The Internet debate between those who affirm and those who deny the evidence for evolution and an old earth usually takes place on the scale of fairly short articles which are accessible to the average reader. Some supposed evidences for a young earth, such as the changing magnetic field of the earth, or the amount of helium in the atmosphere, can be readily disposed of in just a few pages.
On the other hand, there are topics where the scientific issues are more complex and subtle. In such cases, it seems useful to present a comprehensive examination of all the main points in one write-up. For instance, one of the top 10 evidences for a young earth claimed by Answers in Genesis is the observation of soft tissue in some dinosaur fossil bones. To the layman, this seems to indicate that that these bones cannot be tens of millions of years old as mainstream science says. Rather than trying to address just a few of the scientific issues with soft tissue in a piecemeal manner, I decided to write a fairly long essay which discussed all of the key scientific findings up to that point. This enabled the efficiently addressing of all the substantive young earth claims associated with this topic, and provided a single reference to which readers could be directed.
Every few years some seemingly well-credentialed Young Earth (YE) creationist publishes a new book which is touted as the final demolition of evolution. The sweeping claims in such a book are then regarded as established facts by the consumers of YE creationist literature. It seems helpful in such cases to systematically work through such a book, and compare what the author claims to what the full data actually show. This sort of fair and thorough rebuttal will typically make no impression on dedicated YE creationists (since they rigorously filter everything through their particular interpretation of the Bible), but it can prove enlightening to someone who is on the fence, trying to sort out what the truth really is.
For instance, when John Sanford’s book, Genetic Entropy, was first published in 2005 it was hailed as the definitive proof that modern evolutionary theory is a complete failure. The central claim of that work is that all genomes are (and have been since The Fall) relentlessly deteriorating due to the buildup of unselectable harmful mutations. Jubilant YE creationists widely referred to that book to bolster their beliefs. The author was a respected retired botanist from Cornell. In my own case, a fellow evangelical Christian handed me a copy of that book in 2008, assuming that it would bring me over to the anti-evolution camp. At that point I had not made up my mind about the scientific case for or against evolution, and Genetic Entropy seemed convincing at first reading. Being a professional researcher, I wanted to read some in-depth critical review of the book, and then balance the pros and cons in my own mind.
However, I could not find a thorough critical review. In the end, I wrote my own chapter by chapter review of Genetic Entropy, as a means of clarifying issues for myself and to respond to my well-meaning YE creationist friend. The net result for me personally was to conclude that the evidences presented against evolution were complete failures, if all the facts (not some cherry-picked subset) are laid on the table. (It happens that writing that review of Genetic Entropy was what launched me into blogging on faith and science – – since no other thorough scientific review of this controversial book seemed to be available, I decided to implement a WordPress blog to put it, and some other material I had drafted, out on the internet for the benefit of others.)
All of this goes to show why I am highlighting here the Evograd blog. The proprietor of this blog, a graduate student in evolutionary biology who prefers to remain anonymous, has produced a relatively few but very weighty studies which treat timely, highly technical subjects. I don’t think his work is as well known as it should be, considering how it directly and thoroughly confronts some key YE creationist claims.
I first became aware of this blog when looking for commentary on Replacing Darwin, by Answers in Genesis’s Nathaniel Jeanson. This book appears to be the latest, greatest “demolition of evolution” touted by YE creationists. Jeanson has a PhD from Harvard, which is supposed to lend credibility to his work.
The only in-depth critique of this book I was able to find was by Evograd. He systematically exposes Jeanson’s erroneous assumptions and faulty logic. The first seven out of planned ten posts on the blog have been completed. (Evograd’s fans are waiting for the last three installments to appear, but more pressing matters have taken up his time). Replacing Darwin is a long, sprawling, and dense treatise, and so Evograd’s responses are likewise lengthy, diverse, and detailed. I’ll mention a few points here, but won’t try to summarize all the issues.
“Part 6: Jeanson’s Fulcrum Fails” treats chapter 7 of Replacing Darwin. In that chapter Jeanson claimed that the actual, observed amount of mitochondrial mutational differences between various species is much, much lower than predicted by standard evolutionary timescales – – and therefore, the biosphere (and indeed the earth) must be much, much younger than posited by mainstream science. But…the Evograd blogger notes that Jeanson used a mutation rate for mitochondria that is about ten times too high, and also did not take into account the elementary math of how the apparent rate of substitutions will tend to slow down for more ancient lineages even if the actual rate is/was constant. These errors (and others) led Jeanson to grossly overestimate the mitochondrial mutations entailed by “standard” evolutionary theory. When those errors are corrected, the data are in fact consistent with evolution.
The seventh and latest installment, “Part 7: A Nuclear Catastrophe“ has links to all the previous posts in the series on Replacing Darwin. In this technically dense post which cites a wide range of relevant literature results, Evograd debunks a number of Jeanson’s claims concerning DNA in the cell nucleus.
Tomkins on the Human Vitellogenin Pseudogene: Who Needs Signal When You Have Noise? – – Reptiles and birds produce eggs with substantial yolks. The yolk nourishes the embryo as it grows and matures in the egg, prior to hatching. The vitellogenin gene is involved in producing the yolk. That is its function in birds and reptiles, as can be clearly demonstrated. (In some species, this gene has been duplicated, so there is more than one copy of it in the genome, but the function is the same). In modern placental mammals like humans, there is no need for the function of the vitellogenin gene. Human embryos get their nourishment from the placenta, not from an egg yolk, so they have no need of the protein product of the vitellogenin gene. Thus, over the tens of millions of years since the emergence of modern placental mammals, most of this gene has mutated away. However, some mutated, nonfunctional fragments of the vitellogenin gene still appear in the human genome, in a location corresponding to the locus of the functional gene in chickens. Standard evolutionary science holds that mammals descended from egg-laying common ancestors with reptiles, and so finding these deactivated “pseudogene” fragments in this location is a confirmation of evolution. 
In response to this evidence for common ancestry, a YE creationist scientist, Jeffrey Tomkins, published an article in an Answers in Genesis journal, claiming that one of these gene fragments is in fact functional. Tomkins identifies it as a key part of a gene that affects neurological processes in the human brain. This claim has been cited as fact by YE creationists all across the internet, and used to deflect the evolutionary evidence of the vitellogenin gene. Enter Evograd: in this article linked above, he eviscerates Tomkins’ contention of functionality, showing that each of Tomkins’ seven lines of argument is utterly worthless. This is another virtuoso performance by the Evograd blogger, showing a keen grasp of subtle technical points and wide command of the relevant literature, combined with clear writing style and ability to focus on the most important issues.
More Evograd articles on the evolutionary significance of pseudogenes:
Articles dealing with human chromosome number 2.
This chromosome 2seems to represent a fusion of what in all other higher primates are two separate chromosomes (typically called 2A and 2B). In the human chromosome, the actual point of the fusion of the two original chromosomes can be discerned, pointing to common ancestry between humans and other primates.
[and also, in Part 7: A Nuclear Catastrophe , Evograd demolishes Tomkins’ claim (retailed by Jeanson) that a functional gene spans the fusion site in Chromosome 2]
Some other excellent reads on the Evograd blog:
 A “pseudogene” is a recognizable DNA sequence derived from some functional gene, but which no longer expresses the original protein. For instance, humans have many nonfunctional genes (i.e. pseudogenes), which in other animals are functional genes involved for odor recognition. (Presumably as humans developed higher visual acuity, they became less dependent on sense of smell, and so natural selection was relaxed for retaining these olfactory genes). These pseudogenes, both the coding DNA and related regulatory regions, were originally fully functional (prior to accumulating disabling mutations), so it is not surprising to find that some bits of some pseudogenes have become used in the regulation of some other, still-functional genes in the genome. Opponents of evolution cite these discoveries of functionality as though they overturn the status of pseudogenes as pseudogenes, but that is misleading nonsense.
Per Wikipedia on the definition of pseudogenes:
Pseudogenes are segments of DNA that are related to real genes. Pseudogenes have lost at least some functionality, relative to the complete gene, in cellular gene expression or protein-coding ability. Pseudogenes often result from the accumulation of multiple mutations within a gene whose product is not required for the survival of the organism, but can also be caused by genomic copy number variation (CNV) where segments of 1+ kb are duplicated or deleted. Although not fully functional, pseudogenes may be functional, similar to other kinds of noncoding DNA, which can perform regulatory functions. The “pseudo” in “pseudogene” implies a variation in sequence relative to the parent coding gene, but does not necessarily indicate pseudo-function. Despite being non-coding, many pseudogenes have important roles in normal physiology and abnormal pathology… Pseudogenes are usually characterized by a combination of homology to a known gene and loss of some functionality. That is, although every pseudogene has a DNA sequence that is similar to some functional gene, they are usually unable to produce functional final protein products.
[Housekeeping note: in deference to the primacy of his work, if a reader here is unhappy with some of the technical conclusions of the Evograd blogger cited above, please leave your comments on his blog, not mine]