Malevolent Desiger News - How Breast Cancer is 'Designed'

Malevolent Designer News

How Breast Cancer is 'Designed'

Image: thomasandreas/iStock/Getty Images Plus

How Breast Cancer Arises | Harvard Medical School

Bear in mind that Creationists believe all parts of the human body, indeed all parts of every living organism, were intelligently designed by an omniscience and omnipotent god. With omniscience comes inerrant foresight of the consequences of any particular design, so, whatever the design does, must be the intended outcome of the design, or else the designer is not omniscient and needs to wait to find out what its design does.

In that case it can't be described as omniscience, but still being intelligent, it should be capable of discarding a design that doesn't do what it wants and starting again. In other words, it should be capable of ensuring that anything it designs does exactly what it wanted it to do, and should do it efficiently, with minimal waste and with the minimal complexity.

In other words, omniscient or not, its designs should comply with the basic principles of intelligent design - minimal waste, minimal complexity and maximal fitness for a clear purpose and endurance over time.

Sadly, for creationists that's not what we see; instead, we see evidence of utilitarianism. Whatever conveys a short-term benefit in terms of producing more offspring that go on to reproduce, is retained, regardless of any long-term detriment, provided the short-term benefits outweigh the long-term detriments. However, the result is often suboptimal compared to what it would have been had there been no detrimental effects, or had the design been more efficient at what it does.

One of the pieces of evidence for utilitarian design is the replication of the entire genome in every cell in multicellular species, when only a small portion of it is needed in specialised cells, and a characteristic of multicellularity is cell specialisations. This ludicrously wasteful method of cell reproduction, retained because it was the method used in the ancestral single-celled species, has meant that a complex system of epigenetics is needed to turn off the unwanted genes and to ensure just the right genes are active when needed. It also requires another complex mechanism for detecting and repairing the frequent mistakes that replicating billions of base pairs of DNA inevitably produce, because the method of replication is far from perfectly designed.

For more about epigenetics and why it is needed, see The Unintelligent Designer: Refuting the Intelligent Design Hoax, pp. 109-115

The result is two of the hallmarks of bad design - prolific waste and unnecessary complexity. And now, as shown by this piece of research by Harvard Medical School scientists, harmful consequences. As though the risks of developing a cancer due to run-away replication of cells, as sometimes happens when cell replication goes wrong, the scientists have discovered that one of the types of one of the commonest cancers, breast cancer, is caused when the sex hormone, oestragen, needed for reproduction, enhances the probability of things going wrong and producing a cancer.

Traditionally, creationists faced with this sort of evidence against intelligent design, resort to religious mumbo-jumbo and start gibbering about 'The Fall' allowing 'sin' to enter the world, as though there is some other intelligence, empowered by 'sin' against which their supposedly omnipotent god is powerless, or this thing called 'sin' is itself capable of intelligently creating things. But what of these problems - the result of cell replication going wrong because of the sex hormone that in needed for reproduction in women, did their putative designer not design? Cell reproduction or sexual reproduction?

The research and its significance are explained in a Harvard Medical School press release by Ekaterina Pesheva:

Religion News - Californian Christians Demand the Right to Spread Hate and Disinformation

Religion News

Californian Christians Demand the Right to Spread Hate and Misinformation

Pro-Trump Christian extremists join the failed Coup on Jan 6, 2021

Christian Supporters of Donald Trump pray outside the U.S. Capitol January 06, 2021 in Washington, DC.

Win McNamee/Getty Images

Religious broadcasters seek to reverse California law aimed at quelling online hate speech

In a tacit acknowledgement that religions promulgate hate and division, and spread disinformation, The National Religious Broadcasters (NRB), an association of Christian media outlets, is joining a coalition opposing a Californian law that would require social media operators such as Facebook and Twitter to publish their policies for removing hate speech from their platforms.

In effect, NRB's president and chief executive officer, Troy Miller, is campaigning for the right of Christians to retain the special privileges of spreading hate and misinformation with impunity when he declared in a statement:

In an environment where much religious viewpoint expression is considered ‘controversial’ speech, NRB is acting to stop the weaponization of new laws against Christian communicators.

Catholic Child Abuse News - They're Still at it in San Francisco

Catholic Child Abuse News

They're Still at it in San Francisco

Salvatore Joseph Cordileone, Archbishop of San Francisco.
Refusing to release names of accused priests.

Why is San Francisco’s top Catholic shielding pedophile priests? | San Francisco News | sfexaminer.com

It's been a while since I wrote about the paedophile ring known as the Catholic Church, because the stories have become so commonplace that they had dropped out of the mainstream new.

Many people assume the much-vaunted reforms supposedly implemented by the Catholic Church at the behest of Pope Francis to protect potential abuse victims from their priests, have been successful and put a stop to the routine sexual abuse of minors by priests and nuns that had become the norm throughout the Catholic world.

However, not all senior Catholic clerics have signed up to these reforms. It seems that the instinct of some, such as Archbishop Salvatore Cordileone, of San Francisco, is to protect the paedohiles and facilitate their abuse of minors for recreational sex.

According to this report in the San Francisco Examiner:

Creationism in Crisis - Does Reality Really Exist? Science is Still Working On It.

Creationism in Crisis

Does Reality Really Exist? Science is Still Working On It.

Great Mysteries of Physics: does objective reality exist?

One of the more hilarious arguments against science that I have had levelled at me by a Creationist is that you can't prove reality exists, and yet the whole of science claims to be a description of reality and the scientific method is an examination of it based on materialist principles.

The conversation was ended abruptly with the traditional condescending insult when I pointed out that he was trying to persuade me that reality doesn't exist in order to justify his belief in a creator of it!

Whether or not reality exists as we see and experience it, or whether what we see is an optical illusion or an emergent product of the underlying structural chaos of spacetime is irrelevant to our everyday lives, or course. If you're shot to death by a gun, or hit and killed by a bus, you're just as dead, whether or not the gun or bus actually exists.

