Biology
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Overviews of all views within the Evolution-Creation Debate Spectrum:
Overviews of and dialogue between 4 Christian standpoints (Young Earth Creationism, Old Earth Creationism, Theistic Evolution, and Intelligent Design), including more in-depth discussion of the crucial flaws and defenses of each | Four Views on Creation, Evolution, and Intelligent Design (Counterpoints: Bible and Theology) (2017)
Overviews of roughly 6 camps (not necessarily Christian) across the entire spectrum of the origins of life debate (Naturalistic Evolution, Non-teleological Evolution, Planned Evolution, Directed Evolution, Old Earth Creationism, and Young Earth Creationism), discussing the views more from the viewpoint of their underlying assumptions | Mapping the Origins Debate: Six Models of the Beginning of Everything; eBook text online at Wright Library
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Evolution:
Updated discussions of the many layers of evolution: The genetic (modern Synthesis), Evo-devo and the epigenetic (extended synthesis) | Evolution Evolving: The Developmental Origins of Adaptation and Biodiversity - Kevin N. Lala, Tobias Uller, Nathalie Feiner, Marcus Feldman, Scott F. Gilbert (2024)
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Intelligent Design:
A comprehensive book for Intelligent Design debates, philosophy of science etc. (interestingly, even talks about the inflaton field!) | Signature in the Cell: DNA and the Evidence for Intelligent Design - Stephen Meyer (2009) (The website for the book, on which you can find praises/critiques of the book up until 2012)
Specified Complexity (as termed Specified Complexity; in statistics, it is equivalent to the concept of Randomness Deficiency) | The Design Inference: Eliminating Chance Through Small Probabilities - William Dembski (1st edition in 1998)
Classical Text on Kolmogorov complexity which will help you gain a rigorous understanding of complexity and randomness | An Introduction to Kolmogorov Complexity and Its Applications - Ming Li and Paul M.B. Vitányi (1st edition in 1994)
A book from the secularist (agnostic) corner that proposes structuralism and typology, and presents criticisms of evo-devo, epigenetics, and proposes homology as actually against evolution | Evolution: Still a Theory in Crisis - Michael Denton (2016)
There are people who say that ID proponents don't realize that convergent systems with feedback can search for the islands of function. This characterization is naive. ID proponents obviously recognize that there are cells and selection processes. The challenge to evolutionists is simply to show that there is a convergent system with feedback at the level of abiogenesis, and at every or at least most degrees of DNA length (No. of base pairs).
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Basic Observations about the main debate:
tl;dr:
Paleontology and interpretation problem of fossils, Eigen's Paradox (for DNA error-correcting), mutation rate
Apart from redefining types and taxa and whether they can be stable concepts to be used to discuss evolution (a consistent evolutionist can very well reject their absolute validity and just say they are nominal, with univocal reality being the actual configurations of the DNA base pairs and its interaction with the environment), paleontology remains the main battlefield for evidence for and against evolution. A rebuttal of Denton's view that there are too few transitional forms by talkorigins.org frankly admits the evidence and merely replies that Denton is too strict:
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"Now to the fossil record. Similar to the creationists, Denton proposes that there are not enough transitional forms in the fossil record, and that what transitional forms do exist are rather dubious in nature because they do not show soft organ changes (since organs aren't fossilized) and are not intermediate in every single characteristic. Thus, Archaeopteryx lithographica, perhaps the most famous transitional form of all time, is inadequate because its wings and feathers were fully formed. Never mind that Archaeopteryx sported more reptilian skeletal characteristics than it did avian ones, and ignore the fact that its skeletal characteristics very closely match a class of wingless reptiles called therodonts that existed around the same time and in the same geographical location. It is apparent, then, that Denton's standards for labeling a fossil a "transitional form" are unreasonably restrictive."
