Forums → WEPR → Long link

The study is looking at variation, and uses artificially bred lines to make it faster. I agree, the mechanisms that form variation are not different in artificially and naturally selected lines; that is not the point I was trying to make. The issue is with the specific changes. My point is, artificial selection favours arbitrary characteristics desired by humans, disregarding any occasional disadvantage for the organism; because it was bred for an artificial environment where such disadvantages can be dealt with. In a natural environment, such disadvantages would be out-selected, hence why using artificially selected cripples as evidence against large-scale variation in a natural environment is nonsense.

As for the rest of the study, I am currently writing a full review of the article (except for the intro since I already addressed that part) including an assessment of the study, it'll just take me some more time.

Nobody should be using it to attack religion.

What should be and what is are two different things. Welcome to the real world, it sucks more often than not but at least there's a real sense of accomplishment when something gets done.

It's also important to remember that merely because our understanding of the mechanics of an idea is wrong or incomplete, it does not mean that the idea itself is.

That is true. But when our understanding of the mechanics is wrong you can hardly call that idea a fact. With a flawed understanding of the mechanics an idea can't be proven and we have to be that much more critical of it. Without properly working mechanics, the idea doesn't work and shouldn't be accepted. If the mechanics we think are part of it are proven to not work that way then the theory, as it exists, has been falsified. You can't just excise the parts that don't work and still call it a theory (or worse, a fact) because that's not how science works. A theory can't be restructured without evidence supporting the new parts, otherwise it's not sufficiently proven to act as a theory.

To long link, long reply. As mentioned before, I did not review the introduction a second time.

In the following, the author of the article linked in the OP is simply termed 'the author'.

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Mutation - Natural selection

"That is evolution's only tool for making new creatures"
Actually, there is also recombination, genetic drift (see ring species), hybridisation, horizontal gene transfer, developmental changes, ...

"Thus all the right mutations (and none of the destructive ones) must happen at the same time by pure chance. That is physically impossible"
Indeed that would be highly improbable, and it is not happening in organisms as far as we know. The author is making an unreasonable and baseless assumption. Mutations in gonadic cells that do disturb vital parts will lead to an early abort of the foetus in most cases, those that do not will be established.

The author denies even the possibility of beneficial mutations, but there are actually documented cases of such mutations: we know they happen.

- Wikipedia: Pesticide resistance
- RationalWiki: vivid examples of beneficial mutations
- Andian village developed tolerance to arsenic
- Evolution is still happening: Beneficial mutations in humans

As for the precise effects of beneficial mutations and their establishment, I listed below some studies I found discussing the extent and limits.

- Sniegowski P.D., Gerrish P.J. 2010. Beneficial mutations and the dynamics of adaptation in asexual populations. Phil Trans R Soc B 365:1255-1263
- Orr H.A. 2010. The population genetics of beneficial mutations. Phil Trans R Soc B 365:1195-1201
- Kirkpatrick M., Peischl S. 2012. Evolutionary rescue by beneficial mutations in environments that change in space and time. Phil Trans R Soc B 368

The Drosophila study on classical sweeps:
- Burke, Molly K., Joseph P. Dunham, Parvin Shahrestani, Kevin R. Thornton, Michael R. Rose, Anthony D. Long. 30 September 2010. Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature, Vol. 467, pp. 587-590.
What does the abstract of the study tell us? It begins by stating that so far, genomic studies of adaptation have been done in asexual systems with small genomes. They used sexually reproducing Drosophila for their experiment that they bred to have a faster development. Their result is that "Signatures of selection are qualitatively different than what has been observed in asexual species; [...]", stating that classic sweep models insufficiently explain the adaptation seen in their flies; other models do a better job of explaining it. They conclude that classic sweeps probably don't contribute substantially to changes of life history characters.
One of their cited sources gives evidence that other mechanisms like soft sweep may contribute:
- Hermisson J., Pennings P.S. 2005. Molecular Population Genetics of Adaptation From Standing Genetic Variation

