Unintelligent Design - How The Same Function Evolved Twice - Once in Vertebrates And Again in Insects

Sunset over University of California - Irvine

Diagram of an insect compound eye.

Credit: Bugboy52.40 via Wikipedia (CC BY-SA 3.0 Deed)

UC Irvine study shows similarities and differences in human and insect vision formation – UCI News

Regardless of the different structures in the compound eyes of insects and the eyes of vertebrates, at the heart of them both is a light-sensitive molecule, 11-cis-retinal, also known as 'visual Chromophore', but these are produced in two different ways from the same starting compound - β-carotene - which in humans is obtained from eating plants like carrots which are rich in Vitamin A from which β-carotene is derived.

This is one of those examples which are so common in biology, of where, had it been intelligent, the same designer could have used a process it had designed earlier but did not, instead it designed an even more complex way of doing the same thing, giving the lie to claims that the same 'intelligent' designer designed living things, insects and vertebrates have two different ways to achieve the same product - 11-cis-retinal; the second being the more complicated of the two.


Although the earliest vertebrates appeared about 518 million years ago, so predating the first insects by about 130 million years, the creationists dogma of omniscience which they traditionally ascribe to their putative designer god, would mean this alleged designer was already aware of the less complex way to make 11-cis-retinal, when if supposedly designed the vertebrate method.

Besides, creationist dogma also says they were all created on the same day - 10,000 years ago.

Malevolent Design - Another Arms Race Between A Parasitic Worm And Its Host - Or is It Just Unintelligent Design?

Cane Toad, Rhinella marina

Cane Toad, Rhinella marina

A secret war between cane toads and parasitic lungworms is raging across Australia

The subject of parasitic arms races throws creationists into a bout of cognitive dissonance from which they can only emerge with a hefty dose of double-think and self-deception, telling themselves that it's perfectly logical to hold two diametrically opposite and mutually contradictory views simultaneously, like believing that the term 'circle' describes a spere but the term 'square doesn't describe a cube.

They need to believe that, whilst it is central to their dogma and the belief on which all their god of the gaps and false dichotomy fallacies relies - that there is only one creator god capable of whatever it is they are waving as 'proof' or its existence, and at the same time believing that parasites were created by a different creator, over whom their omnipotent god has no powers and who goes toe to toe with it in parasite-host arms races.

Sadly for creationists, they were denied the argument concerning a second creator by their guru and Deception Institute flunky, Michael J Behe, who used the evolution of parasites like Escherichia coli and Plasmodium falciparum (the malaria parasite) as 'proof that their god is the intelligent designer behind the 'design' of all living things.

So, let's do what Behe unwittingly did and remove the second, evil designer from the equation, and see where it leads.

A case in point is the recently discovered arms race between the Australian cane toads and the lung worm parasite that infests their lungs:

Unintelligent Design - The Heath Robinson Way Legumes Get Nitrates

Image by Miha Creative/Shutterstock

Mechanism of Plants Obtain Nitrogen by Supplying Iron to Symbiotic Bacteria | Research News - University of Tsukuba

Creationism's 'intelligent' designer is nothing if not inventive. In fact, it's so inventive that it keeps on reinventing things it's already invented and designing new ways to do things it's already designed a way to do. It's almost exactly like it has no way of remembering what it did yesterday and using those designs and inventions today - a bit like a motor-car manufacturer who reinvents the wheel, or the steering mechanism every time it designs a new model.

Take, for example, the way most plants obtain the essential nitrates they need to make proteins. Nitrogen is abundant in the atmosphere (about 79%) where it exists as diatomic molecules N₂, in which form plants can't assimilate it. Instead they depend on soil bacteria, the 'nitrogen-fixing' bacteria such as Azotobacter and Clostridium which convert N₂, into ammonium (NH₄⁺ which forms salts with other minerals in the soil, in which form it can be taken in through the roots of plants. Apparently, it was too simple to give plants the same metabolic pathways that the nitrogen-fixing bacteria have so they could make their own ammonium, so a more complex and less energy-efficient way to get nitrates into plants had to be invented.

A small amount of ammonia (NH₃ is also produced by the action of lightening on atmospheric nitrogen and this, together with nitrates produced by industrial pollution is dissolved in rainwater and finds its way into the soil. Other bacteria, fungi and other soil organisms also release nitrates from decaying plant and animal matter in the soil.

Unintelligent Design - How A Design Blunder Causes Inflammatory Diseases, Especially In Later Life

Endosomes (magenta) collect around mitochondria (blue) after infection with virus HSV-1, which attacks mtDNA (green) and causes its release.

Credit: Salk Institute

Faulty DNA disposal system causes inflammation - Salk Institute for Biological Studies

In another example of the ramshackle Heath Robinson design process that created humans, scientists today published their findings that show how when a cell process goes wrong, as it frequently does, the result can be a serious health condition, causing suffering and unhappiness.

