evolution which provides the same data irrespective of what we think about the universe as a whole.

Finally, keep in mind here that I have studied thermodynamics -- I took a grueling, horrific 300-level physical chemistry class in thermodynamics as an undergraduate for my undergraduate degree (which was in biochemistry), and it comes up in some applied contexts in clinical medicine as well.
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5. You're concerned that the evolutionary record is incomplete, and hasn't shown that life can be generated de novo. Well, welcome to science. It's all incomplete. You're just being selective in deciding which field's incompleteness bothers you the most. Thermodynamics is incomplete considering that the whole proposition of the universe being an open or closed system is based on non-experimental theoretical astrophysics.

I'm sure you're familiar with string theory, which is the attempt to mathematically unify gravitation, electromagnetism, and the strong and weak nuclear forces. Well, no one has done this convincingly yet, and it's being attempted with such bizarre leaps of mathematics that one wonders whether these efforts will constitute anything beyond a rational mathematical statement that is not physically demonstrable. So here, in 2008 now, we do not yet have a way of making gravity physically coherent with thermodynamics. So which one would you like to throw out? It seems that you're more convinced about thermodynamics than evolution, so would you like to throw out gravity? Or if you're going to hold onto gravity and throw out thermodynamics, does that mean that evolution is ok after all? And what about the fact that macroeconomics, which is a science, has not been unified with thermodynamics either? Does that mean that the falling housing market in the United States is physically impossible?
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I find these arguments you've offered to be quite inauthentic, because you've somehow convinced yourself that you're truly taking on the meat of the matter with evolutionary biology. But you're not, not by any stretch, and this is because you just don't understand how your limited background in evolution, thermodynamics, the scientific method, and the culture of science make it impossible for you to raise a scientifically sound critique. Just as I cannot formally take down Wittgenstein or Kant without a formal background in philosophy, and I cannot critique a symphony without a formal background in music theory. Give me 2 minutes and I'll find you a scientific article that I can critique -- it's what we learn when we study science -- journal critique is a central part of science education. But again, you're NOT critiquing the science, you only THINK you are.

So who are you to raise these critiques, then? You're a very bright and articulate theist who WANTS to find a problem with evolution -- and you're not acknowledging this bias that hits you from the very start.

And that's why I contend that you're not being true to yourself here, nor are you even being true to your faith. If you were being true to your faith, you wouldn't pick and choose when to make faith-based arguments and when to make science-based arguments. You could say "Evolutionary biologists can do whatever the hell they want, they can do an experiment that generates life for all I care and show it's the world's best proof of thermodynamics. But God still had a hand in it, whether or not they can prove it. Period." THAT would be authentic. Or you could say, as some do, "The spiritual world supercedes the physical world. Thus, the physical can deceive us and anything scientists generate can be doubted." Again, this is a position of faith that doesn't try to take a scientific point of view.

And if you find anything lacking in modern science, it's not by virtue of your extensive exposure to it. You're observing it from outside, not from within. Science is very microscopic, very methodologic, very mechanical, and very descriptive. So for you to critique its ultrastructure is almost meaningless unless you've extensively explored its workings.
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So here is an opportunity for you to take on science at its own level. Here are some really cool evolutionary biology studies that I want you to critique -- not object to on some loose idealistic grounds, but really critique. The abstract will give you an introduction, but you need to concentrate on the methods and the results, which are the meat and bones of science. In this journal (PLoS - the Public Library of Science) -- the methods are placed towards the end of the paper.

Incidentally, if you do nothing other than read the fantastic introduction to this first paper, you'll see how evolutionary biology is constantly revising itself as new things are discovered. And you'll also see how conclusions are grounded in data and are weighted by the strength of the data.

PLoS ONE: Homeotic Evolution in the Mammalia: Diversification of Therian Axial Seriation and the Morphogenetic Basis of Human Origins

PLoS ONE: The Evolution of Mammalian Gene Families

PLoS Genetics - Adaptive Evolution of Conserved Noncoding Elements in Mammals

And a critique of any scientific study goes as following: 1) what was the research question or hypothesis? 2) were the methods sound? 3) are the results fully reported? 4) what are the implications of this study in the context of the scientific literature? 5) are the conclusions applicable to sample sets outside this study?

Paul

A multiple exposure, on film, of flights taking off from Logan Airport in Boston.

First, I've been honored to have a debate like this with someone who is much more educated than I, and that you would take me seriously enough to give me the quality of responses that you have. Your qualifications in science are both impressive and far, far beyond my own. :eek:

At the same time, I'm sure you've realized that for me this comes down to examining world views as much as science (though science is obviously still important). I'd be interested to know if you've spent any time studying world views and cultures and how they affect a person, group, culture, or society, or if you have had significant cross culture experience that forced you to examine world views not only of others, but also of yourself?

