I think the problem is that the humanities thought of themselves as being scientific. They simply are not. The problem of the humanities is that story-telling has become equivalent to established fact. This can be seen in things like the DaVinci Code, Hegellian Dialectic view of history, and most of source criticism (and several other literary criticisms).
What's really funny is when people try to perform source criticism on modern works, just to have the authors reveal the true history of the work. It shows that while these are amusing exercises, there's really no factual basis to them.
Actually, faith was the driving force for the origin of modern science. Ultimately, science relies on a huuge amount of faith -- faith that the universe is governed by rational, unchanging laws. That faith came from the faith that we had a rational, unchanging creator. Science was the search for the why's and how's of how God worked. It did not close scientific inquiry -- it opened it up.
I hope you're aware that Ankylasaurus has a complicated nasal passage of "unknown function". Why do you assume that the description is false? We know of many current animals that do the same, although much smaller.
"If your theory *predicts* new evidence, you have something useful, not merely an entertaining story."
That sounds a lot like evolution.
"Early evolutionary theory predicted extinct species."
The evidence for extinct species already existed before evolutionary theory. You can't really say that evolution predicted it.
However, creationists (i.e. Mendel) were the ones that came up with Genetics. Mendel believed that genes showed that there were limits to variation, a claim which still has not been disproven by evolutionists (mutation expands the amount of variation slightly, but this still does not impact the overall argument of limitation of variation).
"Go find some evidence that dinosaurs lived in the same time period as writing/farming/animal-domesticating/civilization- creating humans. Find any evidence."
How about the coelacanth fish? It was believed to only exist 70 million years ago, on the basis of the rock layers in which it was found (no fossils of coelacanth fish after the dinosaurs). Yet, eventually we found them at a fish market -- unchanged after all that time, no less!
Then you add in the exceedingly accurate detail of the drawings of Pteradactyls by native americans who called the Thunderbirds. You think they just "made up" an animal that happened to look exactly like pteradactyls?
At the very least this shows that you cannot base extinction dates on fossil evidence. Some think that this indicates that the geologic column doesn't mean what most say it means.
That's assuming that the geologic column is correct. There are several species that were thought to be extinct based on their position in the fossil record, but were later found in meat markets in certain geographic areas. They are _only_ found in rocks dating back to the dinosaurs, and not in any "younger" ones. Yet they are extant today.
The following dinosaurs (among others) have been described in writings by human, and has even spawned a new field - paleocryptozoology:
* pteradactyls -- these were called "Thunderbirds" by native americans
* Ankylosaurus -- called "Leviathan" in the Bible.
* Brontosaurus -- called "Behemoth" in the Bible.
Pteradactyls are especially interesting, as the native american drawings of Thunderbirds match pretty much exactly what we have in museums.
There is a lot of doubt in the geologic column, especially now that we have more data on just how fast geologic structures can form. For example, stratified rock has historically been used to show that a rock formation underwent years and years of sediment deposition, and could essentially be counted like tree rings. However, recent volcanic eruptions have shown that such sediment deposition can literally be laid down in HOURS.
Actually, embryology developments have shown that when you place DNA into a developing animal from an egg, the embryo, as long as it lives, retains mostly just the properties of the original organism, not the transplanted DNA.
"In theory, yes. But since nobody will ever do that, it's not much of a feature."
We would sure use that, here.
"In fact, you can use good old "ln" to create multiple different views of sets of files reflecting different information."
Except that using "ln" is arduous, and would probably not allow you to do complex querying.
"But nobody ever does."
Because you only get a subset of the features for a WHOLE LOT MORE work. How many office workers do you know that would even understand the concept of "ln"?
I haven't used beagle, but here's the general case for large-scale meta-data searching:
If I'm looking for information on, say, the E-Zuper project I working on at work. This allows me to turn up everything that refers to it, whether its an email, a document, a bookmark -- anything. And note that two of those things only exist within certain applications -- the email and the bookmark aren't physical files. They are conceptual objects.
Likewise, you could say, "look at everything I did yesterday", and turn up emails, website visits, documents, etc.
Or you could say, "show me everything by Stan Sterner" and the same thing would happen.
For those of us whose data repositories are diverse and not always file-based, it would be a great blessing. Not to mention that meta-searching is useful even just with normal documents.
If you can assign arbitrary meta attributes, you can bypass the limitations of a traditional directory structure. For example, I can search and find documents that I'm supposed to have completed by tomorrow, if I include an attribute such as "date-needed" on those files. This will pull from every folder (which are likely arranged by project, not date). I could also add priority tags, and search by priority.
"For instance, in your placental/marsupial example, these species are really not as similar genetically as they appear visually."
Do you have a link? I have been searching for a while for some data on how marsupials and placentals compare in their molecular phylogeny, but couldn't find anything (actually, I think I found something which referenced a single marsupial, but I was hoping for more complete information).
"Indeed, they're really not as similar morphologically as they appear visually, when you get down to it; there are differences other than merely placental/marsupial."
There are a few differences, certainly, but many evolutionary textbooks actually make quite a big deal about how similar they are, and that looking solely at morphology might place them in the wrong part of the evolutionary tree.
"And no, these organisms do not have completely different selective pressures; they do indeed live in similar ecological niches."
You are confusing selective pressures and ecological niches. They are different. An ecological niche is the function you play within a given environment. Selective pressures are what cause changes. Wolves and mice occupy different ecological niches, but being in a niche doesn't cause a mice to become a wolf. Selective pressures are what cause change -- adaptation to environment, etc. What you seem to be proposing is that in two vastly different environments, the same body forms arose independently to cover not-yet-existing ecological niches.
"an inability to consistently place species in the hierarchy (e.g. the genetic hierarchy doesn't match up with the morphological hierarchy, etc.) That does not happen."
Take a look at many of the recent phylogenic studies, and note how many of them are surprised by the number of times X has arisen independently in the environment. Each of these "surprises" is an example of what you are saying.
A good site which follows such things fairly well is Creation Safaris.
"Now who's being circular. You can't use myths about Noah's Ark in order to prove other myths (the Bible). In point of fact, we have no evidence that Noah's Ark actually existed, even if some people THOUGHT (and still do think) it did."
You missed the point of the quote. In Josephus's day, the evidence was still around. I'm sorry they didn't take pictures in order to satisfy every skeptic that decides that the historians of that day were wrong simply because they disagree with modern preconceptions about the world.
The point of mentioning the flood is that it is all part of the same history, including a large part of the explanation of fossil distribution (like, explaining why nearly all fossil tracks go uphill).
"This is nonsense, as the entire fossil record shows. Hell, even Answers in Genesis has the old "mutations are bad" on their list of "arguments creationists shouldn't use". (Instead, they advocate the even vaguer "genetic information decreases argument".)"
Perhaps you should go back and read both what I said and what AiG says. We're basically saying the same thing on this one. However, the fossil record isn't nearly as clear as you think. For example, human tracks have been discovered in earlier sediments than evolutionists want to admit, so they simply called them austrolopithecus tracks, even though they do not match the foot bones of the austrolopithecus. Numerous inconsistencies has been shown. You should take a look at this discussion of homology.
"Genomic studies certainly show new genetic networks arising."
Genomic studies are only valid if evolution is assumed to be true. Certainly if you have already assumed evolution, if you saw different information in genome A and genome B, then you would assume that it arose through evolution. But that is not the equivalent of proof, or in fact anywhere near that.
We have not seen new networks of genes forming, even after thousands of generations of bacteria and fruit flies. We simply have not observed any case where new networks of information arise simply through mutation.
"No, we can't watch that happen on laboratory scales, but so what?"
Then in what way is it proven? All you have without that is:
different genomes have different genes
You can't say that one arose from the other. If you are using evolution to interpret the data, you can't use the interpretation as evidence for evolution. The data itself -- different genomes having different genes -- says nothing about how those genes got there.
"And what is it, exactly, about epigenetics that throws doubt on the whole of modern evolutionary biology?"
I didn't say that it did. I simply said that some heritable changes in organisms is not the result of new or even different genes, but of epigenetic mechanisms.
"If we find out a new way of transmitting heritable adaptations other than mutations in the DNA sequence, so what?? It just introduces one more way that evolution can happen, thus strengthening evolutionary theory."
Actually it strengthens design, because you have unused adaptations being carried around by animals before they are put to use, and a mechanism which causes them to be put into play. Evolution can't look ahead to see what kinds of adaptations it needs to pre-code into its genome to be adaptable for the future.
"Yeah, if you want to make up your own definition of the word "evolution".
The part you forget is how much we actually agree on. We agree on change over time, on genetics, on the existence of mutations, and likely on epigenetic change. The part we disagree on is that these processes are capable of producing the abundance of life we see on earth out of initial single-celled life. This requires a building up of systems, of an increase in the complexity of interactions. This is what your example failed to show. If evolution simply means "change in allele frequency of populations over time", then you and I have no argument. However, wrapped up in evolution are the notions of universal common ancestry and specfied complexity without design. I disagree with both of those notions.
"In particular, evolution does not require the creation of "information", whatever that is. (Creationists never provide a means of measuring this quantity to see whether it's being increased or not.)"
http://www.trueorigin.org/spetner2.asp
"Even if you did want to argue that evolution has something to do with "increasing information", mutations can and do add completely new genes to the genome, by known and observed mechanisms. What about that do you think is incompatible with your (heuristic, folk) definition of "increase in information"? How are you going to define that away so that new genes can never add information?"
You forget that in living things everything occurs in systems. See the above article. He gives some good ways to measure complexity in biological systems, including:
* Level of catalytic activity
* Specificity with respect to the substrate
* Strength of binding to cell structure
* Specificity of binding to cell structure
* Specificity of the amino-acid sequence devoted to specifying the enzyme for degradation
Biological systems are not just single enzymes acting alone. There are enzymes that build up and tear down, which have to coordinate with each other. They have to work in unity together, in a very specified way.
"No, they announced that they're not publishing anything on intelligent design. And if an editor bypassed the normal peer review process to publish something on flat-Earth theory, I'd probably issue a resolution to that effect too."
The normal peer review process was not bypassed. It was peer-reviewed by three specialists.
"What was said was that scientists like to break existing theories."
That doesn't make them less immune to groupthink, which was my point.
"Creationists don't even have the evidence to take down a minor theory."
And strangely, ever since Darwin it seems that mere stories have been substituted for scientific evidence and taken as fact, as long as it conforms with evolution.
I have, on occasion, gone there. I don't like it for several reasons:
1) too many posts 2) most people are there just to hear themselves talk 3) there is very little good argument there, and a whole lot of name-calling. Some of it is scientific-sounding name-calling, but name-calling nonetheless.
"Incidentally, you must talk to different creationists than I do. They won't even admit different species are related, let alone different genuses within a family."
AiG, ICR, and all the other major creationists websites all agree that speciation occurs, and in fact, at least AiG believes that it occurs at a much faster rate than evolutionists believe. The difference is that none of these organizations believes that complex biologic machinery can arise by chance. If none of the creationists you've talked to has heard or read any of this material, I'd suggest you choose better friends:)
"Why should they agree? They're two different methods."
Unless one is completely wrong, the method of determining phylogeny should not matter -- it should point to the same tree.
Otherwise, how would you know which one is correct? By morphology? But then again, you are the one proclaiming that morphology doesn't provide the answers one may think it does.