And of course, it’s another example of how we can tell humans weren't intelligently designed by an omnibenevolent god who wants to minimise the suffering in the world, but by a mindless, amoral natural process that has no option but to settle for the sub-optimal as long as it’s better than nothing.

The discovery, by researchers at the Salk Institute and their colleagues at UC San Diego , is the way when mitochondrial DNA (mtDNA) goes wrong and the cell tried to dispose of it, some of it leaks out into the cell, the cell’s immune system treats it like the DNA of a parasitic organism and sets up an immune response which caused inflammation.

Given the origin of mitochondria in our Heath Robinson contraptions we call cells, this is hardly surprising since mitochondria started out, probably as the free-living bacterial prey of another prokaryote, possibly an archaeon. They then became symbiotic, providing the cell with free ATP in return for protection and nutrients in the form of sugar, water and oxygen. Because they need to provide a handful of enzymes to do this with, and they are self-replicating, they retained a small amount of their original DNA while giving up most of it to the host cell's nucleus.

Unintelligent Design - How Scientists Are Overcoming The "Designer's" Incompetence

Credit: Dingzeyu Li via Unsplash

Systemic lupus erythematosus

World-first discovery may enable an effective long-term lupus treatment - Monash University

Readers may recall my recent article on Lupus and why women are nine times more likely to suffer from it than men, because the epigenetic process for switching off genes on their X-chromosome sometimes goes wrong and produces proteins that induce an immune response to their own tissues.

From a creationist perspective, this can only be for one of two reasons: either the designer was incompetent, or this was by design. The choice being either incompetence, or malevolence and misogyny.

Now a team of researchers at Monash University, Clayton, VIC, Australia, have reported success in finding a way to overcome this design defect - which begs the question: if scientists can do it, why couldn't an omnipotent intelligent designer? Could the answer be that the human immune system was not designed by an omnipotent, intelligent designer, but is the result of a mindless, utilitarian process that inevitably produces sub-optimal 'designs' that can't be scrapped and redesigned?

But that is the kind of thought that would cause panic in the mind of most creationists because it would raise the terrible spectre of wondering if they could be wrong.
The Australian team have just published their results, open access, in Nature Communications. They are also explained in a Monash University news release:

Unintelligent Design - How Scientists Are Learning to Do What Creationism's 'Intelligent' Designer Found Too Difficult - Or Didn't Want To Do!

The proteins needed to create limb progenitor cells are marked with different colors under a microscope.

Images: Yuji Atsuta/Tabin lab

The proteins needed to create limb progenitor cells are marked with different colors under a microscope.

Images: Yuji Atsuta/Tabin lab

The Surprisingly Simple Recipe for Starting to Grow a Limb | Harvard Medical School

Visit any site of a supposed Marian miracle, such as Lourdes, now selling 'miracle cures' that almost never work and those that do can be attributed to the medication the pilgrim was receiving prior to the visit, or to spontaneous regression, the placebo effect or a psychosomatic condition, and you may find lots of crutches supposedly left there as testament to the cure of mobility disorders, but what you will never find is the artificial limb discarded by someone who had a spontaneous regeneration of an amputated limb.

Or visit any of the lucrative travelling, carefully stage-managed 'faith healing circuses' where people appear to be 'cured' of all manner of ailments at the touch of a 'healer', who, for perhaps obvious reasons, never works in a hospital, and you will never witness the regeneration of a limb, or even part of a limb. Not even a finger or toe.

And before some-one cites, the 'Miracle of Calanda', this is such an obvious hoax that it's a miracle anyone believes it.

Despite having allegedly created a universe from nothing and all living things from dirt, creationism's god appears to be incapable, even with the help of his miracle-working mother, to be able to regrow a human limb.

The problem is one of the designer's own making (if you believe creationists) because it would involve the epigenetic resetting of the cells at the end of the stump, so they become stem cells again, capable of making all the different specialist cells in a limb, like bone, muscle, skin, nerves and blood vessels and growing to the right shape in the right place. That was a once-only ability in the developing embryo.

Epigenetics, as I have written about many times, is necessary because the cells of a multicellular organism replicate the same way our single-celled ancestors did - by replicating the entire genome every time in every daughter cell. But the benefit of multicellularity is that cells are specialised so only need a few genes, not the entire genome and having the wrong genes active in a specialist cell would be detrimental, so most of them need to be switched off by the epigenetic system. A problem which could have been avoided by any omniscient, omnipotent designer by just replicating those genes that were going to be needed by the specialist cells, but not something a mindless, natural process with no foresight, no reverse gear and no means of scrapping a bad design and starting again, could have avoided.