I also thank you for the compliment about my rhetorical skills, but unfortunately I feel like I have to disagree, as I feel like I've done a poor job throughout at expressing what I want to, while at the same time muddying everything up by going on a wild goose trying to "disprove" evolution and "prove" supernatural involvement, simply because that is my "best guess". As I look back, even to my first post, I realize that I have made one argument after another based on the idea that the supernatural has affected the development of the universe, and I regret that for two major reasons. First, because such arguments are not inherently scientific, and you justifiably disregard them as science. Second, because it makes it very unclear when my arguments could actually be coming from a neutral view. If those arguments have any usefulness whatsoever in this discussion, it would only be to demonstrate that conclusions that appear self-evident in from one world view might be self-contradicting from another world view, and vice versa, even thought the information used by both was the same. That said, I still wish I would have avoided going that direction at all.



And I want to point out again that I'm by no means saying that science should use the supernatural as an explanation, but I think a healthy dose of "we don't know" or "it doesn't make sense yet" would do science a lot of good, and lend it a lot more credibility in my eyes. Anyone may disagree, and I understand that from your perspective the "not know" parts seem very small and the "known" parts seem overwhelmingly convincing, but of course from my perspective I would disagree with you. And yes from your point of view my opinions would appear to be based on a very limited amount of knowledge and a lot of trust in logic, but, nonetheless, they are what I'm seeing from here. Of course this is in general an observation from the "outside", and you have every right to agree or disagree with it. But, just as a side thought, sometimes it is people on the "outside" of a system that can see more clearly what would be very difficult to see from the "inside". And IMO, this is very often the case when world views are involved.

Of course, I realize that I have my own biases, and this discussion with you and others has helped me to see where some of them have/had influenced the way I was thinking about the subject. And honestly, that was part of my hope in this thread (and joining this forum in general) that by placing my thoughts at the mercy of other world views I would be able to learn and better understand my own world view and its biases.

But after all this, I still bring my (personal) observation that there seem to be problems and gaps big enough that the naturalist scenario painted by modern society and science is not close to being "self evident" or authoritative unless the naturalist world view is already assumed. Of course I haven't been able to prove that to you, and your responses haven't shown it to be false to me.



First, I have previously agreed and do so again that the 2nd Law of thermodynamics (and its technical definition of entropy) have nothing to do with evolution. When I bring it up I am discussing the universe as a whole, not evolution, with the purpose of seeing if a naturalist world view is at play. I realize that you don't find this appropriate, but it is of interest and significance to me.

Your objection to using logic to examine science is confusing to me. If you'll forgive me, I will once again use a crude analogy to explain my dilemma: Suppose a magician shows you a hat, you examine it and find nothing abnormal. He takes the hat, steps a few paces back, and proceeds to pull a rabbit out of the hat. He claims that his hat makes rabbits. Would you believe him based on your observation that a rabbit came out of his hat? Or would you look for hidden compartments, mirrors, empty space in his sleeve, and anything else that could explain how it happened? And if you never figured out the trick, would you assume that his hat really did make rabbits? No, because logic tells you that hats don't make rabbits. So why does logic have no bearing on our interpretation of evidence? Am I not understanding your argument? :confused:

Darwin

But isn't that in essence what science is doing if it assumes that there must be a natural answer (a closed naturalist system) to every problem? Again, not that they should assume the supernatural either, but if there was the question of whether or not a natural explanation exists, I think science would take a different posture altogether when it decides what theories are authoritative or not, as every theory would have to pass a certain amount of logical plausibility, not simply be the "best guess" (no matter how developed it is).



But finally, for one last twist:

If, in fact, I have defined science wrongly to include the notion of an unbiased world view- one that allows for all things logically possible, even those that science might not be able to explore- and that science is justified in assuming a natural answer for everything, no matter how problematic, then I withdraw my complaint entirely. Of course that would leave the possibility that science could come to many conclusions (and assume them to be authoritative) that could be far removed from reality. I would also have a much diminished view of science's ability or interest in truthfulness, but nevertheless, all of my complaints would be inconsequential.

Here are links for the pictures:

Here is Spare Change again:
http://www.pbase.com/drpablo74/image/72879049.jpg

This is the setup for Spare Change:
http://www.pbase.com/drpablo74/image/72879911.jpg

This shows the setup better. This is Blue Rose (also done entirely in a traditional chemical darkroom, including the blue tone):
http://www.pbase.com/drpablo74/image/72086028.jpg

And here is the setup including the camera, which uses 4x5" film.
http://www.pbase.com/drpablo74/image/72082732.jpg

[quote]First, I've been honored to have a debate like this with someone who is much more educated than I, and that you would take me seriously enough to give me the quality of responses that you have. Your qualifications in science are both impressive and far, far beyond my own. :eek:[/quote]
It's been my pleasure to participate. As you are experiencing, science has implications outside of science, because it penetrates into our view of ourselves and our world. Maybe it's that I do a lot of teaching, or that I'm in clinical medicine in which I interact with patients who are not educated in science or medicine all the time -- but it would be a foolish scientist who only takes colleagues seriously!