"You can see this happen on a small scale with bacteria becoming resistant to anti-biotics. The changes in the bacteria are very physical. But I suppose this is not macroscopic enough for you."
I know of many ways that bacteria become resistant, and I don't think any of them qualify as evolution.
1) Natural selection -- the resistant bacteria live, the non-resistant ones died. No new information, in fact we're losing information within the population.
2) Plasmids -- antibiotic resistance can be transferred between bacteria through plasmids. These plasmids are already in existence, and no new information takes place.
3) Removal of a pump -- if a mutation of a gene causes a bacteria to _lose_ the ability to pump a large class of material in, some of which happens to be antibiotic, this can hardly be qualified as the kind of evolution required to go from minimal complexity to maximal complexity, because we're going the wrong way. If instead you showed that brand new kinds of cellular pumps were being generated in response, and not as the result of plasmids or any other pre-programmed response, that would be something.
"I don't suppose you believe all the 'historical' accounts of ancient gods and goddesses, atlantis, fantastic creatures like cyclopses, etc etc?"
As I pointed out, the difference is that there is agreement among cultures that the event happened, and for a long time artifacts of the event remained in public viewing.
"in which case you would have to claim that all our dating methods, and huge amounts of other research are false"
There are many reasons to believe that is the case.
"Scientists have looked honestly at evolution. There is no other possibilities."
There are many scientists who disagree. Or do you think Jonathan Wells, Michael Behe, Ariel Roth have done nothing scientific in their entire careers? Why did the Smithsonian's peer-reviewed biology journal include an article on Intelligent Design? If the editor was biased, how did such a prominent scientist come to be biased towards Intelligent Design if all the evidence points away from it? This whole "the argument is closed" idea is nothing more than a power grab.
"Your own link has shown that at least one creationist 'evidence' is full of dishonest reporting."
You don't think that evolutionists are capable of dishonest reporting? This is silly. The fact that there exists one or many dishonest reports from creationists does not invalidate creationism. The same is true of evolutionists.
"As I've said before, creationism does not make any usefull predictions."
The fact that Brutus killed Caesar does not make any useful predictions. The question is if it is true. Creation, by its very definition, is speaking of one or multiple singular events. To say that singular events don't happen because they aren't subject to mathematical reasoning is silly.
"Scientists love any break in current theory because it always gives insights to improved theorems. If they were outraged, it would be because of the quality of research."
The statement of the Biological Society of Washington is amusing at best. Instead of criticizing research methods or other scientific grounds, they simply announce that now it is a matter of policy not to publish ideas that are counter to the status quo. They said that it is outside their normal scope (Taxonomy) which Sternberg fairly easily repudiates in his answer.
"Scientists love any break in current theory because it always gives insights to improved theorems. If they were outraged, it would be because of the quality of research."
I love it when people say "scientists can't be wrong because they are scientists. It makes them superhuman with regard to the influences that happen to mere mortals."
Also I forgot to point out that selective pressures do not necessarily maintain or let genes fall into disrepair. Many pseudogenes are very highly conserved.
"See, again, a theory needs to be able to make predictions, otherwise it is not a scientific theory."
This is correct, and to the degree that evolution makes predictions, I and other creationists have found little problem with it. If you are talking about evolution == genetics, then for a large part of "evolution" we are in total agreement.
"Again, what mendel thought has little relevance on current theory."
Except that he hasn't been shown to be wrong.
"A quick search for this only turned up religious sites, and no scientific papers"
Here is Talk.Origins on the matter:
http://www.talkorigins.org/faqs/dinosaur/blood.h tm l
I'll let you decide what to make of it all.
"I'm glad you think that, but I still have not seen any evidice of this."
How about historical accounts? Do historical accounts simply not matter when evolution contradicts them? Or should we believe the historians? Here is what Josephus said:
" However, the Armenians call this place , the Place of Descent; for the ark being saved in that place, its remains are showed there by the inhabitants to this day.
Now all the writers of barbarian histories make mention of this flood, and of this ark; among whom is Berossus the Chaldean. For when he was describing the circumstances of the flood, he goes on thus: "It is said, there is still some part of this ship in Armenia, at the mountain of the Cordyaeans; and that some people carry off pieces of the bitumen, which they take away, and use chiefly as amulets, for the averting of mischiefs."--Hieronymus the Egyptian also, who wrote the Phenician antiquities, and Manases, and a great many more, make mention of the same. Nay, Nicholas of Damascus, in his ninety-sixth book, hath a particular relation about them; where he speaks thus: "There is a great mountain in Armenia, over Minyas, called Baris, upon which it is reported, that many who fled at the time of the deluge were saved; and that one who was carried in an ark, came on shore upon the top of it; and that the remains of the timber were a great while preserved. This might be the man about whom Moses the legislator of the Jews wrote" (Josephus, Antiquities of the Jews, I, iii, 5 and 6, translated by William Whiston).
"Way to twist things there. There is no 'upwards' or 'downwards' to evolution."
Yes and no. Evolution certainly says that everything started out as simple life forms. Obviously these simple life-forms had to gain complexity in order to engender life as we know it today. Therefore, evolution must account for this increase in complexity. If there is no mechanism in evolution to account for increase in complexity, then universal common ancestry is false. The fact is that even with beneficial mutations there is not a known case of increasingly complex system.
"I am not attacking your beliefs."
Didn't think you were.
"But I do not want my children to be taught religous doctine as though it is truth or scientific in nature."
Interestingly, noone is asking for this. So, great! What people _are_ asking for is an honest look at evolution, where it fits the data, where it doesn't fit, and what the other possibilities are.
"If you want to form an opinion, read books on how evolution works, read books on the scientific process."