And yet medical scientists investigating the problem believe they have discovered the basic principles involved, which turn out to be "surprisingly simple", so well within the capabilities of even creationism's rather limited god.

The scientists, led by Harvard Medical School geneticists, have published their findings in an open access paper in a Cell Press journal, Developmental Cell and explain it in a Harvard Medical School news release by Stephanie Dutchen:

Unintelligent Design News - Why Women Are More Prone To Lupus Than Men - Evolution, Or Does Creationism's God Just Hate Women More?

The classic 'butterfly rash' of systemic lupus erythematosus (SLE)

Lupus and other autoimmune diseases strike far more women than men. Now there's a clue why

In my days as an operational paramedic, I once had to move a 26 your old women to hospital because lupus had made her so ill her blood pressure was below the safe level to maintain her renal function.

It was so low I couldn't even sit her up to carry her down stairs without her losing consciousness, so I had to run a couple of units of IV fluid into her to bring it up enough to make it safe to move her. She really was profoundly ill and at death's door. But such was the nature of the profession that, having delivered her safely to hospital and handed her over to the care of doctors and nurses, that was the end of my role in her care, so I never heard the outcome.

The autoimmune condition, lupus erythematosus, is caused by a malfunction of the immune system in which something triggers it to turn against the sufferer's own body instead of the invasive pathogens from which it has evolved to protect us. Although, of course, a creationist would hotly dispute the idea that a system like our immune system evolved at all, and would insist that it was intelligently [sic] designed by their favourite, evidence-free, supernatural deity without whom nothing can be created, presumably because they believe chemistry and physics don't know how to behave without a magic god telling them.

But an intelligently-designed immune system would only malfunction and turn against the person it is supposedly designed to protect if it were either incompetently designed or malevolently designed and is doing what it was designed to do - randomly increasing the suffering in the world. The evidence is that lupus is far more common in women than in men by a ratio of 9:1, which begs the question, does the designer just hate women more than men or was he more diligent when designing men's immune system then when designing women's?

The answer, as anyone who understands anatomy and physiology and particularly, evolution, will tell you, is that as an evolved system, we can expect compromises and a lack of perfection because evolution is a utilitarian process with no foresight and no reverse gear, so we are stuck with a sub-optimal immune system that evolved in an ancient ancestor, maybe even a pre-vertebrate ancestor. Certainly, all known vertebrates have one, and some, like that of bats, is far superior to ours.

Now a team of researchers at Stanford University School of Medicine, Stanford, CA, USA have worked out why lupus is far more common in women than men. Ther results are published, open access, in Cell and explained in a Stanford Medical news release. But first, a little AI background:

Unintelligent Design - The Unintelligent Evolution of Sea Grasses 100 Million Years Before 'Creation Week'

Neptune grass (Posidonia oceanica) in the Mediterranean Sea.

Photo: Gabriele Procaccini, Stazione Zoologica Anton Dohrn Naples.

Little Neptune Grass (Cymodocea nodosa).

Photo: Thorsten Reusch, GEOMAR

Use it or lose it: How seagrasses conquered the sea - GEOMAR - Helmholtz-Zentrum für Ozeanforschung Kiel

Sea grasses are the only flowering plants to become fully submerged, having evolved from three independent lineages some 100 million years ago in fresh water and transitioned into marine plants. This appears to have been facilitated some 86 million years ago by a whole genome tripling, which created plenty of spare DNA which could mutate harmlessly to create new genetic information - something deemed 'impossible' by creationist dogma. Since then, they have undergone further evolutionary adaptation by gene loss - something else that creationist dogma says is impossible.

Now an international group of 38 researchers coordinated by Professor Dr. Yves Van de Peer, Ghent University, Belgium, Professor Dr. Jeanine Olsen, University of Groningen, Netherlands, Professor Dr. Thorsten Reusch, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany, Dr. Gabriele Procaccini, Stazione Zoologica Anton Dohrn of Napoli, Italy, and the Joint Genome Institute, Berkeley, California, United States of America, sequenced and analyzed the genomes of three of the most important seagrass species – the iconic Mediterranean endemic Neptune grass (Posidonia oceanica), the broadly distributed Little Neptune grass (Cymodocea nodosa) and the Caribbean endemic Turtlegrass (Thalassia testudinum), to discover what evolutionary changes had enabled this transition.

Anyone who has holidayed on the Mediterranean coast may be familiar with the 'Poseidon balls' that wash up on beaches. These example of emergence of order from chaos are the result of the fibrous remains of Poseidon grass leaves being rolled along the seabed at the tidal interface to form long rolls which then break up and get rolled further into balls, as I relate here.

