This was written after his landmark “Signature in the Cell” book. He responds to some criticism of his work there.
This is an excellent and detailed book going over specific evolutionist claims. My notes here only reflect a few general principles.

Here is a summary of the book which he gives toward the end. 4 specific scientific critiques of the inadequacy of Neo-Darwinism in this book are
“1. Neo-Darwinism has no means of efficiently searching available combination space for functional genes and proteins and consequently
2. It requires unrealistic unrealistically long waiting times to generate even a single new Gene or protein, and the new mechanism cannot produce body plans because
3. Early acting mutations, the only kind capable of generating large-scale changes, are also invariably deleterious and
4. Genetic mutations cannot in any case generate the epigenetic information necessary to build a body plan.”

Darwin saw the lack of transitional fossils as the one big problem in his theory. He hoped later researchers would find them, but no one has. Dogmatic Darwinists are more confident about the theory than Darwin himself was. Darwin was at least able to confess the weakness of his theory when it came the lack of transitional fossils.

One Chinese scientist pointed out that in China you can’t question the government, but you can question Darwin; in America you can question the government, but you can’t question Darwin!

Scientific literature in every field are raising serious problems with Neo-Darwinism.

Darwin was all about a universal common ancestor, and natural selection being how we have variety today.

Evolutionists say the soft and hard parts of animals had to evolve at the same time since the animal couldn’t survive with just the soft part.

There are many fossils of soft parts of animals which goes against Darwin’s longtime theory.

Many fossils are even more complex than the animals of today, which goes against Darwin’s simple to complex theory.

There are Precambrian fossils of tiny soft animals, but not of transitional fossils; if even the tiny soft animals were preserved then necessarily the other transitional animals would have been too. Lots of data indicates that the transitional animals never existed, and this is true even though many pre-Cambrian environments were ideal for fossilization.

With how much we know about the fossil record now we can’t claim that these transitional fossils might be out there somewhere. It’s like reaching into a bag of marbles and pulling out blue, red and yellow. At first you think the whole rainbow might be in there, but as you keep pulling out marbles and you only get the same three colors, so you can’t keep saying that it’s likely that the whole rainbow is in there, much less the whole spectrum of colors between each color.

Scientists now see the Cambrian explosion happened in a much shorter duration of time than previously thought.

They say the Cambrian explosion is like one minute of a 24-hour day when compared to the age of Earth. Evolutionists play word games to try and make it seem like they came in an explosion which took many millions of years, claiming a series of explosions etc. Evolutionists are always trying to find ways to make the Cambrian explosion appear less explosive.

Meyer does lots of debates and discusses some of those in the text. (Note – he is one of the greatest debators.)

Many fossils which aren’t even animals are claimed to be intermediate animal fossils.

There are many leaps in complexity in a relatively short geologic time, which natural selection cannot account for. They have been called ‘quantum leaps.’

Neo-Darwinism is similar to classical Darwinism, requiring significant amounts of time, and Neo-Darwinism focuses on mutations. They claim that in the Cambrian and Ediacaran periods that significant mutations took place over 40 million years, which is not nearly enough for natural selection to make those changes. That’s why they call these ‘explosions.’

The first principle is do not fool yourself, you are the easiest person to fool. If you fool yourself, you’ll fool others.

They come up with names for intermediate branches on their phylogenic tree when no discoveries of those animals have been made, it’s just a name a placeholder!

Scientists will admit amongst themselves weak points of their theories, but in public they deny or undermine those points.

Homologous structures were known to be signs of a common designer until evolutionary theorists foisted their dogmatic view on everyone, insisting that these rather mean a common ancestor.

Evolutionists downplay the Cambrian explosion claiming that millions of years of evolution caused that explosion, but that this evolution was all hidden!

Scientists admit that there is overwhelming evidence in the fossil record that animals evolved long before evolution theory claims they would have.

Note – this does not refer to deep time, this refers to the order that fossils are found.

Scientists admit that whenever you see a time in geologic literature, you should demand uncertainty.

Scientists claim that we already know that life evolved from a common ancestor, so they automatically reject findings which don’t agree with that conclusion.

Scientists admit there is no tree of phylogenic life pointing to a common ancestor. Genes do not give information about evolutionary relationships.

Molecular and anatomical data frequently disagree, leaving scientists arguing about how to classify them.

We know of many many cases when similarity does not indicate common ancestry. Evolutionists repeatedly invoke convergent evolution in an attempt to uphold their theory from collapse, while convergent evolution goes against all of their homology arguments. The whole phylogenic tree is based on similarity being a reliable indicator of ancestry, and as we see they don’t have this anymore.

There’s no consistent coherent way to organize all animals into a family tree.

Imagine that you’re invited to a reunion of distant family. You get there and you’re supposed to organize yourselves into first cousins, second cousins, etc. based on appearance and common ancestry stories. But the more you talk to the people at the event, the more you realize you don’t have the same story and not many people there look like you at all. This is what we have with the animal classification and the phylogenic tree of life. (The analogy breaks down when you consider that all humans were from a common human ancestor, but all living things were not.)

Punctuated equilibrium theory is a way to try to confront the stasis in the fossil record, in other words the lack of transitional fossils which Darwin’s gradualistic theory requires. Punctuated equilibrium is about long periods of nothing happening and then lots of things happening and then back to long periods of nothing. (The only reason they have long periods of nothing is to account for traditional evolution time.) Gould was very popular for advocating this.

Meyer debunks allopatric speciation and punctuated equilibrium. These theories require unusual speed and flexibility.

Mendel showed that Darwin’s idea of blended inheritance is not correct. The discoveries of Mendel posed many problems for Darwin’s theory.

Mutation is an editor, not a composer.

The probability of the production of a new gene or protein is astronomically small. With the amount of time they are giving us it’s not even close to enough time to even make this a possibility. Even with billions of years if you took a single phrase and mixed up that phrase and added random letters onto it you couldn’t get a complete library.

Richard Dawkins had a computer program recreate a phrase but this does not really mirror natural selection because natural selection isn’t given a phrase to look for.

Before any beneficial protein gene folding by way of random natural selection, functional benefits would long be lost.

Chapter 11 goes over a guy who allowed an article that questioned evolution to be peer-reviewed and published in an academic journal – the guy was promptly fired.

Evolutionists make claims about genes evolving which are as unsupported as alchemists lead turning into gold.

Evolutionists make claims about gene mutation very similar to taking a book, rearranging its paragraphs randomly, rechanging the spelling of words, reordering the page number, the page arrangement etc., and expecting a more advanced book to be made from this random process.

(Note – Remember: evolution is all about natural selection, which means things will naturally, left to themselves, do this stuff. Nature dissembles, it destroys. Only supernatural God creates.)

Evolutionary biologists use the term de novo to refer to unexplainable sudden changes. (New terms don’t solve problems.)

Evolutionists don’t bring up mathematical probabilities of things they propose. Evolutionary scientists have tried to find ways around the mathematical statistic problem but are now beginning to face the facts.

You can’t swap jeans around like Lego bricks.

Meyer points out various animals with specific features that could not have evolved gradually.

Evolutionists oversimplify the mathematical probability of evolution by oversimplifying organisms, oversimplifying mutations, oversimplifying how things were made, oversimplifying what a mutation can do, oversimplifying everything and ignoring the fact that many systems require multiple parts to be assembled at once.

Given the current age of Earth there’s not enough time for one single gene to evolve, much less an entire series of evolutions making animals and humans.

Evolutionists come up with wildly imaginative scenarios and on the rare occasion when they attempt to put them to the test, the tests fail.

The types of mutations that do occur are not the types of mutations required by macroevolution.

There’s no sufficient variation which means there can be no sufficient selection which means there can be no evolution of species.

Neo-Darwinism does not account for the genetic or epigenetic origins of life. Meyer goes into great detail on these subjects.

The Cambrian explosion remains a profound problem for evolution. Microevolution observed in nature only explains survival of the fittest, not arrival of the fittest.

Neo-Darwinism depends on three claims.
1. that there are variations
2. that natural selection selects among those variations and
3. that favored variations survived to future generations. They are variation, natural selection, and heritability. This is the triad of evolution.

Evolutionists proposed wild-eyed theories without giving any chemical or biological explanation of how those could be feasible.

Any self-organizing components in chemistry are extremely basic, nowhere near the complexity of DNA. Scientists admit that self-organization is really more a slogan than a theory.

Note – the Jurassic Park line “life finds a way” is just another pro-evolution slogan trying to suggest that major things can happen naturally without supernatural direction or supernatural creation.

Genes do not and cannot generate new epigenetic information.

Darwinists are in trouble when you point out that natural selection wouldn’t allow for much variety, so how you going to get all the variety? Darwinists have tried to talk about various non-working gene duplication etc. theories but are stuck with this problem. It makes their time for random mutations much longer, once again excluding evolution as a possibility in the time frame we are given by modern scientists.

Scientists admit that evolution is speculative.

The whole point of natural selection theory is to explain design without designer.

Note – why do people who believe God used evolution accept evolutionary timetables? Those are timetables which would supposedly be required if no designer was involved.

It’s not just that nature does not look like it evolved, nature specifically looks like it was designed.

Computer simulators of evolution have a target sequence, but natural evolution should not have a target sequence. Natural selection lacks foresight. Generic mutation simulators need to have a forward-looking direction, and this is precisely what nature and natural selection do not have.

Interdependent logical interactions show design (not natural selection, which is the heart of evolution theory).

See The Anarchist Manifesto.

The Cambrian explosion does not support the Darwinian idea of a bottom-up evolution.

Agassi (a contemporary of Darwin) pointed out that in the fossil record, we see various prototypes which indicate intelligent design. All these years later that still appears to be the case.

The book “The invisible Man” by GK Chesterton is about how someone was murdered while four honest guards did not detect the murder. It was the mailman who clearly walked up and into the house and back out – they just didn’t suspect him.
This is like how nature clearly shows an intelligent designer – it’s just that the scientists are unwilling to acknowledge the designer.

The commitment to materialism in science causes them to reject intelligent design. It’s not that materialism is what the evidence shows, it’s their only allowed framework, even when the evidence points elsewhere (great full quote here if you can find it).

Scientists have decided by fiat to exclude anything involving intelligent design and this is greatly hindering scientific progress, limiting the types of theories that are tested, etc.

We shouldn’t be committed to abstract criteria about whether something is scientific or not. There are disagreements about what science is. Rather we should focus on whether or not something is true.

There are unobservable things like magnetic fields etc., and gravity force, yet those are clearly science, so why is intelligent design by an unseen designer not considered scientific?

(Note – and yes, we can detect the impact of God, just like we can detect the impact of gravity, magnetism, etc.)

Similar logic and reasoning are used for intelligent design and Neo-Darwinism. They are 2 different conclusions.

Experience shows us that things are made by cause and effect design, so why wouldn’t nature be the same?

We have sufficient evidence to say causal design made nature, though we don’t have all the details of how, and this is logical.

They used to think there was junk DNA, that much of the genome was not necessary because it was leftover trial and error from evolution’s natural selection; now they are finding there is no junk DNA. See the Endcode Project.

Evolution’s monopoly on science today stifles discussion.

Scientific materialism followed (Note- we might say ‘is the fruit of’) Darwinism, claiming that there is no purpose in life, no purpose for Earth, etc.

Neo-Darwinism specifically denies that natural selection is guided in any way. They say the appearance of design is an illusion.

You can’t insist that science and religion are two separate fields and at the same time call for harmonization of science and religion.

Note: great point, Either they work together making one connective truth, or one of them is wrong.

“Why attempt to reconcile traditional Christian theology with Darwin’s theory as Collins tries to do if the theory itself has begun to collapse?”

The new atheism is built on top of (note- or ‘is the fruit of’) Darwin’s theory.

Intelligent design doesn’t insist that there wasn’t something before Earth and what we see was designed.

Note – these matches teachings of the restoration, that God built from existing materials, and that God isn’t the first God (there is no first God).

Intelligent design shows life can have a purpose, there can be a god.

Intelligent design detects and identifies creation, it doesn’t just say there’s a designer. The ability to detect design brings science and faith into real harmony. This prevents feelings of anxiety and promotes feelings of wholeness and hope. We need landmarks and steadying points of reference. We need a father to call out to for help when we are troubled.

Intelligent design has faith affirming implications.