Creationism in Crisis - Evolution or Malevolent Design? More Zoonomia Headaches for Creationists

Creationism in Crisis

Evolution or Malevolent Design? More Zoonomia Headaches for Creationists

Image: istock

The Zoonomia Project

USC researcher uses mammal DNA to zoom into the human genome with unprecedented resolution | Keck School of Medicine of USC

The Zoonomia Consortium was formed in 2015 by a group of scientists from several institutions, including the University of California, Davis, the University of California, Berkeley, the University of California, Santa Cruz, and the Broad Institute of MIT and Harvard. The goal of the consortium was to develop a comprehensive database of animal genomes that could be used to study and compare the genetic basis of traits across different species.

In 2020, the Zoonomia Consortium published a paper in the journal Nature describing the results of their work. The paper, entitled "Zoonomia Consortium, A comparative genomics multitool for scientific discovery and conservation," provides an overview of the consortium's approach and the tools they developed.

The Zoonomia database includes genomic data from over 100 species of animals, including mammals, birds, reptiles, and fish. The database is freely available to researchers and includes a variety of tools for analyzing and comparing genomic data, such as genome browsers, alignment tools, and gene expression analysis tools.

The Zoonomia Consortium's work has significant implications for conservation biology, as it allows researchers to compare the genetic basis of traits across different species and identify genetic factors that may be important for species survival. For example, researchers could use the Zoonomia database to identify genes that are associated with disease resistance or tolerance to environmental stressors, which could inform conservation efforts.

Reference:

Lewin, H.A., Robinson, G.E., Kress, W.J. et al. Zoonomia Consortium, A comparative genomics multitool for scientific discovery and conservation. Nature 587, 240–245 (2020). https://doi.org/10.1038/s41586-020-2876-6

chatGPT3 "Tell me about the Zoonomia Consortium, with references." [Response to user question]
Retrieved from: https://chat.openai.com/

Yet more evidence of mammalian common origins and the lack of intelligence in design, or, if we assume design, then evidence of malevolence, has emerged from the Zonomia Consortium this week.

Researchers at the University of Southern California (USC) Keck School of Medicine have used their database of the genomes of 240 different mammal species, to work out why humans suffer from diseases despite being the end-point of millions of years of evolution that might have been expected to weed out predisposition to diseases.

It turns out that most of the genes that lead to diseases are in a group of highly conserved genes that are common to all mammals. These genes appear to be highly constrained in evolutionary terms, meaning that any mutations would have been seriously deleterious so making their carriers less successful in competition with carriers of the normal allele.

As the USC Keck School of Medicine news release explains:

“Why do humans have disease if they went through millions of years of evolution?” It’s a question Steven Gazal, PhD, assistant professor of population and public health sciences at the Keck School of Medicine of USC, hopes to answer.

Gazal is part of an international team of researchers who have become the first to precisely identify base pairs of the human genome that remained consistent over millions of years of mammalian evolution, and which play a crucial role in human disease. The findings were published in a special Zoonomia edition of Science.

Gazal and his team analyzed the genomes of 240 mammals, including humans, zooming in with unprecedented resolution to compare DNA. They were able to identify base pairs that were “constrained” – meaning they remained generally consistent – across mammal species over the course of evolution. Individuals born with mutations on these genes may not have been as successful within their species or were otherwise not likely to pass down the genetic variation. “We were able to identify where gene mutations are not tolerated in evolution, and we demonstrated that these mutations are significant when it comes to disease,” explains Gazal.

The team found that 3.3% of bases in the human genome are “significantly constrained,” including 57.6% of the coding bases that determine amino acid position, meaning these bases had unusually few variants across species in the dataset. The most constrained base pairs in mammals were over seven times more likely to be causal for human disease and complex trait, and over 11 times more likely when researchers looked at the most constrained base pairs in primates alone.

The dataset was provided by the Zoonomia consortium, which according to the project website, “is applying advances in DNA sequencing technologies to understand how genomes generate the tremendous wealth of animal diversity.” Gazal gives credit to Zoonomia for making this type of data available to researchers and anticipates it will be widely used by human geneticists. “It’s a cheap resource to generate, as opposed to datasets generated in human genetic studies,” says Gazal.

His team’s findings are a significant step forward, as Gazal notes, “we do not understand 99% of the human genome, so it is fundamental to understand which part has been constrained by evolution and is likely to have an impact on human phenotypes.” Their discoveries and methods could become crucial tools for further research.

The next step for Gazal and his team is to repeat the process with a primate-only dataset. By restricting the subjects, they hope to focus on functions of DNA that appeared more recently in human evolution. “We expect this to be even more useful in determining information on human disease,” says Gazal.

More detail is included in the structures abstract to the team's paper published in the special Zoonomia edition of Science:

Structured Abstract

INTRODUCTION

Thousands of genetic variants have been associated with human diseases and traits through genome-wide association studies (GWASs). Translating these discoveries into improved therapeutics requires discerning which variants among hundreds of candidates are causally related to disease risk. To date, only a handful of causal variants have been confirmed. Here, we leverage 100 million years of mammalian evolution to address this major challenge.

RATIONALE

We compared genomes from hundreds of mammals and identified bases with unusually few variants (evolutionarily constrained). Constraint is a measure of functional importance that is agnostic to cell type or developmental stage. It can be applied to investigate any heritable disease or trait and is complementary to resources using cell type– and time point–specific functional assays like Encyclopedia of DNA Elements (ENCODE) and Genotype-Tissue Expression (GTEx).

