Thursday 7 January 2021

Unintelligent Design News - Science Reveals a Ludicrously Complex System

A human cell is featured during mitosis with its chromosomes (gray areas) aligned. The region known as the kinetochore (colored with yellow, red and cyan markers) is the origin of the checkpoint signal that acts as a safety check against premature cell division and is the focus of UC San Diego researchers’ study.
Wait for Me: Cell Biologists Decipher Signal that Ensures No Chromosome is Left Behind - UC San Diego News Center

News today that scientists have discovered how cells ensure the faithful copying of every last piece of DNA as cells divide to produce the trillions of cells in a multicellular organism.

But why is this highly complex system needed, especially when the process of epigenetics is going to turn most of it off to create cell specialisation on which multicellular organisms depend for the division of labour into functional tissues and specialised organs, and what does this tell us about a hypothetical designer who would come up with something this complex to get around a problem it created earlier?

Firstly, why is this process needed in the first place?

The UC San Diego news release explains the problem:
Starting as a single cell, organisms undergo millions of generations of divisions to ultimately generate the bones, heart, brain and other components that make up a living being. The mainspring within this intricate process is the transfer of DNA through each subsequent cell split within discrete packets called chromosomes. It’s critical that all chromosomes are duplicated and precisely distributed through every generation of cell division. If the inherited chromosome components are altered, even slightly, birth defects and certain cancers can result.
To summarise then, the process is necessary because without it, the risks from imperfect replication are so high and can even be fatal - a powerful driver of evolution!

An embryo of a roundworm (C. elegans) is shown undergoing its first division. The embryo expresses fluorescent probes that mark the chromosomes in magenta and the microtubules—the filaments that separate the chromosomes—in gray.

Credit: Desai Lab, UC San Diego
To ensure that the process is completed there has to be a 'signalling' process to tell the cell to halt until everything is completed from the previous division. The scientists at UC San Diego led by Professor Arshad Desai and Dr. Pablo Lara-Gonzalez used a special fluorescent probe to monitor the three-part process involved in this quality control mechanism. They concentrated on a pathway in the cell known as the 'spindle checkpoint'. This pathway is activated at a site on the Chromosome called the kinetochore - the attachment point where protein fibres are attached to the chromosomes to pull them apart.

They found that when these protein fibres are not attached, they send out a 'wait for me!' signal which halts the process until attachment is complete. This mechanism ensures that every chromosome is attached before they are pulled apart so none are left behind. They discovered that this mechanism involves a key 'matchmaker' protein that causes two other constituents that would not normally associate together, to come together to form the chemical signal. This ensures that these signals don't arise inadvertently in other locations in the cell and at inappropriate times.

Their findings were published in Science on January 1, 2012:


During cell division, kinetochores couple chromosomes to spindle microtubules. To protect against chromosome gain or loss, kinetochores lacking microtubule attachment locally catalyze association of the checkpoint proteins Cdc20 and Mad2, which is the key event in the formation of a diffusible checkpoint complex that prevents mitotic exit. We elucidated the mechanism of kinetochore-catalyzed Mad2-Cdc20 assembly with a probe that specifically monitors this assembly reaction at kinetochores in living cells. We found that catalysis occurs through a tripartite mechanism that includes localized delivery of Mad2 and Cdc20 substrates and two phosphorylation-dependent interactions that geometrically constrain their positions and prime Cdc20 for interaction with Mad2. These results reveal how unattached kinetochores create a signal that ensures genome integrity during cell division.

So, now we need to ask why this complex mechanism was needed when, as I said earlier, most of the DNA is going to be deactivated anyway by the epigenetic system to produce the necessary cell specialisation. Here is what I wrote about epigenetics and what the existence of this complex mechanism has to say about any putative designer who could come up with this solution to a problem of its own creation, in my popular book, The Unintelligent Designer: Refuting the Intelligent Design Hoax, which is hated by Creationists:
Briefly, epigenetics is the study of how various genes are turned off in different cells as they become specialised during embryonic development. The actual mechanism, the epigenetic processes itself, are beyond the scope of this book but what interests us here is what this means for our understanding of evolution and, more importantly, why the processes are needed.

The interesting thing from an evolutionary perspective is the fact that, when DNA in the form of a chromosome is replicated in cell division, the epigenetic ‘settings’ are also replicated, so any genes which were switched off in the parent cell will also be switched off in the daughter cells. It seems that, as cells differentiate and become specialised to perform specific functions as the embryo develops, genes can be switched off but they don’t get switched on again, so cells derived from one layer will have all the epigenetic settings of that layer, and some more. The descendants of those cells in turn will have all those settings plus some of their own. And so on until in the fully formed individual all the specialised cell types will have their unique set of epigenetic settings, so liver cells will have different active genes to, say, muscle cells or brain cells


Epigenetics is necessary because in multicellular organisms, any advantage of multicellularity is only realised by specialisation of cells and their arrangement into organs carrying out specialist functions. Many of these functions are only necessary in the first place because of multicellularity, of course. Mammals need digestive, respiratory and circulatory systems to get oxygen and nutrients and remove waste to the cells too far removed from the surface to do it the way single–celled organisms do it – by direct exchange with their environment.

Evolutionarily speaking, multicellularity gave some organisms an advantage over others, but it comes at a price. One of the prices is the complex system of epigenetics and the need to reset and start again with each new individual.

But why is this needed anyway? It is needed because, just like single–celled organisms, the cells of multicellular organisms inherit all the DNA of their parent cells regardless of their eventual function as specialised cells in specialised organs. Unless the unnecessary and unwanted genes are turned off there would be no specialisation and so no benefit from multicellularity. The last thing you want is your brain cells producing the digestive enzymes your pancreas secretes or your kidney cells producing the contractile proteins in your muscles. You want your cells to be specialised and be good at doing what they are specialised to do – and nothing else. When cells start becoming generalised and doing other things they are called cancer.

So what any ID model needs to explain is why any intelligent designer would arrange it so that all cells (with one or two limited exceptions) contain all the DNA of the entire organism when they only need a few special genes to function? Why is this complex system of epigenetics necessary in the first place? Why would an intelligent designer not design things so that as cells become specialised, they only get the DNA they need?

Instead, we have the ludicrous situation of prolific waste of resource in replicating all the DNA – with its attendant risk of going wrong – to have most of it permanently switched off in almost every one of our 70 trillion cells. Then we need a mechanism for resetting it and starting again in the newly–fertilised zygote.

In epigenetics we have a few exciting challenges for biology; for creationism we have as good an example as you can wish for of designer incompetence. We have prolific waste, needless complexity, a clear failure to plan ahead and needing to make the most of a bad job, and of a ludicrously complex ‘solution’ to a problem of its own making because, apparently, the designer lacked the wit to rethink the problem and start again.

How this can be described as intelligent design is quite beyond me. It requires definitions of ‘intelligent’ and ‘design’ that are unrecognisable and indistinguishable from the normal definitions of ‘gross incompetence’ and ‘stupidity’.

For evolutionary biology, of course, epigenetics is as nice an example as you could wish for of the utilitarian, pragmatic nature of evolution, where natural selection can only act on the here and now and where any solution, no matter how suboptimal, will be adopted it if gives an advantage. It is an example of how, like the example of RuBisCo in Chapter 5, evolution has no reverse gear and cannot scrap a suboptimal solution and start again with a better one, as any intelligent design process should be capable of.

Living multicellular organisms are now stuck with the complexity and waste of epigenetics because that gave an advantage, despite the inefficiency and waste, of multicellularity over single–cellularity for some, but by no means all, organisms. Very many organisms remain single–celled of course, and very many remain prokaryote rather than eukaryote. Evolution does not have a plan and is not trying to achieve anything.

Now we learn that even before the system of epigenetics kicks in to begin shutting down most of this faithfully replicated DNA, there needs to be another complicated mechanism to ensure fidelity of the copying process.

Assuming you've been taken in by the Intelligent [sic] Design hoax, you now have to believe that your putative designer not only lacked the wit to realised it was going to need to specialise cells in the multicellular organisms it was designing but never thought to build that in from the start and just copy the genes into the specialised cells that they needed. After all, it wasn't as though any of these specialised cells were ever going to need all the other genes as some point in the future. None of them were going to revert to stem cells or take on other unrelated specialities, yet this designer went to those lengths to ensure all the DNA was copied, much of it needlessly, because the danger from getting it wrong was potentially lethal!

So we have massive complexity to solve a small problem of its own making and prolific waste of the material to make this mostly redundant DNA and the mechanism to replicate it faithfully!

Creationists believe this designer is highly intelligent, omniscient, and a brilliant designer, far surpassing the design abilities of a human designer. Strangely, it exactly resembles a designer without a plan and no understanding of the basic principles of good design. Exactly like a mindless, utilitarian, natural process, in fact.

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