Going through Climbing Mount Probable right this minute.
"Please do not blindly listen to what your creationist friends are telling you."
I don't. However, it might interest you to know that my most vocal creationist friends actually used to be evolutionists until they actually started looking at the facts. They had simply assumed that evolution was the mechanism God used to create, until they examined the evidence for evolution and went "wait a minute..."
Remember, that there is a HUGE cultural bias against anything remotely regarded as being anti-evolutionary in nature. Take the recent fiasco with the Proceedings of the Biological Socie
It's not just that -- it's that at the beginning of multicellular life, we have the sudden appearance of almost every known body plan. There is no evidence whatsoever that these came about gradually. Darwinism predicts that the changes in species happens by a gradual process, that small changes add up to big changes. Yet in the Cambrian rock, we have all of the big changes appearing all at once. There is no evidence that any of this is the accumulation of small changes. Neo-Darwinism simply has no way to account for this, and it usually winds up with Darwinists claiming that the evidence is bad or that we need another mechanism for larger morphological changes in organisms.
You are mistaking circular reasoning as proof. Case in point:
"In fact, all our alignment algorithms are based on the theory of evolution, and it's been shown that including ideas such as evoltionary trees in alignment algorithms drastically improves alignments."
Or, to word another way, "in order to get back good phylogenic trees, we have to bias the search towards it."
"The fact that mendel was a creationast has nothing to do with current thought."
Mendel's argument was that because genes are preserved and recombined in whole form, that it does not provide the gradualistic power to transform one species into another, and instead provides boundaries beyond which species cannot go. Even with mutations, this hypothesis has not been shown to be incorrect.
"Whatever you want to call it, it is not a scientific theory and has no place in a science classroom."
Neither is Universal Common Ancestry. It, too, is a historical stance.
"Given that there is no evidence for it other than a myth, it also does not belong in a history classroom."
No evidence? There's actually quite a bit of evidence if you remove your evolutionary preconceptions. For instance:
* Dinosaur bones have been found with hemoglobin products and unfossilized, which would have disintegrated if they had been around for millions of years
* Many mechanisms show evidence of irreducible complexity. While irreducible complexity is not completely proven, attempts to disprove irreducible complexity have not been successfuly. The best I've seen is showing that one or two pieces of bacterial flagellum can have other uses, not that one could line up intermediate stages between those other uses and actual flagellum.
* Noah's Ark has been known throughout history, and only in the last thousand years has it been unfindable. 2000 years ago ther were regular pilgrimages to go and see it.
* The primary progress of genetics is actually downward, as an initial good creation followed by degeneration would suggest. Downward evolution is the norm. Blind cave fish, the numerous genetic diseases in humans, and the general direction of inheritted mutations all point downward. There are instances of modifications that are beneficial, but none of them involve the creation of whole systems of proteins, which is required for evolution to work. Also, some are confused by epigenetic modifications that are heritable. These are not mutations, these are pre-coded, yet heritable, adaptations that can be triggered in organisms.
"This is not a vacuous procedure that dismisses any misplacement in the hierarchy as convergent evolution; different features in the same species consistently being placed in different locations in the hierarchy would count as a falsification of evolution."
This does happen quite frequently, and it is always explained away as convergent evolution. Just look at the placental/marsupial convergence. Two independent flying squirrels independently developed my random mutations over millions of years, with little difference except being a marsupial instead of a placental? Or the tasmanian wolf versus the placental wolf? Or the placental saber-tooth tiger versus the marsupial? These are not just one or two features, these are entire convergently evolved genus and species. The "same ecological niche" idea is nice, except that the placentals and marsupials grew up in completely different environments, and thus completely different "selective pressures", but yet both lines produced a flying squirrel.
"Andit's obvious that you're going to get different locations depending on which genes you sequence, because a proper location depends on all the genes, especially when comparing highly conserved sequences to non-conserved sequences."
Man, can't you recognize a circular argument when you see it? Is there a way to know before looking which sequences are going to be highly conserved? No, there isn't. What about unconserved? Nope. In fact, there are a lot of highly conserved sequences in pseudogenes which were quite surprising, and evolutionists still have no idea why. Thus, the reason for calling something unconserved or very highly conserved is that it doesn't match what a phylogenic analysis would expect.
Note that all algorithms which take several genes into account for determining phylogeny are actually heuristically biased towards a traditional phylogeny, because there just isn't enough processing power to look at all the possibilities. In addition, there are extreme differences between studies done based on maximum parsimony and maximum likelihood.
"Example?"
http://dml.cmnh.org/1998Dec/msg00381.html
"The data show no such thing. You made that up."
I can't find the reference right now, but there was an article which showed the various mechanisms by which cells worked, and pointed out that there wasn't a good intermediate system between these systems, and the evidence, based on phylogenic analysis of the DNA, indicates that the common relative of all groups had to have contained all of the systems originally. Sorry I can't find the reference. I'll post it if I run across it again.
"Nevertheless, if systematics routinely led to classifications of species on widely different parts of the tree depending on what you're looking systematics would be a failure. However, that doesn't happen."
Most of the times where the classification works reliably is only within a family or genus, where creationists and evolutionists would likely agree that a given set of creations came from the same ancestors.
"Biological Proceedings of the Royal Society" claims that the crab form evolved five separate times based on DNA phylogeny. Another article places turtles as the closest relative of birds. In the arthropods, the DNA phylogenies do not agree at all with morphologic data. In New Mexico, two species of Salamander that are often indistinguishable even to experts have been found to have very different genomes.
Slashdot Mirror
I think the problem is that the humanities thought of themselves as being scientific. They simply are not. The problem of the humanities is that story-telling has become equivalent to established fact. This can be seen in things like the DaVinci Code, Hegellian Dialectic view of history, and most of source criticism (and several other literary criticisms).
What's really funny is when people try to perform source criticism on modern works, just to have the authors reveal the true history of the work. It shows that while these are amusing exercises, there's really no factual basis to them.
Actually, faith was the driving force for the origin of modern science. Ultimately, science relies on a huuge amount of faith -- faith that the universe is governed by rational, unchanging laws. That faith came from the faith that we had a rational, unchanging creator. Science was the search for the why's and how's of how God worked. It did not close scientific inquiry -- it opened it up.
And to think we replaced it with _English_. Oh, the humanity!
I've patented lawyers. They should be turning around and attacking you back very soon. Or perhaps attacking themselves.
It's been available for years for people who know latin.
I hope you're aware that Ankylasaurus has a complicated nasal passage of "unknown function". Why do you assume that the description is false? We know of many current animals that do the same, although much smaller.
"If your theory *predicts* new evidence, you have something useful, not merely an entertaining story."
That sounds a lot like evolution.
"Early evolutionary theory predicted extinct species."
The evidence for extinct species already existed before evolutionary theory. You can't really say that evolution predicted it.
However, creationists (i.e. Mendel) were the ones that came up with Genetics. Mendel believed that genes showed that there were limits to variation, a claim which still has not been disproven by evolutionists (mutation expands the amount of variation slightly, but this still does not impact the overall argument of limitation of variation).
"Go find some evidence that dinosaurs lived in the same time period as writing/farming/animal-domesticating/civilization- creating humans. Find any evidence."
How about the coelacanth fish? It was believed to only exist 70 million years ago, on the basis of the rock layers in which it was found (no fossils of coelacanth fish after the dinosaurs). Yet, eventually we found them at a fish market -- unchanged after all that time, no less!
Then you add in the exceedingly accurate detail of the drawings of Pteradactyls by native americans who called the Thunderbirds. You think they just "made up" an animal that happened to look exactly like pteradactyls?
At the very least this shows that you cannot base extinction dates on fossil evidence. Some think that this indicates that the geologic column doesn't mean what most say it means.
That's assuming that the geologic column is correct. There are several species that were thought to be extinct based on their position in the fossil record, but were later found in meat markets in certain geographic areas. They are _only_ found in rocks dating back to the dinosaurs, and not in any "younger" ones. Yet they are extant today.
The following dinosaurs (among others) have been described in writings by human, and has even spawned a new field - paleocryptozoology:
* pteradactyls -- these were called "Thunderbirds" by native americans
* Ankylosaurus -- called "Leviathan" in the Bible.
* Brontosaurus -- called "Behemoth" in the Bible.
Pteradactyls are especially interesting, as the native american drawings of Thunderbirds match pretty much exactly what we have in museums.
There is a lot of doubt in the geologic column, especially now that we have more data on just how fast geologic structures can form. For example, stratified rock has historically been used to show that a rock formation underwent years and years of sediment deposition, and could essentially be counted like tree rings. However, recent volcanic eruptions have shown that such sediment deposition can literally be laid down in HOURS.
Actually, embryology developments have shown that when you place DNA into a developing animal from an egg, the embryo, as long as it lives, retains mostly just the properties of the original organism, not the transplanted DNA.
"In theory, yes. But since nobody will ever do that, it's not much of a feature."
We would sure use that, here.
"In fact, you can use good old "ln" to create multiple different views of sets of files reflecting different information."
Except that using "ln" is arduous, and would probably not allow you to do complex querying.
"But nobody ever does."
Because you only get a subset of the features for a WHOLE LOT MORE work. How many office workers do you know that would even understand the concept of "ln"?
I haven't used beagle, but here's the general case for large-scale meta-data searching:
If I'm looking for information on, say, the E-Zuper project I working on at work. This allows me to turn up everything that refers to it, whether its an email, a document, a bookmark -- anything. And note that two of those things only exist within certain applications -- the email and the bookmark aren't physical files. They are conceptual objects.
Likewise, you could say, "look at everything I did yesterday", and turn up emails, website visits, documents, etc.
Or you could say, "show me everything by Stan Sterner" and the same thing would happen.
For those of us whose data repositories are diverse and not always file-based, it would be a great blessing. Not to mention that meta-searching is useful even just with normal documents.
If you can assign arbitrary meta attributes, you can bypass the limitations of a traditional directory structure. For example, I can search and find documents that I'm supposed to have completed by tomorrow, if I include an attribute such as "date-needed" on those files. This will pull from every folder (which are likely arranged by project, not date). I could also add priority tags, and search by priority.
"For instance, in your placental/marsupial example, these species are really not as similar genetically as they appear visually."
Do you have a link? I have been searching for a while for some data on how marsupials and placentals compare in their molecular phylogeny, but couldn't find anything (actually, I think I found something which referenced a single marsupial, but I was hoping for more complete information).
"Indeed, they're really not as similar morphologically as they appear visually, when you get down to it; there are differences other than merely placental/marsupial."
There are a few differences, certainly, but many evolutionary textbooks actually make quite a big deal about how similar they are, and that looking solely at morphology might place them in the wrong part of the evolutionary tree.
"And no, these organisms do not have completely different selective pressures; they do indeed live in similar ecological niches."
You are confusing selective pressures and ecological niches. They are different. An ecological niche is the function you play within a given environment. Selective pressures are what cause changes. Wolves and mice occupy different ecological niches, but being in a niche doesn't cause a mice to become a wolf. Selective pressures are what cause change -- adaptation to environment, etc. What you seem to be proposing is that in two vastly different environments, the same body forms arose independently to cover not-yet-existing ecological niches.
"an inability to consistently place species in the hierarchy (e.g. the genetic hierarchy doesn't match up with the morphological hierarchy, etc.) That does not happen."
Take a look at many of the recent phylogenic studies, and note how many of them are surprised by the number of times X has arisen independently in the environment. Each of these "surprises" is an example of what you are saying.
A good site which follows such things fairly well is Creation Safaris.
"Now who's being circular. You can't use myths about Noah's Ark in order to prove other myths (the Bible). In point of fact, we have no evidence that Noah's Ark actually existed, even if some people THOUGHT (and still do think) it did."
You missed the point of the quote. In Josephus's day, the evidence was still around. I'm sorry they didn't take pictures in order to satisfy every skeptic that decides that the historians of that day were wrong simply because they disagree with modern preconceptions about the world.
The point of mentioning the flood is that it is all part of the same history, including a large part of the explanation of fossil distribution (like, explaining why nearly all fossil tracks go uphill).
"This is nonsense, as the entire fossil record shows. Hell, even Answers in Genesis has the old "mutations are bad" on their list of "arguments creationists shouldn't use". (Instead, they advocate the even vaguer "genetic information decreases argument".)"
Perhaps you should go back and read both what I said and what AiG says. We're basically saying the same thing on this one. However, the fossil record isn't nearly as clear as you think. For example, human tracks have been discovered in earlier sediments than evolutionists want to admit, so they simply called them austrolopithecus tracks, even though they do not match the foot bones of the austrolopithecus. Numerous inconsistencies has been shown. You should take a look at this discussion of homology.
"Genomic studies certainly show new genetic networks arising."
Genomic studies are only valid if evolution is assumed to be true. Certainly if you have already assumed evolution, if you saw different information in genome A and genome B, then you would assume that it arose through evolution. But that is not the equivalent of proof, or in fact anywhere near that.
We have not seen new networks of genes forming, even after thousands of generations of bacteria and fruit flies. We simply have not observed any case where new networks of information arise simply through mutation.
"No, we can't watch that happen on laboratory scales, but so what?"
Then in what way is it proven? All you have without that is:
different genomes have different genes
You can't say that one arose from the other. If you are using evolution to interpret the data, you can't use the interpretation as evidence for evolution. The data itself -- different genomes having different genes -- says nothing about how those genes got there.
"And what is it, exactly, about epigenetics that throws doubt on the whole of modern evolutionary biology?"
I didn't say that it did. I simply said that some heritable changes in organisms is not the result of new or even different genes, but of epigenetic mechanisms.
"If we find out a new way of transmitting heritable adaptations other than mutations in the DNA sequence, so what?? It just introduces one more way that evolution can happen, thus strengthening evolutionary theory."
Actually it strengthens design, because you have unused adaptations being carried around by animals before they are put to use, and a mechanism which causes them to be put into play. Evolution can't look ahead to see what kinds of adaptations it needs to pre-code into its genome to be adaptable for the future.
"Yeah, if you want to make up your own definition of the word "evolution".
The part you forget is how much we actually agree on. We agree on change over time, on genetics, on the existence of mutations, and likely on epigenetic change. The part we disagree on is that these processes are capable of producing the abundance of life we see on earth out of initial single-celled life. This requires a building up of systems, of an increase in the complexity of interactions. This is what your example failed to show. If evolution simply means "change in allele frequency of populations over time", then you and I have no argument. However, wrapped up in evolution are the notions of universal common ancestry and specfied complexity without design. I disagree with both of those notions.
"In particular, evolution does not require the creation of "information", whatever that is. (Creationists never provide a means of measuring this quantity to see whether it's being increased or not.)"
http://www.trueorigin.org/spetner2.asp
"Even if you did want to argue that evolution has something to do with "increasing information", mutations can and do add completely new genes to the genome, by known and observed mechanisms. What about that do you think is incompatible with your (heuristic, folk) definition of "increase in information"? How are you going to define that away so that new genes can never add information?"
You forget that in living things everything occurs in systems. See the above article. He gives some good ways to measure complexity in biological systems, including:
* Level of catalytic activity
* Specificity with respect to the substrate
* Strength of binding to cell structure
* Specificity of binding to cell structure
* Specificity of the amino-acid sequence devoted to specifying the enzyme for degradation
Biological systems are not just single enzymes acting alone. There are enzymes that build up and tear down, which have to coordinate with each other. They have to work in unity together, in a very specified way.
"No, they announced that they're not publishing anything on intelligent design. And if an editor bypassed the normal peer review process to publish something on flat-Earth theory, I'd probably issue a resolution to that effect too."
The normal peer review process was not bypassed. It was peer-reviewed by three specialists.
"What was said was that scientists like to break existing theories."
That doesn't make them less immune to groupthink, which was my point.
"Creationists don't even have the evidence to take down a minor theory."
And strangely, ever since Darwin it seems that mere stories have been substituted for scientific evidence and taken as fact, as long as it conforms with evolution.
I have, on occasion, gone there. I don't like it for several reasons:
1) too many posts
2) most people are there just to hear themselves talk
3) there is very little good argument there, and a whole lot of name-calling. Some of it is scientific-sounding name-calling, but name-calling nonetheless.
"Incidentally, you must talk to different creationists than I do. They won't even admit different species are related, let alone different genuses within a family."
:)
AiG, ICR, and all the other major creationists websites all agree that speciation occurs, and in fact, at least AiG believes that it occurs at a much faster rate than evolutionists believe. The difference is that none of these organizations believes that complex biologic machinery can arise by chance. If none of the creationists you've talked to has heard or read any of this material, I'd suggest you choose better friends
"Why should they agree? They're two different methods."
Unless one is completely wrong, the method of determining phylogeny should not matter -- it should point to the same tree.
Otherwise, how would you know which one is correct? By morphology? But then again, you are the one proclaiming that morphology doesn't provide the answers one may think it does.
"You can see this happen on a small scale with bacteria becoming resistant to anti-biotics. The changes in the bacteria are very physical. But I suppose this is not macroscopic enough for you."
I know of many ways that bacteria become resistant, and I don't think any of them qualify as evolution.
1) Natural selection -- the resistant bacteria live, the non-resistant ones died. No new information, in fact we're losing information within the population.
2) Plasmids -- antibiotic resistance can be transferred between bacteria through plasmids. These plasmids are already in existence, and no new information takes place.
3) Removal of a pump -- if a mutation of a gene causes a bacteria to _lose_ the ability to pump a large class of material in, some of which happens to be antibiotic, this can hardly be qualified as the kind of evolution required to go from minimal complexity to maximal complexity, because we're going the wrong way. If instead you showed that brand new kinds of cellular pumps were being generated in response, and not as the result of plasmids or any other pre-programmed response, that would be something.
"I don't suppose you believe all the 'historical' accounts of ancient gods and goddesses, atlantis, fantastic creatures like cyclopses, etc etc?"
As I pointed out, the difference is that there is agreement among cultures that the event happened, and for a long time artifacts of the event remained in public viewing.
"in which case you would have to claim that all our dating methods, and huge amounts of other research are false"
There are many reasons to believe that is the case.
"Scientists have looked honestly at evolution. There is no other possibilities."
There are many scientists who disagree. Or do you think Jonathan Wells, Michael Behe, Ariel Roth have done nothing scientific in their entire careers? Why did the Smithsonian's peer-reviewed biology journal include an article on Intelligent Design? If the editor was biased, how did such a prominent scientist come to be biased towards Intelligent Design if all the evidence points away from it? This whole "the argument is closed" idea is nothing more than a power grab.
"Your own link has shown that at least one creationist 'evidence' is full of dishonest reporting."
You don't think that evolutionists are capable of dishonest reporting? This is silly. The fact that there exists one or many dishonest reports from creationists does not invalidate creationism. The same is true of evolutionists.
"As I've said before, creationism does not make any usefull predictions."
The fact that Brutus killed Caesar does not make any useful predictions. The question is if it is true. Creation, by its very definition, is speaking of one or multiple singular events. To say that singular events don't happen because they aren't subject to mathematical reasoning is silly.
"Scientists love any break in current theory because it always gives insights to improved theorems. If they were outraged, it would be because of the quality of research."
Read for yourself Richard Steinberg's account. For fairness, I'll give you Panda's Thumb's Rebuttal.
The statement of the Biological Society of Washington is amusing at best. Instead of criticizing research methods or other scientific grounds, they simply announce that now it is a matter of policy not to publish ideas that are counter to the status quo. They said that it is outside their normal scope (Taxonomy) which Sternberg fairly easily repudiates in his answer.
"Scientists love any break in current theory because it always gives insights to improved theorems. If they were outraged, it would be because of the quality of research."
I love it when people say "scientists can't be wrong because they are scientists. It makes them superhuman with regard to the influences that happen to mere mortals."
By the way, here's the original article:
http://www.pnas.org/cgi/content/full/94/12/6291
Also I forgot to point out that selective pressures do not necessarily maintain or let genes fall into disrepair. Many pseudogenes are very highly conserved.
"See, again, a theory needs to be able to make predictions, otherwise it is not a scientific theory."
This is correct, and to the degree that evolution makes predictions, I and other creationists have found little problem with it. If you are talking about evolution == genetics, then for a large part of "evolution" we are in total agreement.
"Again, what mendel thought has little relevance on current theory."
Except that he hasn't been shown to be wrong.
"A quick search for this only turned up religious sites, and no scientific papers"
Here is Talk.Origins on the matter:
http://www.talkorigins.org/faqs/dinosaur/blood.h tm l
I'll let you decide what to make of it all.
"I'm glad you think that, but I still have not seen any evidice of this."
How about historical accounts? Do historical accounts simply not matter when evolution contradicts them? Or should we believe the historians? Here is what Josephus said:
" However, the Armenians call this place , the Place of Descent; for the ark being saved in that place, its remains are showed there by the inhabitants to this day.
Now all the writers of barbarian histories make mention of this flood, and of this ark; among whom is Berossus the Chaldean. For when he was describing the circumstances of the flood, he goes on thus: "It is said, there is still some part of this ship in Armenia, at the mountain of the Cordyaeans; and that some people carry off pieces of the bitumen, which they take away, and use chiefly as amulets, for the averting of mischiefs."--Hieronymus the Egyptian also, who wrote the Phenician antiquities, and Manases, and a great many more, make mention of the same. Nay, Nicholas of Damascus, in his ninety-sixth book, hath a particular relation about them; where he speaks thus: "There is a great mountain in Armenia, over Minyas, called Baris, upon which it is reported, that many who fled at the time of the deluge were saved; and that one who was carried in an ark, came on shore upon the top of it; and that the remains of the timber were a great while preserved. This might be the man about whom Moses the legislator of the Jews wrote" (Josephus, Antiquities of the Jews, I, iii, 5 and 6, translated by William Whiston).
"Way to twist things there. There is no 'upwards' or 'downwards' to evolution."
Yes and no. Evolution certainly says that everything started out as simple life forms. Obviously these simple life-forms had to gain complexity in order to engender life as we know it today. Therefore, evolution must account for this increase in complexity. If there is no mechanism in evolution to account for increase in complexity, then universal common ancestry is false. The fact is that even with beneficial mutations there is not a known case of increasingly complex system.
"I am not attacking your beliefs."
Didn't think you were.
"But I do not want my children to be taught religous doctine as though it is truth or scientific in nature."
Interestingly, noone is asking for this. So, great! What people _are_ asking for is an honest look at evolution, where it fits the data, where it doesn't fit, and what the other possibilities are.
"If you want to form an opinion, read books on how evolution works, read books on the scientific process."
Going through Climbing Mount Probable right this minute.
"Please do not blindly listen to what your creationist friends are telling you."
I don't. However, it might interest you to know that my most vocal creationist friends actually used to be evolutionists until they actually started looking at the facts. They had simply assumed that evolution was the mechanism God used to create, until they examined the evidence for evolution and went "wait a minute..."
Remember, that there is a HUGE cultural bias against anything remotely regarded as being anti-evolutionary in nature. Take the recent fiasco with the Proceedings of the Biological Socie
It's not just that -- it's that at the beginning of multicellular life, we have the sudden appearance of almost every known body plan. There is no evidence whatsoever that these came about gradually. Darwinism predicts that the changes in species happens by a gradual process, that small changes add up to big changes. Yet in the Cambrian rock, we have all of the big changes appearing all at once. There is no evidence that any of this is the accumulation of small changes. Neo-Darwinism simply has no way to account for this, and it usually winds up with Darwinists claiming that the evidence is bad or that we need another mechanism for larger morphological changes in organisms.
You are mistaking circular reasoning as proof. Case in point:
"In fact, all our alignment algorithms are based on the theory of evolution, and it's been shown that including ideas such as evoltionary trees in alignment algorithms drastically improves alignments."
Or, to word another way, "in order to get back good phylogenic trees, we have to bias the search towards it."
"The fact that mendel was a creationast has nothing to do with current thought."
Mendel's argument was that because genes are preserved and recombined in whole form, that it does not provide the gradualistic power to transform one species into another, and instead provides boundaries beyond which species cannot go. Even with mutations, this hypothesis has not been shown to be incorrect.
"Whatever you want to call it, it is not a scientific theory and has no place in a science classroom."
Neither is Universal Common Ancestry. It, too, is a historical stance.
"Given that there is no evidence for it other than a myth, it also does not belong in a history classroom."
No evidence? There's actually quite a bit of evidence if you remove your evolutionary preconceptions. For instance:
* Dinosaur bones have been found with hemoglobin products and unfossilized, which would have disintegrated if they had been around for millions of years
* Many mechanisms show evidence of irreducible complexity. While irreducible complexity is not completely proven, attempts to disprove irreducible complexity have not been successfuly. The best I've seen is showing that one or two pieces of bacterial flagellum can have other uses, not that one could line up intermediate stages between those other uses and actual flagellum.
* Noah's Ark has been known throughout history, and only in the last thousand years has it been unfindable. 2000 years ago ther were regular pilgrimages to go and see it.
* The primary progress of genetics is actually downward, as an initial good creation followed by degeneration would suggest. Downward evolution is the norm. Blind cave fish, the numerous genetic diseases in humans, and the general direction of inheritted mutations all point downward. There are instances of modifications that are beneficial, but none of them involve the creation of whole systems of proteins, which is required for evolution to work. Also, some are confused by epigenetic modifications that are heritable. These are not mutations, these are pre-coded, yet heritable, adaptations that can be triggered in organisms.
"This is not a vacuous procedure that dismisses any misplacement in the hierarchy as convergent evolution; different features in the same species consistently being placed in different locations in the hierarchy would count as a falsification of evolution."
This does happen quite frequently, and it is always explained away as convergent evolution. Just look at the placental/marsupial convergence. Two independent flying squirrels independently developed my random mutations over millions of years, with little difference except being a marsupial instead of a placental? Or the tasmanian wolf versus the placental wolf? Or the placental saber-tooth tiger versus the marsupial? These are not just one or two features, these are entire convergently evolved genus and species. The "same ecological niche" idea is nice, except that the placentals and marsupials grew up in completely different environments, and thus completely different "selective pressures", but yet both lines produced a flying squirrel.
Funny that.
"Andit's obvious that you're going to get different locations depending on which genes you sequence, because a proper location depends on all the genes, especially when comparing highly conserved sequences to non-conserved sequences."
Man, can't you recognize a circular argument when you see it? Is there a way to know before looking which sequences are going to be highly conserved? No, there isn't. What about unconserved? Nope. In fact, there are a lot of highly conserved sequences in pseudogenes which were quite surprising, and evolutionists still have no idea why. Thus, the reason for calling something unconserved or very highly conserved is that it doesn't match what a phylogenic analysis would expect.
Note that all algorithms which take several genes into account for determining phylogeny are actually heuristically biased towards a traditional phylogeny, because there just isn't enough processing power to look at all the possibilities. In addition, there are extreme differences between studies done based on maximum parsimony and maximum likelihood.
"Example?"
http://dml.cmnh.org/1998Dec/msg00381.html
"The data show no such thing. You made that up."
I can't find the reference right now, but there was an article which showed the various mechanisms by which cells worked, and pointed out that there wasn't a good intermediate system between these systems, and the evidence, based on phylogenic analysis of the DNA, indicates that the common relative of all groups had to have contained all of the systems originally. Sorry I can't find the reference. I'll post it if I run across it again.
"Nevertheless, if systematics routinely led to classifications of species on widely different parts of the tree depending on what you're looking systematics would be a failure. However, that doesn't happen."
Most of the times where the classification works reliably is only within a family or genus, where creationists and evolutionists would likely agree that a given set of creations came from the same ancestors.
"Biological Proceedings of the Royal Society" claims that the crab form evolved five separate times based on DNA phylogeny. Another article places turtles as the closest relative of birds. In the arthropods, the DNA phylogenies do not agree at all with morphologic data. In New Mexico, two species of Salamander that are often indistinguishable even to experts have been found to have very different genomes.