But the question the team addressed was not how the Poseidon balls form but how did the sea grasses evolve? This is the subject of their paper in Nature Plants and a press release from GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany:

Unintelligent Design - How Ovulation Goes Wrong Because It Wasn't Intelligently Designed

[left caption]

[Right caption/credit]

Gene expression atlas captures where ovulation can go awry | Cornell Chronicle

Back in the late 1960s and early 1970, in what seems like a different lifetime now, I was a senior research assistant in the Oxford University/MRC Neuroendocrinology Research Unit, researching the hormonal control of ovulation in guinea pigs. Two of our tools were radioimmunoassays I had adapted for measuring extremely low levels of a hormone in guinea pig anterior pituitary glands known as luteinizing hormone (LH), and another similar assay for measuring the level of the steroid progesterone in guinea pig blood.

Sadly, having worked for close on two years towards producing a research paper with hundreds of assay results, thousands of microscope slides, hundreds of electron micrographs and a freezer full of samples waiting to be assayed, the government pulled the rug from under our feet by withdrawing our research funding, and I was made redundant, so my work was never published. Disillusioned and with a young family to support, I left research and perused a career in the NHS Ambulance Service instead - but that's a different story, and not relevant to the subject of this blogpost, which illustrates how much science has progressed in the last 50-60 years.

Researchers are no longer researching the hormonal control of ovulation but the fine details of the genetic control of the process of ovulation at the cell level, and what they've found is that the process is far from intelligently designed by anything resembling a perfect, omniscient, omnipotent designer. It is a process that is so complex that it can, and does, go wrong. An intelligent designer who didn't want random women to be unable to shed viable eggs, could have designed a less complicated process, but you can depend on creationism's putative intelligent[sic] designer to never do something simple when there is a far more complicated and wasteful way to achieve the same result.

The research, published a few days ago in Proceedings of the National Academy of Sciences, was led by Iwijn De Vlaminck, associate professor of biomedical engineering in Cornell Engineering, and Yi Athena Ren, assistant professor of animal science in the College of Agriculture and Life Sciences. The paper’s lead author is Madhav Mantri, Ph.D., now a postdoctoral researcher at Stanford University.

The team used a form of RNA tagging to map the gene expressions that occur during ovarian follicle maturation and ovulation in mice.

This spatial transcriptomics map depicts the cell types of a mouse ovary undergoing hormone-induced ovulation

The research is explained in a Cornell University Press release:

Malevolent Designer News - How To Keep Ahead In The COVID Game Against Creationism's Divine Malevolence - Keep Being Boosted

How long does immunity last after a COVID infection?

Creationists stuck with the evidence of parasites and viruses that appear to be designed for two purposes only - making more copies of themselves and increasing the suffering in the world by making us sick and die - traditionally try to ride two horses. They blame something else, like 'The Fall' or 'Sin' for them, whilst still arguing that their putative designer god is supreme in all things and the only entity capable of creating complex organisms.

They also get in a terrible muddle when asked whether their 'designer' god included an immune system to protect us from these parasites when it designed us before 'The Fall', in which case it was planning for it all along, or whether there was a subsequent upgrade to V.1.2, in which case it couldn't have been omniscient and had to redo its design to account for the unforeseen.

But whatever rationalisation creationists can think up for these mutually contradictory beliefs, we are left with the fact that viruses like the SARS-CoV-2 virus and our immune system are locked in an arms race, in which human medical science has had to get involved because the immune system isn't fit for purpose, and the protection it gives us is only temporary.

Meanwhile, medical scientists, aware of the fact that evolution by natural selection is going to continually produce new variants of the virus and that these viruses may become better at evading our defences, continue to apply that knowledge and develop new vaccines against the latest variants.

The following article by Lara Herrero, Research Leader in Virology and Infectious Disease, and Wesley Freppel, Research Fellow, Institute for Glycomics, both of Griffith University, Australia explains why regular vaccination with boosters to keep out immune system primed for the latest iteration of the arms race with a latest version of the virus. The article is reproduced from The Conversation under a Creative Commons licence, reformatted for stylistic consistency:

Malevolent Design - How The Divine Sadist Makes One in Three Infected Babies' Future Lives Difficult Even If They Recover From Bacterial Meningitis

Photo: Getty Images

Bacterial meningitis damages one in three children for life | Karolinska Institutet Nyheter

Left untreated, bacterial meningitis is usually fatal, but even if it is treated with antibiotics and the patient recovers, creationism's divine sadist who designed the bacteria, ensures one in three of them will be lefts with varying degrees of disability, including mental impairment, blindness, deafness or loss of motor control that will be with them for life.

This is the conclusion of a new study published two days ago in JAMA Network Open. It was conducted by a team under the leadership of Federico Iovino, associate professor in Medical Microbiology at the Department of Neuroscience, Karolinska Institutet.

The team compiled data on 3,500 people who contracted bacterial meningitis as children between 1987 and 2021 and compared them to just over 32,000 matched controls from the general population. The average follow-up time was 23 years.