RESULTS

Using constraint calculated across placental mammals, 3.3% of bases in the human genome are significantly constrained, including 57.6% of coding bases. Most constrained bases (80.7%) are noncoding. Common variants (allele frequency ≥ 5%) and low-frequency variants (0.5% ≤ allele frequency < 5%) are depleted for constrained bases (1.85 versus 3.26% expected by chance, P < 2.2 × 10−308). Pathogenic ClinVar variants are more constrained than benign variants (P < 2.2 × 10−16). The most constrained common variants are more enriched for disease single-nucleotide polymorphism (SNP)–heritability in 63 independent GWASs. The enrichment of SNP-heritability in constrained regions is greater (7.8-fold) than previously reported in mammals and is even higher in primates (11.1-fold). It exceeds the enrichment of SNP-heritability in nonsynonymous coding variants (7.2-fold) and fine-mapped expression quantitative trait loci (eQTL)–SNPs (4.8-fold). The enrichment peaks near constrained bases, with a log-linear decrease of SNP-heritability enrichment as a function of the distance to a constrained base.

Zoonomia constraint scores improve functionally informed fine-mapping. Variants at sites constrained in mammals and primates have greater posterior inclusion probabilities and higher per-SNP contributions. In addition, using both constraint and functional annotations improves polygenic risk score accuracy across a range of traits. Finally, incorporating constraint information into the analysis of noncoding somatic variants in medulloblastomas identifies new candidate driver genes.

CONCLUSION

Genome-wide measures of evolutionary constraint can help discern which variants are functionally important. This information may accelerate the translation of genomic discoveries into the biological, clinical, and therapeutic knowledge that is required to understand and treat human disease.

Using evolutionary constraint in genomic studies of human diseases.
(A) Constraint was calculated across 240 mammal species, including 43 primates (teal line). (B) Pathogenic ClinVar variants (N = 73,885) are more constrained across mammals than benign variants (N = 231,642; P < 2.2 × 10−16). (C) More-constrained bases are more enriched for trait-associated variants (63 GWASs). (D) Enrichment of heritability is higher in constrained regions than in functional annotations (left), even in a joint model with 106 annotations (right). (E) Fine-mapping (PolyFun) using a model that includes constraint scores identifies an experimentally validated association at rs1421085. Error bars represent 95% confidence intervals. BMI, body mass index; LF, low frequency; PIP, posterior inclusion probability.

Abstract

Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.

Patrick F. Sullivan et al.,
Leveraging base-pair mammalian constraint to understand genetic variation and human disease.
Science 380, eabn2937 (2023). DOI:10.1126/science.abn2937

© 2023 The Authors. Published by American Association for the Advancement of Science.
Reprinted with kind permission under license #5553150959442

The significant points, that creationist will avoid like the plague, are:

• The evidence of common ancestry of the mammals in the study.
• The lack of any evidence that the scientists were rejecting the TOE as an explanation for the observed facts.
• The inevitable conclusion that if a magic designer designed genes to cause diseases, then the designer can only be described as malevolent; it this was an accident, then incompetence is the only explanation.
• Even if, as 'theistic evolutionists' argue, an invisible supernatural deity was guiding human evolution, it was either incompetent, or malevolent, in allowing genes that caused diseases to be conserved in the evolving human genome.

But those who want to feel important, as the conscious creation of a mighty god who made everything just for them, are hardly likely to allow little considerations like those to make them feel they might be less important than they want to feel.

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Creationism in Crisis - How a 'Macro-Evolutionary' Change can be Produced by Changes to a Few Genes

Creationism in Crisis

How a 'Macro-Evolutionary' Change can be Produced by Changes to a Few Genes.

A transient change in expression of one gene (Shh) can produce a cascade of developmental events leading to the formation of feathers instead of scales

© UNIGE / Cooper & Milinkovitch

Sablepoot bantams

Scales or feathers? It all comes down to a few genes - Medias - UNIGE

Lurk a while in any Evolution vs Creationism group in the social media and you can guarantee a creationist will try to argue that a given example of evolution which they have probably just deamnded be provided, and which conforms to the scientific definition of evolution - any change in allele frequency over time - is not real evolution because it wasn't 'macro-evolution' which they will define as a change in 'kind' or the evolution of a new species, even the evolution of new structures - whichever definition they think stands the best chance of winning.

I've been at this for long enough to remember how, when the early internet 'bulletin boards' on CompuServe had morphed into thriving debate 'forums', creationists would simply argue that there was no such thing as evolution, full stop! It simply never happened; not in the slightest. No Way! Everything was created exactly as it is today during 'Creation Week' a few thousand years ago! Any evidence to the contrary was a forgery by evil scientists or had been planted by Satan.

Then, in the face of so much evidence, particularly the very large number of living and extinct species and the impossibility of them all being collected together in a few days, herded onto a wooden boat and surviving for a year, they began to concede that there had indeed been evolution, but only limited to evolution withing species, and evolution moreover at a phenomenal rate, far exceeding anthing proposed by biologists, so as to produce the millions of species from a few 'kinds' that survived the genocidal flood their putative creator had inflicted on its creation, just a few thousand years ago.

What creationists are doing is moving the goal-posts by redefining a well-understood scientific term to place it beyond what science actually claims, so they can demand evidence of something that no evolutionary biologist ever claimed - that a single mutation produced a new species or that one species gave birth to another in a single event, ignoring the fact that evolutionary biologists understand the evolution is normally a slow process which takes place in the species gene pool, with the instances of new species arising by, for example, hybridization, being rare exceptions, but nevertheless, natural processes, not requiring supernatural entities to explain.

So, ask a creationist now wedded to the notion that real evolution needs to be 'macro-evolution' to define a reptile 'kind' and a bird 'kind' and they will normally define a reptile 'kind' as having scales and a bird 'kind' as having feathers, ignoring the fact that paleontologists have discovered several feathered dinosaurs (reptiles).

Now, present a creationist with an example such as the one in this research paper, where changes to a small number of genes resulted in what they would define as 'macro-evolution', i.e., a change in 'kind' because that change in chickens results in them growing feathers where they normally grow scales, showing the feathers are simply evolved scales.

