The Engineering Problem in Evolution

The Engineering problem

Stephen J Gould [one of the two scientists behind punctuated evolution] said in his book "The Structure of Evolutionary Theory": I recognize that we know no mechanism for the origin of organismal features other than conventional natural selection at the organismic level [pg 710]

Here's a 20-min vid on how punctuated equilibrium doesn't solve the problem

Let's illustrate one of the difficulties with the fish to amphibian transition. There had to be changes from:

1) obtaining oxygen from water to directly from the air,

2) change from permeable scales to impermeable skin,

3) ventral, anal, and tail fins would have to go from steering to a) weight-bearing and b) to providing locomotion,

4) a two chambered, one loop heart system would have to transform into a three chambered, two loop heart.

And all of these changes had to happen 

1) in concert, 

2) on a molecular level and 

3) while that species remained the fittest for its environment. The genetic code had to change in multiple proteins throughout multiple systems within the fish, all at basically the same time.

For example, the Cambrian explosion, the unparalleled emergence of organisms between 541 million and approximately 530 million years ago at the beginning of the Cambrian Period. The event was characterized by the appearance of many of the major phyla (between 20 and 35) that make up modern animal life.

As I said gradualism seemed plausible if there were 100's of millions of years for a system of hit or miss chance, but there is not; take that element away, as Punctuated Equilibrium and the Cambrian explosion shows, then design [a purposeful, intentional, guided process with a goal in mind] is the much more likely candidate than a purposeless, unintentional unguided process without a goal.

This is part of a larger argument that can be found here

The DNA Problem - Updated

There are dozens of DNA based micromachines in our bodies like the ATP Synthase which is a dual pump motor. The ATP Synthase has dozens of different parts; each is a protein which is formed from long strings of amino acids – 300 to 2,000 base pairs – which must be in a particular order, so they will fold correctly to perform a certain function.

But are there enough events since the universe formed to account for the ATP Synthase?

Let's do the math to calculate the total possible events since the Big Bang. 

If every particle in the observable universe [1 × 10 to the 90th power] was an event that occurred every Planck second [5.4 × 10 to the 44th power] since the beginning of the universe [4.32 × 10 to the 17th power - in seconds] there would be a max of  2.3328x10^152 events since the beginning of the universe.

A single average sized protein of 150 amino acids would take 7.2x10^195 to form via an unguided, purposeless, goalless process. That's more the amount of events in the entire history of the universe.

Also, there are vastly more ways of arranging nucleotide bases that result in non-functional sequences of DNA, and vastly more ways of arranging amino acids that result in non-functional amino-acid chains, than there are corresponding functional genes or proteins. One recent experimentally derived estimate places that ratio—the size of the haystack in relation to the needle—at 10^77 non-functional sequences for every functional gene or protein.

And we have many, many different kinds of these micromachines in our bodies. For instance, the ATP Synthase, the dual motor pump mentioned earlier, is part of the Electron transport chain; four other DNA based, multiple part micromachines.

Sorry, but the math just doesn't hold up for a purposeless, unintentional unguided process without a goal for all those necessary genetic changes in multiple proteins in multiple organs that needed to for the fish to amphibian transition. Not to mention all necessary genetic changes in multiple proteins in multiple organs for the 20 to 35 of the major phyla in the Cambrian explosion.

DNA as information and a language.

In modern biology and information theory, DNA is considered to be literal information, not just a metaphor. Computers use a binary code (0 and 1) to store data. DNA uses a quaternary (Base-4) code. The "meaning" of the DNA is not determined by the chemical properties of the sugar-phosphate backbone (the physical medium), but solely by the sequential arrangement of these bases. This is identical to how the meaning of a software program is determined by the sequence of code, not the silicon of the chip.

DNA follows specific rules to be read by the cell. DNA follows a strict set of rules that dictates how the information is read, similar to grammatical rules in human language. The cell reads DNA in groups of three bases called codons. For example, GCA is the command for the amino acid Alanine. This is a fixed "word length" syntax. The cell machinery does not read one base or two; it reads exactly three.