(futher down)
"Every once in a while, a new transitional form turns up and strengthens the evolutionary pattern inherent in the fossil record . But in any case, to deny that the ones that already exist are what they appear to be is a sure indication of unreasonably strict criteria for transitional forms.
We have seen that Denton's assault on evolutionary pattern has failed. The "problems" he points out with the evolutionary interpretation of the data have turned out to not be problems at all. It has additionally been shown - thanks to transitional forms, true homologous structures, and the various novelties that appear in embryological and molecular realms not subject to selective pressures - that deriving a typological pattern from the data is itself a problematic undertaking."
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Thus on this point of hard evidence, it seems that evolutionists and anti-evolutionists will keep talking past each other due to different interpretations of the same evidence. A person's belief in evolution can be gauged by how much he is willing to say in the face of this collection of paleontological evidence.
One of the notes from the website is just plain denial:
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"2A creationist critic responded to me at this point by saying that all dogs are members of the same species, and that their variation thus does not constitute evidence for evolution. However, this critic misses my point entirely. What I was attempting to show was that large structural change could occur naturally. The fact that such change can occur within the same species makes the case for macroevolution stronger, not weaker."
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It does not make the case for macroevolution stronger. This is just plain question-begging. The whole question should be reformulated as: Is gene-sequence change (mutation and muration rates, the basis for macroevolution) responsible for large structural changes, or are isolated gene pools, evo-devo factors and epigenetic changes (the latter two as bases for microevolution rather than macroevolution) responsible?
Stephen Jay Gould's punctuated equilibrium is only a statement at the species level, and not at the class level (per his comment on The Panda's Thumb). Therefore it is admittedly not appropriate to use it to argue with evolutionists about fossil change. The timescale is just different.
Can the mutation rate provide a cap on macroevolution? We can compare the mutation rate of the proposed ancestor of the Asian Elephant (specifically the subspecies Indian Elephant), the Woolly Mammoth (M25 sample), towards the Asian Elephant (0.4-0.6% genetic difference over 1.2 million years, so 5 × 10⁻9 per basepair per year), and the mutation rate of the Asian Elephant itself (5.3 × 10-9 per generation, with generation time at 31 years, so a de novo substitution rate of 1.7 × 10⁻10 per basepair per year). If the mutation rate for the Woolly Mammoth to the Asian Elephant is faster (30 times faster) even given this more generous estimate of the Woolly Mammoth's temporal distance from the Asian Elephant today, then we need to see how other factors make it faster. Since this is a sample gene among a larger population, we need to account for the population as well to know the true range of the gene pool and therefore the true genetic distance it needs to cover. This would involve finding the closest genetic ancestor among Woolly Mammoths to this particular Asian elephant being compared, but we might not have that. We could therefore guess in the opposite direction by taking the genetically closest Asian Elephant to that particular Woolly Mammoth.
Analyzing the evolution-creation debate:
Enlarging the phenotype-space is valid as a rough support for evolution, if we calculate phenotype distance similarly to the distance between two points on a Euclidean space with multiple, mutually-orthogonal axes. Quantum, step-like changes (not to be confused with quantum mechanics) across phenotypes can produce a close-to-continuous fitness-spectrum that can fit multiple environments. Say, for example, 1 step in the x direction and 2 steps in the y direction, which produces a phenotype distance of 5 squared, smaller than 3 (if all 3 steps were taken in the same direction, say x). Actual calculations would determine the weight of each mutation by itself and paired with different distributions. Evolutionists will haggle on how much certain mutations or combinations of mutations can travel over from one species to another with a noticeably "novel" trait. They will also make the regions between the pockets more "forgiving" of mutations that are not-quite-there. If selection is hyper-sensitive, then no travel will be possible. Small deviations from one species will be quickly killed off before the next step of travel takes place. If selection is weakly sensitive, then deviations in all directions will be possible, and the tree will look more like a web with no identifiable "branches" giving structure to the "tree."