What does that mean? It means one single model does not explain every observed adaptational change in the observed population, that there are differences between certain biological traits and possibly between sexual and asexual species. Interestingly when you look at the sources cited in this study, you find studies that did find evidence for the establishment of beneficial mutations:

- Herring C.D., Raghunathan A., Honisch C., Patel T., Applebee M.K., Joyce A.R., Albert T.J., Blattner F.R., van den Boom D., Cantor C.R., Palsson B.O. 2006. Comparative genome sequencing of Escherischia coli allows observation of bacterial evolution on a laboratory timescale
- Barrick J.E., Yu D.S., Yoon S.H., Jeong H., Oh T.K., Schneider D., Lenski R.E., Kim J.F. 2009. Genome evolution and adaptation in a long-term experiment with Escherischia coli

For Lenski's experiment, please refer to this link:
- RationalWiki: Richard Lenski

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Microevolution - macroevolution

The assertion made here is that the evolutionary theory cannot be true because Darwin could not anticipate everything. It ignores (and admittedly the quoted article forgot to address this (or at least the part quoted by the author)) that today we know a lot more than Darwin did. I named at the beginning several mechanisms that favour speciation other than mutations, an important structure being the Hox genes. You can read some about it here:

- Myers, P. 2008. Hox genes in development: The Hox code. Nature Education 1(1):2
- Hox genes and animal body plans

And since the evolution of the eye and wing is addressed, we have today a pretty good understanding of how they evolved.
Here is some more reading material:

- Wikipedia: Evolution of the eye
- Eye evolution
- Why the eye? - Understanding Evolution

- Dinosaur World - Wing Evolution
- National Geographic - From Fins to Wings
- Towers M., Signolet J., Sherman A., Sang H., Tickle C. 2011. Insights into bird wing evolution and digit specification from polarizing region fate maps. Nature Communications 2:426

I add here two links on the evolution of the turtle shell since I mentioned it in a previous post and it is relevant here.

- Lyson T.R., Bever G.S., Scheyer T.M.,Hsiang A.Y., Gauthier J.A. 2013. Evolutionary Origin of the Turtle Shell. Current Biology 23(12):1113-1119
- Smithsonian: Ancient turtle

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Orphan genes - the final blow?

This one is interesting. I had not read about Orphan genes before (or likely just forgot what little I had learned of them). They are apparently genes that form de novo in organisms, which is unusual to say the least. But what exactly is meant here by de novo? It means the gene coding sequence did not evolve in the classical sense, but emerged through other processes. These processes are not yet completely understood and are being investigated; but it seems there are already promising investigations (see links).

Now let's look at the point made by the author. He uses a quote stating that "The probability that a functional protein would appear de novo by random association of amino acids is practically zero." That is true - I agree. That is one of the points that creationists often get wrong about the evolution of complexity. The author goes on comparing this quote directly with orphan genes and uses it as evidence that de novo formation (in the sense used right before) is actually possible. That is wrong - I disagree. Why? Simply because it is not the same kind of 'de novo'. Yes, I am aware that this looks like a bad excuse, but I assure you it isn't. The probability that random amino acids form a fully functional protein by chance is practically zero; but in the case of orphan genes we have different starting conditions. From what I could gather, orphan genes appear within start and stop codons in sequences that previously did not code for a protein. That does not mean that there are a bunch of unassociated molecules that would suddenly form a complex protein all by themselves against all probability. We have a sequence which gets modified by certain mechanisms and ends up coding for a protein. The chance that the sequence modification happened base by base randomly is equally low as the chance of random amino acids forming a functional protein, so we can exclude single nucleotide mutations. The third link below provides some potential mechanisms, "such as gene duplication, frame-shift fixation, creation of overlapping genes, horizontal gene transfer, and exaptation of transposable elements". Notice that I mentioned horizontal gene transfer at the beginning. Note also that while orphan genes occur in many species, they only make up 10 to 30% of all genes in a genome, according to the author quoting his source #45. Note, furthermore, that orphan genes do not disprove the classical mechanisms of gene evolution for the remaining 70 to 90% genes.
In a way, instead of disproving evolution we end up with just one more tool for "macroevolution". I am eager to hear more about ongoing research on orphan genes, for sure.

