(November 18, 2013 at 6:20 pm)Statler Waldorf Wrote: I could make the exact same argument but in reverse. If the science supporting Darwinism were really that compelling they would get it published in the Journal of Creation or the Answers Research Journal. Science and [/i]Nature[/i] have a religious-like commitment to the Darwinian paradigm so if your paper questions that commitment there is no way it is getting published no matter how good the science is. We saw this when the Smithsonian published that letter by Meyer in its journal- people lost their jobs and the article was merely questioning the adequacy of the Darwinian model. It’s a corrupt system.
Professional journals accept the basic tenets of evolutionary theory as they accept the basic tenets of the theory of gravity. At this point in the research into it, it’s a flat-out given that genomes of populations change over time, and that they have done so for millennia. It’s just beyond a doubt. There is no way we will ever discover that this does not- and did not- occur (well, I can think of one way. If a deity or a powerful alien presented itself to everybody, proved its power, and told us it personally diddled around in genomes to make it look as if this was true, and showed us how it did that, I guess we’d have to accept that such an entity had fooled us, and was a total asshole for doing so).
Are there open questions? Sure.One of the reasons Tomkins’s Chimp/human genome paper was so interesting to me is that it IS an open question as to exactly how much direct homology there is, and how much direct homology matters. I was tantalized by Venter’s seeming proposition that there might be several different lines of nucleotide evolution, but he’d have to do pretty major work to get that ball rolling, and I don’t think he’s interested.
I know you don't like it, but there's too much evidence for evolution. I've spent years studying and observing the behavior of genomes, and short of the above scenario, I can't see anything but smaller quibbles about unresolved issues of change- which is wonderful, since it would be sad never to have another discovery. If you can't accept it, OK. I have come to realize that each person views the world differently. I would love for you to see the beauty and connection to all life that comes from evolutionary study, but you don't, and that's that.
I'll respond to the rest, but I'm about played out with this discussion- it's beating our heads against each other at this point, and I'm too damned busy recently for long posts and long arguments. I lose track.
Quote:McClintock’s idea was not questioning the grand paradigm though and that is the difference. She’s a Darwinist; so she was merely rocking the boat a bit, not completely capsizing it as someone who argues for a 6,000 year old Universe is doing.
I’m not going to argue about McClintock, although she’s a better analogy than you know. And you aren’t rocking or capsizing the boat with YEC, SW. It’s having absolutely no impact at all in the scientific community. Scientists are only mildly worried about the ID camp (and that’s only because of textbooks), and never think about you guys at all. Sorry. The papers by Tomkins are the only papers that even resemble scientific research papers, and they would never get published in a respectable scientific journal, and not because of bias against YEC. They’re dishonest, they ignore mountains of conflicting data, and they use appropriate tools in a smoke-and-mirrors way. They’re just not very good, and at least one of them is very bad. When I have more time, I’ll look more carefully at the others, but at a glance, they were WAY less useful than Tomkins’s work. I am pleased to have seen his work, though, and I thank you for selecting it for me.
Quote:It is not reasonable to assume the Dawkins would quote himself in context on the cover of his own book?
This is where it gets boring. Are you just being difficult?- it’s hard to tell. Dawkins did indeed write a whole books about how the appearance of design can fool you- until you look at the evidence. I understand that you feel that cuts both ways, and if one were going to ignore the huge amount of data on changing genomes, or present contrary research, you would have a case. You read one paper by Tomkins on chromosome fusion, which is spectacularly dishonest, and ignore the rest. His data there is absolutely meaningless in the context of the larger body of research, but most folks won’t know it, because they’ll believe his outright falsehoods. I'm sorry you have chosen that path- the fusion research is absolutely gorgeous, and bounteous.
Quote:Well I believe the evidence supports the idea that there are limits to how far the genomes of animals and plants can be altered. You can get thousands of different breeds of dogs from a single canine ancestor but you will never get anything other than a canine. A Chihuahua and a Great Dane are still both dogs.
Oh, Statler Waldorf. I had started to think you were better than this old crocoduck canard. There is absolutely no way I’m going to waste time on this line of argument. If you believe this nonsense, more power to you. I will say that getting introduced to the concept of the “baramin” was extremely hilarious and even kind of interesting. Again, I have learned from the papers you gave me, and that's always good.
Quote:Well the fact that we can still breed many species with one another today (lions with tigers, cougars with leopards, potatoes with peppers, and so on) would indicate a very recent divergence right?
