Creationist Confusion, page 7

When I was talking about 'use it or lose it' I meant the species as a whole. (Not Lamarkian)
Without occasional malaria the sickle cell might at some point disappear from the genepool. So I guess I mean all potentially beneficial genes should be utilized by some portion of the species to keep those genes active as an adaptive trait.

Thanks for your clarification. I don�t think we are at odds at this issue.

It seems to me that the scrambling and re-pasting of genetic material together is 'designed' to create genetic variation. I am not sure if something like this happens in non-sexually reproducing species. But this was probably a big step in accellerating change in genetic code.

Interesting use of the term designed given the context of this thread. Again, this is not in dispute. I think it should be quite clear from my previous posts that synapsis and crossing over (not with John Edwards) IS a way of creating genetic variation. You�ve missed the point though. This merely reshuffles EXISTING genes. It doesn�t create new ones. No one suggests that reshuffling a deck of cards somehow generates a new package.

Have you heard of the 'Red Queen Theory'? Running/changing as fast as you can just to stay in place. Pathogenic organisms/viruses are constantly changing and the only way potential target organisms can keep up is to adapt and change rapidly too.
We do have immune systems, but this isn't sufficient defense against many organisms. It works often as a 'second time around' defense system.

Not sure why you mention this. There is no disagreement here.

I find it hard to believe there are not occasional transcription errors. In clone reproduction organisms this would pass the variation on.

Sorry, but this indicates that you don�t understand genetics, cellular replication, or transcription/translation. I didn�t say there weren�t occasional transcription errors. I said that transcription errors are not passed on to the next generation. This is absolutely true� time to break out that Bio101 text.

I also am inclined to think there are any number of errors that happen during Prophase one of Mieosis.

Again, this was discussed and acknowledged. Errors due occur. As you pointed out, overwhelmingly such errors have a negative consequence. You can believe whatever you wish, but it doesn�t make it true. You can search the literature until you�re blue in the face, and I can almost guarantee you, you will not find any examples of mistakes in meiosis leading to a positive change.

I have heard speculations that viruses have introduced variation of the genetic code. If these spred to or are in the reproductive cells these variations would be spread to offspring. We are very aware of severly injurious viruses like the flu, but it seems quite possible that there are a lot of more benign viruses, that because they are not injuriously apparent are not hunted for and therefore not noticed. It could be that many chunks of what we call our (human) DNA is actually some ancient virus that has been incorporated into our DNA.

This speculation about viruses certainly does exist. And you are correct, for any changes to be observed in higher organisms, germ-line cells must be affected. Viruses can be implicated in swapping of genetic information between certain species. But I must again point out the distinction between existing genes and creation of genes de novo. Viruses can shuffle genetic material around, and again, it doesn�t create new genes. I suppose it�s possible that there could be some sort of �exon shuffling� going on and generation of fusion proteins. However, if we talk about what we can observe: Fusion proteins have a history of distinctly being not beneficial, think: leukemia. Viruses have a history of ranging from innocuous or not necessarily harmful to completely fatal. Again, I would challenge one to search for information regarding the benefits of contracting a particular virus. This notion, that viruses are potential sources for macroevolutionary change, was postulated some time ago. Researchers still haven�t found this example of beneficial viruses, and not for lack of looking.

I believe the mechanisms for splicing genes may have come originally from observing certain viruses.

While I won�t address the veracity of this particular issue here, but even if it were true how is splicing of existing DNA info into the genome of the same or a very similar organism (based on the host range of viruses) evidence for macroevolution? Obviously the genes will still be there. Generally, when homologous recombination occurs, it replaces the existing gene, doesn�t usually duplicate it. Insertion of viral genomes into the genomes of it�s host tends to be very specific. When it�s not, problems tend to develop, again think: cancer.

It has been speculated that the mitocondria is actually an organism that combined with a nuclear cell.
Perhaps the nucleous was originally a cell within a cell.

Its called endosymbiosis. The theory isn�t that the mitochondria combined with a nucleus, rather it�s that a free living bacteria was engulfed by a free living cell, and have since become dependent on each other. Although once again the evidence for this is spotty at best. It is noteworthy that while the mitochondria do possess a genome, it is truncated, and not complete. Certain mitochondrial proteins are encoded in the nucleus. If it ever was a �free-living� organism, it certainly is no longer capable of sustaining itself outside of the cell. I am not sure what the relevance of proposing a �nuclear-endosymbiotic� theory is. I would also point out that you are virtually alone in this speculation. In all fairness, endosymbiotic theory does make efforts to account for the translocation of mitochondrial genes to the nuclear genome. I suggest reading said evidence prior to supporting this (or any) particular theory.

I can see where one might think that the virtual sameness between individuals in a species might imply that there isn't much to work with for creating original genes. But chimpanzees are only 2% different from ourselves.

First of all, given that human genome has just barely been sequenced, and only for a few individuals, and that to my knowledge NO chimp genome is complete, this is not really a good estimation of the homology. Furthermore if you�d actually read these papers, you�d realize that these experiments were performed using genome hybridization experiments and DNA �melting� curves coupled with kinetic analysis. This type of analysis is not good at discriminating between point mutations, insertions/deletions of large repeated regions of sequence, and other important facets of genomes. Let�s talk about what we DO KNOW about human and chimp DNA: Humans have 23 pairs of chromosomes while chimpanzees have 24. Some evolutionists believe that one of the human chromosomes has been formed through the fusion of two small chromosomes. To my knowledge all known chromosome fusions or translocations are overwhelmingly harmful, again, think leukemia.
At the ends of chromosomes a string of repeating DNA sequences called a telomere exists. This telomere prevents chromosomes from shortening through successive rounds of DNA replication. Chimpanzees and other apes have about 23 kilobases of telomeric repeats. Humans have much shorter telomeres, only 10 kilobases long. Humans are unique among all primates in this capacity. The Y chromosome in particular is of a different size and has many markers that do not line up between the human and chimpanzee. Scientists have prepared a human-chimpanzee comparative map of chromosome 21. �[L]arge, non-random regions of difference between the two genomes,� were observed. They found a number of regions that �might correspond to insertions that are specific to the human lineage.� The size of the chimpanzee genome is 10% greater than the size of the human genome, while certainly genome size and complexity are not necessarily related it is an interesting fact. Generally, these types of differences are not included in calculations of percent DNA homology. In what is one of the most extensive studies to my knowledge that compares human and chimp DNA, researchers compared roughly 19.8 million bases. Sounds like a lot, but represents less than 1% of the genome. They calculated a mean identity of 98.77% or 1.23% differences. However, this study only considered substitutions, ignoring insertions and deletions. A study by Britten (Britten, R.J. 2002. Proc. Natl. Acad. Sci. 99:13633-13635 examined the insertion/deletions between humans and chimps. In this study Britten looked at 779 kilobase pairs to carefully examine differences between chimpanzees and humans. It was in agreement with previous studies demonstrating about 1.4% of the bases had been substituted (98.6% similarity). However, in addition to this a much larger number of insertion/deletions were discovered. The large majority of these were 1 to 4 nucleotides in length, although there were some that were > 1000 base pairs long. Interestingly, the insertion/deletions added an additional 3.4 % of unique base pairs.

Previous studies that have focused on substitutions only have missed what is probably the greatest contribution to the genetic differences between chimps and humans. Missing nucleotides from one or the other seem to account for more than twice the number of substituted nucleotides. While the number of substitutions is about ten times higher than the number of insertion/deletions, the absolute number of nucleotides involved in insertion/deletions is greater. These insertion/deletions were reported to be equally represented in the chimp and human sequences. Thus, the insertions or deletions are not occurring in just the chimp or in just the human, which is suggestive of intrinsic differences in the genome rather than a modification of a pre-existing genome.
Furthermore, using percentages conceals an important fact: If 5% of the DNA between humans and chimps is different, this amounts to something like 150 Million DNA base pairs that are different between them, in addition to the things discussed above.

Meanwhile, other studies have demonstrated a remarkable similarity in the nuclear DNA and mtDNA among modern humans. Available DNA sequences from humans are so similar that some scientists conclude there is a �recent single origin for modern humans, with general replacement of archaic populations� (see: Knight, A. et al. 1996. Proc. Natl. Acad. Sci. 93:4360-4364.). Estimates for a date of a �most recent common ancestor� by the evolution camp places the �recent single origin� about 100,000-200,000 years ago. These estimates were based on comparisons with chimps, assuming a chimp-human common ancestor approximately 5 million years ago. Other studies using pedigrees or generational mtDNA comparisons have yielded a much more recent �most common recent ancestor,� and the creationists will love this, even one at ~6,500 years (See: Heyer, E., et al. 2001. Am J Hum Genet 69:1113-1126, Parsons T.J., et al. 1997. Nat. Genet. 15:363-368, and Sigurgardottir, S., et al. Am J Hum Genet 66:1599-1609). Bolded ref. indicates ~6500 year MCRA reference.

The above examples only further demonstrate that the conclusions of scientific investigations can produce different outcomes depending on how the study was performed. Humans and chimps have 95% or >98.5% homologous DNA depending on which nucleotides are included in the analysis and which are not. Modern humans can be shown to have a single recent ancestor <10,000, 100,000-200,000, or 5 million years ago depending on which relationships are assumed and which types of mutations and genomic differences are considered. I actually think I already posted most of this stuff in this thread in one of my discussions with Nygdan.

Note: I use the term 'junk' DNA because i don't know what the proper term for it is.

The more proper term, although quite possibly still incorrect, is non-coding DNA, while it�s not believed by ANYONE to encode protein information, I suppose other coding information is possible.

Junk is not necessarily useless, but often just out-dated.

Wrong� junk DNA is not outdated. Just because we don�t know all of the functions of a particular stretch of DNA doesn�t mean it�s out-dated or useless. That�s hubris. It�s like the appendix and all the other supposedly vestigial organs. A function may or may not be discovered for these things, but there is no justification for describing it as useless.

But much in the manner that junk people collect is sometimes put to use, this genetic material is available for use as new genetic combinations.

Again, this reflects on your lack of understanding of what is meant by the term junk DNA. Furthermore, I fail to see how EXISTING genetic information can be described as a source of new genetic information, unless you are talking about random mixing and shuffling of large regions of DNA, much like that which occurred in Brundle-Fly. While I suppose this is �possible� there is NO evidence to suggest that anything resembling that happens in genomes.

If certain chemicals are present they stimulate cells in the developing embryo to be whatever organ/tissue they are being called on to be. It could be with all this un-utilized (junk) gene code that if the right chemical stimulation were present many other traits/structures might be expessed.

