Darwin’s Black Box by Michael Behe – Book Highlights & Commentary

Introductory Note: This was an excellent book demonstrating the complexity of biological systems, and how absurd it would be to believe that they evolved by chance natural selection. Biological organisms were clearly created. They are far more complex that cars, and no one would claim the car evolved by natural selection.

Also check out Behe’s video course on Intelligent Design & Evolution: Course | Michael J. Behe (michaelbehe.com)

Note- the author starts off the book saying that he’s ready to accept a very old Earth. This of course is a critical flaw in his analysis.

Darwin could not see microbiology he knew that the eye was for seeing but he did not know how it saw; he did not have answers to these questions
The cell is Darwin’s Black box. He had no clue how it worked.

If your friend says he jumped over a couple feet you believe him. If he says he jumped across 10 or 15 ft you are skeptical and surprised. If he says he jumped across the Grand Canyon you don’t believe him. Then he claims that it took him years to do it and that there were buttes but he stood on in the canyon which took a long time to appear and which went away quickly after he had jumped. It’s absurd. Someone who claims that they made many small jumps to get across a large chasm in the past but that the things that jumped on are no longer there is very hard to believe. (Note- truly evolution is a system of belief, aka faith.)
Evolution makes huge leaps for which there are no evidence.
There are unbridgeable chasms even at the smallest levels of life.

Darwin had to convince people that complex organisms could be made slowly.

Vision was a black box for Darwin. He and his contemporaries had no clue how it worked. What he thought was simple is actually extremely complex involving many proteins enzymes etc.; multiple systems going at once. These aren’t just leap to leap, these are huge distances.

Darwinism explains micro evolution well, but it is a farce to explain the origins of life the origins of species, the main thing that Darwin was getting at.

Little kids think a box can be an airplane (think Calvin & Hobbes) because they don’t know how the airplane works. There are scientists now taking a similar approach about evolution and the origin of life.

Scientists used to think that cultures growing in a liquid could spontaneously generate because the flies appeared to spontaneously generate on meat. The key problem was to think that the flies and the cultures were extremely simple. A similar problem exists evolution of complex organs like the human eye. Darwin made it seem very simple but it is not.

Neo-Darwinism was made by various sciences getting together and deciding what to do with evolution theory. This all came out before biochemistry. Now that we have biochemistry that must be revisited as biochemistry debunks it.
Darwinism is becoming less popular within and without of the scientific community due to many questions the theory cannot answer
Scientists admit that the theoretical framework and evidence for Neo-Darwinism is weak.

There appears to have been a biological Big bang, many species coming on scene at once. (Note: the “Cambrian Explosion” in the fossil record of advanced lifeforms appearing is from the flood of Noah wiping out many animals and fossilizing them in a unique environment able to convert bone into rock, something that isn’t happening today.)

Mathematicians insist that even with current dates of how old the Earth might be, that’s not nearly enough time for claimed evolutionary changes in species.

Scientists are upset that 1. there are no transitional forms and 2. that species have different but very definite limits as to how much they can change and 3. that systems appear suddenly and 4. that natural selection cannot account for the diversity etc.

There have always been well informed respected scientists who find Darwinism to be inadequate.

Most scientists will say they believe Darwinism but they believe it based on authority, based on what others have said.

Scientists are afraid to debate natural selection which is ironically unscientific. True science doesn’t fear scrutiny challenge and debate.

When Dawkins (arch evolutionist) tries to support the evolutionist view of the bombardier beetle evolving, he fails to explain how all those chambers, muscles, etc. would have evolved gradually. Many of the parts aren’t necessary for the system and wouldn’t have just showed up by and by. Even if you come up with a story of what might be beneficial here and there and how it might evolve, it still fails to explain the details of the extremely complex processes that would need to take place for such a story to come about. All they can say is that it might happen. That’s not very scientific.

Dawkins talks about the eye and explains it as a series of complex systems coming together. He never explains how those complex systems came to be in the first place. It’s like saying a stereo is made out of putting together an amplifier and a CD reader etc. without explaining how those parts first came to be and how they were assembled. Evolutionists use dramatic oversimplification in an attempt to make it seem more plausible for something to have happened by chance.

These explanations given by Dawkins are extremely simple and do not justly describe how these things came to be. They are illogical assumptions that everything would be just right by chance.

There are “irreducibly complex” systems which have no use until everything is in place. Natural selection can only choose systems that are already working.

You can make the case that multiple complex systems evolved at the same time just in time for a complex organism who needs all those multiple systems to live, but this is an empty argument, you might as well argue that the Earth popped into existence yesterday by chance.

Evolutionists submit that evolution isn’t always gradual, but they say it has to be gradual when explaining complex apparently designed objects like eyes because without gradual all you have is miracle. Can’t have it both ways.

A mutation can change one step of instruction such as ‘place the legs on the head rather than on the abdomen’ but a mutation can’t change the entire instructions such as ‘instead of build a fax machine, build a radio.’

There are tens of thousands of different molecules involved with things like the eye and the bombardier beetle; you can’t say that you know those all just evolved and came together. It is speculation, it is belief.
To debate about whether such evolution could randomly occur is like 19th century scientists debating about butterflies being able to spontaneously generate out of meat. Again, we simplify too much. And as we see the increasing complexity of these systems, the idea of random evolution to create them becomes less and less likely.

A mousetrap is an example of an irreducibly complex system; without all the parts there it doesn’t catch any mice. Not only do you need to have all parts present at once, but all the parts need to be fine-tuned with just the amount of spring just the right positions etc. An irreducibly complex system is assembled all at once.

Just because a bike is a precursor to a motorcycle doesn’t mean the bike turned into the motorcycle. Biological evolution is limited to slight modifications and there’s nothing about a bike that you can slightly modify into an engine or fuel tank. Natural selection in a bicycle manufacturing plant cannot produce a motorcycle. There is no example in history of major biological changes.

Note- there is the supposed Cambrian explosion but that is merely the fact that many fossils appeared seemingly out of nowhere, it’s certainly is not step by step proof of evolution. The reality of the Cambrian explosion was the flood of Noah which brought about special conditions to fossilize many animals which in other conditions would have simply decayed.

In order to understand the barriers to evolution you have to understand the complexity of biological systems

Part 2 – this is where the complicated stuff is and I won’t attempt to give many notes here.

Ch. 3

Cells are run by molecular machines.

We make machines which efficiently do tasks but in biology if there is a microscopic machine doing a simple task efficiently, if that had to evolve, it would have had to learn that task too.

What something is made of and how it works are two different things, which are both extremely complex.

Evolutionists have very creative minds, they can come up with stories to explain evolution of anything, but they’re just stories.

While modification goes on systems are non-working.

The evolutionary literature explaining how these complex things would come to be is severely lacking. Further, the papers disagree with each other on the roads that would be taken, etc. They don’t take into account mechanical details; they just make big generalizations.

Nobody knows how the flagella evolved. No research accounts for it etc. Some 40 different proteins are involved. Same for the cilia wherein some 200 different proteins are involved.

Cartoons show extremely complex systems going through a series of events to set off a single trap, it’s humorous because everything has to work exactly right to get the trap to go off, if one part of the whole sequence didn’t work the trap wouldn’t work. This is similar to evolution and it’s laughable. In biology there really are very complex systems which have an end function which is very specific and it cannot be accounted for by evolution.

Note- it’s like the old Paley’s pocket watch in the desert analogy. If you find a pocket watch in the middle of the desert, do you conclude that it was put there by someone who owned purchased or created it, or do you conclude that it evolved randomly?

Ch. 4

Blood clotting is a very complex system of many interconnected parts. It has to form only when and where it is required or the whole system clots and dies. No one on earth has any idea how the coagulation current came to be.

Each tiny little step in evolution has such small odds that it’s utterly ridiculous to consider it. It’s not just a small chance that one thing would evolve into another thing, it’s a small chance that a very small part of the evolution would happen. And when we talk small we mean infinitely small odds, making this more of a fairy tale storybook than science.

Natural selection only works if there’s something useful already there to select from. Necessary proteins wouldn’t just appear with nothing to do until other stuff arrived.

If one thing goes wrong in a whole delivery the package will not reach its destination and it may as well have never been sent.

Extremely complex processes take place billions of times a day in the cells of our bodies. Science is stranger than fiction. It cannot be accounted for by random evolution no matter how much time you give.

Note- Whenever we prove Darwin’s macroevolution theory wrong they just expand the age to an older and older Earth and universe. They can only play this game for so long; Darwinism is truly on its way out.

We see many irreducibly complex systems working together in even bigger irresistibly complex systems, and the mathematicians have said repeatedly that the current age allowed for the Earth and universe is not nearly nearly nearly enough for these things to happen randomly; they would need to be at least billions and billions and billions and billions and billions and billions times billions and billions and billions and billions and billions of years older to give the remote chance. But as we can see this is nonsense, you can’t just sit around and take seriously a theory that requires so small odds. The smacking obvious answer is that the Earth and universe were designed by a designer! You just can’t get around that.

Irreducibly complex systems are all or nothing, you can’t just add one part now and later add another part, or the system doesn’t work.

You can’t say that some parts of the cell were used for other functions before they were used in their current functions. It would leave a very lousy cell that would not sustain life.
A single flaw in the cells process pathway and you die. If cells evolved as incomplete structures our ancestors would have died too.

There’s no literature on the evolution of vesicles and many other topics in the evolution of microbiology.

Part 3 What Does the Box Tell Us

The chemical soup life experiments failed miserably. Much guidance was given, and no complete life made, etc.

There isn’t a single book or article in the literature explaining the microbiological evolution. There are books and papers which say sequences but none of them say how those sequences came to be.

A combination lock, if you keep trying different combinations, perhaps you eventually get half the letters right, this is not progress, you still can’t open the lock, life can’t reproduce to the next generation the “lock” fails. If the code is “Mary had a little lamb”, the random choices with lots of time would just as soon spell out “Lets go to the park” or some other random sentence; the direction of the evolution wouldn’t be aimed at or kept. No one says which letters are held to produce the correct sentence.

Some say that if there is a designer why isn’t nature more perfectly designed, but this is not the point of science. The point of science is to see whether or not design is obvious. We cannot guess the psychology of the designer as to why certain systems would be imperfect.

Note- of course sin results in damaged systems, ever since the fall of Adam our bodies have been fallen and broken, tending toward decay and death; and when this life is viewed as a probation test to see how we respond to weakness, it is better understood why systems are intentionally imperfect.

Vestigial organs which have no apparent use are claimed to be by-products of trial-and-error evolution from past species, however these supposedly useless organs turn out to be extremely important in immunity etc. Just because we don’t know why something is there doesn’t mean it’s useless.

Once design is taken seriously by scientists, the academic literature will be much more rigorous, require much more hard data, and tolerate much less storytelling.

The author says there’s a possibility of old earth with intelligent design. (Note- I don’t see a need for it, old earth was specifically theorized to get rid of a creator. Evidence is piling up against old earth theory.)

Ch. 11 Science Philosophy and Religion

The discovery that life was made by intelligent design is one of the single greatest discoveries of all science.

About 90% of Americans believe in God and about half attend religious services regularly.
The army employs chaplains. Businesses and sport teams gather for prayer. As a country we honor people like Martin Luther King who’s actions were deeply rooted in a belief in God.

In 1925 the John Scopes trial involved Scopes a teacher who volunteered to be arrested for a law to not teach about the Creator in science. There’s a movie about it Inherit the Wind (1960).

(Note- Inherit the Wind makes the preachers and creationists look like idiots, and the evolutionists to be the only ones with level heads and sense. The creationists don’t even try to use any scientific evidence, so the evolutionists simply take the side of “science”, and claim that the religious are in the way of all science, and that evolutionists to refute creationism simply poke at supposed errors of the bible. The issue was completely avoided, that Darwinism is impossible scientifically.)

One man who performed many science experiments was going to be hired but was asked in the interview if he believed in evolution, he said no he believes in the biblical account of creation, and for this he was not hired.

Science these days is less of a pursuit for truth and more of a game played by the rule that the supernatural can never be invoked. Professional scientists in university accept this rule even when they privately believe in God, as most of the population does.

A designer can’t be put in a test tube but neither can extinct (supposed and missing) common ancestors. We can see the lingering effects of a designer (just like how they claim to see lingering effects of the missing common ancestor)

Scientists try to place the original of life in the universe in a tiny box, but it cannot be done.

Evolutionists want to force parents to teach children evolution.

Note- one way they are accomplishing this is by putting more and more restrictions on homeschooling. Use this freedom while you still have it.

The fear that science with supernatural conclusions would ruin science is not founded.

It is not a strange conclusion that life was designed by an intelligent agent; rather that is the obvious and natural conclusion.


Over the past decade since the book this book was originally published we have learned much more about microbiology, how things are even more complex, and this strengthens the case of intelligent design.

Some say that these irreducibly complex systems could be used for other things as they break into simpler machines. But this is devolution not evolution.

The author never said that parts of the irresibly complex system couldn’t be used for something else. He said the removal of one part causes the whole system to stop functioning; it doesn’t necessarily cause the individual parts to stop functioning.

Mouse traps weren’t made by a handful of toothpicks getting together and deciding to be a mousetrap.
You might as well assume that half of your car’s transmission will jump out of your airbag. Essential components don’t happily come out of accessories.

Richard Dawkins said biology is the study of living things that appear to have been designed. Thus we see that even to the diehard Darwinists design is evident. It’s not just some conclusion we draw when we can’t think of anything else. It’s what we conclude when we get in touch with our inner ingenuity. Any engineer can pick out something that’s been designed for a purpose and he can usually pick out the purpose by looking at the structure of the objects.
The difficult thing would be to make the claim that random evolution is responsible for these things.
The burden of proof is on the one who denies what he can plainly see with his eyes. In the absence of an explanation, we are rationally justified to assume complex things like Mount Rushmore were designed, not just evolved.

“All sciences begin with speculation, only Darwinism ends with it.” Authors promoting evolution acknowledge this, that their work is speculation.

Assertions that microscopic machines evolved are based in speculation, not calculations and experiments.

There are no detailed Darwinian accounts for the evolution of anything.

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