Not necessarily.
Quote: If such species diverged millions of generations ago we would expect their ability to produce viable offspring with one another to have been lost.
Not necessarily. Interbreeding ability is an open question for nearly all closely related species, and the definition of “species” using that criterion has been abandoned by nearly everyone outside of textbook writers, for several reasons. Genomics is not a very old science, and not a very precise one, yet, and observing the behavior of organisms in labs and zoos leaves much to be desired in research. There is a rich body of work on this very question. The logic you have presented here is one-dimensional and not in line with current thinking.
Quote:Yes, but I would prefer that we did it more like Darwin and Newton did. They merely published their work and then it was available for everyone to see rather than a handful of anonymous reviewers rejecting it before it saw the light of day. If the methodology is poor it will be pointed out. People are biased, envious, and dishonest creatures; believing they can review someone else’s work they disagree with honestly is merely a pipe dream I am afraid.
SW, this DOES happen in journals. If it’s a paper of any importance in any field, grad students and their profs will chew it to death in journal club, and springboard off the research- which will lead to problems if the original research isn’t solid. I once helped developed a complex series of primers for an extensive PCR experiment based off another lab’s paper. They didn’t work and didn’t work and didn’t work, and finally the other lab (who was involved) redid their original work and found it was bad work. They retracted and we were pissed off for wasting time.
And you may not know this, but Stephen Meyer’s latest book was reviewed by
Science a month or two ago. It wasn’t reviewed well, but it will bump his sales, and
Science knows it.
Esquilax is doing just fine is his conversation about peer-review with you, so to keep this conversation to a reasonable length, I'm going to defer to him on this question.
Quote:A natural occurrence is simply what we observe when God is governing his creation in a regular and predictable manner (the Earth revolving around the Sun for example). From our perspective it is inaccurate to say that everything runs on its own and God merely has to step in from time to time.
Interesting. So you believe that nothing occurs due except by the direct governance of your God at all times? He doesn’t, say, set up systems that work and leave them to do their thing once in a while? Every atom and every physical process is under direct orders at all times?
Quote:I agree that the operational sciences deal solely with the natural; this is because empirical science requires direct observation and repeatability. This being said, there is nothing in the scientific study of origins that disallows for inferring the involvement of a creative agent.
Obviously not, since creationists and evolutionary biologists alike do it all the time.
Quote: I think we both agree that science cannot demonstrate naturalism- which is rather ironic because many scientists today adhere to naturalism and pretend that anyone else who does not is not a real scientist.
I’m not sure what you mean by “demonstrating” naturalism. Science provides data about the universe we live in, which data we then try to find parsimonious explanations for.
Quote: I completely reject naturalism but am able to still work in my field just fine. In fact, I have never run into an instance where I have arrived at a conclusion differing from that of my non-creationist colleagues.
That’s good to hear.
Quote:As for your point about supernatural events in the past always having a natural explanation, I do not feel this is accurate at all. I am aware of no purely natural and material explanation for donkeys talking, axe heads floating, water being turned into wine, and people being dead for three days and then resurrecting and ascending to Heaven. I also doubt that you believe we will ever find a material explanation for such events.
I am still not sure what it would take to convince you that the supernatural did in fact exist. It seems that you have created a system that will never allow that to happen.
I also see no natural explanation for many other miraculous events in many other old books. Gods turning into swans, raping women, and fathering children is DEFINITELY not a natural occurrence. Neither is riding winged horses (and quite a few old religious texts claim that one). Do you believe Muhammad had a winged horse? Why are your magical stories special? There is no evidence at all (other than all our knowledge of horse and wing anatomy) to suggest that winged horses could not ever have existed, or that Muhammad could not have had one.
It's not just YOUR old holy stories that are hard to swallow. It's ALL of them- and all making so many competing claims. Yawn.
Quote:I am still not sure what it would take to convince you that the supernatural did in fact exist. It seems that you have created a system that will never allow that to happen.
Evidence, dude. Show me the winged horse. Show me the talking donkey. Please do NOT show me the raping swan, unless you have it on a leash.
It would also help if all theists,or even all Christians, could agree on anything about the nature of a creator/deity. There are plenty of your own people who disagree with you vehemently, and plenty of other religions with old holy books that make competing claims that they believe in as strongly as you do yours.
It would also help if I knew less about the behavior of evolving genomes.