As the news release from the Karolinska Institutet explains:

Unintelligent Design - The Heath-Robinson Contraption In A Western Honey Bee's Gut

Western honey bee,
Apis mellifera

Study shows western honey bee synthesizes food for its intestinal bacteria

A feature of creationism’s putative intelligent [sic] designer's designs is that they are almost always ingenious but overly complex for the task and often cobbled together from components designed for other purposes.

Just like a William Heath-Robinson contraption, where everyday objects such as a coal-scuttle full of coal, is a counterweight, every piece of string is made from short pieces of string knotted together and a simple task is made far more complicated than it need be.

And yet it works, just about, no matter how inefficiently, and removing just one component would make the whole thing fail - what creationists call 'irreducible complexity' but what a proper intelligent designer would probably call, 'bloody stupid'. Creationism's 'intelligent' [sic] designer wouldn't have lasted a term in design school.

Just such a Heath-Robinson machine has recently been discovered in the gut of the Western honey bee, Apis mellifera. Its purpose is to solve the problem of digesting the food the bee eats, for which it needs the help of 8 species of bacteria and other microorganisms that live in the bee's gut. Some of these bacteria are needed just to clean up the waste produced by other bacteria. 8 species is low compared to other species; humans, for example, need about 20 different species.

Apparently, giving bee's the same enzymes the bacteria use was far too simple and not nearly complex enough for the divine Heath-Robinson designer.

But even that wasn't complicated enough because one of the bacteria can't live on sugar alone, even though honey bees can, so the honey bee manufactures nutrients to feed to this bacteria.

How this was discovered was the subject of a recent paper in Nature Microbiology by a team of researchers led by Professor Philipp Engel in the University of Lausanne's Department of Fundamental Microbiology (DMF) in Dorigny. Their research is explained in a news release from the University of Lausanne (translated from French):

Unintelligent Design - How Creationism's Heath-Robinson Designer's 'Design' Causes Cancer

Pit Head (c. 1930) William Heath Robinson

Deregulation of Alternative RNA Splicing Promotes Pancreatic Cancer Pr | Moffitt

William Heath-Robinson was an English eccentric illustrator of ridiculously over-complicated solutions for (mostly) imaginary problems. His 'labour-saving' devices often took more people to operate them than the labour they saved.

His designs usually incorporated the most unlikely of objects, such as pianos or stacks of books to stand on, bent sticks to hold things up, pulleys and levers, held together with pieces of string, which never failed to have a knot in them because they had been made from shorter lengths tied together. And the amazing thing was, when you looked at them, it looked though they really would work, and if you took any component away, the whole thing would fail.

What he probably didn't appreciate at the time, was how closely his 'intelligent' designs resembled the designs of creationism's putative designer, but they are almost perfect metaphors for the detail beneath the superficial appearance of design in living organisms, especially the processes and mechanisms that look irreducibly complex.

Take, for example, a consequence of the failure of a 'Heath-Robinson' mechanism for correcting a problem with how RNA is built using templates in DNA which are scattered over several sections of DNA instead of being in a single, contiguous lengths. The different fragments of RNA that this initially produces must then be spliced together (just like William Heath-Robinson's pieces of string).

And of course, being a 'Heath-Robinson' machine, even this little section of the process of protein production is not simple. Splicing is a complex process involving the protein, RBFOX2, and when this fails in pancreatic cells, the resulting faulty RNA molecules can lead to cancer and metastasis of those cancer cells is itself facilitated by reduced RBFOX2.

How the failure of this correction mechanism causes pancreatic cancer was discovered by an international team of researchers led by Assistant Professor, Karen Mann, Ph.D., of the Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA, with colleagues from The Tisch Cancer Institute; St. Jude Children’s Research Hospital; the Agency for Science, Technology and Research in Singapore; and the University of Otago in New Zealand.

Of course, the real problem here isn't with the designer but the mindless design process that produces these over-complicated, utilitarian 'Heath-Robinson' solutions to problems. DNA is RNA's data store and, so long as it works better than what went before it, there is no pressure to sort out and 'defrag' the DNA, so the irreducibly complex 'Heath-Robinson' machine might fail and cause pancreatic cancer occasionally, but the proteins the pancreas produces are worth the occasional failures, and mindless evolution has no concern for the suffering caused.

Here is how the team described their findings in Nature:

Creationism in Crisis - How Mindless Evolution Took A Giant Ape To Extinction

A reconstruction of Gigantopithecus blacki.

Image: Garcia / Joannes-Boyau

The Extinction of the Giant Ape--A Long-standing Mystery Solved--Institute of Vertebrate Paleontology and Paleoanthropology

Gigantopithecus blacki, the largest hominoid that ever lived.