Just as sentences have capitalization and periods, DNA has specific instructions for "Begin reading here" and "Stop reading here." If these periods are missing or mutated, the cell produces a run-on protein that is usually dysfunctional. Because DNA is read in triplets, starting at the wrong letter shifts the entire "frame," turning a functional sentence into gibberish (much like how removing the "T" from "THE CAT" leaves "HEC AT...").

In English, the word "apple" stands for a red fruit, but there is no physical reason the letters A-P-P-L-E must represent a fruit. It is an agreed-upon convention. In biology, the codon AAA codes for the amino acid Lysine. However, the codon AAA does not physically look like Lysine, nor does it chemically react directly with Lysine.

On one end, the tRNA (a bridge between the genetic code on messenger RNA and the specific amino acids that build proteins) reads the code (AAA); on the other end, it carries Lysine. The cell uses a complex set of enzymes to ensure the right amino acid is attached to the right tRNA. This shows the relationship is symbolic: the cell "knows" that AAA means Lysine, essentially following a dictionary. This symbolic representation is a hallmark of information systems

Specific codons correspond to specific amino acids, which are the building blocks of proteins. DNA is a "blueprint" or "software program" that the cell's machinery reads to assemble functional proteins. These proteins, the machines built from the DNA blueprint, do almost all the work in your body.

The better explanation for the various DNA based micromachines in our bodies is design

OBJECTIONS

The evolution isn't by chance objection

This is correct to a point. Natural selection acts on the results of various genetic mutations. Traits that provide a survival or reproductive advantage in a specific environment become more prevalent in the population because individuals with those traits are more likely to survive and reproduce, passing on their genes.

However, genetic mutations are random. The likelihood of a random mutation resulting in a harmful/neutral effect is much greater than resulting in an advantageous effect, as they seem to be very rare.  And there is no natural selection or survival of the fittest to  “guide” the process of genetic mutations - it’s always random.

I was challenged on this with this comment: Mutations are not random they are constrained and probabilistic. Natural selection is absolutely a non-random process that preserves traits that improve survival and reproduction generation after generation. It’s literally nature “deciding” which mutations stay and which do not, that’s biased, not random.

Random: An outcome that is unpredictable and lacks a specific pattern or direction. In a "purely random" process, every possibility has an equal chance of happening (like rolling a fair die).

Biased: An outcome that is weighted or "steered" in a specific direction. It is not purely chaotic; certain results are favored over others due to constraints or external forces.

It's true that the genome uses chemical markers on DNA and DNA packaging (wrapping around histone proteins) to flag critical areas to recruit DNA repair machinery, this does not help show that naturalistic evolution is the best explanation. To have protection zones in DNA seems like a hallmark of design. That's why a military plane, like the A-10 Warthog, can come back all shot to hell, because none of it vital parts were hit. That is by design!

So, I would argue that this protection/repair of the vital bits is better explained by design rather nature since it seems to imply that there is a goal or purpose. 

Finally, DNA doesn't have offspring,  so natural selection can't explain anything concerning the development of our DNA based micromachines, or how proteins are formed. 

The design objection

Please don't say that design [purposeful, intentional guided process with a goal] is unscientific, since:

1) SETI looks for design [or artificiality - i.e. not generated by natural processes], 

2) an arson investigator can tell if a fire came about naturally or was started by a human, 

3) the police can determine if a death was natural or at the hands of a human, 

4) an archeologist can say whether it’s a just rock or an arrowhead, etc. 

5) we can determine whether a virus, like Covid-19 was designed or was natural. 

An appeal to a designer is accepted in every field of inquiry, including biology. An a priori non-design stance for evolution seems to be an a priori ideological conclusion, rather one that is driven by the facts  

This is a God of the Gaps argument.

