There are certain “Forbidden Questions” that scientists, particularly biologists, aren’t allowed to ask if they want their careers to continue smoothly and the research funds to keep flowing. After all, whether they are consciously aware of it or not, their field adheres to the Naturalistic Assumption, the assumption that all things in nature must be explained without resorting to things that are outside of the laws and forces of nature.
This is assumed in scientific research and when scientists communicate with the public, and it takes on the form of an ideology, similar to a religious doctrine which must be accepted by its adherents. The problem is, adhering to an ideology can prevent scientists from seeing when the evidence is pointing in a different direction.
Since the Naturalistic Assumption has become a doctrine, by definition the evidence can’t point to anything that doesn’t have a natural explanation, even if that explanation is just a tall story. In fact, I would suggest that the presence of a story is an indication that the assumption of naturalism may be at fault.
This assumption also leads to false reasoning. Since many scientists believe they have to explain everything by means of natural causes, it creates the illusion that God doesn’t need to exist, and therefore doesn’t exist. After all, what is left for him to do? Everything God could have done, scientists insist nature can do on its own.
But if nature can’t actually do it all by itself, then scientists have created a self-imposed illusion upon themselves, and by extension the general public who rely on them for information.
However, let’s step back from the Naturalistic Assumption for a moment, and ask ourselves one of the Forbidden Questions. It is forbidden because scientists aren’t allowed to entertain the possibility of any alternative to naturalism without risking their careers. But the bottom line is, naturalism is just an assumption. It’s an ideology, a worldview, a doctrine of faith adopted by the scientific community. When we recognize this, we are free to put it aside and ask all the questions we like.
Evolution is fundamentally a bottom-up design approach. Simple things gradually become more complex. Smaller genes gradually produce larger ones. Things are pieced together through billions of years of trial and error. There is no plan or foresight. If something works, it’s only because countless variations have failed, and an almost endless number of organisms have died to discover what works best.
The particular Forbidden Question I will focus on in this chapter is this: when we remove our evolutionary lenses, does life actually exhibit evidence of top-down design? Does the evidence we have actually fit this better than bottom-up design?
In a human trial, the same evidence is available to both the defense and the prosecution. The verdict depends on how that evidence is interpreted, and which interpretation better fits the facts. But if we only ever hear from one side, or only allow the evidence to be interpreted in one way, then it would be a crooked trial.
I have already spent many chapters discussing the bottom-up design approach by means of mutations and natural selection. Now it’s time to look at the evidence through a different lens, one where life was actually designed and planned from the beginning. Does life make more sense from this viewpoint? Does the evidence support this idea?
I think there are ten major lines of evidence for a top-down design approach to life. First, consider the fact that life on Earth is critically dependent on language – specifically, the language used to translate coded sequences into proteins, called the “genetic code.” Even the simplest of lifeforms have ribosomes that are able to read sequences of code and turn them into proteins. A genetic code must have been in place before genes could begin to be stored and then translated into proteins.
Furthermore, science has shown that, out of a million different approaches, the one used by nature is optimal in many aspects.1 How did nature manage to find such an optimal system? If it was trying out myriads of different genetic codes, how could proteins evolve and be produced in such an environment, since the meaning of a gene would change depending on the shifting language?
If you change one codon to mean a different amino acid, then you shift the meaning of all the genes in the genome using that codon. They would become different proteins and may even lose their functions. This suggests a top-down design approach, where the language is defined first, before anything can be written down in that language.
Curiously, the gospel writer John, while he didn’t have the genetic code in mind, said essentially the same thing. If we take the “Word” as the language of DNA, and the information stored in a DNA molecule, which cells need to build proteins, life could be summed up in the same way that John does: “In the beginning was the Word,” and that “all things came to be through this one, and without this one, not one thing came to be which has come to be.” And finally, “the Word became flesh.” 2
The literal Greek of this verse reads, “the Word became flesh and tabernacles in us.” I have already shown how the Hebrew Tabernacle depicts the eukaryotic cell. Our flesh is made of eukaryotic cells, which are miniature tabernacles.
The second line of evidence for top-down design is the way information is protected from mutations and damage. When copying the genome, error correcting processes reduce errors to a minimum, and I suspect they may be optimized based on time and space constraints. Without these processes, daughter cells would receive a genome riddled with errors.
Furthermore, thousands of nucleotides are damaged in the DNA molecule of cells every day. Without damage repair systems working hard each day, the cell’s genome would quickly lose critical information.