[quote]At the same time, I'm sure you've realized that for me this comes down to examining world views as much as science (though science is obviously still important). I'd be interested to know if you've spent any time studying world views and cultures and how they affect a person, group, culture, or society, or if you have had significant cross culture experience that forced you to examine world views not only of others, but also of yourself?[/quote]
I'm a first generation American, all of my grandparents are / were Holocaust survivors, and my two living grandparents are quite conservative Jews (and used to be orthodox). I've done medical work in four African countries, in the Amazon, with Native Alaskans, and with immigrants/refugees from all over the globe. I spent three years as a post-doctoral fellow at Harvard in infectious diseases and tropical medicine, and my areas of academic subspecialization are AIDS and tropical diseases. So I am constantly taking care of people from other countries and cultures, and I collaborate with many African researchers and physicians. I speak Spanish and French and a tiny bit of Twi (from Ghana). Furthermore, I love learning about the societies that I'm exposed to, and I've read a lot of epic literature from some of the ancient West African civilizations. I've had a lot of exposure to Islam in my time in Senegal and Gambia, and I've done some studying of Hinduism and Buddhism (Japanese Buddhism especially after visiting about 8000 Zen and Shinto temples during a week-long visit to Kyoto a few years ago). I collect ethnographic artwork (I have around 50 African sculptures, masks, textiles, musical instruments). So in summary, I completely immerse myself in other cultures, and I merge them with my own views of myself. And that's part of the reason I'm here.

I don't let these other facets of my life "contaminate" science, which in pure form takes shape on its own terms, but when I go in the other direction -- by applying science to human life (i.e. medicine), I must find ways to make things logically understandable to patients. Sometimes this is as simple as sitting down when I talk to them so that they don't get a sense of how busy I am. Sometimes it means printing out articles for them and translating them into lay terms. And often it's catering my therapeutic approach (when possible) to their fears and priorities.

At any rate, what is your background?

[quote]First, because such arguments are not inherently scientific, and you justifiably disregard them as science.[/quote]
THIS is what I'm looking for in authenticity. It's ok to believe (unempirically) in the supernatural, and to criticize the cultural role of science in that context. But it doesn't make sense to criticize science itself for not taking responsibility for supernatural propositions. Probably 99% or more of the people in our country believe in science to some extent or another -- because it's just so self-evident in the things we invent and the things we describe. But 90% believe in God. So the two are not culturally mutually exclusive, and whether or not they can be rationally unified doesn't make them incongruous in the individual minds of many people.

[quote]conclusions that appear self-evident in from one world view might be self-contradicting from another world view, and vice versa, even thought the information used by both was the same. That said, I still wish I would have avoided going that direction at all. [/quote]
No need to regret this -- because by virtue of our discussion you're going to undergo some process of refining the way you organize or express your ideas the next time this comes up for you! That's why this discursive process is so useful.


[quote]And I want to point out again that I'm by no means saying that science should use the supernatural as an explanation, but I think a healthy dose of "we don't know" or "it doesn't make sense yet" would do science a lot of good, and lend it a lot more credibility in my eyes. Anyone may disagree, and I understand that from your perspective the "not know" parts seem very small and the "known" parts seem overwhelmingly convincing, but of course from my perspective I would disagree with you.[/quote]
This is what I meant by the difficult position you're in when you're outside of science. Science is FULL of "we don't know" or "it doesn't make sense yet". We see it, think it, and talk about it EVERYWHERE. And what we don't know is far greater than what we do -- in fact we don't know what we don't know. Think about how paradigm shifts and major discoveries in science open up whole new lines of research inquiry that weren't even anticipated beforehand. But the reason you feel obligated to make a point of this, and the reason you think science is arrogant about it, is simply that the mainstream reporting of science to laypeople is heavily weighted towards new discoveries. Unknowns and great areas of research do come up, but only in terms of scientific promise-- what are scientists working on next -- not in terms of scientific unknowns.

[quote]But after all this, I still bring my (personal) observation that there seem to be problems and gaps big enough that the naturalist scenario painted by modern society and science is not close to being "self evident" or authoritative unless the naturalist world view is already assumed. Of course I haven't been able to prove that to you, and your responses haven't shown it to be false to me.[/quote]
What you call the "naturalist world view" is turning into a sort of targeted label for you. So I need you to step away from that terminology for a second. What you're describing as such, or as a "naturalistic bias", is a viewpoint that has been espoused since Aristotle -- that we can learn about the world by observing it. Science has gotten very abstract and complicated, at least from a lay vantage point. But this emphasis on observation IS self-evident. You know that you cannot walk through walls because of life experience with walking and with walls -- this is simple observational science. And we know that gravitational force is independent of mass because we observe that a 1 ounce marble and a 10 pound rock will hit the ground at the same time. And all of experimental science, while methodologically intricate, is still doing the same thing. This is not a worldview -- this is simply a process of learning about the world by making controlled observations -- and it's part of being a rational human with many (more than 5!!) senses.

