My first disclaimer is that I am not an evolutionary biologist. I am a molecular biologist, but I do know my way around evolutionary biology.

This claim is not merely false, it is gibberish. The concept of "perfect species" is categorically in error.

Evolution is simply the heritidable change in gene frequencies in populations due to selective pressure. At least, that was the classical view, we now understand genetic drift to be almost as important. The selection will ultimately be determined by the environment, and so phenotypic divergence will occur as a result of whatever phenotypic changes are entailed by useful mechanisms for increased procreation and hence the frequency of those allelles in that environment. As a result, phenotypes diverge. Your twit friend has it backwards. Life started from a common ancestor and the arms of the phylogeny diverge outward, they never converge. Never. It's impossible. I don't quite think this poor deluded twit understands that all modern organisms are just as "evolved" as any other on the phylogenic tree. A modern bacteria is just as "evolved" as a modern human. And they are just as adept at surviving. There is no such thing as a perfect organism, and evolution does not have eschatology, and arms of a cladogram never converge, by nature of the types of mutations that occur (homology is driven by duplicative errors) the phenotypic diversity increases with time, that is to say that because of the increase in homologous sets, the collective genome tends to diversify, and once two arms of the cladogram are genetically seperate, they do not meet again. It's probabalistically impossible. And evolution does not work "towards" anything, and lastly, the relationship between genes (which do diverge at constant rates) and phenotypes is not directly proportional. Not by a long shot. That's six errors that demonstrate your interlocutor doesn't even know what the fuck he's even debating!

Never, ever use the phrase survival of the fittest. It's a meaningless phrase. It was coined by idiots in the popular media. 

A seventh piece of ignorance. The number of possible allele recombinations is greater than...well, certainly greater the number of brain cells he is in possession of.

Not really. Deleterious allelles can stay for numerous reasons. However, I do not think that is one of them. The primary reason is if they are recessive in heterozygous organisms 

I congratulate you, but do you mean to tell me that this idiot was trying to debate evolution without being based in the laws of the Punnett Square? Shouldn't you have pointed out that engineers, for example,  need to know addition and subtraction before they can design buildings?

Because he's an idiot. There is no process difference between "micro" and "macro". "Macroevolution" is just a broad term which refers to any evolutionary change which involves speciation. Although there are some creationists who challenge that speciation is impossible because species by definition can only exchange genetic material with those of the same species, such statements require egregious understanding of basic genetics. For one, the concept of "species" entails by virtue of its meaning a continuum of possible genomes with small differences such that sexual recombination is still possible (In asexual organisms, the concept of species is even more arbitrary). When examining species which have diverged from each other from a common ancestor tracing back, say, 50 million years, the intra-species genomic changes will be neglibible compared to the inter-species genomic differences. Generally speaking, when two human genomes are sequenced at random, they will differ in approximately 0.1% of the sequence. Which would compare to a much greater percentage between a human and a mouse which also needs to take chromosomal polymorphism into account. When dealing with such disparities, we refer to what is called the fixed difference, that is, the difference that will hold true of inter-species mutation for any two representatives of the two species being selected because the intra-species difference is negligible in comparison. 

So, to understand how speciation works, at least, at an extremely basic level, it is necessary to understand that any gene frequency that is now a characteristic of the whole species began as a mutation in a single organism. If this organism exists in a breeding population of size N, for sexually recombining organisms, than for diploid oragnisms, the initial allele frequency of the mutation which later spreads throughout any population is obviously (N/2). The change and rate of change of this allele will depend on consequences. If it is deleterious, like most, it will probably be eliminated quickly. If it is selectively neutral, it can spread via sampling error, the general rule is that for any neutral mutation, it will take 4N generations in a population of constant size N, to spread through the genome. As for benificial mutations, such spreads are determined by virtue of their ability to propogate, by which I mean increase the survival and procreation of the organisms which hold it, and so, itself. This holds true regardless of whether one accepts gene centers evolution. 

There is really no difference between micro and macro. When there are two species which are recently diverged from a common ancestor, their fixed difference will be hard to measure, because the intra-inter species differences will not be as clear as for a solidly established divergence that occured, say, 100 million years ago from their common ancestor. Speciation simply reflects that genome changes are continuum by nature, and there is no functional or process difference in the selection processes, it is simply the compounding effect of...well, more time, generally speaking. The laws of biology dictate that evolution will occur. Because mutation rates for each gene remain constant for that gene based on its functionality, the general rule of thumb on a molecular level is more time=more divergence. This is called the molecular clock and is firmly established by modern molecular phylogenics, making use of a class of nucleotide sequences called fibrinopeptides. 

A thorough misunderstanding of the law of biogenesis, which eliminates the ancient view that maggots, for example, are spontaneously generated from meat. Spontaneous generation is impossible, but the law of Biogenesis has no comment on a long, complex process of chemical evolution.

Its not merely under scrutiny, it has been successfully refuted. As you pointed out, chemical evolution is a well established process, and if not DNA, precursor molecules such as RNA and pre-RNA systems were definitely the antecedants of modern DNA-based organisms. The RNA world and chemical evolution are well-established and reasonable principle. The same principles apply to the replication of much simpler molecules that also function by templated polymerization. Ribozymes certainly predated enzymes. This is unsurprising since polynucleotides can encode information by serving as a template to guide synthesis of their own copies, and ribozymes can do so by autocatalysis. Because they do not form base-pairing or any anologous tempalte structure, polypeptides do not have this ability.

Certainly. I currently think, although I could be easily wrong, that PNA is the most likely candidate. RNA systems come from PNA systems and DNA systems from RNA systems. RNA nucleic acids are too large to have been the first precursor of DNA. As for proteins, those most likely originated before DNA-based organisms, in ribozymes that could bind amino acids. They've obviously overtaken ribozymes since they are much better catalysts, but there are still plenty of ribozymes in modern day cells that give clues to their ancient evolutionary origins. Ribosomes are ribozymes, so are snRNP and snoRP and miRNP complexes.

Indeed. thank you for bringing this up. Most opponents of evolution wouldn't know the modern synthesis if it walked up to them and kicked them.

Nor I. I enjoyed reading your post.

A wise man once said "Giddem-while-they're-young." Barring that, we'll need an old atheist, a young atheist, and a gallon of holy acid.