A God of the Gap argument assumes an act of God as the explanation for an unknown phenomenon. But I’m not citing an unknown phenomenon or a gap in our knowledge. I am using the inference to the best explanation and citing what we do know about DNA, the difference between fish and amphibians, in order to choose between design [purposeful, intentional guided process with a goal] over a purposeless, unintentional unguided process without a goal.

DNA isn't really information objection

There are abundant scholarly sources that explicitly define DNA as information or instructions.

Central Dogma of Molecular Biology - talks about information or instructions in the cell: The flow of genetic information in a cell is from DNA to RNA to proteins. This paper clearly states the scientific conclusion that DNA is a code/blueprint and that the particular order of its bases is where the information/data for constructing the organism is stored.

Molecular Biology of the Cell Quote: "The complete set of information in an organism's DNA is called its genome, and it carries the instructions for all the proteins the organism will ever synthesize. It clarifies that biologically, the information in DNA is not a metaphor, but a literal instruction set for synthesizing proteins, which are the physical machinery of the cell.

The Major Transitions in Evolution Revisited - They categorize the history of life into major transitions (e.g., from single cells to multicellularity) and define these transitions by how "genetic information is organized and transmitted." This source moves beyond simple cell mechanics and argues that the history of life is essentially a history of information processing and storage improvements.

DNA which holds the permanent genetic blueprint, while RNA carries out instructions to build proteins (mRNA), forms ribosomes (rRNA), and transports amino acids (tRNA)

Here's a simple breakdown:

DNA (The Blueprint): Stored in the nucleus, DNA contains the complete genetic code for all the proteins your body needs.

Transcription (Copying the Recipe): A specific gene (protein recipe) is copied from DNA into messenger RNA (mRNA).

mRNA (The Delivery Truck): This mRNA copy travels out of the nucleus to the cytoplasm.

Ribosomes (The Protein Factory): These organelles read the mRNA sequence.

Translation (Building the Protein): Transfer RNA (tRNA) brings amino acids (the building blocks) to the ribosome, which links them in the correct order, creating a protein

DNA isn't a language ojection

There are abundant scholarly sources that explicitly define DNA as language similar to human language.

See The Language of Genes - David Searls, a pioneer in computational biology, wrote this landmark paper for Nature. He argues that the tools used to analyze human language (linguistics) are mathematically identical to those needed to analyze DNA. He explicitly uses "syntax" and "grammar" to describe how DNA is structured. Not only that, but he compares the arrangement of genes to sentence structures, showing that DNA has a hierarchical grammar where "nouns" (genes) and "verbs" (regulatory elements) must be placed in a specific syntactic order to function. He demonstrates that DNA is not just a linear string of data but has a "context-free grammar" (a specific type of linguistic structure in the Chomsky hierarchy), allowing for complex dependencies similar to nested clauses in English.

See also The linguistics of DNA: words, sentences, grammar, phonetics, and semantics 

Linguistic Terms Used: Words: Codons (groups of 3 bases); Sentences: Genes (strings of codons that form a complete thought/protein); Grammar: The chemical rules that dictate how these "words" can be combined.  The author argues that this is **not** merely a poetic analogy but a distinct mathematical similarity between the structure of human language and the structure of the genetic code.

DNA-Binding Specificities of Human Transcription Factors  - The researchers found that proteins (transcription factors) read DNA not just as individual letters, but as words and compound words. They discovered that when two proteins bind to DNA sequence together, they don't just sit next to each other; they alter the binding instructions, effectively creating a compound word with a new meaning, similar to how joining fire and fly creates firefly, which is distinct from the two separate words.

Thus, we have plenty of scholarly research that shows DNA as a literal language with grammar, syntax, punctuation, and words.

Design provides no testable mechanism, no predictive model, and no explanatory gain

This objection has no basis in fact:

1) Design relies on the known cause of Agent Causation (intelligence), which is the only known cause of specified information. 