Frankly, I’m sorry the conversation has come to changing people’s minds, because I think we both know that isn’t going to happen. For me, it’s an interesting look into a weird perspective, and one that is useful to understand. The YEC camp isn’t dangerous to the functioning of science or public science education, so I’m not particularly interested in changing your mind.
And understand that I am not aggressively ASKING you for this evidence. I am responding to your question of what it would take.
Quote:If Christ was willing to allow you to go poking around in his genome of course. 
How is the writers of the gospels being unaware of germ theory relevant to the story of the resurrection?
It would be mean of a resurrected person to deny excited scientists the opportunity- just for a day, maybe.
My point with germ theory is that I don’t consider people who knew next to nothing about the behavior of bodies to be authorities on any behavior of any body. Ancient medical texts are fun to read, but are pretty whacked on most aspects of human biology.
Quote: I actually think that is one of the most compelling aspects of the Bible in general, the miracles described in the Bible would still defy our understanding of science today; which is not consistent with people simply witnessing natural events they merely did not understand at the time.
If those miracles occurred today, yeah, that would be great. A resurrection would blow the lid off our understanding of life and death (and it’s worth mentioning that people claim to be resurrected all the time- I think there’s even video footage of some of it). A talking donkey would be awesome and would be inexplicable given what we know about donkey anatomy (that poor donkey could probably never expect to see the outside of a research facility again). Bummer that they don’t happen today so we can see them.
Quote:In order to avoid the circles we’d have to have this discussion at more of an epistemic level. We’re too far down the conceptual scheme to have much common ground.
Well, at least we’re conversing politely. That is much more than you can say for many internet discussions of this variety- and I'm too tired and busy recently to have much conversation about anything. You should post a picture of a crying baby to goad me into a stiffer upper lip.
Quote:You seem to be conflating two very different areas of science here. Yes, a supernatural explanation would not be allowed in the empirical sciences because it is not a repeatable event because of its irregularity. However, to say that inferring that all matter is the result of creation is unscientific because we cannot test it is not completely accurate. We also cannot directly test or repeat the origin of life that supposedly took place 4.3 billion years ago; this does not mean that all theories of abiogenesis are therefore unscientific. In the scientific study of origins it is completely appropriate to make an inference to the best possible explanation, even if that explanation involves creation.
I don’t believe I am conflating anything. I agree with the above statement. There is limited data, and currently no way to recreate the experiment of early life. I’m pretty convinced by the work in support of an early RNA world, but can we know for sure? No.
Quote:Are you really suggesting that if we did not know how the Egyptians built the pyramids we’d have to infer that they were the result of unintelligent natural processes? We have no idea how Stonehenge was built and yet we know it was the result of a creative mind; it would be ridiculous to argue that those rocks naturally assembled like that. If it is scientific to make such inferences in regards to the pyramids and Stonehenge then it also too must be scientific to make them in biology and cosmology.
And we’re back to being fooled by appearances. We aren't making particularly shocking inferences about the pyramids. know a great deal about early peoples and their ability to create large stone objects. Since there are no contemporary written records for the construction of the pyramids or of Stonehenge, it could be that aliens put them there (or that God did!). But they are clearly things created by people. How do we know? We know a lot about people and their technological progress. We don’t know anything about a creator or its abilities or technical progress. So it’s an uncompelling argument, especially when we know for a fact that people lived in those areas at those times, and we don’t know for sure there is a deity, or if there is, if it created us, or if it did, it still interferes, and so on and so forth.
Quote:If the primary research were arguing for the natural formation of the pyramids or the formation of the faces on Mt. Rushmore by wind erosion I would still believe (and correctly so) they were the result of an intelligent creator. I see no reason as to why biology and cosmology have to be any different. I believe that you need to justify why you allow such inferences to be made in the fields of engineering, archeology, sociology, and anthropology but not in biology or cosmology; as of right now it appears to be nothing more than special pleading.
Nope. All is evidence-based. You like the idea that evidence about past events is merely inference- but it isn't, in any of the fields you have mentioned. But I always like it when creationists talk about special pleading. It’s not a conversation I want to have again, and I’m sure you’ve had it before as well, so let's spare ourselves.
Quote:We cannot study the origin of life 4.5 billion years ago either; is this idea unscientific too? Your definitions of supernatural and natural seem to be a bit self-serving as well.
No, we cannot directly study the origin of life, and we may never be able to. I'm comfortable with that. I don't think that's a self-serving attitude. If a mystery remains, so be it.
Quote:I do not see the relevance of this; yes there is evidence for the supernatural worldwide.
I think you do see the relevance: because the claimed supernatural events often are in support of other religious ideas. For instance, a resurrected boy in India would put a dent in Jesus’s specialness, I think. And somehow nobody ever puts forward solid evidence for these supernatural events, either. Have you ever watched one of those ghost shows? THAT’S their evidence.
Quote:
Quote:I have done no such thing. I have said, very reasonably, that it is wise to look for natural explanations first, and I haven’t seen any evidence yet.
You did not only say that though, you also said that when we cannot find a natural explanation for something you adhere to the faith position that there is simply one we have not found yet. This means-that no matter how compelling the evidence is-you will never conclude that the supernatural exists.
No, I said it’s wise to look for natural explanations first. If a boy in India WAS resurrected, would you believe it? Would you suspect he was in Jesus’s league? No. First you’d think “fraud.” If all the evidence pointed to a genuine resurrection, you’d look for something different about that body. If there was nothing different about the body, and he wasn’t a fraud (say the whole death and resurrection was taped by medical authorities you trusted), what would you have to conclude? There is special pleading here, but I think it’s yours. Why not accept the resurrection stories that occur all the time? If you know the answer to this question, then you know why I’m dubious about your resurrection story.
Quote:Why do you keep bringing up witches? I am not seeing how they are analogous to God creating and governing everything.
I like witches. It’s a fun supernatural concept. Plus, the world is full of people who claim to be real witches doing miraculous supernatural things. I met one who claimed she could curse people with death. Do you accept their stories? Why or why not?
Quote:What do you mean by a natural source?
A known reason for a body to be sick. If you had a terrible medical mystery hurting your body, wouldn’t you expect your doctors to keep trying to find out what it was and if they could fix it? Or would it be OK for the doctor to shrug, call it a miracle, or a witch’s curse, and walk off the job?
Quote:You have said such a thing, and multiple times. You have said that supernatural explanations are not allowed in science and that when we cannot find a natural explanation for something we must assume one still exists.
No. I’ve said that science cannot study supernatural processes. If one occurred, it would outside of the purview of science. That is NOT the same thing as saying science doesn’t allow for the supernatural. And yes, I think it’s wise to look for natural explanations. You do, too, or you’d accept every resurrection story, and you’d never go to the doctor.
Quote: Then you turn around and ask for scientific evidence supporting a supernatural event
Well, I’m NOT asking for evidence of miracles. You asked me what it would take to convince me, and I said that evidence would. That’s not asking for anything- it’s answering your question. I already know you can’t provide evidence of the supernatural. That’s why I don’t believe in it. Maybe a ghost will appear to me and change my mind.
*snipped your imaginary conversation*
Quote:Quote:If the implications are magical or supernatural, they don't belong in a science journal because those things are outside the purview of science.
You keep asserting this, but I see nothing in the definition of science that makes this the case.
Science, again, exists to study the studyable. Journals are filled with things that can be studies using the scientific method. If something can’t be studies by the scientific method, it doesn’t belong in a science journal. That doesn’t make all things that can’t be studied by the scientific process invalid. For instance, sometimes a poem I have read many times strikes me very hard and opens up new ideas to me when it never did so before. Was it the right time in my life? The right combination of thoughts just before reading it? The right piece of music played that morning? A few words said by someone else the day before? There is no way to study this phenomenon scientifically (and no reason to- I like the unpredictability of poetry’s impact on me), and if I wrote a nice essay about it, all scientific journals would surely reject it- not because my experience is invalid, but because it’s outside the purview of science. It's unscientific, and a totally valid and wonderful experience that I often have.
Am I being clear with this example? I'm not sure.
Quote: Secondly, why do you ask for scientific evidence supporting supernatural creation when you admit it cannot exist by stipulation?
Again, I’m not asking. I’m answering your questions. And I DON’T know that supernatural events cannot or have not occurred. I await one happening to me with bated breath. If the ghost of my grandfather appeared and had a conversation with me that only he could have had, and this event was witnessed by someone else so I could know I was not insane, I’d be convinced that ghosts exist. Ta-da!