The gene sequence will have to travel from one adaptable pocket to the next. Evo-devo and epigenetics will turn those steps into jumps. The whole debate is about how plausible is the jump from one to the next, and fossils give clues to how those jumps actually happened (and incidentally, how they could happen). Evolutionists will therefore "continuitize" the available pockets as much as possible, and both "continuitize" and "amplify" the travel distance per gene mutation as much as possible. Evo-devo and epigenetics do cover a lot of distance, and therefore phenotypes could be chunked into a smaller number of genes. Is the chunking enough?
Most evolutionists will want to allow the whole tree of life (or tree of phenotypical-pockets) to converge to one point. The one tree could have "roots," but those multiple roots must too converge through mutative-biological mechanisms to one point. This is a testament to the incredible life-fitness of the cell. Michael Denton is the dissenter who thinks the phenotypical pockets only converge to multiple trees of life with no overlap between trees at the biological-mutative level (Typology), but could be "linked" to more fundamental physical constraints (Structuralism) or other factors. Denton is therefore an interesting evolutionist that gives us a gauge on the religiosity of the whole evolution camp. He is like the open-minded evolutionist who is sending an invitation to the physicists to calculate a higher probability of cell-like life formation. Evolutionists therefore would want him if they wanted to solve more convincingly the abiogenesis problem (the physicist/chemist side), but that would sacrifice the validity of pure, biological evolution.
Can creationists leverage the problems of evolution without tacitly assuming other non-problematic features of evolution? Yes. All creationists have to do is point out the difficulties (the early appearance of angiosperm, the Cambrian explosion etc.) naturally arise when post-fall physical laws run against Creation initial conditions and discontinuous curse-events that potentially change the laws of the universe. This limits the use of science to purely predictive purposes and severely limits its use in retrodictive explanatory purposes past the curses and past the moment of Creation.
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Young Earth Creationism/Young Universe Creationism:
Young Earth Creationist Cosmology that can account for the old-age of stars | A New Creationist Cosmology: In No Time at All - Part 1 (2010), 2 (2011), and 3 (2011) -- the book it was based upon: Starlight and Time - Russell Humphreys (1994)
A partial-apparent age treatment | Scientific Creationism - Henry Morris (1974)
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Basic observations on apparent age and non-essential features:
The definition of non-essentiality is still far too broad (since essentiality is unreasonably limited to the Garden of Eden in only the first six days), and practical concerns (e.g. navigation over broad distances) that may arise in future non-fall scenarios are not considered among the essential features.
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Apparent Age:
Good discussion about different varieties of Apparent Age views of the universe (I think partial apparent age would be the appropriate view) | Asa3
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The detailed sequence of starlight would have the function of allowing humans to appreciate the deeper beauty of math and the night sky were humans not fallen and continued to receive direct revelation from God about the natural world. Thus it would merely extend the season-marking and beauty function of basic starlight up to the time when humans would be able to detect the intricate details and start micro-season marking (if, say, history at the femtosecond scale became an interesting project for humans in a supposed perfect world). Do not deny God's possibilities. There should not be just meaning in starlight in an "ancient pre-fall world" and a "modern post-fall world," but also a didactic function about what the world could be in a sadly contrafactual "modern non-fall world."
Humility in crediting God with honesty does not just have to be in asserting that there were non-essential details that have to be respectfully reconciled with a Biblical account, but humility should be exercised even in the interpretation of the details that were taken to be "non-essential" in the first place. How are we sure that we can only interpret detailed sequences as only something analogous to a "non-essential seal of authenticity"? Even as a partial apparent age-r, I could simply extend "essentiality" to include any didactic purpose in the future (indeed, detailed sequences of starlight were never a problem before, and has only now started to give us information about stars that keep its current state consistent with physical laws going both forward and backward in time; how can we venture to say that these details are non-essential?). In short, do we really know what would a minimum apparent age universe without non-essential details would look like? Or do we haggle unreasonably on what is non-essential?
I do not think the last sentence in the summary is honest enough: "This theory is scientifically supported, theologically satisfactory, matches our common sense intuitions about the reality of our experiences, and provides a solid foundation for science and for living by faith." Apparent age is in every way scientifically supported, theologically satisfactory and provides a solid foundation for science and even more so for living by faith, but I suspect that all the reasons that push one to prefer actual old age is snuck into the reasons of "common sense intuitions." Simply put (and to paraphrase Bertrand Russell), your common sense intuition just might not be common.
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One harmonizing of old age universe laws and young-age universe history that ends up being complete but non-testable, and was rejected by both religious and scientific circles | OMPHALOS: An Attempt to Untie the Geological Knot
Per Craig Rusbult on the ASA3 website:
Martin Gardner, in Facts & Fallacies (1957), agrees that Gosse "presented a theory so logically perfect, and so in accordance with geological facts that no amount of scientific evidence will ever be able to refute it." Burgeson also agrees: "Gosse argues well that any fiat creation, even by God, must necessarily include unreal history. His arguments need to be taken seriously."
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I also think the author misinterprets Henry Morris' claim here:
"But instead of just defending apparent history, he goes on the offensive against its critics by claiming that apparent age is theologically essential: 'here could be no genuine creation of any kind, without an initial appearance of age inherent in it. ... When one decides to reject the concept of real Creation [with apparent age], there is no scientific stopping-point short of what amounts to atheism. ... It is essentially an affirmation of atheism, a denial of the possibility of a real Creation. (1961, pp 237-238)' Wow. This is quite a claim."
He expands Morris' attack on apparent age to mean an attack on old-universe views. But by this point, Morris' point is the implausibility of anti-Creation views, and therefore more attacking eternal universe views instead of views of the universe with arbitrarily old ages. The point is that no matter how old the universe is claimed to be, there will always be a beginning and therefore an absolute discontinuity with nothingness, and that is where the necessity of Creation will always be located. Apparent age is no longer apparent old-age, but "apparent eternality." As long as this is understood, there is no contradiction between Morris' claim here and Rusbult's.
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There is an objection to non-essential features:
Hill Roberts says, regarding an "apparent age" explanation for how — if the universe is less than 10,000 years old — in 1987 we saw the supernova explosion of a star (or at least what appeared to be a star) that was 170,000 light-years away, If God created stars at such a distance, and intentionally created the starlight already at the earth from the beginning, then in this case (and many others as well) He would have had to encode the starlight with the history of an event (the change from normal star to explosion) that never actually happened — it just "appears" to have happened. If the universe is only a few thousand years old, this supernova has always been a supernova and never an ordinary star. But up until 1987 it was seen in the starlight to have been just an ordinary star. If God altered the history of this part of His creation to appear to be something it wasn't, who's to say what history is real and what history is fake? And why would God tell us to go look at natural history (Romans 1:19-20) to learn about His godly nature and power if natural history doesn't record true history? This would seem to be a problem since that same God tells us He cannot lie — Hebrews 6:18, Titus 1:2. I will not accept that God is a liar, even if it's just a little "white lie" to astronomers. Therefore, I don't think God faked this event in the starlight. It must have really happened 170,000 years ago. {source}
This objection is unsatisfying. The question that can be raised towards this claim is: why is the statement that "it must have really happened 170,000 years ago" taken as absolute, incontrovertible fact? Is it not enough to say that the phenomenon was given to us at an earlier date than what is expected for star maturity? The phenomenon would be "essential" (or even for night-sky-beautifying purposes) for giving us an even more bright and structured signal to define the night sky. It could also be said to act as a proof of a theory that stars reach supernova (should mankind ever come to that theory and use it for further development of science or just take that theory as an object of marvel itself). The same could be said about why the stars should be positioned so assymetrically across the sky instead of symmetrically (which presents problems for determining which way was stellar north). Be creative!
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Homology
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Geology