- Orphan genes: a guide for the perplexed
- Tautz D. and Domazet-loso T. 2011. The evolutionary origin of orphan genes. Nature Reviews Genetics 12(692-702)
- Wissler L., Gadau J., Simola DF., Helmkampf M., Bornberg-Bauer E. 2013. Mechanisms and dynamics of orphan gene emergence in insect genomes. Genome Biol Evol. 5(2):439-55

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Origin of Life research (and "Origin of Life" research, continued)

To start off this section, let me remind you the usual objection: abiogenesis is not evolution, and evolution does not rely on abiogenesis. Evolution, as its name says, explains how already existing life forms change. The burden of explaining the origin of life is all on abiogenesis.

Now as for abiogenesis, the points given by the author are risible. Especially the quote "Deamer's demonstration that we cannot translate lab results to natural settings is valuable" irks me. No it isn't. Apparently he is completely uncritical regarding his own experiment; did he use the most recent findings, did he do everything right, is there a possibility that he simply hasn't found the correct environment for his experiment, is it possible that a factor was missing? No, he contents himself with very little apparently.

It is true that there is not nearly as much evidence in favour of abiogenesis as there is for evolution. However, the author is misrepresenting the current state of research. He only quotes scientists that explain the issues of either abiogenesis as a whole or single points like RNA replication, but he completely leaves out the progresses that have been made in other areas. It is ongoing research with good evidence that we will soon make interesting discoveries.
Below I give some links to the topic; of course the obligate youtube video (exposing Jack Szostak's view, the guy that the author quotes for his slide (one slide! out of a whole presentation!)); but I feel like it is getting old news, so please also find below links showing more recent studies. Have fun.

- The Origin of Life - Abiogenesis - Dr. Jack Szostak
- Noller, F. 2010. Evolution of Protein Synthesis from an RNA World. Cold Spring Harbor Perspectives in Biology
- Herschy B., Whicher A., Camprubi E., Watson C., Dartnell L., Ward J., Evans J.R., Lane N. 2014. An origin-of-life reactor to simulate alkaline hydrothermal vents. J Mol Evol. 79(5-6):213-27
- Uni Muenchen: Labyrinths as crucibles of life
- Barge L.M., Abedian Y., Russell M.J., Doloboff I.J., Cartwright J.H.E., Kidd R.D., Kanik, I. 2015. From Chemical Gardens to Fuel Cells: Generation of Electrical Potential and Current Across Self-Assembling Iron Mineral Membranes. Angew. Chem. Int. Ed., 54: 8184–8187.
- Press release of the above study from NASA's Jet Propulsion Laboratory, Pasadena, California

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Gradual change versus leaps

The modern synthesis of the evolutionary theory encompasses both gradualism and punctual equilibrium, so saying that there are two distinct versions of the theory is not correct. In both cases, the organism continues to evolve. This is easily seen in gradual evolution, but less apparent in phases of morphological 'stasis'. In some cases the species is in sync with a steady environment and hence does not change its appearence significantly for a long time, but even during this stasis the species evolves. An example of this is the coelacanth: while the modern species (plural) look pretty much like their fossil ancestors, they are nonetheless different species (based on minor morphological variations). This is because fossils show mostly anatomy and morphology, which are governed by a small amount of genes only, leaving the remaining bulk of the genome free to vary [1]. A rapid change in morphology within the fossil record can be explained for example based on one population that splits from the rest, evolves in a different environment, and later drives out the original population [1].

[1] Guillaume Lecointre, "Guide critique de l'évolution". Paris, Belin, 2010.