Hmmm� I�m not sure why this non-coding DNA thing needs to be beaten to death this hard, but what can you do? Again making these types of statements really only reflects your lack of understanding of non-coding DNA. It�s called non-coding DNA for a very specific reason. I will attempt to make this reason very clear: Generally because nothing about this DNA sequence suggests it encodes information. Non-coding DNA is made up, in a large part, on repeated sequences of DNA. Repeating patterns in the genetic code don�t yield biological information. Furthermore much of this non-coding DNA lacks the ability to be expressed in the form of promoters, including multiple upstream and downstream promoter elements, and a start codon.

Further it might be we are the particular organisms we are not just because of the particular genetic code we have but also because of which genetic code is expessed. Not sure how the master control genes work. If they create the chemicals that stimulate some particular set of genes to activate (and/or shut some off).

Sigh.

It could be that if you stimulate the right set of genes (perhaps using anachronistic control genes) we would come out as some pre-cursor ancestor creature. Like our ancestor that we share with the chimpanzees. The idea of music and chords comes to mind. A master control gene is like pressing a key on an organ that plays an entire chord. We are a set of harmonies that are played with our genetic code, but all the harmonies for many of our ancestors may infact be intact within us. Keys just waiting idle unplayed.

Sigh� sounds like someone�s seen �Altered States� too many times.

It brings to mind the sick examples of a dropsila fly with fully formed leg growing out of its head and other oddities. They show that the code for any of our organs/structures/tissues is in any cell. I speculate that they may be vastly more than that. With the activation of the right set of idle master control genes we would be some other creature. This might be synthesized with using the chemicals created by some idle master control gene.

These master control genes you keep referring to are called homeobox or hox genes. I agree, antennapedia (legs instead of an antenna) is a bizarre thing to do to any creature, even a fruit fly. That each cell contains a complete genome is not in dispute, unless you are talking about immune cells. Thus you are correct: each cell possesses the blueprint for the entire organism. Altering of hox genes has never produced a new structure. A leg in place an antenna is NOT a new structure. If you happen to possess a superfluous third nipple (Krusty

) no one would argue this was a �new structure.� Similarly, legs sprouting from some poor fruit fly�s head is not a new structure, and certainly not an improvement.

We may have many creatures within us.

Profound. But really genetic evidence suggests otherwise, traits that are permanently lost are permanently lost. I challenge you to find any examples of re-emergence of a lost trait.

Often what passes for new technology is just the re-combination/re-use of old things/ideas. This seems very likely the case with genetic code. The wings of birds were on their ancestors, forelimbs. The flippers of Dophins and many marine mammals are from the limbs of ancestors. I think the feelers of many organisms are thought to be adapted limbs.

Slank, certainly I am aware of the idea of homologous structures between organisms, which incidentally, doesn�t pan out at the molecular or developmental levels. However, I would ask you to zoom out even further. Are you going to postulate that the flippers of Dolphins are somehow descended from the bacterial flagellar motor? It�s nice to be able to look at things that all have four limbs and assume they must all be related, however it is nothing more than assumption, and an assumption that often stands in opposition to existing evidence.

I apologize, profusely, for the long time it took to type this out. Its inexcusable, I had planned on beign very thorough, but there really is too much here to address in single posts. I've had to eliminate much of it. Also, I was spending some time considering how much the difference between 'facts' and theories and observations that are based in part on theories need to influence the understanding of this. But ultimately I think that a ;common sense' understanding of facts an observations is sufficient.

Originally posted by mattison0922

Phew! Here it is.

I would like to preface this post by again reiterating my intentions here.

My understanding is that you basically feel that macroevolution is seperate from microevolution and i suppose speciation and that, while there is evidence to support it, that evidence isn't iron clad and that it can't be said to be a 'fact'

I am removing a lot, because these are getting unweildy.

As far as archaeopteryx is concerned, i think that enough has been presented on both sides to allow for the points to stand. I'd be glad to discuss more if you want. Hmm, maybe a different thread would be a good way to pickup?

but my point has always been based on the available evidence, we CANNOT argue evolution as being a fact.

here's where something of a problem arises. I'm going to try to make this as unwordy as I can or else I'll probably start rambling.

One is not observing the fact of macroevolution when one looks at archaeopteryx. One hypothesises that archaeopteryx has the intermediate features that it does because of macroevolution.

Now, this does not mean that we are wasting our time when talking about transitionals, because one cannot observe the paleontological scale changes of 'macroevolution', rather one can only have evidence that is consistent with its occurance. -So-, transitionals are evidence of macroevolution having occured, and they tell us what its done and can do, and are relevant to the discussion. Most importantly, no transitionals, (in so far as we can identify them) then no operation of macroevolution in the past, and that in itself means that there would be major problems with the entire idea of evolution.

However, (and I think that this is a good way to reduce the size of these posts) they can be placed aside when talking about the fact of macroevolution and its mechanisms, and one can consider more small scale changes.

For example, chichilid fishes. Now, a fish is still a fish, as is famously said. However, speciation, as in the cesation of gene flow or even its ability to occur between two populations (even by third parties or something) can be said to have occured here. A single parent population has segregated into two distinct populations, and the result has been that they occupy two different 'environments' and have different morphologies between them.

As I have said, I never would have joined this thread if Aeon had not stated that �evolution is a fact.� That kind of dogmatic speech just pushes my buttons.

Yes but, as you have stated, its a fact that populations change over time, your concern is, is it a fact that they change drastically and into other 'kinds' of animals (again tho, I think that 'kinds', while intuitively understandable today, doesn't have real biological relevance)

These references are offered for contextual purposes: What is often promoted is �fact� is something for which there isn�t even a consensus opinion among scientists.

But the consensus is that evolution occurs. None of what you've presented is from scientists who think that it doesn't occur, they don't argue that it occurs, they argue that the particular pathway given, rather than another evolutionary one, occured. Having said that, I do agree that it shows that one can't domatically assert 'birds evolved from dinosaurs, its a fact'. That, most certainly, is deep in the realm of 'hypotheses'. Infact, its so new and there is enough dispute to keep it a 'hypothesis' for now (of course, thats semantics anyway, if a theory is said to be a hypothesis that has stood up to its tests and not been refuted or superseded by a better hypothesis, but whatever)

I haven�t seen you state this here, but are you stating that evolution is a �fact?�

I hope that the above illustrates my stance on the subject. I wouldn't seperate evolution into micro/macro/paleoscale or any of that when I would say that 'Evolution is a fact'. I had actually considered this question for a while. After all, what the heck do I care if evolution is a fact or a 'extremely well supported theory' or even a 'moderately well supported theory, and one that hasn't been superseded by any bettter theories yet'? So when I look at it, I am comfortable with the change in allele freq.

Your objection is of course acknowledged. However this quote was offered for historical perspective, particularly when coupled with the quote from Raup. Again these refs. are offered in refutation re: the statement that evolution is a fact.

This of course rams right up against the issue of what evidence for macroevolution should be, and what macroevolution itself is. Raup notes that transitions are rare, considering that gradualistic/anagenic evolution would mean that there should be a large number of intermediate forms. If macroevolution is taken to mean only these very large transitions, then yes, I agree, those very large transitions haven't been observed in nature; but, and this is important, its only not been observed if one is talking about transitions between different 'kinds' of animals. For example, experiments on selection and genetic manipulation in flies have resulted in viable populations of complete freaks, with different numbers of body segements and limbs comming out of their heads. Nature, not recognizing the human distinction between 'kinds' of animals, isn't going to say 'well, this is so radically different that its not a fly and therefore I will prevent it from existing.' I mean, if flies can exist, and I agree that this is different because its something that happened experimentally in a lab, but if flies can exist in populations where the features are so radically different, is there any reason to think that, say, fish with bony limbs can't benefit and change under selective pressure to develop supporting limbs? So in this way, macroevolution is a fact. Change in populations is observed, in the wild. Speciation is observed, in the wild. And, since the fruit fly and other laboratory experiments show that there is no limit to the 'plasticity', why not state its a fact? But I wholeheartedly agree that its not a fact that birds evolved from dinosaurs, or that tetrapods evolved from some particular group of pre-tetrapods, that is all theory.

In many ways, I don�t feel like we are coming from different perspectives. While I understand the context of these particular quotes, it�s nice that you are elaborating for the rest of the post. My continued assertion: stating evolution is a fact is not science, it�s dogma.

Interestingly enough, this [punctuational evolution] is where some of my biggest problems with evolution began. There is no reasonable mechanism postulated for the rapid change suggested by the fossil record.

Well, as you know from the massive amount of trees that have been sacrificed to the 'Punk Eek' debate, this is not somethign that should probably be discussed here in detail.. I would only put forward that the mechanism that causes the punctuational pattern is promoted as Gould and Eldridge as being Mayrs 'peripatric speciation' mode, wherein speciation, instead of happening in large populations over a large area, happens in very small populations that are practically isolated at the periphery of the species range.

places like say The British Museum have impeded this kind of research. Why?

Why should the BM grant more access to archaeopteryx? Wickramasingh's analysis was teribly flawed and the specimins are clearly not frauds. Also, the BM doesn't control all the specimins. Are you suggesting that the most rational answer is that they know its a fraud and are covering it up?

Perhaps you�d care to comment in the flawed methods used by Wickramasingh, especially in light of the flawed analysis of Spetner.

The spetner analysis was only flawed in that it didn't take particular note of there not being the same anomolous substance on the control portion. The thing is, the lack of the substance on the control section of the slab without any fossil material is consistent with the stuff being a preservative that was selectively applied to the fossi surfaces, rather than the entire slab surface. Now, I don't know if there is preservative or anything else in all the areas, but that would be consistent with wickramasingh's analysis. Also, I think that the chemical make-up of the substance being consistent with a preservative is rather suggestive of it being a preservative.

At the end of the three days of presentations, [Alan] Charig [chief curator of fossil amphibians, reptiles, and birds at the British Museum�BH/BT] orchestrated a concerted effort to summarize the ideas for which consensus exists. The general credo runs as follows: Archaeopteryx was a bird that could fly, but it was not necessarily the direct ancestor of modern birds.... A communiqu� expressing the unanimous belief of all participants in the evolutionary origin and significance of Archaeopteryx was adopted, in order to forestall possible misuse by creationists of apparent discord among scientists (1985, 5:179).
Personally, I find it interesting and somewhat disheatening that the scientists at the meeting felt constrained to adopt a unanimous resolution concerning the �evolutionary origin and significance of Archaeopteryx� solely to prevent creationists
I think that that is a good thing. Most creationists are anti-rational, anti-scientific, and anti-intellect. Oh, surely, several of them use scientific sounding analyses, and in particular the chemists in the ID movement are using techniques that are very scientific sounding, but ultimately their positions are entirely those of faith, and they are anti-scientific. I mean, if the conclusion that evolution is a fact is dogmatic, then what is it when one looks to the bible as absolute literal truth and tries to conform the evidence to it?