These error correcting and damage repair processes need to be in place at or near the start of life on Earth, so that genetic information can be preserved. The existence of these systems is consistent with a top-down designer who wanted to ensure organisms had the ability to preserve their genetic information, both for themselves and for future generations.
However, a bottom-up approach has the dilemma that these mechanisms would need to evolve in a highly unstable environment, where stored information would be mutated and degraded rapidly, before the systems needed to preserve it could come about. Furthermore, these systems limit mutations, yet evolution relies on mutations for better designs to come about.
The third line of evidence for top-down design is the existence of entire protein “libraries” available to each organism.
Earlier on we conducted a thought experiment where I showed that small proteins could potentially evolve on their own. But an important question we never actually asked is: why would they?
A hypothetical RNA World gets on just fine without proteins, because RNA does all the work. According to evolutionary theory, nature also gets along perfectly well without new proteins and functions ever coming along, because the new ones mostly evolve out of existing ones that are happily doing something already.
In other words, nature has no reason to bother evolving anything new, because it has no hopes, dreams or future ambitions. An organism’s primary goal is to survive and reproduce. If a new function or feature comes along, it is the result of incredible serendipity.
Engineers find solutions to problems. But according to evolutionary theorists, nature first finds a “solution,” and then it somehow finds a “problem” for the solution to solve. For example, it first evolves a new protein, and then somehow “recruits” it to perform a role in an organism that didn’t need it before.
By contrast, a top-down designer can decide exactly what is needed to build the organism, and then give it access to a library of proteins encoded in genes, so it can build itself based on the blueprints in its genome.
If the designer wanted to reproduce a function, feature or part that was in another organism, he could simply copy and paste the proteins and modules of code involved, either from the other organism or from master plans stored elsewhere, and then make any adjustments as necessary. If a new function was needed, he could invent the proteins and blueprints for it, either right there, or more likely he would plan for the function in advance.
This is also what computer programmers do. They often rely on “libraries” of functions that can be called up when needed, and they can copy and paste whole “modules” of code used in other programs. They don’t wait millions of years for code to evolve, and engineers don’t wait millions of years for parts to evolve either.
But if nature relies on evolution, it can’t plan for a nuclear pore complex in the future, and then hope that just the right proteins come along, in just the right quantities, and get posted to just the right places in the cell.
All lifeforms have access to their own protein libraries that often consist of thousands or tens of thousands of functioning proteins, each one built, in many cases, out of hundreds of amino acids.
Scientists can perform experiments where they mutate a gene or take it out of action entirely, and see what effect this has on the organism. They have discovered that many proteins perform critical roles, and in a few cases, even a single mutation can cause disease.
Some mutations don’t seem to matter, but if you mutate a protein enough, it will usually lose its function, because the sequence of amino acids determines the folded shape of the protein. Mutate it too much, and it’s likely to become a different shape, not suited to the job it was supposed to perform. In other words, many or even most proteins seem to be optimized for a particular job.
Every living organism on the planet contains its own library of proteins, and there are many overlaps across the spectrum of life. Evolutionary theorists argue that this is evidence of common descent – that all branches of life are descended from a universal common ancestor. However, it’s also evidence of common design.
If you designed a dog, and then wanted to design a cat, would you start, to pardon the unintentional pun, from scratch? It would be far more sensible to simply copy and paste lots of the stuff that makes up a dog, such as genes and blueprints that make blood, bones, teeth and so on. To make a cat, you would then need to modify the shape and size, and make it a little more aloof.
Some proteins don’t quite fit the branches of the supposed tree of life, so biologists argue that they got there by horizontal gene transfer. Bacteria can do it, so they assume higher life forms can do it too, even though they don’t seem to have the equipment for it. But even if we assume that higher organisms can acquire whole genes perfectly intact from other organisms, how does the recipient know what to do with a gene that has just been transferred to it?
This is a similar problem to the one we faced when trying to stitch together two smaller proteins into one, except it is many orders of magnitude more difficult, because the newly inserted gene has to somehow find a functional role in the genome, and perhaps a new address label. However, an intelligent designer could transfer genes horizontally, vertically or any other way he wanted, and design the system so it could accommodate new genes.
Computer programmers re-use whole libraries of code for many different programs, and nature does the same thing. Proteins for essential life functions are re-used across the board, often with some tweaks for the specific organism. This is what we would expect from a top-down design approach. It would match what computer programmers and engineers do every day.
The fourth line of evidence for top-down design is the overall robustness of protein interactions. For example, in a large study of over 1,800 species ranging from bacteria to primates, and millions of protein interactions, researchers found that every species had backup plans that allowed its protein machinery to find workarounds when problems arose.3
As usual, the researchers attributed this to evolution, but why would evolution bother to evolve backup systems? It has no foresight. But this is something a smart engineer would build, in anticipation of a potential fault or emergency. Across the spectrum of life, organisms come equipped with many backup systems, suggesting planning and forethought in their design.
The fifth line of evidence for top-down design is the cellular postal system. Earlier on I posed the riddle of how a protein gets an address label, in order to be transported to various places in the cell. And how does a new body part come about, without a zip code for the part?
A top-down design approach makes this easy. A city planner who was planning a new district would make sure it had a zip code, along with street names and house numbers, so the new residents could get their mail.
The sixth line of evidence is the constant re-use of design blueprints among organisms. Evolution is a tinkerer. Genomes must mutate, in order to have a chance of coming up with new designs and functions. Yet time and time again, biologists find similar designs and features in organisms of all shapes and sizes.
Most eukaryotic cells have an inner compartment, the nucleus, surrounded by a double membrane that contains nuclear pore complexes (or NPCs). There are some fairly minor differences across life, but they all share the same core shape.
When biologists see this, they use the term “conserved.” What they mean is, all organisms with this feature sprang from a common ancestor in the distant past, but the feature hasn’t changed much, even over assumed vast periods of time or across widely different creatures in that branch of the tree of life.
In the case of the NPC, because it plays such an important role in the survival of an organism, biologists argue that evolution can’t tinker with it to the same extent as it could perhaps do with other parts, and hence it stays roughly the same.
In one sense, this sounds perfectly reasonable. After all, if the nuclear pore complex fails to function, important material can’t get in or out of the nucleus, and the cell dies. Therefore, any mutations that stop the NPC from working will be ruthlessly weeded out by natural selection.
However, this doesn’t explain why the NPC has retained its core shape across the spectrum of life over a supposed billion or more years of evolution. Even if its shape is optimal, and evidence suggests that it is, why don’t we see nature at least testing out myriads of other designs? Why do they all have eight spokes? Why do we not see NPCs with six or nine spokes? Is there really only one way of designing an NPC? If so, how does nature know what it is?
There are also plenty of examples of features and functions that have supposedly evolved again and again independently in different branches of the hypothetical tree of life. Evolutionary theorists call this “convergent evolution.” I would suggest that convergence and conserved features are actually evidence of top-down design.
For example, to design a frog, you first need access to the blueprints that make up all the parts of a frog, from small things such as nuclear pore complexes, to the proteins and blueprints required for building organs such as hearts, eyes and brains. If a designer has already created other organisms with these core functions, then creating a frog isn’t much of a leap.
However, designing the ability of a frog to actually leap would be an interesting engineering challenge, and would probably require new proteins and functions, or at least re-purposed ones. A top-down designer is in a far better position to achieve this, knowing the desired outcome in advance, than an evolutionary bottom-up approach.
The fact is, across the spectrum of life, creatures use many of the same parts in their bodies. This is why evolutionary theorists argue for a universal tree of life, with each species evolving from a common ancestor. However, I would suggest it is also evidence of a designer who re-uses the core designs of particular features, but then endows certain types of creature with unique or distinctive features, such as the ability of a frog to leap, an owl to swivel its head, and a cat to stand precisely half in and half out of a door you’ve just opened for them.
Industrial manufacturers do the same. A car maker doesn’t reinvent the wheel every time it wishes to design a new car. It uses the same wheel blueprint, even though it might embellish the design, or adapt it to suit a newly designed vehicle. The fact that all vehicles have roughly the same shape of wheel doesn’t mean all cars evolved from a common ancestor out of an ancient Ford deep sea vent. Instead, they were designed based on common blueprints.
But according to evolutionary theorists, we are not allowed to apply this logic to biological life. Still, there’s no good reason why we can’t, if we put aside the assumption of naturalism. Many organisms share common features, including proteins, which have then been adapted to suit the particular type of creature. This could be seen as evidence of top-down design.
The seventh line of evidence for top-down design is that life already exhibits a top-down approach in its control of genes.
Think about the exquisite control that was needed to turn you from one tiny cell into a fully-grown human. The early cells needed to divide numerous times. They gradually needed to specialize to form different tissues and organs. Proteins needed to be switched on or off, or expressed in greater or lesser quantities, at just the right times. You needed to be kept alive during this entire process, even before you had a heart. Once your heart had been formed, blood needed to be pumped around your developing body, and energy needed to be circulated, despite the fact that you were constantly changing shape.
Some of this process is controlled by feedback loops at a local level, but the overall development of an organism is strictly controlled by gene regulatory networks in the genome. If this weren’t the case, you would just be a big clump of the same kind of cells – maybe a big ball of neurons, or a big eye; or maybe you’d have a random number of fingers, or arms that extended almost without end. If the development of an organism requires such careful and intricate top-level planning, why would this not be true of life itself?
Top-down control and regulation is necessary for many of life’s processes. Recall the way the pond-dwelling Oxytricha breaks up its genome into nearly a quarter of a million pieces, and then rearranges them into 16,000 chromosomes. All of this requires elegant top-down control, but we are told to believe the process supposedly came about by the shuffling of nucleotides. Is this really plausible?
The eighth line of evidence for top-down design is the high level of efficiency of cellular processes. In the book of Revelation, God declares: “Look! I am making all things new.” 4 This happens quite literally all the time in the cell. Parts are disassembled, recycled, and replaced with new parts constantly.
Some biologists think this is inefficient, but I would argue it is supremely efficient. First of all, there is very limited space in a microscopic cell, so only making what it needs when it needs it makes sense.
Second, with physical machinery, wear and tear may cause the equipment to become less effective over time, or even to break down. However, if something stops working in a cell, there is a strong possibility the cell dies. Therefore, by constantly renewing the machinery, this eliminates the problem of wear and tear, and ensures its parts are constantly at or near peak performance, minimizing the chance of anything breaking down.
As another example of efficiency, biologists have shown that some proteins perform more than one role. For example, when the cell is undergoing division and the nuclear pore complex is disassembled, some of the proteins that made up the NPC go on to help in the process of cell division, when they might otherwise be floating around doing nothing. This is highly efficient.
Evolutionary theorists argue that this is an example of how one function could have evolved out of another function. But this implies one of the functions wasn’t being performed before, which invites the question of how cell division took place without it.
However, an engineer would perhaps want to employ those proteins while they are hanging around waiting for cell division to take place. Why not draft them into use, precisely as nature does? This is evidence of smart design.
The ultimate example of efficiency is the human genome itself. It contains the control sequences and plans for every stage of human development, along with the blueprints for tens of thousands of proteins, and thousands of molecular machines needed to build a person. In other words, an entire human being consisting of trillions of cells is coded for in just 3 billion letters in a DNA molecule. Clearly the genome must use plenty of algorithms and be highly efficient.
This is stored in a molecule you can’t see with your eyes. As a size comparison, it’s the equivalent of taking a length of string that could stretch around the Earth ten times, and putting it inside a chicken egg. This is incredible efficiency.
The ninth line of evidence for top-down design is the magnitude of the engineering feats and inventions we find in nature. These are explained by evolutionary theorists through the use of simple stories, or meaningless phrases such as, “the eagle’s telescopic eyesight evolved to help it catch prey” or “the frog’s ability to leap evolved to help it survive.” These aren’t explanations. They’re simply assertions. And pretty glib ones at that, because in the evolutionary paradigm, every feature that sticks around long enough does so because it conveys a survival or reproduction advantage, so that life is ultimately just about sex (or replication, if you’re bacteria) and the survival of your offspring.
But nature is full of incredible inventions that demonstrate amazing variety and ingenuity. Anything we humans have invented, nature probably got there first. Reading and writing? Ribosomes and reverse transcriptase beat us to it. Electricity is an essential component of modern life, and yet the body used it before we did, because cells use proteins called ion channels to create a positive electrical charge, which can be turned into electrical pulses called action potentials.
The Internet is an incredible network of computers talking to one another, but neurons also form vast communication networks in the brain and nervous system. Humans thought they were smart when they first learned to send electrical signals down a wire, the basis for early forms of telecommunication; but a DNA damage repair system beat us to it, sending electrons down the DNA spiral to look for faults.
We use gears to drive at different speeds, but the planthopper got there first, literally using the same kind of gears we use in vehicles, to jump hundreds of times its body length.
It took knowledge, intelligence and ingenuity for us to come up with many of our inventions as humans, but according to evolutionary theorists, the shuffling of nucleotides was able to come up with such inventions in nature.
In reality, I would suggest this couldn’t happen, because, to take just one example, the invention of gears requires an understanding of engineering principles that can’t be discovered by changing letters in a DNA sequence. The two processes are at completely different levels of complexity.
However, a top-down designer with a solid grasp of engineering principles could give the planthopper its gears, and create proton pumps and electron transport chains so that subatomic particles can be shuffled around to create energy.