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Fossil record

This part begins with a common misconception, it also illustrates why many biologists don't like terms like "missing link" or "transitional species"; they are too easily misunderstood. The author explicitly expects to see "works in progress" to validate evolution. This is ignoring that in order to be consistent with how evolutionary mechanisms work, every single link, every single species, every single organism has to be a complete animal or plant; otherwise it would in all certainty be out-selected. Another misconception that is implied here is that a "transitional" characteristic evolves for the purpose of the modern body part; this however is just as wrong. Examples include limbs (evolved in shallow water in lurking predators, only later used as an exaptation to terrestrial mode of life in tetrapods); wings (only later used as an exaptation for flight (link), the turtle shell (expanded and dense ribs that were first used for improved diving dynamics and only later used for protection), and many more. I think a quote from the above link on flight evolution brings it to the point: "Evolution has no sense of future; the here and now is the only place where evolution occurs. It is imperative to keep this in mind when considering the origin of flight. Lineages of organisms are not designed for some future purpose; they are changed by opportunities to which they can respond and by the selective processes that their environment imposes on them. "
Nonetheless, we have in several cases a very consistent fossil record displaying the evolution of animals and plants over time, another topic on which the author is not up to date.

Concerning the claim that we have no fossil ancestors at all for complex invertebrates or fish, this is not quite true, see links below.

- Smith M.R., Caron J.B. 2015. Hallucigenia's head and the pharyngeal armature of early ecdysozoans. Nature 535:75-78
- Yang J., Ortega-Hernandez J., Gerber S., Butterfield N.J., Hou JB., Lan T., Zhang XG. 2015. A superarmored lobopodian from the Cambrian of China and early disparity in the evolution of Onychophora. PNAS 112(28):8678-8683
- Donoghue P.C.J., Keating J.N. 2014. Early vertebrate evolution. Palaeontology 57(5):879-893

It should go without mention that the fossil record is not perfect due to the nature of preservation and excavation. Especially in a period when life forms were less likely to leave fossils (conditions that preserve soft-bodied fossils such as in the Burgess Shale are exceptional in that aspect). Luckily genomic studies help palaeontologists where no fossil evidence can be found, as in the study linked below.

- Spang A., Saw J.H., Jorgensen S.L., Zaremba-Niedzwiedzka K., Martijn J., Lind A.E., van Ejik R., Schleper C., Guy L., Ettema T.J.G. 2015. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521:173-179

As for the author's criticism on the study linked below, what is in the abstract called "compilation of the patterns of fossil and molecular diversification, comparative developmental data, and information on ecological feeding strategies" is apparently what the author calls 'story-telling'. I see nothing wrong with the assumption that evolution occurred either, to expect that each and every study should contain a full argumentation of all the evidence at hand before doing any experiment is nonsensical. Furthermore the study is a projection, not the final word on the topic.

- Erwin, Douglas H., Marc L., Sarah M.T., Erik A.S., Davide P., Kevin J.P. 2011. The Cambrian Conundrum: Early Divergence and Later Ecological Success in the Early History of Animals. Science 334:1091-1097

The argument with the compound eye of arthropods is moot. An organ already that performing is subject to less selective pressure and hence will not change radically. Note however that the eye is not exactly the same, so evolution did occur. The two following paragraphs of the article don't seem to contain any apparent point. As for the coelacanth, I already mentioned this previously: the fossil species are extinct, the modern species changed very little in appearance as their environment was stable. And yes, we now know they weren't the earliest walking fish, they are not even considered tetrapods. We can thank the substantially larger fossil record of today for this insight. Same goes for the Archaeopteryx: the reason why it isn't considered as a direct link anymore is because we have a much more detailed fossil record of the avian dinosaurs nowadays. Different animal, same point: evolution did occur between Protozygoptera and modern dragonflies, or else they would be considered the same species. The morphological changes are evidently so small that a five minute look at a drawing of the fossil and a medium-quality photograph does not reveal any visible difference. The platypus is evidently a mammal with convergent and novel characters (bird-like snout (without the keratin), poisonous talon). The issue with the avian and equine family trees has been previously addressed: of course they are all fully formed! That is congruent with evolution.

As for the comments about phylogeny, one thing worth noting is that categories like 'family' or 'class' have lost relevance as the data is far more complex than Linnaeus could foresee (also, while his system is still used in its bases, modern phylogenetic relationships are often at a discrepancy to Linne's ideas, as morphology is not the only criterium). Today we keep the genus and species level, everything above is referred to as a taxon (pl. taxa). The author's confusion with modern phylogenetic relationships is therefore somewhat understandable.