Ahhhh, then you see my point. The point is there are so many different issues with respect to this stuff that to argue it a fact is absurd.

I will have to insist however that the transitionals are not promoted as observations of the fact of evolution, but are rather theorized to be the results of evolution. In that way they can allow people to study evolution. But the fossil record itself isn't 'evidence' of the fact of evolution. However, it would be rather difficult to explain the fossil record if evolution doesn't occur, and in that way its supportive of macroevolution. But, in a way, thats 'overkill'. Macroevolution is said to be a fact because of the laboratory evidence. Really, what one might best look at is darwin and his peers. When darwin came around, he wasn't arguing that evolution occurs, he was arguing that it occurs through natural selection. The genetic, most of the paleontological, and even some of the observational evidence, didn't exist in darwin's time. Yet many naturalists considered that it was a fact that evolution occurs, they could see that populations of organisms aren't static and arent composed of disctinct invariable types.

To prematurely discuss some issues in this post: Gravity is not a controversial theory, (notice I didn�t say fact). The reason is because the effects are consistently observed and measurable.
But gravity particles and gravity waves aren't observed. In a similar sense to evolution, its only thought that the planets and such move because of gravity. Their movement and nature conform to the requirements of gravity and the predictions of gravity theory are generally met. I'll agree that gravity is generally accepted as occuring, but then again people aren't personally offended at the idea of gravity. The anti-evolution position is normally a visceral emotional one, and half the time there isn't even a concern that animals evolved, only offense taken at the idea that man evolved.And of course there are some people who argue that gravity doesn't occur or that its the result of an entirely different phenomenon. Most of those people are generally loons tho. Of course, even in the physical sciences, there are some suggestions and attemps at 'unifying' gravity along with other forces. And also the fact that gravity doesn't work at extremely small distances, and may even work differently at very large distances (but thats a more controversial issue) show that radical changes to the theorys of just what gravity is are possible and infact probable or even, completely necessary. And even just regular old gravity has changed, Newtonian gravity was superseded by Einsteinian gravity. If Gravity in that sense was a fact, then Einstein's advancement wouldn't have been possible, or at least it would be wrong. So the situation is analagous to evolution. Gravity obviously is occuring, and its doubtful that anything coudl demonstrate that it doesn't, while on the other hand there are a variety of theories as to how it works and such and they have been changing eversince a Theory of Gravity was first proposed. This makes the variety of opinions and theories relevant to evolution all the less surprsing, since gravity is a 'fundamental' force of nature, while evolution is suubject to chemical physical and 'biological' 'laws'.

Homologous structures, initially thought to be controlled by descent with modification and natural selection of genes, are continuously being demonstrated to be controlled by DIFFERENT genes at the molecular level.
Such as what? And is it all of them? This aspect might demonstrate that particular homologies aren't homologous, but there are still homologies across the natural world. The hox genes for example, are the usual 'poster boy' of homology.

Clear to who, clear to you? Not clear to every scientists in the field.

its a quasi walking ape showing a trend torwards increasing brain size and human like facial and dental features. What else could a transitional between a man and a chimp look like?

I�m sorry, but similar features does NOT necessarily imply similar ancestry. It�s not an unreasonable assumption, but it�s not a fact.
But it cannot then be stated that these organisms aren't related. The point isn't that the ape-man transition is a factual observation of macroevolution, the fossils aren't breeding and giving birth in front of us in the first place. The point is that these fossisl can't be said to not be intermediates, their features are intermediate between the 'types'. They show that the 'type' doesn't actually exist, because they are inbetween it. Similarly archaeopteryx with its combinations of features, most broadly the hands, tail and head of a reptile with a hallux and feathers, show that, irregardless of what archaeopteryx is, that there isn't a 'bird type'. That all the features of birds are in other animals, espcially the prime features of feathers. The 'type', the kind, is an accident of the history of nature. If whatever the heck archaeopteryx and the other dinobirds and some dinosuars were still around, people probably wouldn't have any concept of a bird type, or at least it woudl be a very different concept, one that included ground running barely feathered no beaked sharp tooth long tailed screaming monsters that rip things apart with their hands.

These would of course argue against the factual nature of evolution, and again point out the speculative, not factual nature of the theory.

I think that the rejection of any 'transition' in the fossil record can't refute evolution, no more than any transition can 'prove' the factual nature of evolution.

. In fact, the DNA sequences for all people are so similar that scientists generally conclude that there is a �recent single origin for modern humans, with general replacement of archaic populations.

But this in itself is evolution. They are citing that evolution occured. I understand and agree that it shows that there is some controversy and disagreement on the specific patheways of evolution, but this only is an issue for the theory on the pathway.

To be fair, the estimates for a date of a �most recent common ancestor� (MRCA) by evolutionists has this �recent single origin� about 100,000-200,000 years ago. In contrast, studies that have used pedigrees or generational mtDNA comparisons have yielded a much more recent MRCA�even 6,500 years
! I'll have to check that one out, thats a very strange thing to get. 6,500 years ago was 4,500 BC, practically the historical era. I've read about there having been a populational 'bottleneck', one that is proposed to account for the genuinely surprising closely relatedness of humans and the low variability. I've often heard that the whole modern human population is less variable, in terms of genetics even not just phenotype, than -populations- of chimps. Not all 'chimpkind' as a whole but just subpopulations of groups of chimps. No reference on that, its one of those 'factoids' that just sticks in yer head.

here is ASU's Institute of Human Origns take on it

Did you insert this for a point of personal irony? Just Curious.
? No, i thought that it would make a good 'generalized' statement on it. Why? I think I am missing something.

I am sure that you are aware of �convergent evolution� as Aeon felt it necessary to point out to me.

Also, on convergent evolution, if it were to occur, it'd be an example of macroevolution. So you can't maintain that australpithecines are animals that have converged on the human type, and still say macroevolution doesn't occur. Unless you would say that they were all instantaneously created and the similiarity isn't due to convergence or any other evolutionary phenomenon.

Point taken. I was using the point of convergence to illustrate the fact that different explanations are offered when evidence doesn�t fit the currently accepted scenario. The point was that because things are similar doesn�t prove common ancestry. It may suggest it, but there could be other reasons for the similarity.
Well, phylogenetics and cladistics are more or less based on this similarity idea in combination with parsimony and some other aspects. however, cladistics isn't the fact of evolution. Cladistics is an attempt, based on theoretical considerations, to reconstruct hypothetical phylogenies. Each 'cladistic tree' is a hypothesis in and of itself. THey can, and of course routinely are, be refuted, rejected, and replaced. Homology is very suggestive that evolution occurs, but it is theoretical. IOW evolution explains homology, homology doesn't explain evolution.

Based on observable evidence, such as the rate of natural, unrepaired mutation in an organisms DNA for example

And you are stating that its too slow to lead to a strengthening of the limbs over the general timespan involved? I mean, the move from a perch to a lizard is a big jump, but from a bony limbed shallow water fish to a more boney limbed terrestrial amphibian?

While your point about existing variation is taken, existing variation in genetic structures in unable to account for the appearance of new genetic information,
Perhaps this is the greatest stumbling block then. If the genetic evidence demonstrates that, despite appearances, evolution cannot occur, if it refutes the idea that evolution occurs, then that woudl be significant.

This is not the point. The point is that there is considerable dissention

There is considerable dissention on the transitions, but none of the authors cited argue that evolution doesn't occur. As far as any of them can tell, and say, it does occur. They simply argue that a different set of archosaurs evolved into birds, or that a particualar organism is more terrestrial than usually thought, but the factual occurance of evolution is not based on this weak, theoretical transitions. Indeed, you are quite right, there is dissention and lack of consensus on some of these aspects, but there is a consensus that evolution occurs.

On Kow Swamp man and the differences betwen sapiens and erectus, only slightly features distinguish man from primitive apes in the first place. And I think that the point about the Kow Swamp specimin is that, its not erectus, its sapiens, and this means that erectus has a suite of features that are not found in sapiens. Of course, those features are "quantatative" in a sense, not qualitative. IE erectus has no chin or a smaller braincase, whereas modern man and kow swamp man has a larger braincase and more of a chin, differences in degree, not in kind, which is acceptable under the understanding of the differences between species.

We can�t look at the specimen as a whole without analyzing the individual components of that whole. If parts of the whole don�t add up though, HOW is the whole going to add up?

Perhaps I am being obtuse but I am not entirely sure I understand the comment. erectus, or any organism, doesn't need say one or two characters that are not had in any other organism in order to be considered a distinct species. They can have quantitative differences than other organisms, they can have no characters that are unique in and of themselves, but are merely 'more' or 'less' than others, ie more expanded, less vaulted, more keratinized, more sculptured, etc etc. Look at foxes and wolves. These are differences of degrees. Or even dogs and cats. Extend the snout, alter the musculature, allow the claws to retract, these aren't immpossible changes that would so radically alter the genome that the organism couldn;t function. If a fruit fly can have legs growing in place of antennae or have entire bod y segments lost, or duplicated, then surely these sorts of changes are possible. (agian, I'd hedge that there is a difference between hypothesised changes in the fossil record and deliberate changes in the lab, but it does show that the genome can be altered, that, as complex and interconnected it is, it can be radically altered, and, even in the fruit fly experiements, the changes were brought about by exposing the organisms to radiation and the like, not be selectively designing the freaks).

Nygdan, I�m sorry but this absurd, and doesn�t take evolution as a whole into account. There absolutely are kind barriers.

Ah, this is a strong statement, and probably the one we should try to focus on.

There are multiple very real, very difficult barriers that must be explained for this theory to be a �fact.�

The issue that I have with this is that, just what are these 'kind' barriers? For example, one could've said that feathers were a kind barrier, that they are something that had to have been formed ad hoc and at once. But they don't have to be. There are plausible antecedants to flight feathers in the fossil record. Given that, even tho we can't state as fact that "dino-fuzz" evolved into feathers, we can say that there isn't anything barring feathers from evolving. The 'kind barrier' of feathers doesn't exist, because feathers aren't limited to any kind of animal. And the tetrapod limb, similarly, there is nothing 'kind like' about it. Its just a limb with some bones. Its not far fetched to say that it could've come from more primitive antecedents, even if, as in other cases you've brought up, the genetic information has altered radically also. Its not insurmountable change, given that flys can have their entire body plan altered and survive. I understand that it ends up meaning a lot of changing of the genome, but obviously the genome can withstand change. At least thats how I understand it to be.