The tenth line of evidence for top-down design is the foresight displayed in nature. According to evolutionary theory, natural selection doesn’t have foresight. It just selects from what is available at the time. Yet even in the evolutionary paradigm, nature continually comes up with new inventions that seem to anticipate future developments. This suggests intelligent planning rather than just luck.
The invention of a genetic code and a ribosome was necessary for proteins to be produced. At the same time, neither of these would be of any use without the existence of encoded genes in a genome.
Most of the chemical reactions required to sustain life would be far too slow without enzymes, which often make those reactions happen millions of times faster. But life can’t afford to wait around for enzymes to evolve. The organism would be dead without them. Nature anticipated this need, by providing each organism with the proteins it needs to produce chemical reactions, along with the enzymes needed to rapidly accelerate those reactions. This would be the hallmark of a designer who knows in advance what is needed to achieve a desired end result.
In evolutionary theory, proteins can be accidentally duplicated, and then after the copy manages to find a new form, it can somehow get recruited to perform a useful new function in the cell, even though there is no recruitment agency to do this, and no system to give them new address labels when necessary. Yet nature continually shows foresight, by giving proteins functions and address labels.
The invention of mitochondria, the powerhouses of the cell, anticipated the existence of multi-cellular life which would require much more power.
The invention of chromosomes, and the special equipment needed to compress, decompress and read the DNA sequences, anticipated the much larger genomes that would be required by multi-celled organisms. In other words, nature supposedly invented the ability to store the vastly bigger genomes needed by cats and humans, before it could ever conceive of a cat.
The development of nuclear pore complexes and the nuclear envelope around a cell nucleus anticipated the need for greater control over the cell in eukaryotes.
Somehow, cells also became “pluripotent,” able to become many different types of cell, which anticipated the development of plants and animals. For example, human red blood cells jettison their nucleus, and they utilize hemoglobin proteins to carry oxygen around the body. Single-celled organisms don’t have a body as such, and some creatures such as insects don’t need oxygen to be actively transported, because they are small enough to rely on it being passively circulated. But this also limits their size.
According to evolutionary theory, the lucky invention of red blood cells allowed creatures to grow bigger, which would then give them a survival advantage. In other words, nature solved a problem creatures didn’t know they had – namely, being too small.
But red blood cells aren’t the only things needed to transport oxygen around a body. An organism needs a cardiovascular system made up of a heart, blood vessels and capillaries, and a respiratory system involving lungs, airways and air sacs. The two systems also need to work together, to get oxygen from the respiratory system and into the blood. You need red blood cells to transport oxygen, but also a transportation network to be in place, for red blood cells to be of use. This requires foresight.
Neurons are another type of cell, with the ability to transmit electrical and chemical signals. As well as having a cell body containing a nucleus, most neurons also have special equipment including an “axon” and “dendrites.” The axon looks like a tail with a sheath around it, and it transmits electrical impulses. Dendrites receive signals from other neurons across contact points called “synapses.”
Neurons work together in large numbers to create a communications network. They are, in effect, network devices. Therefore, the invention of the neuron anticipated that creatures would have brains and nervous systems, which suggests foresight.
Furthermore, to build a creature out of these different cell types, the first cells divide repeatedly, and then cells go on to specialize into specific types – such as skin, brain and blood cells. This means the blueprint for each cell type must be built into the organism’s very first cell, and the timing for the production of these specialist cells must also be written into its genetic blueprint.
In other words, the plan for the development of an organism is already fixed from the beginning, and there is no easy mechanism to invent new cell types such as neurons, let alone whole organs such as brains and hearts. Yet evolutionary theorists insist that the shuffling of nucleotides somehow managed to do it.
I would suggest a far better explanation is that neurons and blood cells, and all the machinery needed to fully utilize them, such as brains, nervous systems and hearts, were built by a designer who would know in advance where the creature’s brain or heart would be, and could put the plans for their construction into the organism’s very first cell.5
1 Freeland, Hurst, “The Genetic Code Is One in a Million”, Journal of Molecular Evolution, 1998. 2 John 1:1-3,14. 3 See the article “Species evolve ways to backup life’s machinery” by Tom Abate, posted at earth.stanford.edu on February 14, 2019. 4 Revelation 21:5. 5 A much more extensive discussion of the idea of foresight in nature can be found in the book Foresight: How the Chemistry of Life Reveals Planning and Purpose by Marcos Eberlin, published by Discovery Institute Press, 2019.