Finally some free time to respond to this, sorry for the long wait.
I'm not sure where to start, so this may come out somewhat disjointed.
Education - I see many problems with how I and many others were taught about science as a whole. The sections that describe the method and how we have come to certain views are glazed over, while the rest is presented as fact. This leads people to think of science as simply a collection of facts, without realizing its inductive nature. It leads to conversations where "Science says X” response: "oh, a new fact” rather than wondering why and how that conclusion came about.
I could go on a huge rant about my dislike of current education, but to sum it up, I hate multiple choice and how failure is near impossible. In terms of evolution, through high school it was presented very lightly with basic examples (finches, population stuff, etc.). I wish they would have explored Origin of Species and Darwin's reasoning, then gone on to revisions and different views. As it is central to modern biology, rather than being a single unit, I think a whole HS course or courses should be presented to science students.
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My mountain analogy is actually a great way to view evolution, as we can measure separation of species and change. I mentioned H-W equilibrium and you laughed about it, saying that any population is in H-W. The application of it is that one can compare populations that are individually in equilibrium to see if there is interbreeding. This was done on the Komode bear population in British Columbia to see if gene flow was being disrupted by water separation (among other things). This comparison can be used to measure growing separation between groups in what is considered one species (usually the testing is done on microsatellites (tandem repeats) for which selection is generally neutral {Huntington's would be an exception}). On the other side, we can measure separation by silent mutations in genes. Once gene flow is cut off between groups, that mutations to their genes are now independent. So, when we look at gene and evaluate the conserved regions as well as silent mutations an estimate of the divergence can come forward. (though mutations are generally seen as random, there are trends, such as A<->T and G<->C mutations being more prominent).
Gene duplication can also play a role in this, as we see the majority of duplicates being silenced within a short time geologically if 2+ groups separate there is a 50/50 chance that opposing genes will be silenced which will oppose breeding (due to double null states at the gene in offspring). With the rate of gene duplication quite high, this opposing factor could be quite strong. I have read a recent paper on this that I can dig up if you want.
Natural selection- Though it is mainly seen as the large scale 'survival of the fittest' or 'survival of the most reproductively fit' it also extends right down to the genes. When we look at genes why do we see so many silent mutations? This would be due to the amino acid at that position being important so that a change (unless to a similar aa) would be detrimental. We see structures such as the 7 trans-membrane domains being conserved, or related to my work, specific positions in opsins being conserved as they lead to different wave length sensitivity. So, not only does natural selection cull at the gene pool level where those with the highest Darwinian fitness succeed, it operates at the gene level. I don't see this phantom hand guiding evolution at all, I see an indifferent world where things live and change or most often die out due to events, changes in the environment, competition and so on.
I think it is cool that bacterium that have evolved the ability to eat
synthetic fibres such as nylon. If you think about it, how could that come about? I would say that the mutation that led to this ability probably arose many times in the bacteria, however they had no function in other instances so were selected against. When the fibre was present and the variation arose again, all of a sudden it is useful and advantageous. Just an interesting factoid, back to the discussion.
In the cases you've mentioned about asteroid strikes and so on, those could be considered natural selection but are usually called bottle necks, or after the event founder effect, etc. In those cases it may just be survival of the luckiest, then selection would resume on the remaining population as you said.
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Evolution, expectations, etc. - Your definition of macro-evolution is very different from the norm I run into. Usually it is just "large changes" which is ambiguous and allows for moving the goal-posts. Most commonly it is that the creationist doesn't think speciation happens. Matters your concept of species, if it is inability to interbreed and/or produce fertile offspring that has been demonstrated, at that point usually the goal is moved so that no amount of evidence will "prove" macroevolution. The definition presented was "evolution of life from simple, one celled organisms (or less), to all life we see today". So, macroevolution is the whole chain of descent from single celled organisms until now (I'm unsure if you also meant that multiple macro-evolutions from different primitive life occurred that is why you think more variation should be present, rather than the branching tree pattern). Drank way too much coffee this morning, pissing like a race horse...
I will admit, we cannot directly prove the entire chain. We can however give loads of indirect evidence for common ancestry. To answer your questions on why not more variety and completely strange things, this is due to common descent ie. descent with modification. An interesting way to think of this is that if I had pictures of all my ancestors going back and those of my dog, at a certain point they would be the same. It may sound kind of ridiculous, but it would be the same with a banana, though much further back. You've already seen most of the evidence, and to me it is quite conclusive. In terms of comparing anatomy, we see similarity between limbs such as arms, wings, fins, flippers, etc. This would be expected if they had all arisen from an ancestral feature (fin-like legs of a tetrapod amphibian IIRC). We would also expect basic genes to be conserved, such as those dealing with cellular maintenance and basic processes. Going back to the banana example, last I heard we share 50% of our genes with them. Keeping on the gene route, the closer the point of divergence the greater the genome similarity we would expect to find, which is exactly what we see. Though the number keeps changing (as some scientists put out papers way too early) the similarity of humans to chimps is very high ~98%. This does not mean we came from them, but that we share a common ancestor. As I've pointed out before with the quote from Yellow, biochemical similarity also points to ancestry - amino acids used, carbon basis, nucleic acids, and so forth. The case for human descent is very strong, bones, genetics, retrovirus insertions and so forth. You mentioned Neanderthals and how we don't come from them. Interestingly, until that was found out all I heard from creationist was that it was a diseased human; I would say finding out it was a divergent hominid does more damage to the creationist case. That makes it so that we have human like animals divergent from us, which kind of destroys us as "special creations". Am I willing to bet my soul on it? Once again, that has no place in my world. Soul, sin, saviour, they are a meaningless trinity to me.
In regards to transitory fossils, I'm unsure why people expect the divergent point to be half and half. It could look like neither, or the branch on one side stay relatively similar whiles the divergent species changes. So even though I share an ancestor with a banana, half man, half banana fossils shouldn't be expected (I know that's pretty sili).
You thought that I had changed from strict gradualism to a more punctuated approach, not really. I never actually said it had to be extremely slow, I think it can be gradual, or can move quickly (both in geological time scale though). It depends on selective pressures, variation, natural events, etc. To see how much change selection can have, simply look as what we have done with dogs. We didn't cause the variation, we simply selected certain features and now we have great danes and shait-zu's, with have huge morphological differences. I see natural causes doing the same thing but on a longer scale and less towards the purposes of another organism (like cows having big udders because man wants their milk and has bred them so, wouldn't be likely to happen naturally. Though I do consider humans natural and just another animal, the selective pressures we have imposed are "artificial"). You want to know how new organs came to be, and my answer would be they aren't new, rather modifications or new functions of pre-existing organs. For example the heart, I can see quite easily how it could have come to be, starting with such features as contractile vacuoles and cytoplasmic streaming, to single chamber pumps leading up to current multi-chamber hearts. Perhaps this is simplistic, but the modification of existing parts follows from common ancestry. If you reject descent, then "we don't know" would seem best. The false dichotomy of evolution v. creation has many creationists thinking if they destroy evolutionary theory, creation wins by default. This is not true; creation would need its own positive evidence.
I asked earlier about what evidence you wanted, and gave the dog giving birth to a pinecone example, in the next section I will explore that among other things.
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Designer - When I asked about the pinecone, you responded that that would be evidence for macroevolution. That was kind of a test, as if a dog birthed a pinecone, or a cow begot a chicken, evolution would be dead. Evolution makes certain predictions, such that one generation to the next large scale changes are not expected. A change of that sort would go against common descent and destroy the theory. Now let us look at design, it would fit with design just fine. Here is the major problem, no matter what happens it fits with design. It is definitional; the designer can do anything so anything that is evidence of evolution can automatically be attributed to a designer. An even bigger problem is that design doesn't seem to give any predictions, unless you want to start doing psychology on the supposed designer, which I'm sorry, but comes off as absurd ex. "He clearly did not like the dinosaurs". Why suppose one designer, why not a family. The extinction events were when he was distracted with the wife and kids and forgot to take care of earth. Then his daughter created the dino's, but when he found out he punished her by sending an asteroid to wipe them out. Or you could have it that there are competing designers, for weapons/defences, body plans, biochemistry, etc. Why not have a pantheon of designers/gods?
I know you hate outside sources, but from a recent panda's thumb comment:
"RBH:
The point is painfully simple: absent any constraints on what the designer(s) can or will do, there is no conceivable control condition that could make the discrimination we need, no condition that could disprove its(their) actions in anything resembling Behe’s “thought experiment”."
If you’re going to use this argument, then you have to carry it all the way through. How can you be sure that some intelligent designer hasn’t watched and affected the results according to his/her/its whims for every scientific experiment ever conducted? You can’t restrict this argument to just evolutionary biology experiments. How do you know that it isn’t possible that everytime an astronomer looks through his telescope, she only sees what the designer wants her to see? How do you know that the designer didn’t affect Newton’s calculations or Darwin’s observations?
This is in the same category as the question ‘how do you know we all didn’t spring into existence five minutes ago with all our memories of experiences the way they are?’ In other words, its a meaningless objection.
Design pretty much destroys science as a whole, this unrestricted meddler could be doing anything, and no matter the evidence or result we get could be attributed for it. Such as how sharks could have been wiped out then recreated due to some fondness in the designer. On the other side, why would it see the need to create in such a way to lead us on, a way that shows common descent? Just to screw with us?
I do see the "let's see how this works" in organisms, but rather as short order selection for survival than a plan. The massive extinction rate and stupidity of how things are put together speak of a natural system not one that was planned out. Look at pathways in a cell, some are akin to Rube Goldberg machines, the watch analogy really doesn't fit.
On the point of progression, I don't really see what is around now as inherently better than what came before. Look at humans and how wasteful in terms of energy use we are. If you want to personify evolution we are kind of a last ditch effort. I see evolution as change, and that what works now is favoured, no overall plan. Through natural selection if the environment stays similar what works starts to conform to that, but what works in one area may be quite poor elsewhere. Or advantages to one creature would be harmful to another (ex. antibiotic resistance). When people think that human are so great and above other creatures, it doesn't make sense to me. We are simply the current dominant macroorganism, bacteria and insects far outnumber us. We are unique in some attributes, but nothing special.
In terms of body plans, AFAIK, most came about in the Cambrian Explosion. As for why, it's been a long time since I covered that topic. IIRC it was about exoskeletons and primitive bone structure that allowed new species to diverge. It isn't really an area I've explored, but I'll be sure to read up on it when I get time. How many mutations from fin to leg, or how exactly exoskeletons came about, honestly I don't know. I'd say likely novel mutations such as those that led to nylonase.
I wanted some type of resolution, but doesn't look like that is going to happen, sorry about that.
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Faith - Please don't tell me once again that I need faith to accept evolution, I hold it in accordance with the evidence. Mutations happen, changes due to variation and selection happen, gene duplication, etc. are witnessed, we know they exist. Some other parts are indirect evidence, but they point the same direction. This designer is not, we don't even know it exists.
Just a side point, from your talk about the designer I don't know how you can say it is sometimes formless. To me structure determines function, a pile of all the elements in a person isn't a person. A fork made of ice ceases to be a fork after it melts. So a being lacking any form, lacks function as well.
Why do you suppose the designer is anthropomorphic anyway? Looking at the world, plants seem like a favoured creation, as well as unicellular life, why couldn't the designer be tree or insect or bacteria like rather than humanoid.
I guess what it comes down to is that evolution is bottom up natural design, while creationism is top down intellectual design.
My point is really that evolution is a very reasonable thing to endorse, with lots of evidence on its side and predictive power. Does this mean that it will ultimately be correct? No, it doesn't assure it. However, I think it is the most rational position to hold on the matter of "how we got here?”
Apologetics -
Hm, until recently I had never heard anyone use that outside of defence of religion (mainly christianity). When you said Patterson was an apologist, I took that as creationist trying to defend the bible.
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That's about all I have to say for now, didn't intend this to be so large but it turned out that way. The reading I've done has been worthwhile, though it probably wasn't what you'd have liked, it has actually made evolution seem all the more reasonable conclusion. I do want to thank you for getting me thinking more, I became quite lazy this past summer. Now I've exploring books on many new subjects such as truth/justification as well as broadening my understanding of evolution and science. Will probably be a few years until I have a good grasp of the areas I'm interested it, but it should be fun learning.
Later,
Kraft