Now, of course you are not a fan of the Talk Origins newsgroup's archive, but there is a page about this subject.
www.talkorigins.org...
www.talkorigins.org...
www.talkorigins.org...

I note them because they do discuss the issue, and because they have the references relevant to the issue at hand. I, however, haven't been able to read those particualr references. The case made in them is that, infact, new structures can arise from old ones, and that 'arbitrary' gene sequences can result in functional ones.

I think that one of their notes is intersting:

According to Shannon-Weaver information theory, random noise maximizes information.

Its interesting because 'information theory' is often brought up, and it can be a counter-intuitive subject.

I will reiterate the is no proposed reasonable mechanism to account for the formation of new genetic information.

I do not understand. Why are mutations an insufficient source of new variation/information? Mutations are known to occur, they alter the genome, why aren't they able to alter it in such a way that results in a slightly different phenotype? And why can't natural selection act on this to result in new structures? I'll agree that the process isn't entirely understood, I'll agree that this is a theorectical portion of evolution, but the lack of a complete answer as to how evolution operates isn't in itself a refutation of hte concept or something that allows us to say that the factual observations of change in populations don't occur. We see change in populatins within a species. We see the evolution of new species. We see the induced but drastic alteration of the genome. We see evolution occuring, and, insofar as we do see that, we can state that evolution is a fact.

Dawkins for a refutation of this concept.

Which of his books refutes this?

On the out of place skulls, I am generally unfamiliar with the literature on them, so I can't really say anythign more than I already have.

1. �new� species that are �new� to man, but whose �newness� remains equivocal in light of observed genetic �variation� vs. genetic �change� (as discussed above), and/or because a species of unknown age is being observed by man for the first time.

If I understand this correctly you are saying its an issue because, say, in chichilids the new species isn't particularly different than the old right? Its just a different variation on the same type right?

2. �new� species whose appearance was deliberately and artificially brought about by the efforts of intelligent human manipulation, and whose status as new �species� remain unequivocally consequential to laboratory experiments rather than natural processes.

Indeed, human based selection is what inspired, some say, Darwin to come up with natural selection. The agent of selection isn't necesarily whats important here. Afterall, the humans didn't create ad hoc a new gene or set of genes and work out how it could be inserted into the organisms without disturbing their genome to the point of destruction. They selected for traits. Nature, too, can Select for traits. But, this sort of thing is the theory of natural selection, not the fact of evolution. The fact that the populations can be changed so radically is enough to show that evolution occurs. Infact, aren't you arguing that it doesn't occur, not that it occurs at the direction of any intelligence, man or god?

In neither of the above examples cited by Isaak was the natural (i.e., unaided) generation of a new species accomplished or observed, in which an unequivocally �new� trait was obtained (i.e., new genetic information created) and carried forward within a population of organisms.

in 5.9.1of this one of those pages one finds that multicellularity was observed to have occured in a unicellular organism Chlorella vulgaris, and in 5.9.1 Nakajima and Kurihara 1994 observed multicellurlarity in a bacterium, Shikano et al observed a morphological change of a size increase of 13 times the original size, from short rods to long filaments along with a size increase of 13 times. The human element shouldnt be rejected as 'design', since often all they are doing is providing selection pressure, or causing more exposure to radiation and thus an increase in random mutations. If the problem is that a totally new structure hasn't been observed to have evolved in nature de novo, well, thats not exactly what is expected to be the fact of evolution. Bird wings, for example, needn't have evolved out of nothing and all at once. Its the 'progressive' change that is the key to it. The change in a population of finches to have beaks that are stronger and larger than before, and a shift in diet from small plants to large hard shelled nuts has to be evolution. The new variation did not exist before, its new variation and new information. Yes, finches had beaks to begin with, but they didn't have those kind of beaks.

not just variations within a type of organism but the emergence of entirely new organisms.

Well, if its a question of massive change into entirely different sorts of organisms without any human selection, then I agree, this has not been observed. This does not mean macroevolution does not have a factual basis. Organisms speciate, and organisms change. Thats all that is required for macroevolution.

Definitions of �species� and (therefore) �speciation� remain are and varied, and by most modern definitions, certain changes within organism populations do conveniently qualify as �speciation events.� However after many decades of study, there remains no solid evidence that an increase in both quality and quantity of genetic information (as required for a macro-evolutionary speciation event) has happened or could happen.

Entire chromosomes have been seen to have duplicated and freed up for all sorts of selective pressure. And genes and even sets of chromosomes. And variation beyond the ancestral populations range has been observed to occur, this isn't 'hidden' genetic information, this is natural selection eliminating the unfit/promoting the fit and ever present mutation resulting in new random variation about the new mean.

As for Dobzhansky�s fruit fly experiments, it should be pointed out that an example of a laboratory-induced physiological change in a specimen, even if it involves genetic change, can hardly be considered proof that NATURAL evolution occurs, since the change did not take place without the deliberate activity of man.

But that deliberate change is often nothing more than providing a selective pressure, or in some cases merely exposing them to more radiation. Heck in one they only provided a maze with two alternate routes and rewards in them. There's no reason to think that this invalidates the changes, anymore than setting up a chemical reaction implies that it doesn't happen in nature.

Furthermore, a genetic, mutational change alone, while it may qualify as microevolution, does not demonstrate evolution per se: Evolution does not require just change, but progressive change,
On this I would have to disagree. Evolution is merely change, progressive or non-progressive. From the human viewpoint, and from a current temporal viewpoint, it certainly often looks like things have been progressive. But, for example, Eohippus wasn't under pressure to become the modern horse. It was under various pressures at variuos times and different populations of it evolved in all sorts of directions. Progression is not required. In particular it shouldn't have anythin to do with the appearance of a new trait.
In Dobzhansky�s work, numerous varieties resulted from radiation bombardment: fruit flies with extra wings, fruit flies with no wings, fruit flies with huge wings, fruit flies with tiny wings. In the end the only thing produced was fruit flies! Dobzhansky meddled with the genetic code

But he didn't directly and specifically alter it. He, in a sense, caused possibly hundreds of years of random, no directed mutations to occur over a few generations. And the result was entirely new body plans. If mere mutations can produce that, then what is supposed to prevent them from causing anything else? And these organisms needn't be more fit, becuase there was no selective pressure. Think about it, without selective pressure, all those changes occured. What would happen if there was selection and time for it to act on the organism?

Even the bird to dinosaur transition almost starts to fall 'below the level of kinds' of animals and into the 'microevolutionary' change level.

BS. Dinosaur to bird transitions have never been classified as microevolution. Please point out a reference where this is referred to this way.

The change from somethign like herrerasaurus to modern pigeons is of course huge, and I am not claiming that, if one accepts the existence of 'kinds' (which I do not accept as a biological term) is 'inter-kind' change. What I am saying is that the change from things like archaeopteryx to birds, or microraptor and other very bird like dinosaurs shows that the 'morphological gap' between birds and dinosaurs is extremely small. Birds, again, have extremely few features that dinosaurs don't. How can one seriously contend that more co-ossification of vertrebrae is huge and fanatastic 'inter-kind' change? Or more reduction of the tail bones, or more fusion of the hand bones? Kinds simply do not exist in biology.

I would again encourage you to consider the big picture and the amount of genetic information to be added to go from E. Coli like organisms to homo sapien like organisms�. Really, seriously ponder that for a while, and I encourage you to try and answer it for yourself.

With over 4 billion years of time and a nearly infinite number of generations? Selective pressure in small 'microevolutionary' steps can produce practically any 'macroevolutionary' patter. Induce multicellularity, cause differentiation of cells, let entirely different organisms meld into the same one, throw in new genetic information with viruses, increase some of the different types of cells and decrease the others. All the changes involved, they are mind boggling in terms of 'raw' evolution, in terms of raw factual uncontroversial and seemingly powerless changes in a population. But with direction, with natural selection, they become workable. With speciation they become accelerated and with limits to plasticity they become 'progressive'.

.

I was sold on evolution until the subject of the primordial cell came up, then I started seriously researching it.

Well, at least if there is anyway to reject modern biology, that would be it. Its the great unknown in it all.

Gravity seems to hold up very well at all levels except the quantum level.

As before, which gravity? Newtons, einsteins? Tommrrows?

[qujote] Similarly, you can mix two organic reagents together and get coherent repeatable results time after time.
And you can seperate populations and apply selection and get speciation.

[quiote]However the result of evolution is merely inferred, and never observed (macro).
The only thing that is not observed are the paleontological scale changes, which are not the 'factual' observation of evolution.

This is the essence of my argument, notice how I didn�t say gravity is a �fact.�

Well, I think that most people would say that gravity is a fact, and that, after all, the initial problem was that most people were saying 'evolution is a fact' when it isn't. I'd say that evolution is as much a fact as gravity. And, similarly, that macro-evolution has as much to do with micro-evoltion as gravity at, say, the scale of feet and inches has to do with gravity as the scale of AU or galaxies.

But, if we want to talk about which theories are better supported, ie Einsteins theories on gravity and Darwin's theories that natural selection occurs, well, that would be a different sort of thing that talking about it being a fact.

If you want to reject "macroevolution" because you've never witnessed it, then you'd also have to reject almost any chemical reaction, or the existence of transitional states within those reactions that are too small to see or too ephemeral to be 'observed' in the same manner than you want to observe macroevolution.

Please see my above rebuttal. While reactions can�t be observed, their results can be measured with some degree of reproducibility. Furthermore transition states can be studied; there are entire fields of study devoted to this,
Yes, but, interestingl, a transition state in a chemical reaction doesn't necessarilly exist. Similarly, one can draw the structure of a series of resonance structures of an organic molecule, but one realizes that this 'thing' is just a construct of theory, and that the actual thing doesn't truly conform to any of those structures. Nonetheless, one can predict the products of reactions with it and list the properties of the 'resonance chemical'. That doesn't mean that, merely because the true nature of the transition isn't understood, that the reaction isn't occuring.

one of the major one�s is drug development. I specifically did a major portion of my graduate work re: enzyme thermodynamics and transition state analogs.

Christ. And you still find time to read a forum about reptiloid illuminati pyramid builders from planet x eh?