Evolution in Action - Giant Spiders Spreading Across Southern USA

Slideshow code developed in collaboration with ChatGPT3 at https://chat.openai.com/

The Jorō spider, Trichonephila clavata

Joro spiders aren’t scary. They’re shy.

A rather beautiful large spider is rapidly spreading across the southern USA, aided by a couple of attributes that enable it to adapt to human habitation, in a stunning example of how the environment can select for species fitted to live and thrive in it. A related species, T. clavipes, has already established itself in southern USA.

The spider, Trichonephila clavata, is a very large, but harmless (to humans), Jorō spider, the subject of a recent research paper in the journal Arthropoda. The research, carried out by researchers, by Andrew K. Davis and Amitesh V. Anerao of Odum School of Ecology, University of Georgia, Athens, GA, USA.

The study shows that, in a classic example of how particular traits can enable a species to extend its range, T. clavata is good at living alongside humans. Rather than being aggressive, which most people would assume is the reason it is out-competing native American spiders, T. clavate is particularly shy and non-aggressive. Despite their size and warning colouration, they are harmless to humans and pets. They will only attempt to bite if picked up and trapped and even then, their fangs aren't large enough to pierce human skin.

Interestingly, their avoidance strategy is to remain completely motionless for about an hour when disturbed, unlike most spiders which normally resume activity after few minutes, leading the researchers to classify them as 'shy' rather than aggressive.

The research is explained in a University of Georgia press release:

New study suggests the massive spiders are gentle giants, mean people no harm

One of the ways that people think this spider could be affecting other species is that it’s aggressive and out-competing all the other native spiders, so we wanted to get to know the personality of these spiders and see if they’re capable of being that aggressive. It turns out they’re not.

They basically shut down and wait for the disturbance to go away. Our paper shows that these spiders are really more afraid of you than the reverse.

One thing this paper tells me is that the Joros’ rapid spread must be because of their incredible reproductive potential,” Davis said. “They’re simply outbreeding everybody else. It’s not because they’re displacing native spiders or kicking them out of their own webs.

Dr. Andrew Davis, lead author Odum School of Ecology, University of Georgia, Athens, GA, USA.

Despite their intimidating appearance, the giant yellow and blue-black spiders spreading across the Southeastern U.S. owe their survival to a surprising trait: They’re rather timid.

According to a new study from the University of Georgia, the Jorō (Joro) spider may be the shyest spider ever documented.

The researchers compared more than 450 spiders’ responses to a brief and harmless disturbance across 10 different species.

While most spiders froze for less than a minute before resuming their normal activities, the Joro spiders remained motionless for more than an hour.

In fact, Joros are relatively harmless to people and pets. Joros won’t bite unless cornered. And even if you did manage to somehow annoy a Joro into biting you, its fangs likely wouldn’t be large enough to pierce your skin.

A female Joro spider spins its web. The 30mm scale bar is included for size reference.

Credit: Jeremy Howell

Most spiders begin moving quickly after stress, Joros remain immobile for 60-plus minutes

To examine the spiders’ reaction to stress, the researchers used a turkey baster to gently blow two rapid puffs of air onto individual spiders. This minor disturbance causes the spiders to “freeze” for a period of time, going absolutely still.

The researchers tested more than 30 garden spiders, banded garden spiders and marbled orb weavers. They also analyzed similar data from previously published, peer-reviewed papers that assessed the response of 389 more spiders, comprising five additional species.

All of those spiders began moving again after an average of about a minute and half of stillness.

The Joros, however, stayed frozen with no body or leg movement for over an hour in most cases.

The only other spider species that exhibited a similarly extended response was the Joro spider’s cousin, the golden silk spider. Known as Trichonephila clavipes, the golden silk spider and the Joro spider are from the same genus.

A Joro spider feasts on a caterpillar.

Joros may be invasive, but they’re not aggressive

Most people think ‘invasive’ and ‘aggressive’ are synonymous. People were freaking out about the Joro spiders at first, but maybe this paper can help calm people down.

They’re so good at living with humans that they’re probably not going away anytime soon.

Amitesh Anerao, co-author of the study,
Undergraduate researcher, Georgia University, Athens, GA, USA

Officially known as Trichonephila clavata, the East Asian Joro spider first arrived in Georgia around 2013. The species is native to Japan, Korea, Taiwan and China, and likely hitched a ride stateside on a shipping container.

The species has since rapidly spread across the state and much of the Southeast. Joro spiders easily number in the millions now. And there’s not much we can do to stop them from increasing their range.

Davis’ previous research even suggested the invasive arachnids could spread beyond their current habitats and through most of the Eastern Seaboard.

Sunlight streams through the elaborate webs made by Joro spiders

Joro spiders built to withstand human activity

Joros are regularly spotted in areas native Georgia spiders don’t typically inhabit.

They build their golden webs between powerlines, on top of stoplights and even above the pumps at local gas stations—none of which are particularly peaceful spots.

The researchers believe the Joro spiders’ shyness may help them better endure the barrage of noise, vibrations and visual stimuli they consistently encounter in urban settings. Their prolonged freeze response to being startled could help conserve the Joro spiders’ energy.

If you’re wondering how something so mild-mannered could spread the way Joro spiders have, you aren’t the only one.

Arachnophobes can take solace in the Joro spiders’ meek and gentle temperament. But the spiders are likely here to stay.

Figure 2. Behavioral responses of spiders to a mild disturbance stimulus (air puff), from our tests, plus from data presented in published studies (see Table 1). Shown are the mean durations of time spent in a “thanatosis” state after receiving the stimulus.

Davis AK, Anerao AV. (2023)

Copyright: © 2023 The authors.
Published by MDPI (Basel, Switzerland). Open access. (CC BY 4.0)

The researcher’s paper is available, open access, in the journal,Arthropoda:

Abstract

The jorō spider (Trichonephila clavata, originally from east Asia) has been introduced in the southeastern United States, and is rapidly expanding this range, leading to questions about what facilitates this spread. Meanwhile, its cousin, the golden silk spider (T. clavipes), already has a range that covers most of the southeast. In an ongoing effort to understand the behavior of jorō spiders in their introduced range, we undertook the current project to evaluate how they react to perceived threats, which can inform us on how a species interacts with conspecifics, or how well it can tolerate anthropogenic disturbances. We collected mature females of both Trichonephila species, plus three locally common orb-weaving species in Georgia, and we evaluated the time spent immobile after experiencing a mild disturbance (a brief puff of air). We also collected similar “air puff response” data for five other North American species from the published literature. Collectively, the dataset totaled 453 observations of freezing behavior across 10 spider species. Comparing these data across species revealed that most spiders remained immobile for under a minute after the stimulus. Meanwhile, both Trichonephila spiders remained immobile for over an hour, which appears to be unprecedented, and suggests that spiders in this genus are the “shyest” ever documented. This reaction could also allow Trichonephila spiders to tolerate urban environments by remaining motionless throughout each disturbance instead of fleeing.

Davis AK, Anerao AV.
Startle Responses of Jorō Spiders (Trichonephila clavata) to Artificial Disturbance.
Arthropoda. 2023; 1(2):60-67. https://doi.org/10.3390/arthropoda1020009

Copyright: © 2023 The authors.
Published by MDPI (Basel, Switzerland). Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

A classic study showing how traits can facilitate the spread of a species into new territories provided the local environment provides the right selectors, if not, of course, introduction won't succeed. And once again confirming the relationship between a species and its environment and how the latter selects for traits which produce more copies than other alleles.

All perfectly understandable in terms of natural processes, with not a hint that supernatural magic had to be involved at some point.

And yet creationism is still managing to recruit new scientifically illiterate fools into the cult, despite all its counter-factual claims and readily available evidence refuting them.

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Unintelligent Design - Why Evolution is not an Intelligent Design Process

Unintelligent Design

Why Evolution is not an Intelligent Design Process

The Unintelligent Designer:
Refuting the Intelligent Design Hoax

Perfection: The Enemy of Evolution | Duke Pratt School of Engineering

In my book, The Unintelligent Designer: Refuting the Intelligent Design Hoax, I pointed out that evolution differs from intelligent design in three major ways:

1. Prolific waste. Clever design is economical to make and use.
2. Unnecessary complexity. Clever design is minimally complex.
3. Lack of a clear purpose beyond producing more copies of itself.

The first two of these stems directly from the fact that evolution is utilitarian - whatever is better than that which went before it will be retained. 'Better' in this context means whatever produces more offspring that survive to reproduce.

The analogy is shooting arrows at a target and going with whatever method gets you closest to the bullseye, instead of discarding anything that doesn't hit the bullseye dead center. Only evolution doesn't even have a bullseye to aim at because there is no direction or required outcome.

But not so of a design process, of course, even a design process based on trial and error, because an intelligent design process will have a bullseye to aim at, and a preconceived idea of the ideal or optimal solution to the problem the design is intended to solve.

Creationism's putative divine designer, whom most creationists equate to the god of the Bible, Torah and Qur'an, being reputedly both omniscient and omnipotent, would not need trial and error, and would hit the bullseye, dead centre every time, so anything designed by it would never be sub-optimal, inefficient, or utilitarian. To a perfect designer, near enough is never good enough.
One of the many examples of unintelligent design I cited in my book is that of the enzyme known as RuBisCo (Ribulose-1,5-bisphosphate carboxylase/oxygenase), an essential component in photosynthesis. RuBisCo is so sub-optimal that it is the reason there is so much greenery around - plants need tons of the stuff to make enough sugar. Instead of the thousands of reactions per second that most protein enzymes are capable of, RuBisCo manages about four per second and frequently 'mistakes' a molecule of oxygen for a molecule of carbon dioxide, producing a toxic byproduct, wrecking the process, and costing the plant considerable lost energy and slowing the entire process down even further. But, because evolution can only work with what it already has, plants, and everything dependent on plants (i.e., almost all living things on Earth) are stuck with RuBisCo - probably the most abundant organic molecule on Earth and taking an appreciable proportion of the energy it produces in the form of glucose, to make.

Now, in an interesting paper published in the journal Biosystems, Adrian Bejan, the J.A. Jones Distinguished Professor of Mechanical Engineering at Duke University, Duke University, Durham, NC, USA, explains why a 'genetic algorithm', in other words, copying the evolutionary process, may be a better approach than the traditional aiming for perfection approach. A slightly less than perfect solution to a problem is easier to achieve and allows the design process to build on that solution and move on to the next step.

In it, Professor Bejan argues that chasing perfection is a constraint on design while accepting suboptimal solutions frees up more opportunities to explore possible improvements - just like the iterative process of evolution does.

Creationism in Crisis - Not a Single Founder Couple, Not Even a Single Founder African Species

Slideshow code developed in collaboration with ChatGPT3 at https://chat.openai.com/

View of the village of Kuboes, on the border of South Africa and Namibia. DNA samples were collected from Nama individuals who have historically lived in the region.

New UC Davis Research Using DNA Changes Origin of Human Species, Researchers Suggest | UC Davis

New research confirms what had long been suspected - that early Homo sapiens interbreeding with Neanderthals and Denisovans in Eurasia was not the only place and time that hominins had interbred with other related species.

The research co-led by Professor Brennan Henn, professor of anthropology and the Genome Center at the University of California Davis and Simon Gravel of McGill University, has now shown that early hominins interbreed with other hominins in Africa before spreading to Eurasia and then to the rest of the world, so the world population of H. sapiens does not have a single ancestor but is the result of hybridization and remixing of diverged populations.