[quote]First, I have previously agreed and do so again that the 2nd Law of thermodynamics (and its technical definition of entropy) have nothing to do with evolution. When I bring it up I am discussing the universe as a whole, not evolution, with the purpose of seeing if a naturalist world view is at play. I realize that you don't find this appropriate, but it is of interest and significance to me.[/quote]
Well, if you're discussing the universe as a whole, you come upon two problems. First, evolution is one of a million scientific propositions and areas of study (and it's heterogeneous unto itself!) that will fall under the rubric of the universe. So any conclusion you draw about the nature of the universe will affect mechanics, marine biology, geology, and meteorology just as much as it will evolution.

Secondly, it's impossible to be an expert in all sciences at once. So while I know a lot about evolution, I don't know a lot about astrophysics or the origins of the universe. There may be objective truth out there that can scientifically place evolution within every other scientific principle. But that doesn't mean that the scientific disciplines need to be consistent with one another (yet), nor does it mean that an evolutionary scientist or a volcanic geologist need to concern themselves with what astrophysicists are talking about. It's sort of incidental.

[quote]Your objection to using logic to examine science is confusing to me... So why does logic have no bearing on our interpretation of evidence? Am I not understanding your argument? :confused: [/quote]
Yeah, you've missed the point I'm making. My objection is to using logic to critique a science from outside. Any scientific theory is based on a mountain of supportive data. So you aren't going to bring down that theory with logic unless you go to the data proper and show how either the data are flawed or there is a more parsimonious conclusion.

This is exactly how Einstein brought down previous physics. Rather than making a logical, ultrastructural argument about how the "ether" was incorrect, he looked at all the flaws and inconsistencies in that field and created a theory (that he later demonstrated mathematically) that tied all the observations together much more convincingly.

[quote]About the paper (first link): First, I think we both know that I'm not qualified to give a professional critique[/quote]
I know -- I wanted to accomplish a few things. First, to show you that evolutionary science is microscopic, and it's based on studies, not on overarching theories -- so flaws in evolution must be pointed out at the level of these studies. Secondly, to show that nowhere in the papers does a biased worldview appear, because the conclusions drawn are based on the data generated and by reference to other studies. Thirdly to show that it's really hard to penetrate the meat and bones of science as a layperson, so you need to be very careful about what you think you understand. And fourthly, to show how cool this research is on its own merits, irrespective of what the overarching theory states.

[quote]From what I could tell, the whole premise of the paper is that it did happen, that it happened naturally, and that all we have to do is understand it, and as such there is never an attempt to question, prove, or test the plausibility of that premise.[/quote]
Oh come on, that's not in the paper anywhere -- this is the same thing you've been saying all along, and you're now irrationally projecting it onto the paper because it fits your preexisting assumptions.

You need to start out this exercise by forgetting what you think you know and just starting from a clean slate. Don't make any assumptions about the author's viewpoints. Just operate from what he's written.

You're bright enough to go in there and look more specifically. So I'll give you one more chance -- do it with the first paper. Just tell me the following in the best terms you can:

1. What is the research question being asked? (you can get this from the title, practically)
2. What is the hypothesis?
3. What subjects were being studied?
4. What methods were used?
5. What data were generated?
6. What were the conclusions in the context of other science?

All of this is there, and even if you don't understand a lot of it you can definitely identify it.


See again, your eyes take a quick glance at the paper and then wander up away into your preexisting conception. So stop that, dammit!! Just look at the paper and don't ask of it questions it doesn't address.

And by the way, there is no "genetic code for bone". It's a polygenic phenomenon that comes from the development of cells that are indeed of the same lineage of chondrocytes (cartilage cells), but that are capable of depositing hydroxyapatite (a calcium salt) that replaces a cartilage matrix with calcium. This requires a whole physiology that regulates calcium differently, that can produce osteoblasts and osteoclasts from common progenitor cells (osteoclasts are derived from a kind of white blood cell called monocytes), it requires mechanisms for these cells to develop within appropriate tissues in development. This doesn't necessarily require new genes, but it does require physiologically different regulatory mechanisms, mainly from levels of gene expression. And there is CLEAR evidence of where this occurred in evolution -- within the evolution of fish, because the ancestral fish were (and are) cartilaginous, but later fish species had bone.

