Elsie_T wrote:1.) The Stanley Miller Experiment: Miller in 1953 conducted an experiment by reproducing the atmosphere of early earth and he subsequently produced amino acids. The only problem here is, Miller chose a hydrogen-rich mixture of methane, ammonia and water vapor as the make up of the atmosphere, a combination which all scientists reject now. The current hypothesis is that the early atmosphere consisted of carbon dioxide, nitrogen and water vapor. An experiment using these chemicals produces not amino acids, but formaldehyde and cyanide (or embalming fluid!)
Before the Stanley Miller experiment, there apparently was a widespread presumption. According to it, it was impossible in principle that amino acids could have been produced from inorganic matter in any chemical reaction that would occur without something intelligent in charge. Miller's experiment refuted that presumption. The observations made on re-running the experiment with an atmosphere of carbon dioxide, nitrogen and water vapor don't revise the refutation of this broad claim. Stanley Miller may also have made a more specific claim for all I know. (I haven't read his paper.) He may have claimed that his mechanism simulated the way amino acids actually emerged historically. If he did, the revised experiment you describe would refute that specific claim. But it wouldn't prove that abiogenesis is impossible, and it would say nothing about other possible ways in which abiogenesis could have happened. Indeed, several other pathways have been proposed in the meantime, and the most likely candidates today do not depend on any specific assumptions Miller implicitly made about the primeval soup's ingredients.
Elsie_T wrote:2) Ernst Haeckel's drawings of embryos: [...] He was exposed in the 1860's for this fraud, however, these drawings apparently still appear in high school textbooks today.
I haven't carefully followed the history of what Haeckel did, so I don't know that he actually engaged in fraud. But for the sake of the argument, I'll assume that he did -- especially since
talkorigins.org confirms your account. The next question, then, is how that affects our view of what actually happens. How does the picture change if you correct for the fraud and use photographs instead of drawings? As best I remember, photographs are what appeared in my high school textbooks, and they make the same point just as impressively. It is possible, of course, that Haeckel's drawings are still used because they are pretty or something. If so, that would prove that some editors of biology textbooks are lazy and sloppy, but not that the underlying observation about embryology is false.
Elsie_T wrote:3) Java Man is actually on the cover of the 1998 edition of 'The Origin of the Species'. [...] However, what is not so well known is that Java man consists of nothing more than a skullcap, femur, three teeth and a great deal of imagination. In other words, evolutionists created him more out of what he should look like if Darwinism were true.
The Origin of Species isn't copyrighted anymore. Anyone can republish it and hundreds of people have, so there is no such thing as "the" 1998 edition. The fact that one out of several hundred editors made a stupid mistake is not troubling to me. I cannot comment too sepcifically on the substance because I am not familiar with the historic details about Java man. Two points though: For one, a common creationist claim about him is that he was a gibbon, while the standard scientific literature came to see him as a modern human fairly soon. (A similar but much more complete skeleton was discovered on Java in the 1930s.) Point one is that a scullcap, a femur and three teeth are enough to tell the difference between a human and a gibbon forensically. Second point: The story, as best I can make out, shows that darwinist excavators sometimes misattribute a fossil, and that the editors of darwinist books can be as lazy and careless as everybody else. It also shows that Java man, contrary to what Dubois said, was not a common ancestor of modern apes and modern humans. It does not show that modern apes and modern humans have no common ancestor.
Elsie_T wrote:There is also the Neanderthal Man, Piltdown Man, and the Nebraska man, which, I believe are still represented in textbooks?
I have not read every textbook in the world, so I'll restrain myself to talking about the one I was assigned in high school in the 1980s. As I remember it, Nebraska man was not mentioned, Piltdown man was mentioned as a fraud, and Neanderthal Man was discussed as a close relative of modern man, but one that had consistent systematic differences with our species. If I had to write a textbook, I would do nothing radically different.
Elsie_T wrote:How has the scientific community responded to these challenges and has there been any consensus as to an outcome?
The answer varies from case to case, so I can't give you a one-size-fits-all reply. I'll just say that while talkorigins.org is not peer-reviewed, it usually gives a very accurate account of the scientific communities position on the subjects you brought up, if it has one. I warmly recommend searching it.