As the UC Davis news release explains:

Artificial Intelligence - How Appearances can be Deceptive if we Think Like Creationists

Artificial Intelligence

How Appearances can be Deceptive if we Think Like Creationists>

According to a McKinsey report, depending on the adoption scenario, automation will displace between 400 and 800 million jobs by 2030, requiring up to 375 million people to change job categories entirely.

Evolution is making us treat AI like a human, and we need to kick the habit

Readers may have noticed how I've been using the AI chatGPT3 engine recently. I find it incredibly useful for quickly generating information about a topic. The one drawback seems to be that its references don't always check out and it's sometimes impossible to find the paper of book referenced, even. This seems to be a major deficit in its training.

I found it invaluable in developing the coding needed to run the slideshows I'm now frequently including in these posts, although I often needed to remind it of the objective because its solutions were overly complex and sometimes didn't work as I wanted. It also tends to misunderstand the specification and solve a problem that doesn't exist.

But, as the following article by Neil Saunders, Senior Lecturer in Mathematics at the University of Greenwich, points out, there is a natural tendency to treat it like a real human being. I have to admit, I often say please and thank you, and sometimes hesitate before asking it yet again for help, half expecting it to become impatient. This is, of course, a mistake as an algorithm doesn't have emotions and isn't even conscious of its own existence, let alone being 'human' in its interactions with us. It simply responds to our input by pattern-matching and generating output in intelligible English.

And this is what makes it so human; it talks to us like a very polite and infinitely patient human being would. This tendency to assume agency is deeply embedded in our evolved psychology in the form of teleological thinking and explain why credulous creationists assume whatever they don't understand or what isn't immediately obvious, must be the work of an agency of some sort. I have even had creationists argue that atoms can't combine with other atoms, or photons don't know where to go, unless directed to do so by a sentient being - which of course assumes that atoms and elementary particles are sentient and can obey instructions too. Teleological thinking is the basic notion behind 'intelligent design' and arguments from design, such as the refuted Palley's Watch analogy.

It is a simple step then to assume that the 'designer' or directing agent must be the locally popular god, despite the fact that there is no definitive evidence that any god(s) exists or mechanism that could explain the origins of any. The argument is childishly circular - there must be a designer because things look designed; the designer must be God because only God can design things; the 'fact' of design proves the existence of a designer - And of course mummy and daddy believe in the only true god.
But there are dangers in using AI combined with teleological thinking and ignorant credulity because people who think teleologically can be manipulated and those who believe absurdities can be persuaded to commit atrocities.

Here then is what Neil Saunders has to say on the subject. His article is reprinted from The Conversation under a Creative Commons Licence, reformatted for stylistics consistency:

Creationism in Crisis - Researchers Have Worked Out How Butterflies Evolved

Slideshow code developed in collaboration with ChatGPT3 at https://chat.openai.com/

Blue morpho butterfly, Morpho peleides

Kristen Grace/Florida Museum

Butterfly tree of life reveals an origin in North America – Research News

Butterflies first began to diverge from moths about 100 million years ago. It had been assumed that this was to avoid nocturnal bats by flying during the day, but a group of geneticists led by Akito Y. Kawahara, of the McGuire Center for Lepidoptera and Biodiversity in the Florida Museum of Natural History, FL, USA, have now shown that a diurnal existence was made possible by the evolving relationship between flowering plants and bees, which provided an energy-rich source of nectar.

By analysising the DNA from more than 2,000 species representing all butterfly families and 92% of genera, the world-wide team of scientists have traced the movements and feeding habits of butterflies through time in a four-dimensional puzzle that led back to North and Central America. Their results were published, open access, a couple of days ago, in the journal Nature, Ecology & Evolution.

As the Florida Museum news release explains:

Creationism in Crisis - Researchers Observe Multicellularity Evolving in Only 3,000 Generations

Creationism in Crisis

Researchers Observe Multicellularity Evolving in Only 3,000 Generations

Macroscopic snowflake yeast with elongated cells fracture into modules, retaining the same underlying branched growth form of their microscopic ancestor.

A Journey to the Origins of Multicellular Life: Long-Term Experimental Evolution in the Lab | Research

Creationist frauds will often be seen recruiting new fools for their cult by feeding them disinformation about biology and what science, particularly, evolutionary biology supposedly can't explain.

The fact that bearing false witness, in this case against science, is forbidden in the Bible they purport to be defending and by the god they claim wrote it, betrays the fact that their objective if not to promote and defend the Christian religion but to recruit members for a money-making/political cult in order to manipulate and exploit them.

Some of the more infantile creationists may be trying to swell their ranks in the childish belief that the more people they can trick into believing their superstition, the more right it becomes. Those nagging self-doubts are such an existential threat to creationists that cognitive dissonance can give rise to absurd thinking.

One of the false claims you will often see being made is that biologists can't exolain how multicellularity evolved.

That claim can now be easily refuted by reference to an ongoing experiment in a aboratory in Georgia Tech, in which researchers have observed a single-celled yeast evolve into a multi-cellular organism in just 3,000 generations. The researchers have reported their findings in Nature.

In fact, this is only the latest in several lines of research about which creationists will have remained stoically ignorant:

Creationism in Crisis - How a Single-Celled Phytoplankton Evolved

Slideshow code developed in collaboration with ChatGPT3 at https://chat.openai.com/

Like ancient mariners, ancestors of Prochlorococcus microbes rode out to sea on exoskeleton particles | MIT News | Massachusetts Institute of Technology

New research suggests the Prochlorococcus microbe’s ancient coastal ancestors colonized the ocean by rafting out on chitin particles.

Image: Jose-Luis Olivares/MIT

The thing about the Theory of Evolution (TOE), is that it is the basic framework in biology for finding answers to questions.

For example, it was not obvious how an abundant member of the oceanic phytoplankton, Prochlorococcus came to exist as a free-living organism, when they probably started out as organisms that lived close to the shore as biofilms on the seabed.

Prochlorococcus, a prokaryote picocyanobacterium, is the most abundant of the billions of organisms that make up what has been described as a floating forest that soaks up almost as much CO₂ as the world's terrestrial forests and pumps out almost as much oxygen.

It is also the base of the food chain in the oceans.

Prochlorococcus marinus

Creationism in Crisis - Chimpanzee Vocalization Shows Common Ancestry With Humans

Slideshow code developed in collaboration with ChatGPT3 at https://chat.openai.com/

Chimpanzees form complex vocalisations

© Adrian Soldati

Chimpanzees Combine Calls to Communicate New Meaning | UZH News

Creationists insist that humans were specially created separate from the other mammals as a special type of 'life’ and point to unique characteristics as evidence of this claim, not realising that having unique characteristics is what defines any given species. Elephants, for example, could claim to be a special form of life because they have unique characteristics that distinguish them from, say, giraffes or hyenas.

A unique characteristic of humans often cited by creationists is language - in other words, our ability to combine simple sounds into complex words and words into meaningful sentences. So, it will come as something of a shock to creationists to learn that this ability is not a uniquely human ability and that chimpanzees also have that ability, so it was very probably an ability of the last common ancestor of human and chimpanzees that lives some 6 million years ago.

The discovery was made by a team of researchers led by Maël Leroux of the Department of Comparative Language Science, University of Zürich, Zürich, Switzerland, and including researchers from Utrecht University, Utrecht, Netherlands, the Budongo Conservation Field Station, Masindi, Uganda, the Center for the Interdisciplinary Study of Language Evolution (ISLE), University of Zürich, Zürich, Switzerland, and the Department of Psychology, University of York, York, UK.

Their findings were published open access a few days ago in the journal Nature Communications.

The University of Zurich news release, explains the research and its significance:

Creationism in Crisis - Rhino Retroviruses Provide Evidence of Evolution

Slideshow code developed in collaboration with ChatGPT3 at https://chat.openai.com/

Female black rhinoceros, Diceros bicornis bicornis.

Wikipedia
User: Bernard DUPONT

African rhinos share retroviruses not found in Asian rhinos or other related species - Leibniz Institute for Zoo and Wildlife Research

Endogenous retroviruses have long been a bugbear for creationists in that they show convincing evidence of evolutionary phylogeny and common ancestry, so this paper which reveals the recent entry into the genome of the African rhinoceroses but not the Asian rhinoceroses, shows that the African rhinos share a common ancestor more recently than they share a common ancestor with the Asian species. That African ancestor became infected after it split from the common ancestor of the African and Asian rhinos.
The research team was led by Alex D. Greenwood of the Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany.

First, a little about ERV's:

Endogenous retroviruses (ERVs) Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections that have become permanently integrated into the genome of the host organism. They are found in the genomes of most vertebrates, including humans. ERVs are considered "endogenous" because they are passed from generation to generation and are inherited in a Mendelian fashion, just like other genes. The life cycle of a retrovirus involves the reverse transcription of its RNA genome into DNA, which is then integrated into the host genome. Occasionally, retroviruses infect germ cells (cells that give rise to eggs or sperm) and their DNA is inserted into the genome of the offspring. Over time, these integrated viral sequences can become fixed in the population and passed on to future generations.

ERVs provide evidence for evolution in several ways:

1. Shared ERVs among species: ERVs are found in the genomes of different species, and the presence of the same ERV at the same genomic location in different species suggests a common ancestor. For example, scientists have identified a specific retroviral sequence called "HERV-K" that is present in the genomes of humans, chimpanzees, and other primates. The shared presence of this ERV provides strong evidence for a common evolutionary history.
2. ERV distribution and phylogenetic relationships: The distribution of ERVs across different species can be used to construct phylogenetic trees, which illustrate the evolutionary relationships between species. By comparing the presence or absence of specific ERVs in different genomes, scientists can infer the evolutionary history and relatedness of species. This approach has been used to study the evolutionary relationships between primates and other mammals.
3. ERVs as "molecular fossils": ERVs can act as "molecular fossils" that provide insights into ancient viral infections and evolutionary events. By studying the DNA sequences of ERVs, scientists can gain information about the timing of viral integration events and the evolutionary relationships between different ERVs. This information helps reconstruct the evolutionary history of the host species.
4. Functional remnants of ERVs: Although most ERVs have accumulated mutations over time and lost their ability to produce functional viral particles, some ERVs retain functional elements. These functional remnants can have important roles in the regulation of gene expression and embryonic development. For example, certain ERVs have been co-opted by the host organism to play a role in placenta formation in mammals. This co-option of ERV sequences for new functions illustrates the process of exaptation, where existing genetic material is repurposed for novel functions during evolution.

References:

1. Mager, D. L., & Stoye, J. P. (2015). Mammalian endogenous retroviruses. Microbiology spectrum, 3(1), MDNA3-0009-2014. doi: 10.1128/microbiolspec.MDNA3-0009-2014
2. Griffiths, D. J. (2001). Endogenous retroviruses in the human genome sequence. Genome biology, 2(6), reviews1017.1. doi: 10.1186/gb-2001-2-6-reviews1017

chatGPT3, "Tell me all about endogenous retroviruses (ERV's), how they enter the genome and why they are evidence for evolution, with references, please. [Response to user question]
Retrieved from https://chat.openai.com

The press release from the Leibniz Institute for Zoo and Wildlife Research explains the research and its significance:

Rhinoceros belong to a mammalian order called odd-toed ungulates that also include horses and tapirs. They are found in Africa and Asia. Until recently, evidence suggested that throughout their evolutionary history, gammaretroviruses such as Murine leukemia virus had not colonised their genomes, unlike most other mammalian orders. The colonisation process is called retroviral endogenisation and has resulted in most mammalian genomes being comprised of up to ten percent retroviral like sequences. An analysis of modern and extinct rhino genomes headed by the German Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW) now found that African rhinos have dozens of gammaretroviruses in their genomes absent from the genomes of Asian rhino species, such as the Sumatran and Javan rhino, and that the African black rhino has two related groups, one missing from the white rhinos. The restriction of gammaretroviruses to African rhinos and the close relatedness of the viruses to rodent viruses, particularly those of African rodents, suggests that African rhinos were infected by an exogenous viral variant and their genomes colonised in Africa. The work is published in the scientific “Journal of Virology”.