But isn't that in essence what science is doing if it assumes that there must be a natural answer (a closed naturalist system) to every problem? [/quote]
I'm only disregarding the epistemological necessity that evolution and thermodynamics be unified, because they're both independent sciences that don't even look at the same questions -- and are therefore limited from one another. There can't be inconsistencies between them if they're not even asking the same questions. Their validity (in scientific terms) stands or falls based on their own internal merit.

[quote]Again, not that they should assume the supernatural either, but if there was the question of whether or not a natural explanation exists, I think science would take a different posture altogether when it decides what theories are authoritative or not, as every theory would have to pass a certain amount of logical plausibility, not simply be the "best guess" (no matter how developed it is).[/quote]
I don't see how any question of whether or not there is a natural explanation is the problem of science. Science's role in life is to look for natural explanations by looking at nature -- it's only in the natural world and never outside it. By saying this I'm not even tacitly acknowledging a supernatural (which I don't), but just saying that if there IS anything supernatural then it's by definition outside the viewpoint of science. Why? Because if something is independently observible or demonstrable, then it's amenable to any sort of controlled / scientific inquiry, and that sort of makes it not supernatural anymore. If something apparently supernatural yet observible like lightning or plagues or eclipses occurs, then its supernaturality kind of disintegrates once it becomes accessible to science.

[quote]if I can understand just enough to see why chance could not produce the net result of complex life, and that none of the evidence that's ever been presented seems to me to show otherwise, then the "boat" does have a few holes, it's already sunk.[/quote]
See, you have three enormous problems here that are rooted in your own assumptions.

1. Your conception of what CHANCE is. No one in evolution talks about life arising by chance. Life arose because the conditions allowed it, and the conditions allowed it because of the chemical and kinetic nature of the earth 3 billion years ago. That doesn't mean it was inevitable that life would arise, but then again it wasn't inevitable that you be conceived as opposed to 70 trillion alternative combinations of your parents' chromosomes.

2. Your conception of PROBABILITY. You CANNOT CONCEIVE of 3 billion years. You CANNOT CONCEIVE of the amount of chemical and energetic complexity that existed at the time. And you therefore CANNOT CONCEIVE of the number and complexity of chemical interactions that were constantly occurring.

Life exists almost completely because of carbon, hydrogen, oxygen, nitrogen, and phosphorus, which make up the near entirety of our organic molecules. These were highly abundant in the earth from the beginning.

It's already been shown in labs that starting from basic elementary chemicals you can produce organic (complex carbon-based) molecules just by bombarding it with energy. And this basically mimics the conditions of the earth before there was an atmosphere (so there was a lot of cosmic energy) and when the earth was far hotter than it is now.

Do you know what DNA is? It's basically a string of simple molecules -- it's a backbone of simple sugars strung together (deoxyribose in DNA, ribose in RNA, which is much less stable chemically and much more ancestral). The sugars are bound together by a simple phosphate ion (just PO4). And stuck to the sugars are one of four also simple molecules called purines or pyrimidines. These are NOT complicated unto themselves. What's complicated about DNA is the number of sequences it can encode using a 4 letter alphabet.

A cell is nothing more than a balloon of water surrounded by a hydrophobic membrane -- and hydrophobic compounds are easy to derive from simple organic molecules.

The components of cellular metabolism -- molecules that can be split to yield energy, ionic membrane gradients, electron acceptors, can all happen using very simple chemical constituents as well.

Put these permissive conditions on a planetary scale over billions of years, and you have a level of probability that is beyond your powers of conception. It's not random chance, then that life arose -- it was, perhaps, inevitable under those conditions given enough time and enough constancy in the environment.

So what is the probability of life evolving on any planet? As far as we know it's a 1 in 9 chance. But that's a statistically meaningless sample size, and we've never found another planet close enough to scrutinize that has had conditions like ours. So maybe the probability of life evolving is greater than 1 in 9 on planets that are moer similar to earth. It's a big universe out there.

3. You assume that evolutionary science is a done deal, and therefore it lives or dies based on its "holes". This is a fundamental misconception about science. We don't know everything about how babies are conceived, but that doesn't mean that the stork delivers us. We don't know everything about human disease, but that doesn't mean that Galen was right about the four humors.

There is a lot we don't know. And that's why we continue to do research. What we DO assume in science is that we'll find answers if we look hard enough or in the right way. So just because we don't know exactly how life arose doesn't mean that it didn't. Maybe some day the mechanism will be more clear.

But there are big holes in every alternative explanation (i.e. Creation), such as the fact that there is no independently demonstrable evidence of any kind that supports divine creation -- so why should anyone rationally believe it? At least evolutionary theory is rooted in what we observe.

[quote]If, in fact, I have defined science wrongly to include the notion of an unbiased world view- one that allows for all things logically possible, even those that science might not be able to explore- and that science is justified in assuming a natural answer for everything, no matter how problematic, then I withdraw my complaint entirely.[/quote]
I'll say again that science's worldview is that we can understand the natural world by observing it. Pure logic is not all that useful once it's contradicted by empirically demonstrable observations. So science is unbiased insofar as it's willing to accept anything that is demonstrable.

[quote]Of course that would leave the possibility that science could come to many conclusions (and assume them to be authoritative) that could be far removed from reality.[/quote]
And that's why we do the science to begin with. If I put my cosmic elephant crap-ball up against Genesis, the only difference between the two is that more people for more time have accepted the view in Genesis -- but there is no way to independently verify one over the other. If I put Genesis up against science, Genesis has no claim to demonstrability beyond a presupposition of divinity; whereas science will produce a world of observations to support its conclusions.

:eek: Wow, cool set ups... Blue Rose is a beautiful picture.

Glad to see that you have had a lot of exposure to other cultures. I think it does a lot to help a person understand a lot about others. Personally, I grew up (till about 10) living about half the time in Northeastern Brazil and the USA. My dad grew up in Southern Brazil, and my mom grew up in Jamaica. Needless to say, even though I am much more American than anything else, I've never felt 100% apart of any culture, especially since my parents weren't really "Amercican" themselves. Anyway, I've met lots of people from all over- thanks in large part to my dad's aquaintances, and always enjoyed reading books about other cultures. I got to go back to Brazil for a couple of weeks a few years ago, but I'd love to spend some more time there... Last winter my wife and I spent 5 months in Kyrgyzstan teaching English while living with an Uzbek host family and learned a bit of their language as well (since they didn't speak English).

About the papers: I did make my response rather unclear... The response that I wrote was relating them back to my argument, which was obviously not the intent of the writer, so it was not a negative statement about them in particular. Acutally, I found the papers themselves (I read a bit of the one about CNCs as well now) I found to be informative, interesing, well documented, and overall very well done (and a bit above my head).

Oops, accidentially hit the "enter" key and posted the above before I was done...

Anyhow, I think that this idea of bias is important. I think we have both agreed that there can be theistic bias that negatively affects their scientific nuetrality. In a past post you said "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 take this to mean that you think that there can be such a thing as a naturalist bias which would be negative... First, am I right that this is what you meant? And if so, I have a few questions...

What would a naturalist bias be or look like?
How could a scientist tell if they have a bias?
How could a scientist tell if they were working in a system with a naturalist bias?
What would the negative affects be?

Hopefully if we can have some common ground here, it will help clarify our discussion.

That's not what I meant. Someone outside of science (or even a scientist outside his scientific work) can have a naturalistic bias, but you cannot have a naturalistic bias if science is what you're doing. No more so than a basketball referee is biased towards using the rules of basketball and not football to ref a game. To have a theistic bias in scientific research or communications is possible -- it means that you're infusing science with assumptions that have nothing to do with the science itself -- they are inaccessible.

A naturalistic bias, conceptually, doesn't make sense because science is in itself a naturalistic discipline. Like I said, does the Pope have a Catholic bias in his job? I'd argue no -- because his work is defined by the operations and parameters of Catholicism.


If a scientist has a bias of any sort (like a drug company having a bias towards the efficacy of a new drug), it can affect study design, disclosure of results, and presentation to the scientific community. One area of complaint in medicine (and to a lesser degree in science in general) is that people do not often publish negative findings (except as part of a larger study). This isn't all that necessary in science except that you may save someone the time, effort, and money of doing research that's already known to be unproductive. It IS useful in medicine so that we avoid using therapies that don't work or can cause harm.

As for a global naturalistic bias, I think this could certainly take shape in the nonscientific communications of scientists -- like making polemical statements against religion. But that would be nonscientific communication. The best one can say as a scientist is that "religious explanations have great importance to people, but these are not scientifically verifiable and therefore must not be discussed as if they carry weight within scientific thought." Or something like that.

A scientist would be extremely foolish to make leaps of logic in a scientific communication, i.e. assuming truths about the universe that aren't somehow connected to his/her own work via a chain of scientific discovery.

Certainly evolutionary scientists assume that evolution is true in some form or another, but that's because they are building on a pre-existing body of research that leads to no other overall conclusion. There is always going to be disagreement about the specifics, but the basic tools of understanding genetics, of dating fossilized specimens, of mathematical modeling, and of studying morphology are all well-established, and these are the tools of evolutionary biology; the difference between studies are the subjects and the specifics, i.e. to what questions those tools are applied. Qualitatively these assumptions are no worse, however, than I as a doctor assuming that the blood circulates around the body (even though I haven't repeated the 13th century research of Ibn al-Nafis or 17th century William Harvey). I witness the circulation of blood in some ways, whether it's a blood clot in a leg vein dislodging and migrating to someone's lung, or it's giving antibiotics in someone's arm vein to treat an infection in the brain -- it's all based on confidence in past research.

If an evolutionary geneticist starts linking his papers to thermodynamics, string theory, the Big Bang, and the geologic origins of planet earth, and does so in a way that doesn't directly cite related scientific research, then that WOULD be a type of bias. It's sort of like in court: "I object -- assumes facts not in evidence!" That would be an attempt to link disparate areas of study, and pure speculation can be shaped to reflect someone's biases

Okay, I understand how you are saying that there is, in a certain sense, no way to be "natually" biased when attempting to study "natural" science, and on one level I understand and agree with you. It is not the job of natural science to make statements about the supernatural... It is by definition outside of it's considerations. So on this point we agree. I think it's important to push this out a little further though, and hopefully you agree... Keep in mind I am not here trying to argue that anyone (you included) has any biases, I'm just pushing this out theoretically to see where they could be possible.



First, from this example I think you indicated that there is the potential for bias when there is a vested interest. (Is this a fair assumtion, or am I taking that too far?) This article on vested interest is pretty good IMO and rather short, and I think is worth a read (or at least a skim) if you have the time, as it explores the idea much better than I will, and I think it's important to the question I will ask: Vested interest - Wikipedia, the free encyclopedia In short, the idea is that if a certain action has a personal benefit to the person, they are more likely to choose that action. And, from my experience and understanding, this can happen on the subconsious level (and therefore unexamined) just as well as the conscious. I think it's also key to note that there can also be a "collective" version of vested interest.

Second, you indicate 3 or 4 areas of potential influences of bias:
- study design
- disclosure of results
- presentation to scientific community
- not publishing negative findings (which I realize can be of quesitonable value, but as you indicated, is still a point to consider)

So my quesiton is this: Do you think that it is theoretically possible for an individual scientist, or a collective group of scientists, to have any vested interest (conscious or subconscious) in the areas of potential influence that you described as it relates to natural history or evolution? Is it possible that there any potential benefits involved in producing results that support a believable and authoritative acount of naturalistic history?

Sure, just look at the tobacco companies and nicotine research. That's why journals and conferences force people to disclose their affiliations, investments, and sources of funding; and if there is any question of bias you have to look EXTREMELY closely at their methods.


It can go beyond that in an area like science, in which your methodology can be subtly biased to favor your personal interest -- which further biases everything that happens downstream from that point in the methods -- all your results, conclusions, everything.


You're asking this question WAY too broadly. You ask as if a scientist EVER does a study in which the study question and the primary outcome investigates "did evolution occur or not occur?" or something like that. No one studies that question!

People study questions much more microscopically than that (just refer back to the articles I linked). But to answer your question, people certainly benefit from the success of their research. It increases their recognition, makes them more competitive for grants, advances their tenure status, whatever. If they think they're going to get the Nobel Prize for proving that mice can fly, then they're going to work hard at that question. If they for intellectual / professional / monetary reasons are dedicated to discovering some missing link in evolutionary biology, they'll work hard at that question.

But that is different than what you're asking. And it's immaterial anyway, because if someone's research is crappy, then the conclusions they draw are only as good as their results, their results are only as good as their methods, and their methods only as good as their hypothesis.

Well, I wanted to ask a broad quesiton, just to keep finding common ground. It wasn't meant as an argument or an accusation. (Also, for what its worth, I haven't been questioning whether evolution occured for quite a while now. The question I raised later was whether or not current understandings are a good explanation of life as we know it. And even in that context, I would not ask science to use the supernatural as any sort of explanation if the answer was "no", nor to stop looking for a natural explanation. I have been paying attention. )

But are we agreed that there is potential for there to be a benefit to a person or a collective group of people in presenting a believable and authoritative account of naturalistic history? To me that is not immaterial, as a potential benefit would IMO lead to a personal or collective vested interest in something other than complete and unbiased accuracy... This is still not a verdict or anything, of course.

Maybe for someone making a TV special about it, or someone writing a book, or even someone writing a textbook.

Otherwise, the benefit you describe is true only insofar as there is benefit for a person to succeed at their job (and in this it's incidental that some people study evolution and other people study dog psychology). I mean, hit men benefit from killing for cash successfully, scientists benefit from investigating scientific questions effectively.

And the real question about bias in science is whether the methods / results / interpretations suffer from that bias. Science is usually hypothesis driven (I hypothesize, for instance, that the symmetrical four-limb structure of vertebrates is associated with homeobox genes expressed in early embryogenesis blah blah blah --- and the null hypothesis is that they are NOT associated with these genes). Thus, a hypothesis is testable. Bias can force you to inappropriately accept or inappropriately reject the null hypothesis -- and you need to account for this in your study design and your interpretation of data (for example if my cutoff for significance is P < 0.05, and I do 100 comparisons, then by random chance I'll have 5 "significant" relationships among those comparisons whether there is a real relationship or not).