2) Design successfully predicted that "junk DNA" would be functional and that biological change has limits. 

3) Design solves the Information Enigma of the origin of life, which unguided chemical evolution has failed to explain for 70+ years.

NOTES:

Note 1: The math (1×10^90 x 5.4×10^44 x 4.32×10^17) was checked with these two different AI math solvers, here and here both had the same answer: 2.3328x10^152

For comparison, the number of possible ways to order a pack of 52 cards... is 8×10^67.... essentially meaning that a randomly shuffled deck has never been seen before and will never be seen again in our lifetime.

Note 2: 2.3328x10^151 takes into account the entire observable universe, but it's difficult to believe that particles outside the earth would affect evolution. Also, it's calculated from the beginning of the time [13.8 billion years] not the beginning of life [3.5 billion years], so the amount of total events for evolution of life is much smaller. Somewhere around 2.5x10^61.

Note 3: The numbers used for the amount of particles in the universe, the Placnk second, seconds since the Big Bang are from The Physics of the Universe's the Universe by the Numbers page

Additional info 

We Have Been LIED TO About Origin Of Life (Renowned Organic Chemist Speaks Out) [Video]

How Organic Chemistry Convinced Me of the Creator [Article]

Finding God through science – an atheist discovers chemical evolution can’t adequately explain the origin of life [Article]

Scientist Explains HUGE Mathematical Problems For Atheism [Video]

Scientists Are Changing Their Minds (EVIDENCE For God!) [Video]

Fined-Tuned Constants

 

Consider some of the finely-tuned factors that make our universe possible:

• If the strong nuclear force were slightly more powerful, then there would be no hydrogen, an essential element of life. If it was slightly weaker, then hydrogen would be the only element in existence.

• If the weak nuclear force were slightly different, then either there would not be enough helium to generate heavy elements in stars, or stars would burn out too quickly and supernova explosions could not scatter heavy elements across the universe

• If the electromagnetic force were slightly stronger or weaker, atomic bonds, and thus complex molecules, could not form.

• If the value of the gravitational constant were slightly larger, one consequence would be that stars would become too hot and burn out too quickly. If it were smaller, stars would never burn at all and heavy elements would not be produced.

The finely tuned laws and constants of the universe are an example of specified complexity in nature. They are complex in that their values and settings are highly unlikely. They are specified in that they match the specific requirements needed for life.

The following gives a sense of the degree of fine-tuning that must go into some of these values to yield a life-friendly universe:

• Gravitational constant: 1 part in 10^34

• Electromagnetic force versus force of gravity: 1 part in 10^37

• Cosmological constant: 1 part in 10^120

• Mass density of universe: 1 part in 10^59

• Expansion rate of universe: 1 part in 10^55

• Initial entropy: 1 part in 10^(10^123)

The last item in the list — the initial entropy of the universe — shows an astounding degree of fine-tuning. What all this shares is an incredible, astronomically precise, purposeful care and planning that went into the crafting of the laws and constants of the universe, gesturing unmistakably to intelligent design. As Nobel laureate in physics, Charles Townes stated:

Intelligent design, as one sees it from a scientific point of view, seems to be quite real. This is a very special universe: it’s remarkable that it came out just this way. If the laws of physics weren’t just the way they are, we couldn’t be here at all. The sun couldn’t be there, the laws of gravity and nuclear laws and magnetic theory, quantum mechanics, and so on have to be just the way they are for us to be here.

Some scientists respond, “Well, there must be an enormous number of universes and each one is a little different. This one just happened to turn out right.” That’s a possibility, and it’s a pretty fantastic possibility — it assumes there really are an enormous number of universes and that the laws could be different for each of them. One would like to get a look at the universe-generating machine responsible for this abundance. Would it have to be fine-tuned? The other possibility is that our universe was planned, and that’s why it has come out so special.

William Lane Craig has a fantastic video explaining this: