Search This Blog

Thursday, 27 June 2024

technology of the zygote vs. Darwin.

 Let’s Think About a Zygote Like an Engineer


Having read Evolution News for years, contributing an occasional article or two, in addition to my 81-part series on “The Designed Body,” I’ve noticed that there’s a certain way we proponents of intelligent design tend to frame our arguments. We usually provide information on what it takes for life to work, rather than just how it looks (per much of neo-Darwinism). Then we look for reasonable explanations of causation which must include where the information came from to properly produce, assemble, and coordinate all the necessary parts of a given system that we know is absolutely needed for survival (most of that is absent from neo-Darwinism).

But in my collaboration with Steve Laufmann to produce our book Your Designed Body, we came to the conclusion that a different style may be more useful. What we propose is that, in addition to what’s described above, we also engage readers with examples of “problem-solving” just like engineers do it. After all, it takes one to know one. If you’ve never used mental energy to try to solve any one of these hard problems of life, then how can you appreciate what it took to come up with and apply the solution? 

Let’s try the following as an exercise. Once you’ve gone through it, you’ll be better prepared to understand all the causal hurdles that had to have been surmounted. And this will allow you to ask better questions and not be as vulnerable to many of the “just so” stories of neo-Darwinism. 

“Separation of Concerns”

Recently, there was an article in The Scientist, “The First Two Cells in a Human Embryo Contribute Disproportionately to Fetal Development.” It noted a study published in Cell, “The first two blastomeres contribute unequally to the human embryo,” indicating that “a research team showed that, contrary to current models, one early embryonic cell dominates lineages that will become the fetus.” 

The gist of the article was that the current thinking — that it’s at the eight-cell stage where totipotent embryonic cells take the first “fork in the road” of commitment to developing into the fetus or the placenta — may be incorrect. It would now seem that this first “separation of concerns” (as Laufmann and I call it) may take place earlier on, when the zygote divides into the first two blastomeres. 

Ingenious methods were used to label and track the cell lineage from the two-cell to the blastocyst stage:“Thus, they could determine the contribution of each cell to the development of two early structures: the trophectoderm (TE) that becomes the placenta and the inner cell mass (ICM) that eventually produces the fetal tissue.” 

“They are not identical,” explains Magdalena Zernicka-Goetz, a developmental and stem cell biologist at Caltech and the University of Cambridge who is a study co-author. “Only one of the two cells is truly totipotent, meaning it can give rise to body and placenta, and the second cell gives rise mainly to placenta.” She adds, “I was always interested in how cells decide their fate.” The article in The Scientist concludes by telling us that “next, Zernicka-Goetz aims to investigate the features and origins of the differences between clones at the two-cell stage.”

Points to Ponder

It is clear that scientists still do not fully understand how human life develops from the zygote to a newborn and then into a mature fertile adult. One has to wonder what signaling and communication must take place at exactly the right times and in the right orders for all of this to happen properly, never mind where the information and instructions came from. Despite this self-acknowledged lack of understanding, we are told by evolutionary science that it certainly was an unguided and undirected natural process that brought it into being, and not a mind at work, as intelligent design contends. 

What do you think? If you took your car to a mechanic and he told you that he has no idea what’s wrong with it but he’s sure he can fix it, would you engage his services? Just because the scientist is smarter than you about what parts do what and how, that doesn’t necessarily mean that her conclusions about causation are true. After all, in saying that “I was always interested in how cells decide their fate,” she’s attributing agency, a mind at work, to the zygote. So don’t be misled.

Human Life Is a Hard Problem

Actually, life is a series of millions of hard problems that have to be solved all the time, or else. I’m talking about, among many other things, the cellular, metabolic, anatomical, and neuromuscular problems of human life. Let’s start from square one — the human zygote — how each of us began after the sperm of our father joined with the egg of our mother within her womb. That is the one cell from which, within nine months, we developed into a three-trillion-cell newborn with all the equipment we needed to survive. 

If you could go back in time to that moment in your life, be nanosized and micro-pipetted into your own first cell, what would be the first problem you’d have to solve? In other words, once the zygote comes into being, what’s the first thing it has to do? 

Well, if it’s going to become a newborn in nine months or so, it’s got to start dividing. But that won’t happen for at least 24 hours, so you have to consider what else may be more important as the zygote floats within the fluid of your mom’s uterus.

The chemical content of the fluid inside the zygote (high potassium, low sodium) is the opposite of what’s in the fluid surrounding it (low potassium, high sodium). And because these ions can cross the cell membrane, diffusion would naturally make them try to equalize on both sides (inside and outside the zygote) which would spell disaster. So, the sodium/potassium pumps in the zygote’s cell membrane have to kick in right away to keep pushing sodium out and bringing potassium back in, right?

Yes, the action of the million or so sodium/potassium pumps in the zygote’s cell membrane are needed for it to stay alive. But what do they need to do their work?

All work requires energy. So, as with all of life, the first priority of the zygote is to generate enough energy through glycolysis (without oxygen) and cellular respiration (with oxygen). The zygote needs oxygen and glucose (or other substances) to metabolize to get the energy it needs.

And if the zygote’s going to divide into two cells, then four, eight, sixteen, and more, then it’s also going to need nutrients to be able to make more copies of itself. Where does the new human life get the oxygen and nutrients it needs, and how does it make sure of its supply until it becomes a newborn? 

The Engineering Problem

This is how Steve Laufmann and I framed this engineering problem in our book:

All cells need oxygen and nutrients. Early life is no exception. Fertilization results in a zygote, which multiplies through cell division to become an embryo. In the early phase, the embryo gets what is needed by diffusion from the surrounding fluid. This works when there’s only a few dozen cells. But within several weeks the embryo will grow into a fetus, and in a few months into a newborn with trillions of specialized cells organized into coherent, interdependent, finely tuned organ systems. For this to be possible, the embryo needs a better way to get oxygen and nutrients, and to get rid of carbon dioxide and waste materials. If he cannot meet this challenge, he will not survive. But he’s in a special situation, dwelling inside his mother, so he’ll need a solution altogether different from anything else in the body’s inventory — a distinct yet temporary system that can meet this need while he’s developing his permanent internal systems.

We go on to ask a very important engineering question:

How do you build a series of finely tuned, coherent interdependent systems, each necessary for life, and stay alive the whole time? It just wouldn’t do if the body needed to go dead for a while, build some stuff, then come back to life when everything was ready to go. What the child in the womb needs is a complete set of temporary systems to meet the needs of his rapidly growing body, to keep it alive until its own systems are ready to take over. Then at birth, when they are no longer needed, these systems must be discarded as the child transitions to long-term systems.

The Solution Is the Placenta

The  answer to the very hard engineering problem we asked above is the placenta. Somehow or other the zygote has the foresight to know that down the road it will develop into a fetus that requires the placenta for its metabolic and nutritional needs. 

This is how we explain the solution in our book:
           Tissues of the embryo (TE) combine with tissues of the mother (lining of the uterus) to make the placenta — a totally separate organ that provides the scaffolding needed to keep the developing child alive. The placenta enables the mother to sustain the developing child while his internal organ systems and tissues are being fabricated, integrated, and launched. The developing child is, quite literally, on life support between the zygote phase and birth, when his body is finally ready to take over the job.

Up until this recent study it was thought that it’s not until the embryo consists of at least eight cells that some of them start to commit to being part of the placenta (TE). But now it seems that it takes place at the two-cell stage. If your nanosized self is inside the zygote, which lever do you pull to make sure that one of the two forming blastomeres goes down the TE-track? And even more important, where did the lever come from? 

It appears that, based on the findings of this study, the answer to the first question will be the concern of future research. But since, as we are regularly assured, we all know that life came about from the unguided and undirected processes of natural selection acting on random variation, the second question is assumed to have already been answered back in 1859, before we knew any of these intricate particulars and when biological systems were assumed to be vastly simpler than they turned out to be. What do you think? Any questions?

More light ,less heat re:dark matter?

 

The plague of plagues?

 

Predarwinian design vs. Darwinism

 Life Can’t Exist Without Repair Mechanisms, and That’s a Problem for Origin-of-Life Theories


A cell is often described as a factory — a quite extraordinary factory that can run autonomously and reproduce itself. The first cell required a lengthy list of components, layers of organization, and a large quantity of complex specified information, as described by previous episodes of Long Story Short. The latest entry in the series emphasizes yet another requirement for life: an abundance of specific repair mechanisms. 

Damage to the “factory” of the cell occurs on two levels: damage to the stored information (either during replication or by natural degradation over time) and damage to the manufacturing machinery (either from faulty production of new machinery or damage incurred during use). Each type of damage requires specific repair mechanisms that demonstrate foresight — the expectation that damage will occur and the ability to recognize, repair and/or recycle only those components that are damaged. All known life requires these mechanisms. 

Damage to Stored Information

The initial process of DNA replication is facilitated by a polymerase enzyme which results in approximately one error for every 10,000 to 100,000 added nucleotides.1 However, no known life can persist with such a high rate of error, if left uncorrected.2 Fortunately, DNA replication in all life includes a subsequent proofreading step — a type of damage repair — that enhances the accuracy by a factor of 100 to 1,000. The current record holder for the sloppiest DNA replication of a living organism, under normal conditions, is Mycoplasma mycoides (and its human-modified relative, JVCI-syn 3A), where only 1 in 33,000,000 nucleotides are incorrectly copied.3

Following the replication of DNA, a daily barrage of DNA damage occurs during normal operating conditions. Life therefore requires sophisticated and highly specific DNA repair mechanisms. In humans, DNA damage response is estimated to involve a hierarchical organization of 605 proteins in 109 assemblies.4 Efforts to make the simplest possible cell by stripping out all non-essential genes has successfully reduced DNA repair to a minimal set of six genes.5 But, these six genes are encoded in thousands of base pairs of DNA, and the machinery to transcribe and translate those genes into the repair enzymes requires a minimum of 149 genes.6 Thus, the DNA code that is required to make DNA repair mechanisms easily exceeds 100,000 base pairs. Here, we encounter a great paradox, first identified in 1971 by Manfred Eigen7: DNA repair is essential to maintain DNA but the genes that code for DNA repair could not have evolved unless the repair mechanisms were already present to protect the DNA. 

Faulty Production of New Machinery

We  used to think that the metabolic machinery in a cell always produced perfect products. But the reality is that faulty products are unavoidable, resulting in the production of interfering or toxic garbage. All living organisms must therefore have machinery that identifies problems and either repairs or recycles the faulty products. 

The cell’s central manufacturing machine is the ribosome, a marvel that produces functional proteins from strands of mRNA (with the help of many supporting molecules). Unfortunately, about 2-4 percent of mRNA strands get stuck in the ribosome during translation into a protein.8 Not only does this halt production, but it could result in production of a toxic, half-finished protein. 

If the mitochondria could not get “unstuck,” life as we know it would end. In the process of self-replication, a single cell must produce an entire library of proteins, placing a heavy burden on the cell’s mitochondria. But with a 2-4 percent rate of stuck mRNA strands, the average cell would have each of its mitochondria get stuck at least five times before the cell could replicate.9 Therefore, life could never replicate and metabolism would cease unless this problem was solved.

Fortunately, all forms of life, even the simplest,9 are capable of trans–translation, typically involving a three-step process. First, a molecule combining transfer and messenger RNA and two helper molecules (SymB and EF-Tu) recognizes that mRNA is stuck in the ribosome and attaches a label to the half-formed protein. This label, called a degron, is essentially a polyalanine peptide. The condemned protein is recognized, degraded, and recycled by one of many proteases. Finally, the mRNA must also be labeled and recycled to keep it from clogging other ribosomes. In some bacteria,10 a pyrophosphohydrolase enzyme modifies the end of the mRNA, labeling it for destruction. An RNAse (another enzyme) then recognizes this label, grabs hold of the mRNA, and draws it close to its magnesium ion, which causes cleavage of the RNA. Another RNAse then finishes the job, breaking the mRNA up into single nucleotides which can be re-used.

The required presence of tools that can destroy proteins and RNA also comes with a requirement that those tools are highly selective. If these tools evolved, one would expect the initial versions to be non-selective, destroying any proteins or RNA within reach, extinguishing life and blocking the process of evolution.11

Note that the set of tools for trans-translation and protein and RNA recycling are all stored in DNA, which must be protected by repair mechanisms. And, these tools cannot be produced without mitochondria, but the mitochondria cannot be unstuck without the action of trans-translation. Thus, we encounter another case of circular causality. 

Damage Incurred During Use

The normal operation of enzymes or metabolites like co-enzymes or cofactors involves chemical reactions that follow specific paths. Deviations from the desired paths can occur from interferences like radiation, oxidative stress, or encountering the wrong “promiscuous” enzyme. These deviations result in rogue molecules that interfere with metabolism or are toxic to the cell. As a result, even the simplest forms of life require several metabolic repair mechanisms: 

“[T]here can be little room left to doubt that metabolite damage and the systems that counter it are mainstream metabolic processes that cannot be separated from life itself.”12
“It is increasingly evident that metabolites suffer various kinds of damage, that such damage happens in all organisms and that cells have dedicated systems for damage repair and containment.”13
As a relatively simple example of a required repair mechanism, even the simplest known cell (JVCI Syn 3A) has to deal with a sticky situation involving sulfur. Several metabolic reactions require molecules with a thiol group — sulfur bonded to hydrogen and to an organic molecule. The organism needs to maintain its thiol groups, but they have an annoying tendency to cross link (i.e., two thiol groups create a disulfide bond, fusing the two molecules together). Constant maintenance is required to break up this undesired linking. Even the simplest known cell requires two proteins (TrxB/JCVISYN3A_0819 and TrxA/JCVISYN3A_0065) to restore thiol groups and maintain metabolism.12 Because the repair proteins are themselves a product of the cell’s metabolism, this creates another path of circular causality: You can’t have prolonged metabolism without the repair mechanisms but you can’t make the repair mechanisms without metabolism.

An Ounce of Prevention is Worth a Pound of Cure

In addition to life’s required repair mechanisms, all forms of life include damage prevention mechanisms. These mechanisms can destroy rogue molecules, stabilize molecules that are prone to going rogue, or guide chemical reactions toward less harmful outcomes. As an example, when DNA is replicated, available monomers of the four canonical nucleotides (G, C, T, and A) are incorporated into the new strand. Some of the cell’s normal metabolites, like dUTP (deoxyuridine triphosphate), are similar to a canonical nucleotide and can be erroneously incorporated into DNA. Even the simplest cell (once again, JVCI-syn3A) includes an enzyme (deoxyuridine triphosphate pyrophosphatase) to hydrolyze dUTP and prevent formation of corrupted DNA.6

Summing Up the Evidence

Those who promote unguided abiogenesis simply brush off all of these required mechanisms, claiming that life started as simplified “proto-cells” that didn’t need repair. But there is no evidence that any form of life could persist or replicate without these repair mechanisms. And the presence of the repair mechanisms invokes several examples of circular causality — quite a conundrum for unintelligent, natural processes alone. Belief that simpler “proto-cells” didn’t require repair mechanisms requires blind faith, set against the prevailing scientific evidence.   

Notes

Babenek A, and Zuizia-Graczyk I. Fidelity of DNA replication — a matter of proofreading. Curr Genet. 2018; 54: 985-996.
Some viruses have high error rates when replicating, but viruses cannot replicate without the help of cellular life, which requires very low error rates. Some specialized DNA polymerases intentionally operate with lower fidelity on a temporary basis for purposes such as antibody diversity. 
Moger-Reischer RZ, et al. Evolution of a Minimal Cell. Nature. 2023; 620: 122-127.
Kratz A, et al. A multi-scale map of protein assemblies in the DNA damage response. Cell Systems 2023; 14: 447-463.
Hutchison CA, et al. Design and synthesis of a minimal bacterial genome. Science 2016; 351: aad6253. 
Breuer M, et al. Essential Metabolism for a Minimal Cell. eLife 2019;8:e36842 DOI: 10.7554/eLife.36842. 
Eigen, M. Self-organization of matter and evolution of biological macromolecules. Naturwissenschaften, 1971; 58: 465–523.
Ito K, et al. Nascentome analysis uncovers futile protein synthesis in Escherichia coli. PLoS One 2011; 6: e28413
Keiler KC, Feaga HA. Resolving nonstop translation complexes is a matter of life or death. Journal of Bacteriology 2014; 196: 2123-2130.
Mackie GA. RNase E: at the interface of bacterial RNA processing and decay. Nature Reviews Microbiology 2013; 11: 45-57.
“Because RNA degradation is ubiquitous in all cells, it is clear that it must be carefully controlled to accurately recognize target RNAs.” Houseley J and Tollervey D. The many pathways of RNA degradation. Cell 2009; 136: 763-776.
Hass D, et al. Metabolite damage and damage control in a minimal genome. American Society for Microbiology 2022; 13: 1-16.
Linster CL, et al. Metabolite damage and its repair or pre-emption. Nature Chemical Biology 2013; 9: 72-80.