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The "Tree of Life" is falling

This point is not worth dwelling too long upon since I already gave a link that deals with this issue (I repost the link below for convenience). The basic gist is that while the old model of the tree of life is long outdated, we use newer models now. Common descent was never abandoned along with the old model.

- News of the Death of the Tree of Life has been greatly exaggerated

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The big fudge

This part is flat out denial of inheritance and convergent evolution, and a lot of incredulity.

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Design flaws

Apparent 'design' flaws often can be explained from an evolutionary and/or developmental perspective (such as why we suffer from hemorrhoids), and the case of the eye and its apparent 'bypass' of the flaw is no exception.

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Reviving evolution

While Haeckel's drawings of the embryos were not very accurate, it has never been found to be fraudulent. Haeckel's imperfect recapitulation (as opposed to perfect recapitulation, a misunderstanding that even eminent biologists fell for at the time) matched the von Baerian divergence. Karl Ernst von Baer proposed an early similarity and later divergence in embryos: "The general features of a large group of animals appear earlier in the embryo than the special features" (Alec Panchen's Classification, evolution and the Nature of Biology). This is essentially what Haeckel's imperfect recapitulation is about. It is important however to be aware that neither recapitulation nor divergence are laws; while the pattern is observable especially among vertebrates, it is not uniform among all living taxa and there are numerous exceptions.

-Wallace Arthur, 2010. "Evolution: A Developmental Approach", Wiley-Blackwell

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Vanishing vestigials

Funny how he only mentions vestigial organs he can explain away, ignoring vestigial limbs in whales and snakes, for example.

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Violating the law

Entropy can be locally reduced, but as it consumes energy, total entropy will rise. With this simple insight, his argumentation falls apart.

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Mindboggling complexity - proteins

Refer to this article:

- Wikipedia: Irreducible complexity.

Note already the second paragraph of the introduction.

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Duplicate genes

- Bozorgmehr, J.E.H. 2011. Is gene duplication a viable explanation for the origination of biological information and complexity?. Complexity, 16: 17–31.
The study given and linked above analysed the effects of duplicate genes and found that even though they do "contribute(d) to the size and diversity of the genome", duplication alone cannot explain the high level of complexity found in organisms. This is not so much an argument against evolution as it is an argument against the notion held by some biologists that natural selection is the sole cause of adaptation. However it appears more and more apparent that factors other than natural selection can cause adaptation. I would like to note that the study only mentioned the conservative aspect of natural selection on the genotype, although experiments have shown that under changing environments natural selection can also promote genotypic variation.

Furthermore, I found studies that relativise the results of the one just discussed.

- Meyer A., van de Peer Y. 2005. From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). BioEssays 27(9):937-945
- Hittinger C.T., Carroll S.B. 2007. Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449:677-681
- Bergthorsson U., Andersson D.I., Roth J.R. 2007. Ohno's dilemma: Evolution of new genes under continuous selection. Proc Natl Acad Sci U S A 104(43):17004-17009

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Repairing mutations

Genetics 101: while DNA repairing mechanisms deal with the bulk of mutations, neither repair nor replication systems are perfect. Mutations can be overseen, they can even be introduced by the replication/repair systems themselves. Sometimes &quototentially devastating mutations (such as double-strand breaks)" are turned "into mutations that may affect only a single gene product." - Griffiths, Wessler, Lewontin, Carroll, "Introduction to Genetic Analysis", 9th ed., W.H. Freeman and Company, New York.

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Genome size

Genome size does not directly correlate with apparent complexity, but keep in mind that 1) complexity is difficult to quantify, and 2) gene expression may contribute to complexity way beyond simple gene or base numbers.

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Junk DNA

Gene expression, just as I was saying. Research has evidently made progress in this area since the beginnings of genetics. This is just history of sciences: the discovery of new structures that improve our knowledge of genetics. Still, it is unrealistic to assume that every base pair in the sequence currently has a function. Remember at this point the orphan genes: how could a gene form de novo from a random sequence if everything has a function that could be disrupted by such a formation?

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Networks (and 'To the next level')

First please refer again to the previously linked article on irreducible complexity.

The author claims that "The theory of evolution cannot explain how gene regulatory networks came to be." A quick literature search immediately discredits the absoluteness of the author's claim.

- Crombach A., Hogeweg P. 2008. Evolution of Evolvability in Gene Regulatory Networks. PLOS Computational Biology
- Erwin D.H., Davidson E.H. 2009. The evolution of hierarchical gene regulatory networks. Nature Reviews Genetics 10:141-148
- Tsuda M.E., Kawata M. 2010. Evolution of Gene Regulatory Networks by Fluctuating Selection and Intrinsic Constraints. PLOS Computational Biology
- Peter I.S., Davidson E.H. 2011. Evolution of Gene Regulatory Networks Controlling Body Plan. Cell 144(6):970-985

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Many scientists are with us

There is an actual debate, among scientists directly involved with evolutionary theory, about the relevance of natural selection and other mechanisms, see link below. But the quotes of the skeptics given by the author display misconceptions about evolutionary theory. A recurring argument is the random chance; a fallacy by over-exaggerating its role. Random processes are mostly important for creating variation; most selective processes and others involved in adaptation however are precisely non-random, this is essential for evolution and adaption beyond pure random changes.

I am not surprised to see that a handful of scientists are skeptic; it is to be expected. There are debates at pretty much all levels. Keep in mind that there is still a broad consensus on evolution and a mountain of evidence in favour of it. You cannot simply wipe that away.

- Laland, Uller, Feldman, Sterelny, Müller, Moczek, Jablonka, Odling-Smee, Wray, Hoekstra, Futuyame, Lenski, Mackay, Schluter, Strassman. 2014. Does evolutionary theory need a rethink? Nature 514:161-164

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After the "tree of life"

Horizontal gene transfer makes it more difficult to classify bacteria, this is well known. Of course the author seems to think that this automatically discards common descent, which is not the case. The quoted study explicitly says "we cannot rely exclusively on traditional genealogical relationships" and calls for more data from different sources to be taken into account in order to establish a more accurate phylogeny.

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Epigenetics

It seems to me this paragraph contains no concise point. Just a lot of isolated quotes that give a glimpse of the process of scientific discovery.

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The Mind of the Evolutionist

And yet we have documented examples of both island dwarfism and island gigantism. With all due respect for Meiri's opinion, but although some studies found no marked effect, many studies confirm the island rule. Even Meiri states that "We did find consistent evidence that large (> 10 kg) mammals grow smaller on islands. Smaller species, however, show no consistent tendency to either dwarf or grow larger on islands."

In my opinion, those discrepancies are likely a result of different methods of analysis, the existence of exceptions to the rule, and a certain variability of the optimum size and relevance of the rule among taxa. But frankly, this is to be expected when different people analyse something. It does not show that evolutionary biologists like fables, it shows they are doing research.

- Raia P., Carotenuto F., Meiri S. 2010. One size does not fit all: no evidence for an optimal body size on islands. Global Ecology and Biogeography 19(4):475-484
- Aubret F. 2014. Island colonisation and the evolutionary rates of body size in insular neonate snakes. Pubmed
- Jaffe A.L., Slater G.J., Alfaro M.E. 2011. The evolution of island gigantism and body size variation in tortoises and turtles. Biol Lett
- Lomolino M.V. 2005. Body size evolution in insular vertebrates: generality of the island rule. Journal of Biogeography 32(10):1683-1699
- Clegg S.M., Owens P.F. 2002. The island rule in birds: medium body size and its ecological explanation. Proceedings B 269(1498)
- McClain C.R., Boyer A.G., Rosenberg G. 2006. The island rule and the evolution of body size in the deep sea. Journal of Biogeography 33(9):1578-1584

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I hope that along addressing the points of the author, I could clarify some aspects of the issues at hand (ideally all, but I don't see this happening). Now if there is a particular point which you want to address, or a particular study you feel I haven't properly addressed, let me know and we'll discuss that.

Violating the law

Entropy can be locally reduced, but as it consumes energy, total entropy will rise. With this simple insight, his argumentation falls apart.

Genome size

I got poofed in here. What seems to be the misunderstanding/misconception/misinformation/thirst for knowledge? I did get my degree in Biology and so technically am a Biologist you know

Sorry, wish I had poked my head in here sooner. i will have to read over this in more detail, but just glancing over it for a moment on the matter of micro/macro evolution I am left with the same question in my mind that always comes up.
What is preventing these variations from going further to produce a new species and eventually something so different we wouldn't at first seem it as being related to it's ancestry species?

Would they consider pond scum becoming a parasite as macroevolution?
Lethal parasite evolved from pond scum

@Freakenstein I'm waiting for a reaction of Ishtaron to my long reply, but meanwhile I would like to have your opinion on an argument I had with him concerning artificial selection. The link pretends that pushed selection of artificial breeds lead to 'limits' in variation, like infertility, that would prevent speciation, transfering this argument also to natural selection (see the introduction in the OP link). What is your opinion?

So speciation is the incremental progression of an older species to a new one. The word 'species' is defined as a population which is close enough in relation to each other (e.g. DNA sequence) that they can interbreed and produce fertile offspring. The idea is that speciation happens because migrating populations experience different 'challenges' different to what they originally had to deal with, and were previously successful at. Whatever the challenge is, the population (not the individual itself) must adapt to the new changes in environment or risk extinction.

Natural infertility happens genetically. In an ecological case, it is when two species of animals are successfully able to breed, but are not capable of producing fertile offspring; instead, the offspring is infertile. See, infertility within their native population cannot happen ecologically, because a whole population of infertile animals would cease to exist. Genetically yes, but there are specific reasons for that, one is reproductive syndromes that make the individual infertile, but not the population as a whole. One animal being infertile does not affect the population's evolution significantly. It only means this one animal's genome isn't going to be part of the gene pool.

Every one of our dog breeds of Canis familiaris are products of the artificial selection of Canis lupis, bred specifically on different tastes and needs. The lettuce and disgusting cauliflower you eat are descendants of a common ancestor, the mustard flower.

"Evolutionist professors have told this to their students for years, while looking at them with perfect vision"

Did this guy just assume evolution is some kind of perfect hill-climbing algorithm that can find global maxima of optimalility? Perfect vision? Not so much our brain does a ridiculous amount of processing on the garbage our eyes feed them. Human eyes are just a local maximum that can't really be improved anymore since any further changes in the structure to reach a better state would lower the fitness of the animal so it's pretty hard to overcome this.

The author denies even the possibility of beneficial mutations, but there are actually documented cases of such mutations: we know they happen.

Even complex interplay of benefits and lowering of fitness for things like sickle-cell disease. It protects against malaria but then again also causes complications for the host.

Eventually these parts no longer function and they shrink in size.

They don't magically shrink, if the mutation to make them smaller increases the fitness of the organism and allows them to breed more or they or their offspring to survive then yeah you will see the population move in that direction. It's a fitness advantage.

Mutation-natural selection could no more build the vast, intricate networks in living creatures than a beaver could build the Hoover dam.

What are all these horrible analogies doing in the article they discredit the author completely. Like what legitimate insight are they trying to offer.

Then again I'm just a dirty evolutionary psychology student so what do I have to offer. Except extreme skepticism at something borderline an attack ad against evolution.

Yeah evolution can't explain everything about the organisms, like... say my specialty behavior. You can't apply the evolutionary hammer to absolutely everything about animals. But it is still a core component in the tools box that is part of systems view on these questions. Like Dupre's says "the lure of the simplistic" there is a need for a family of models and evolution is one of those models. It is legitimate they are some very straightforward nice things you can apply to say humans that work and explain the problems at hand. This "article" doesn't really offer anything except some misinformation and personal opinions founded on confusion and anger.