Limestone karst landscape in Chongzuo, southern China. The Gigantopithecus sites are located in caves in the steep-sided walls of the mountains. The mountain in the center of the picture is Mulan Mountain. The entrance of Hejiang Cave (#16 in Figure 2) is about three-quarters down from the main peak.

Zhang Y and Harrison T.(2017)

Gigantopithecus blacki was the largest known member of the Hominidae. It lived in what is now southern China but went extinct between 295,000 and 215,000 years ago, leaving only around 2000 fossilised teeth and four jawbones as evidence of its existence. Creationists will need to ignore that fact that this means the entire species lived and went extinct some 250,000 years before 'Creation Week' when they believe the Universe, Earth and all living things were magicked out of nothing.

The reason for its extinction remained a mystery until now, when a team of researchers from Chinese, Australian and American universities have shown that extinction was almost certainly caused by climate change which deprived it of its highly specialised food - tree bark.

The story of its evolution and eventual extinction illustrates the unplanned and mindless nature of evolution by Natural Selection which has no mechanism for anticipating, let alone planning for a major event like climate change causing forest to become grasslands. There is no Plan B because there is not even a Plan A. The large size of Gigantopithecus was probably related to its diet of tree bark, which can be deduced from its teeth and jaw. A large gut being needed to digest, with the aid of bacteria and other microorganisms, a high-cellulose diet. And a large body needs a lot of food to sustain it. Compare the size of the wholly vegetarian gorilla with that of the more omnivorous chimpanzees.

The researchers have published their findings, open access, in the journal Nature and explain it in a news release from the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP), Chinese Academy of Sciences:

Unintelligent Design - How Creationism's Incompetent Designer Tries To Fix It's Bad Design

New Study Reveals Crucial 'Housekeeping' Genetic Elements and Their Potent Role to Fight Cancer｜THE INSTITUTE OF MEDICAL SCIENCE, THE UNIVERSITY OF TOKYO

The thing about Creationism's putative intelligent [sic] designer is that it isn't just your common or garden variety of jobbing designer; it is allegedly omniscient, omnipotent and perfect, so anything it designs should be perfectly designed to do exactly what it does, nothing more and nothing less. Creationists need to ignore that aspect of its designs when it comes to the problem of all the parasites that live on and in the animals and plants it supposedly created or they need to perform some double-think mental gymnastics and blame something else which, even though their putative intelligent designer is the only entity capable of designing anything living, also designs things.

Creationists also need to ignore the fact that good design is minimally complex and pretend it’s a hallmark of good design. But imagine a manufacturing process that is so badly designed that it needs whole layers of sub-processes to correct the mistakes, and then those sub-processes need more sub-processes to correct their mistakes!

Presumably, a creationist would look at that system with its vast array of monitoring and error corrections as evidence of intelligent design, regardless of the waste and inefficiency built into the system. In reality, of course, any competent process designer would get it right first time, or would scrap a bad design and start over, learning the lessons of earlier failures, so designing the perfect system with minimal complexity and minimal waste should not be beyond the wit of a perfect, omnipotent omniscient designer, should it?

Alas, what we see in nature is nothing like perfectly designed processes; instead, we see muddle, waste and inefficiency with layer upon layer of sub-processes simply to cope with the errors in the processes.

An example of just this situation inside the cells of our allegedly intelligently design bodies was discovered recently by a team of researchers from the Laboratory of Functional Analysis in silico (Nakai-lab) at The Institute of Medical Science, The University of Tokyo, Japan, led by Professor Kenta Nakai, head of the laboratory, and Dr. Martin Loza, Assistant Professor, in collaboration with Dr. Alexis Vandenbon, Associate Professor, from the Institute of Life and Medical Sciences, Kyoto University, Japan. Their work was published, open access, in Nucleic Acids Research on December 12, 2023.

The team found as many as 11,000 gene regulators, all needed for basic 'housekeeping' and error corrections within the cell. These are known as housekeeping cis-regulatory elements (HK-CREs). These elements are vital in maintaining cellular stability beyond conventional gene regulation, influencing diverse cellular functions across healthy cell types. Moreover, a subset of these housekeeping elements, particularly those related to zinc finger genes, was found to have reduced activity in diverse cancers, suggesting their role as potential housekeeping tumor suppressors.

These HK-CREs were believed to be simple on/off switches that regulated the activity of housekeeping genes, but that was far too simple for whatever designed this complex process, of course. The Japanese team found that these switches aren't only important for the enhancement of specific genes but are crucial for the basic functions that keep our cells healthy. In other words, they are needed to clean up and correct the mistakes in the basic cell functions.