Other science is more exploratory or descriptive (like the human genome project). And paleontology is somewhere between -- it depends on finding a limited sample set of degraded specimens, and based on dating techniques (which ARE generally accurate) putting these specimens anatomically in the context of morphologically similar things. Bias, then, is related to how accurate your comparisons and your dating techniques are.

You bring up a very good point here. So aside from science proper, do you think that some (or many) of the intitutions considered "scientifically credible" by society (talking mostly American here, since thats where I live) would have a strong vested interest, and with that possibly a bias, toward presenting that "believable and authoritative account of naturalistic history"? Some of the institutions I'm thinking of could be museums (smithsonian comes to mind), TV chanels (Discovery etc.), magazines (National Geographic), etc. This of course would not directly reflect negatively on science (as in your profession) in any way. But for those of us "outside" of science, those presentations of history are what we see the most, so I'd be interested in you opinion. Also, you mentioned writing a textbook... don't you think that is a very important thing to remain honest, as it potentially shapes the thoughts of the future scientists?


I see what you are saying here, and it makes complete sense... but at the same time it demonstrates a kind of trust in the "purity" of the scientist and the scientific communiy. (Not that this trust is automatically invalid, but we are all human after all.) The question that I'm raising is whether or not there is any potential benefit to the scientist or the scientific community that is other than simply investigating effectively. Just to suggest some possible benefits, though there could be others I'm not seeing, and the things I'm mentioning might not be valid...
-Are there sources of funding that would be happy to have this believable or authoritative account?
-Are the personal world views and philosophic beliefs of the scientist(s) supported, unnafected, or negated by such an account?
-Are there potential professional benefits to supporting such an account, due to "pleasing" other people or institutions?
-Are there potential egotistical benefits (recognition) to supporting such an account?
-Are there potential negative results to presenting or pursuing something that seems to sharply conflict with widely accepted theories?

At the same time, I recognize what you said about results being testable, and agree that that does lend some credibility even when "vested interest" might exist. But the possibility for biase, although maybe limited to some degree, still exists. And as you noted, in more exploratory or descriptive sciences, the potential increases. And when looking at the 4 potential areas for bias that you described a few posts ago, the door for potential influence still seems fairly open to me. They seem to be very fundamental to the point of even shaping potential results, as well as the conclusions drawn from the studies, even if the proper methods are used and correct results are found. Your thoughts?

Having spent the last 3 years as a postdoctoral fellow at Harvard, which is as recognized in the sciences as anyone, my sense was that institutionally their interest was in having productive leaders in their respective academic fields. By leaders they want people with notoriety, recognition, and accomplishments. There is a bit of tail-wagging-dog here, because this recognition attracts grant funding and donations for the institution. But at the same time there were people on their faculty with fundamental disagreements with one another. There were other people on the faculty with notably unorthodox areas of research. I don't think the vested interest lies in the theory itself. I think they want leaders in every area of research imaginable -- so they have leaders in everything some of which directly or peripherally addresses evolutionary questions.


I've written some textbook chapters myself. The most important things in writing a textbook chapter are 1) know your audience, 2) be true to the literature, and 3) avoid controversies except when necessary. And as for #3, if you're bringing up new and unpublished research, you need to be clear about it.


Humans are humans. But while some scientists are certainly corrupt or disengenuous, that doesn't mean that there's some kind of conspiracy within science.


No, that's not how grants work. Some funding agencies are more conservative or more fringy than others, but you win funding by showing that you've got a track record, and that you have sound proposals that you can carry through.


It depends what account and what belief system. Every possibility is accounted for, so the answer is yes, yes, and yes. Furthermore, views are much more complicated than science vs religion or natural vs supernatural or evolution vs creation. Some people believe that evolution (incl human evolution) is completely true as described through scientific research -- but God presided over it.


Maybe in a case by case way. But not uniformly.


You don't get much praise for saying the same thing other people have. You get praise for coming up with things that are new.


The biggest problem is being right about what you've proposed and showing it through research. The scientists who deny anthropogenic climate change have had a bitch of a time making any kind of scientific case. Of course it IS harder to get publications and grants and to be a keynote speaker at a national meeting if you're on the fringe -- but again this comes down to research. You shut up your critics with research, not with theories.


Well, only by virtue of their lack of statistical power. But you stick to the evidence you have. Again (and again!) it's about data.


Not if you're consistent throughout!! Hypothesis leads to methodology that tests the hypothesis; methodology generates results; the hypothesis is accepted or rejected based on the results, and the validity (or lack thereof) of the hypothesis is interpreted in the wider context of other science in the field. There are strong studies and weak studies, and this comes down to your method. If your hypothesis is something that's easily testable, then it isn't hard to keep bias out.