We had data from several rhino species where we kept finding large portions of gammaretroviruses. When we used much newer and more complete reference genomes from modern and extinct rhinos we found that only African rhinos had been colonised

Dr Kyriakos Tsangaras, lead author
Department of Life and Health Sciences
University of Nicosia, Nicosia, Cyprus

This ultimately comes down to lack of high-quality reference sequences of wildlife. While things have improved a lot since the first human genome was sequenced, you miss things such as viral history when the databases lack so many species or high-quality reference genomes from many species. It is really another example of why we need more genome reference sequences from wildlife because we don’t know what other things we are missing and which conclusions we draw about presence and absence of sequences that may turn out to be a consequence of too little information.

Professor Alex Greenwood, Senior author
Head of the Wildlife Disease Department. Leibniz Institute for Zoo and Wildlife Research
Berlin, Germany

Retroviruses such as the causal agent of aids, HIV-1, are unique among viruses in that they have to integrate into the DNA of the host as part of their replication cycle. If this happens in the germline in spermatocytes or oocytes, they can become a part of the host genome that is inherited by the following generation and then are present in every cell of offspring bodies. This evolutionary process has happened so often that on average up to ten per cent of the mammalian genome is made up of retroviruses or their remnants. A previous study of available genomes from horses and their relatives suggested that they, along with rhinos and tapirs, had not been invaded by gammaretroviruses, a group of viruses related to mouse and bird viruses that have successfully colonised most mammalian genomes.

Together with colleagues from Australia and Germany the scientific team found that in fact two different viral groups had colonised African rhinos. One of them had only colonised the black rhino (Diceros bicornis) and not the white rhino (Ceratotherium simum) and was evolutionarily younger than the one shared by both. As both groups are restricted to African rhinos the study suggests that the African rhino lineage was infected and their genomes colonised in Africa, and that is why the respective gammaretroviruses are not found in Asian rhinoceros and other rhino relatives.

More detail is given in the team's paper in the Journal of Virology, which sadly lies behind a paywall. However, the abstract is freely available:

ABSTRACT

High-throughput sequences were generated from DNA and cDNA from four Southern white rhinoceros (Ceratotherium simum simum) located in the Taronga Western Plain Zoo in Australia. Virome analysis identified reads that were similar to Mus caroli endogenous gammaretrovirus (McERV). Previous analysis of perissodactyl genomes did not recover gammaretroviruses. Our analysis, including the screening of the updated white rhinoceros (Ceratotherium simum) and black rhinoceros (Diceros bicornis) draft genomes identified high-copy orthologous gammaretroviral ERVs. Screening of Asian rhinoceros, extinct rhinoceros, domestic horse, and tapir genomes did not identify related gammaretroviral sequences in these species. The newly identified proviral sequences were designated SimumERV and DicerosERV for the white and black rhinoceros retroviruses, respectively. Two long terminal repeat (LTR) variants (LTR-A and LTR-B) were identified in the black rhinoceros, with different copy numbers associated with each (n = 101 and 373, respectively). Only the LTR-A lineage (n = 467) was found in the white rhinoceros. The African and Asian rhinoceros lineages diverged approximately 16 million years ago. Divergence age estimation of the identified proviruses suggests that the exogenous retroviral ancestor of the African rhinoceros ERVs colonized their genomes within the last 8 million years, a result consistent with the absence of these gammaretroviruses from Asian rhinoceros and other perissodactyls. The black rhinoceros germ line was colonized by two lineages of closely related retroviruses and white rhinoceros by one. Phylogenetic analysis indicates a close evolutionary relationship with ERVs of rodents including sympatric African rats, suggesting a possible African origin of the identified rhinoceros gammaretroviruses.

IMPORTANCE:Rhinoceros genomes were thought to be devoid of gammaretroviruses, as has been determined for other perissodactyls (horses, tapirs, and rhinoceros). While this may be true of most rhinoceros, the African white and black rhinoceros genomes have been colonized by evolutionarily young gammaretroviruses (SimumERV and DicerosERV for the white and black rhinoceros, respectively). These high-copy endogenous retroviruses (ERVs) may have expanded in multiple waves. The closest relative of SimumERV and DicerosERV is found in rodents, including African endemic species. Restriction of the ERVs to African rhinoceros suggests an African origin for the rhinoceros gammaretroviruses.

Tsangaras K, Mayer J, Mirza O, Dayaram A, Higgins DP, Bryant B, Campbell-Ward M, Sangster C, Casteriano A, Höper D, Beer M, Greenwood AD (2023)
Evolutionarily young African rhinoceros gammaretroviruses.
J VIROL 97, e0193222. https://doi.org/10.1128/jvi.01932-22.

© 2023 American Society for Microbiology.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

To any normal person, evidence like this would confirm evolutionary divergence, firstly between the African and Asian rhinoceroses, then, later between the African rhinoceroses.

It would also show that the scientists are in no doubt that evolution is the fundamental explanation for their findings, with no hint that they believe magic and supernatural magicians were involved, like creationist frauds fool their dupes into believing they increasingly are. Indeed, why would they? What rational, educated adult, with a mental age greater than about 9, believes in magic or supernatural magicians and thinks they should play any part in scientific explanations of real-world evidence?