Given the significant association between cancer and mutations in epigenetic components, every small insight we gain could be key in the ongoing battle against this disease, which has tragically claimed innumerable lives. Through extensive bioinformatics analyses, we aimed to emphasize HK-CREs profound impact on fundamental cellular processes, including their potential as essential housekeeping tumor suppressors.

Assistant professor Dr. Martin Loza, lead author
The Institute of Medical Science
The University of Tokyo, Japan

To summarise at this point then, the housekeeping genes (HKRs) are needed to clean up the errors and mess of a badly designed process, but then they need more genes (HK-CREs) to regulate their activity!

But it gets worse!

Unintelligent Design News - If Scientists Can Do It, Why Couldn't Creationism's 'Intelligent' Designer?

© Max Planck Institute for Terrestrial Microbiology/Geisel

First step towards synthetic CO₂ fixation in living cells | Max Planck Institute for Terrestrial Microbiology

I've written several articles on one of the best arguments against intelligent design - RuBisCo - and include a section on it in The Unintelligent Designer: Refuting The Intelligent Design Hoax. I have also reported on efforts by biomedical scientists to improve on its efficiency and so increase crop yields.

Now we have another research paper which shows how any intelligent designer of photosynthesis could have done a much better job of it but either chose not to or was too incompetent to realise is could have done better, if it really is intelligently [sic] designed and not the result of a mindless, utilitarian process.

First a little refresher on RuBisCo and why it is so inefficient:

Unintelligent Design - Malevolence or Incompetence? - Why Design A Uterus To Grow Fibroids?

Uterine fibroids

Hic et nunc via Wikipedia (CC BY-SA 3.0)

Assistant Professor Stacey Schutte, left, and Research Associate Andreja Moset Zupan study new avenues to treat fibroids in Schutte's biomedical engineering lab in UC's Bioscience Center.

Photo/Andrew Higley/UC Marketing + Brand

Researchers find ways that uterine fibroid cells respond differently from surrounding tissue | University of Cincinnati

Almost 80% of women of child-bearing age will develop uterine fibroids. Although usually not malignant, they can nevertheless be extremely painful, can cause bleeding and can lead to infertility. The economic cost of fibroids has been estimated to be some $9 billion in the USA alone.

Fibroids grow in response to the same hormones, oestragen and progesterone, which cause the endometrium to thicken then breakdown during the menstrual cycle. Now a research team at the University of Cincinnati have shown that cell stretching is also a factor in their growth.

Hormones and uterine stretching as the endometrium thicken and shrinks and during pregnancy and childbirth are, of course part of the normal state of affairs for the uterus that creationists believe must have been designed by their supposedly omniscience, omnipotent designer, so, if we accept that childish notion of magic design by an omniscient supernatural entity, for the sake of argument, we have to assume growing fibroids was all part of the plan, since it is not possible for an omniscient designer to not be aware of the outcome of its design and for it not to design with that outcome in mind.

So, the only alternative, within the creationist paradigm, is that fibroids are the accidental and unforeseen consequences of the design and function of the uterus - which would mean one of three things:

1. The designer was not omniscient.
2. The designer was incompetent.
3. If the designer was both competent and omniscient it must have been malevolent and intended a high percentage of women to suffer the pain and inconvenience of fibroids.

This discovery is the subject of a research paper in the journal F&S Science which, sadly is behind a paywall, but the Abstract in the form of a summary of the paper is available.

Unintelligent Design - Another Ludicrously Complex Arms Race, This Time Between Plants And A Predatory Fungus

Gray Mold, Botrytis cinerea, on green tomatoes

Discovery: plants use “trojan horse” to fight mold invasions | News Running epigenetics a close second for the most obvious evidence on unintelligent design in nature is the ubiquitous arms race; Arms races are a major component of evolutionary biology, easily understandable in terms of evolution by natural selection. One organism (call it Organism A) predates on, or parasitises another (call it Organism B); this creates an advantage for Organism B in avoiding being eaten of serving as the host of Organism A, so any functional defense mechanism is selected for by natural selection. This in turn creates an advantage for Organism A to evolve a mechanism for overcoming Organism B's defences, and so on until a state of equilibrium is achieved in which either one or the other organism is no longer able to evolve further.

This can lead to some extreme adaptations such as the stupidly long neck and legs of the giraffe which is a response to acacia trees evolving longer trunks to place their leaves, flowers and seeds beyond the reach of giraffes. In the process, acacia trees need to produce masses of cellulose to build the trunk and pump water much higher against gravity than if they were low-growing bushes, and giraffes have to maintain a very high blood pressure to keep their brain supplied with oxygen while drinking water places them at risk of predation by lions because they can't stand up and raise their heads quickly or they will lose consciousness. And they need the additional complexity of special valves in their neck veins to maintain a high blood pressure to their brain.

Now, take away acacia trees (imagine a sudden virus that wipes them out) and the giraffe is no longer superbly adapted for its environment; instead, it is severely handicapped, and might even find feeding from an alternative source difficult.