Quote:That’s not completely accurate, there are thousands of articles published yearly dealing with what has happened in the distant past. The past is not directly observable. If scientific journals only dealt with the operational sciences I would agree with you, then creation would not belong in such journals; however that is not the case. Scientists make inferences about the past, and an intelligent cause is a completely valid inference.
This is pretty weak, S-W. Events in the distant past are STUDYABLE. Direct observation is a tool of study which many times cannot be employed. We cannot directly observe the order of nucleotides in a DNA strand, either, but you don’t have trouble accepting their existence, I presume.
Quote:That was my point; such papers do not get published even though the science is legitimate. The only way a creationist can get published in such a corrupt system is to conclude with, “well this is a problem for Darwinism that has not yet been resolved.” Rather than the obvious answer, “Your theory is garbage dummies!”
Now that I’ve read a few of your papers, I have a better point to make here. Tomkins’s science is legitimate. But. His presentation of the state of research before his research is dishonest. His correct technique is rendered useless by applying it dishonestly: for instance, including the Y chromosome in his chimp/human paper without so much as a mention of the vast amount known about the staggering differences between the Y chromosomes of nearly all closely related species, and why this is a nearly useless metric. He says only that other studies prove his point. They don’t. He’s lying- not merely interpreting the data differently. But it looks good to include it, because it’s so different. So he does, without a word about the reality of Y chromosome research. It's shameful.
And I suspect no scientist would be allowed to publish a paper that called another hypothesis “garbage.” Letters, yes, Papers, no.
Quote:Do I get to be Vice President of Journal Club? Since your field is genetics and mine is environmental sciences I doubt we’ll find many articles that we both could adequately analyze.
I don’t have time for another Journal Club anyway. But it’s a fun idea. Perhaps some of you could do it with one of the other papers you’ve been discussing here- make a thread for the sole purpose of picking that particular paper apart bit by bit. It’s a useful exercise- and then you could be President if you start the thread. I'd be quite interested to watch you and Morgan discuss one of the papers you've been discussing from top to bottom, without all the other stuff and other posters in between.
Quote:Where did I say I do not like presuppositions? I only dislike them if people do not honestly identify theirs. Creationists are very honest about their axioms and ultimate authorities. Those who believe in an old Earth presuppose uniformitarianism, but very few are intellectually honest enough to identify this presupposition. That is where I get cranky.
You are the only YEC I have interacted with, but you have definitely been honest about your presuppositions. The ID guys are slimy as hell about it- I apologize for tarring you with that brush. Guilt by association is not something I normally truck with. Again, apologies.
Quote: I am not sure what you mean by primary bench research.
Doing experiments to gather data.
Quote:Quote: I appear to be of a more open mind here: if presented with rock-solid evidence of a supernatural phenomenon, I would have to accept it.
Can you give an example?
I did so above. I’d love to meet a ghost- especially my grandfather’s. I miss him, and it would be a matter of him communicating onformation to me that only he would know (like the last thing he said to me before he died when we were alone), and another witness to make sure I'm not off my rocker.
Quote:There are certain things I know are true through deduction, it would be irrational for me to relinquish that knowledge because of something founded in induction.
Fair enough, although if you're YEC, I'd re-examine your deductions at some point in your life.
Quote:I actually enjoyed the paper on fusion and am a bit disappointed that you seem to merely assert it is unscientific rather than give any specifics. I thought he makes several well-reasoned points, and seems to cast light upon the fact that the whole chromosomal fusion hypothesis is nothing more than a post hoc rescue mechanism used to waive away unexpected evidence.
I called the FIRST paper on your list, not the one by Tomkins, unscientific (and I'm sure you know why, if you've read it). Tomkins has the basics of the scientific method down. The reason the paper on fusion is so bad is that it presents evidence of something we already knew, keeps that fact secret from his readers, and completely ignores the truckloads of other data for fusion evidence while whining about one point of telomere degeneration that was both expected and known prior to his study. He throws in a ton of sciency-sounding language unrelated to his central point, which is just completely useless. This paper exists solely to preach to his own choir in language they will probably never understand. It’s a terrible paper.
I’m glad you enjoyed the paper, but I suggest you read up on the actual science behind chromosome fusion before putting too much stock in it. There is NO unexpected evidence here. None.
And the questions I asked about the chimp/human homology paper were good ones. You shouldn't ignore them if you want to honestly understand what Tomkins is talking about.
Sorry for all the whining about tiredness. I'm at one of those ridiculous points in life. Wah, wah.
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