Another arms race can be seen at the moment is where the SARS-CoV-2 virus is evolving new variants every few months in response to growing herd immunity in its hosts, the human population, due to vaccinations and sub-lethal infections. The virus is getting better at evading our antibodies for long enough for us to pass on the infection to someone else and is tending to be less lethal, so we survive to infect others, even being asymptomatic. Gradually the virus will evolve to become a relatively mild infection that most of us will catch as often as we catch the common cold, and only especially vulnerable people will be made seriously ill by it.

These are just two examples of hundreds of similar arms races in nature; there are even arms races between sexes of the same species as females evolve strategies to retain the ability to only mate with a male of her choice, while males evolve strategies to deprive her of that ability.

But how on Earth can this be explained in terms of design by a single designer, or, including the creationists fallback excuse for parasites, two designers - their supposedly omnipotent, omniscient god and 'Sin'? Would not an omnipotent, omniscient god know in advance what Sin's next response would be and create a design that it couldn't overcome, so an arms race never started in the first place? Or are we to believe that creationism’s god and this 'Sin' thing are equal in all things yet able to conceal their next move from something all-knowing, but powerless to stop its rival? In other words, neither omniscient nor omnipotent.

The notion of intelligent design is quite simply incompatible with the evidence of arms races, for which evolution provides a ready answer.

I have devoted the whole of chapter 3 to arms races in nature in my popular, illustrated book, The Unintelligent Designer: Refuting The Intelligent Design Hoax, but what it doesn't include is this recently discovered arms race between plants and a parasitic fungus, Botrytis cinerea, or gray mold.

Malevolent Design - How A Cat Poo Parasite Can Change Your Personality

Toxoplasma gondii is an obligate intracellular, parasitic protozoan that causes the disease toxoplasmosis. Diagram of Toxoplasma structure.

Image Credit: Designua / Shutterstock

Toxoplasma 'cat poo' parasite infects billions – so why is it so hard to study?

In my last blogpost, I described how the parasitic organism, cryptosporidium, is one of those 'irreducibly complex' organisms that creationists have been fooled by Michael J Behe into believing are proof of their putative creator god, because, so their ignorant intuition tells them, there can only be one intelligent designer capable of designing an irreducibly complex structure such as the bacterial flagellum or the apical complex structure that all members of the Apicomplex phylum characteristically possess.

Sadly for them, though, their reliance on this 'proof' of their god precludes them from arguing that these nasty little pathogens that appear to be designed to make us and other animals sick is the work of another intelligent creator, 'Sin', so the inescapable conclusion must be that their beloved creator god is designing these pathogens to make us sick and to increase the suffering in the world.

As though that wasn't bad enough, we now have another related parasite, also a member of the Apicomplex phylum, that on the face of it, seems to be an even more determined attempt to make us sick. It's a parasite that once you have it, you have it for life, and the evidence is that it manipulates your behaviour and changes your personality too. This then raises doubts about the idea of free will that is a central part of creationist superstition, and notions of 'Original Sin' (that thing that can supposedly create parasites too).

This organism is Toxoplasma gondii which is carried by about 25% of the world's people, so the chance of you or me or any of your friends and family having it is quite high.

Malevolent Design - More Nastiness From The Pestilential Designer, Or God, As Creationists Call It

Infections from a diarrhoea-causing parasite are on the rise in the UK – but experts aren't quite sure why

Cryptosporidium is a eukaryote protozoan parasite which creationists dogma says must have been designed by their favourite designer because that is the only entity capable of designing complex organisms, including 'irreducibly complex' structures.

Embarrassingly for creationists who are hoping to be able to blame 'Sin' for them, they are hung out to dry on the same hook that Michael J. Behe hung them on with the flagellum of the pathological E. coli bacterium, which they now happily wave as 'proof' of their designer good. Protozoans of the Apicomplexa phylum, of which the cryptosporidia are species, all have the apical complex organelle which is essential for them to break into a cell in order to infect it.

The characteristic apical complex organelle of the Apicomplexa phylum

Cryptosporidia appear to have two functions: to increase the suffering in the world by causing gastrointestinal disorders, usually resulting in severe diarrhoea; and to make more copies of themselves to infect more people and animals and spread the suffering more widely. They have no known beneficial functions in respect of humans or their other host species.

The species Cryptosporidium hominis is an obligate parasite on humans, so, according to creationists superstition, must have infected one or two of the Ark survivors, assuming there were no more than two individuals of the species present. Either that, or, according to creationist mythology, it has been created in the last four thousand years, which rules out being created by 'Sin' as a result of 'The Fall', which would mean it predates creationism's genocidal flood.

First, some AI background by way of introduction to the subject: