Unintelligent Design - How Creationism's Heath-Robinson Designer Muddles Through But Still Messes Up.

spB^d-II complex at average resolutions of 3.2 and 3.1 Å.

Quality control during splicing: When an error in the precursor mRNA is detected, the spliceosome is blocked, the recruited control factors interrupt the “normal” cycle, and a molecular short circuit causes the spliceosome to disassemble.

© K. Wild, K. Soni, I. Sinning.

Spliceosome: How Cells Avoid Errors When Manufacturing mRNA

Q. How can you tell when something is designed by a supreme intelligence with the inerrant ability of foresight?

A. It works perfectly, without errors and does exactly what it was intended to do, nothing more and nothing less.

Q. How can you tell when something is 'designed' by a natural, utilitarian process like evolution by natural selection?

A. It works most of the time, even if not very efficiently, is over-complex and so prone to errors and doesn't anticipate change. It also frequently requires additional layers of complexity to compensate for its errors and inefficiency.

Sadly for intelligent design advocates, structures and processes found in nature are almost never perfect and free from errors and, when examined closely, are seen to be error-prone, suboptimal and requiring additional complexity to compensate for the errors and inefficiencies. And these error-correction mechanisms are themselves error-prone and prone to failure.

One such mechanism, the details of which have just been worked out by researchers at the Heidelberg University Biochemistry Center (BZH) in collaboration with colleagues from the Australian National University, is the system of spliceosomes found in eukaryote cells, that correct the errors in messenger RNA (mRNA) before they are transcribed into functional proteins.

The reason these large nuclear proteins are required is because the DNA the mRNA is transcribed from is contains 'introns' - small sequences that are not part of the gene being coded for. Imagine a computer database of words, which, when a retrieved, inserts random letters in the middle of the word.

Refuting Creationism - 183-Million-Year-Old Fossilised Soft Tissue - Stand By For Creationist Lies

The tip of the right flipper with two scales along the trailing edge.

Image: Klaus Nilkens/Urwelt-Museum Hauff

This article is best read on a laptop, desktop, or tablet

Soft tissue from a 183 Million-Year-Old Jurassic Plesiosaur analysed | Lund University

Some palaeontology finds must seem like a god-send to creationist cult leaders looking for something to misrepresent to their dupes, but it has been a few years since Dr. Mary Higby Schweitzer's team reported finding 'soft' tissue in a fossilised dinosaur bone.

Creationists routinely misrepresent this discovery, particularly the discovery of soft-tissue structures in fossilised dinosaur bones. Schweitzer and her team found microscopic structures resembling blood vessels, cells, and proteins in well-preserved fossils, which creationists have seized upon as supposed evidence that dinosaurs lived only a few thousand years ago, rather than tens of millions. However, their claims are based on a fundamental misunderstanding—or deliberate misrepresentation—of both the science and Schweitzer’s own conclusions.

Far from supporting a young Earth, Schweitzer’s findings actually highlight the remarkable durability of biological molecules under specific conditions. Her research suggests that iron particles from haemoglobin help preserve proteins by acting as a natural fixative, similar to formaldehyde. This explains how soft-tissue structures can persist for millions of years without requiring the fossils to be "recent," as creationists falsely claim. Despite Schweitzer’s repeated clarifications that her discoveries do not challenge the vast timescales of evolutionary history, creationists continue to misquote her work to fit their pre-existing religious narratives.

This distortion is part of a broader pattern in which creationists cherry-pick scientific findings, strip them of context, and twist them to manufacture doubt about evolutionary theory. Rather than engaging with the scientific explanations provided by Schweitzer and other researchers, they rely on misleading rhetoric to persuade those unfamiliar with the complexities of molecular preservation. In doing so, they not only misrepresent the science but also the integrity of the scientists behind it. Some creationists even claim the tissue was carbon dated to just a few thousand years old. This is a lie since no such dating was performed because carbon dating is only accurate on specimens less than about 50,000 years old and is never used to date fossils because the original carbon from the living animal is lost in the mineralisation process.

And now we have something else for the frauds to fool their dupes with and win new ignorant simpletons into the creationist cult.

It comes in the form of a report by researchers at Lund University in Sweden which concerns 'soft' tissue found in a fossilised plesiosaur. However, and this is something that creationists will ignore in their eagerness to misrepresent the find - the fossilised tissue is fossilised hard parts of skin, such as scales. There is no question of the fossils being soft tissue. Creationists will also dismiss the fact that the fossil is 183 million years old and will claim the presence of soft tissue 'proves' the dating method is flawed because it must only be a few thousand years old.

Unintelligent Design - An Arms Betwen The Sexes!

Females position their legs to make their bodies look more attractive to a male

Male flies' better vision called the females' bluff | University of Gothenburg

When dance flies mate, females make themselves more attractive by swallowing air and laying their hairy legs along their bodies to look like they are full of eggs. New research shows that the males have developed better eyesight, probably to detect the deception.

As I showed in my books, The unintelligent Designer: Refuting the Intelligent Design Hoax and Unintelligently Designed Arms Races: How Nature Refutes Intelligent Design, the natural arms races that are ubiquitous in nature make no sense as the work of an intelligence. It is simply not an intelligent act to have an ultimately pointless arm race with yourself.

Arms races happen because one side doesn't know the other side's next move but falling behind could be ultimately fatal. Both sides have no option but to use the 'Red Queen strategy' of running ever faster just to stand still. It makes as much sense as playing poker with yourself. As the act of an intelligence, it would mean the designer sees the solution to yesterdays' problem as today's problem to be solved. It probably tells us a great more than they might wish us to know that creationists think this is a sign of supreme intelligence.
The latest such arms race to be revealed by science makes even less sense from an intelligent design perspective if that's possible. This one is an arms race between the sexes in an order of insects known as dance flies and is the result of the two different strategies the males and females use to ensure they get the best mate and so produce the fittest offspring.

Dance flies are (mostly) predatory flies that kill and eat other insects. To attracts a female, males perform a dance with other males in a flying display. The females attract a male by showing him her abdomen in full of eggs and she is ready to be inseminated. The male then pursues the female and presents her with a dead insect as food. She then allows him to mate with her. They will then go off and repeat the mating rituals so both will mate with multiple partners. The female then lays her fertilised eggs in damp soil where they hatch and live as larvae and pupa until ready to hatch and repeat the cycle.

It is in the females reproductive interest to attract the fittest males and she does this by flying in front of him to display a large body full of eggs, while the male concentrates his efforts of pursuing the female most likely to produce a large batch of eggs, and presenting her with a nutritious meal in return for mating with her.

Malevolent Design - How Sudan Virus is Cleverly Designed to Kill 50% of Its Victims

Cryo-EM structure of Sudan ebolavirus glycoprotein complexed with its human endosomal receptor NPC1

New Study Reveals How Sudan Virus Binds to Human Cells | Midwest Antiviral Drug Discovery (AViDD) Center

It's shaping up to be a thrilling month for devotees of creationism's divine malevolence as science finds out just how brilliantly its nasty little parasites are designed to make us sick and increase the suffering in the world, although quite why any normal person would worship a hate-filled sadistic psychopath is even more of a mystery than the mechanism by which it designs and creates organisms.

The latest is the details of how the Sudan virus (a variant of Ebola with a 50% 'success' rate in terms of deaths of its victims) has an improved method of binding to our cells to gain entry and start the killing process. Like Ebola, it binds to receptors on the cell surface, but because it has just 4 different amino acids in its coat proteins, it binds much more efficiently - a factor which probably contributes to its high kill rate.

Malevolent Design - More Brilliance from Creationism's Divine Malevolence

Dengue signs and symptoms

Source: CDC

Female mosquito taking a blood meal

Hijacking of plasmin by dengue virus for infection - NUS Faculty of Science | NUS Faculty of Science

If you're a creationists who follows the latest science (if there is such a thing), you must be bursting with admiration for the ingenuity of your beloved intelligent designer for the way its brilliance at making us sick and spreading more suffering in the world is being revealed by science.

In the last few days, I've reported on how HIV, the virus that causes AIDS, is designed to hijack our cell's metabolic processes to ensure its own survival, and how the zika virus that cause the serious birth defect, microcephaly, in children if their mothers become infected during pregnancy, is brilliantly designed to make our skin produce more of the scent that attracts mosquitoes, so ensuring it is spread as widely as possible.

Now we have a superb example of this skill in malevolent design revealed by researchers from the National University of Singapore (NUS) who have discovered how the dengue virus is designed to make sure as many people as possible are infected by it. And this is breath-taking in its ingenuity. It is spread by the divine malevolence's favourite insect vector - the mosquito.

Refuting Creationism - How Bonobos Help Us Find Something When They Know We Don't Know Where It Is

Kanzi

Image: Ape Initiative

Nyota

Image: Ape Initiative

Don't know something? Apes can tell | Hub

The thing about Creationists is that, whilst they can't make testable predictions and their claims are non-falsifiable, they nevertheless make claims, based not on what the evidence shows, but on what they would like to be true to be as important as they like to imagine they are.

For example, they claim that there are certain features of humans that distinguish us from all the other species (ignoring that all species have unique features, which is what makes them distinct species). Most of these claims will be about our intelligence, social interactions and ethics and our artistic and aesthetic abilities.

Curiously, because they reject the idea that our ability to empathise is the basis of our social ethics, preferring to claim they get their morals from their god because that makes them feel superior to people with a different religion or none, they nevertheless will assert that compassion is one of those uniquely human characteristics that sets us apart from the other animals, so is evidence of our special creation by a magic creator who created everything just for us.

But like so many of their claims, this one turns out to be not only not unique to humans but evidence of common ancestry with the other apes - in this case bonobos, our closest relative. Bonobos have the ability to realise when there is something we don't know and to understand when we need to be educated - something that psychologists beleved was a uniquely human ability.

What information do you have concerning bonobos and their ability to empathise? Bonobos (Pan paniscus) are known for their remarkable capacity for empathy, which has been widely studied by primatologists and psychologists. Their social behaviour demonstrates strong emotional intelligence, cooperation, and conflict resolution skills, making them one of the most empathetic of non-human animals.

Key Evidence for Bonobo Empathy

1. Consolation Behaviour
   • Bonobos console distressed individuals by embracing, touching, and grooming them. Studies, such as those by Frans de Waal and Zanna Clay, show that bonobos, especially juveniles, frequently comfort upset group members.
   • Unlike some other primates, bonobos will console unrelated individuals, suggesting a form of empathy that extends beyond kinship or direct social bonds.
2. Yawn Contagion
   • Bonobos exhibit contagious yawning, particularly when observing familiar individuals yawn. This behaviour is thought to reflect an ability to emotionally resonate with others. Studies indicate that the stronger the social bond, the more likely an individual is to "catch" a yawn.
3. Altruism and Helping Behaviour
   • Bonobos display spontaneous helping behaviour, even in non-reciprocal situations. Research has shown that they will help strangers obtain food without expecting immediate rewards.
   • Experiments at Lola ya Bonobo sanctuary demonstrated that bonobos would unselfishly share food with unfamiliar individuals rather than hoarding it.
4. Cooperative Problem Solving
   • In contrast to chimpanzees, who often engage in competitive strategies, bonobos are more likely to cooperate when solving tasks. Studies show they work together harmoniously to retrieve food, even when dominant individuals could monopolize resources.
5. Emotional Sensitivity and Social Bonds
   • Bonobos are highly sensitive to emotional cues in their group members. Their facial expressions, vocalizations, and body language communicate distress, pleasure, or reassurance.
   • They engage in socio-sexual behaviours (such as genital rubbing) to diffuse tension and maintain social harmony, which may be an expression of empathetic bonding.

Comparisons with Other Primates

• While chimpanzees (Pan troglodytes) also display some empathy, their social structure is more hierarchical and aggressive, often limiting empathetic behaviours to kin or allies.
• Bonobos, in contrast, live in matriarchal societies where social bonds are maintained through affection and non-aggressive conflict resolution, reinforcing their empathetic tendencies.

Neuroscientific Basis

• Studies of bonobo brains suggest that their limbic system (including the amygdala and anterior cingulate cortex) is more developed than in chimpanzees, which may enhance their capacity for emotional processing and empathy.

Conclusion
Bonobos are among the most empathetic primates, capable of understanding and responding to the emotions of others. Their ability to console, cooperate, and help even strangers suggests a deep-rooted evolutionary foundation for empathy, which may shed light on the development of human social emotions.

This was demonstrated by two researchers with Johns Hopkins University's Social and Cognitive Origins Group, published yesterday in Proceedings of the National Academy of Sciences.

Don't know something? Apes can tell

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To get treats, apes eagerly pointed them out to humans who didn't know where they were, a seemingly simple experiment that demonstrated for the first time that apes will communicate unknown information in the name of teamwork. The study also provides the clearest evidence to date that apes can intuit another's ignorance, an ability thought to be uniquely human.

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Key Takeaways

• Apes can intuit another’s ignorance, an ability thought to be uniquely human.
• When apes know their partners are ignorant, they will point them toward missing information.

The ability to sense gaps in one another's knowledge is at the heart of our most sophisticated social behaviors, central to the ways we cooperate, communicate, and work together strategically. Because this so-called theory of mind supports many of the capacities that make humans unique, like teaching and language, many believe it is absent from animals. But this work demonstrates the rich mental foundations that humans and other apes share—and suggests that these abilities evolved millions of years ago in our common ancestors.

Professor Christopher Krupenye, co-author Department of Psychological & Brain Sciences
Johns Hopkins University, Baltimore, MD, USA.

Krupenye and co-author Luke Townrow, a Johns Hopkins PhD student, worked with three male bonobos—Nyota, 25; Kanzi, 43; and Teco, 13, all living at Ape Initiative, a research and education nonprofit. During the experiment one of the bonobos would sit with Townrow, facing each other across a table, the ape on the other side of metal gate. The bonobo would watch as a second person placed a treat, a grape or a Cheerio, under one of three cups. Sometimes Townrow could see where the treat was going, sometimes he couldn't. The bonobo could have the treat if Townrow could find it.

Whether or not Townrow saw where the treat was hidden, he'd say, "Where's the grape?" and then wait 10 seconds. If he'd seen the treat being hidden, during the 10 seconds the ape would usually sit still and wait for the treat. But when Townrow hadn't seen where the treat was hidden, the ape would quickly point to the right cup—sometimes quite demonstratively.

Their fingers would point right through the mesh—it was clear what they were trying to communicate. One, Kanzi, who was very food motivated, would point repeatedly in certain phases of the experiment—he'd tap several times to get our attention and was quite insistent about it.

We predicted that if apes are really tracking ignorance, when their partners lacked knowledge they would be pointing more often and more quickly and that's exactly what they did. The results also suggest apes can simultaneously hold two conflicting world views in their mind. They know exactly where the food is, and at the same time, they know that their partner's view of the same situation is missing that information.

Professor Christopher Krupenye.

The work is the first to replicate in a controlled setting similar findings from the wild that suggest chimpanzees will vocalize to warn groupmates ignorant to potential threats, such as a snake.

The team was thrilled to further confirm apes' mental sophistication.

There are debates in the field about the capabilities of primates, and for us it was exciting to confirm that they really do have these rich capacities that some people have denied them.

Professor Christopher Krupenye.

What we've shown here is that apes will communicate with a partner to change their behavior, but a key open question for further research is whether apes are also pointing to change their partner's mental state or their beliefs.

Luke A. Townrow, first author. Department of Psychological & Brain Sciences
Johns Hopkins University, Baltimore, MD, USA.

This work demonstrates the rich mental foundations that humans and other apes share—and suggests that these abilities evolved millions of years ago in our common ancestors.

Professor Christopher Krupenye.

Next the team will work to more deeply explore the apes' motivations and how they think about other individuals' minds.

Publication:

L.A. Townrow, & C. Krupenye
Bonobos point more for ignorant than knowledgeable social partners Proc. Natl. Acad. Sci. U.S.A. 122 (6) e2412450122, DOI; 10.1073/pnas.2412450122 (2025).

Abstract
Numerous uniquely human phenomena, from teaching to our most complex forms of cooperation, depend on our ability to tailor our communication to the knowledge and ignorance states of our social partners. Despite four decades of research into the “theory of mind” capacities of nonhuman primates, there remains no evidence that primates can communicate on the basis of their mental state attributions, to enable feats of coordination. Moreover, recent reevaluation of the experimental literature has questioned whether primates can represent others’ ignorance at all. The present preregistered study investigated whether bonobos are capable of attributing knowledge or ignorance about the location of a hidden food reward to a cooperative human partner, and utilizing this attribution to modify their communicative behavior in the service of coordination. Bonobos could receive a reward that they had watched being hidden under one of several cups, if their human partner could locate the reward. If bonobos can represent a partner’s ignorance and are motivated to communicate based on this mental state attribution, they should point more frequently, and more quickly, to the hidden food’s location when their partner is ignorant about that location than when he is knowledgeable. Bonobos indeed flexibly adapted the frequency and speed of their communication to their partner’s mental state. These findings suggest that apes can represent (and act on) others’ ignorance in some form, strategically and appropriately communicating to effectively coordinate with an ignorant partner and change his behavior.

A growing body of work suggests that monkeys and apes share with humans rich precursors of theory of mind, the ability to infer the mental states that guide others’ actions (1–3). However, major debates concern what distinguishes human theory of mind in terms of both its functions and its underlying representations. Regarding function, various scholars have argued for decades that what makes humans special is a remarkable propensity for cooperation and that the underlying mechanism is a unique capacity to harness theory of mind to communicate in service of coordination (4). For example, we readily adapt our communication to the knowledge and ignorance states of our partners to change their mental states (5), and behavior, and enable cooperative acquisition of goals. While no research has addressed this ability in nonhuman great apes, two studies shed light on its precursors. First, Grueneisen et al. (6) found that chimpanzees and bonobos can facilitate coordination by adjusting the visibility of their actions for a cooperative partner relative to a competitive one, though their task did not involve communication or experimentally isolate theory of mind. Second, Crockford et al. (7) found that wild chimpanzees may be able to communicate based on a recipient’s mental state: Chimpanzees produced more warning vocalizations in the presence of groupmates who were ignorant about a nearby snake, compared to those who were knowledgeable. However, experiments in controlled and nonthreatening settings are needed to eliminate alternative explanations (e.g., that chimpanzees simply responded to others’ behavior, or were driven by arousal) and to clarify whether this capacity can be deployed flexibly in other contexts and via other communicative modalities. Paradigms with greater control are also essential for isolating the particular cues subjects are sensitive to and constraining the hypotheses about the underlying mechanisms driving this pattern of communication, especially following contradictory findings in captivity (8).

Regarding the underlying representations, a reevaluation of the literature has compellingly shown that controlled studies testing primates’ capacity to represent others’ knowledge or ignorance could be explained by attributing only knowledge-like states called awareness relations (9). This is because past paradigms make positive predictions only about how subjects should act if they have attributed knowledge (e.g., avoid food known to a competitor) but not ignorance (i.e., refs. 1, 3, and 10–12). Thus, no controlled studies have directly tested for primates’ capacity to represent others’ ignorance. One central prediction that distinguishes ignorance representation from deflationary accounts is that only primates who can represent others’ ignorance should be able to act on those representations, for example, through communication.

To clarify the unique functions and representations underlying human theory of mind, we tested whether our closest relatives, bonobos (Pan paniscus), can identify a partner’s ignorance and adapt communication to enable coordination. In a highly controlled preregistered study, captive bonobos could point and remedy a partner’s ignorance. Bonobos could receive a reward that they had watched being hidden under one of several cups, if their human partner could locate the reward. If bonobos can represent a partner’s ignorance and are motivated to communicate based on this mental state attribution, they should point more frequently, and more quickly, to the hidden food’s location when their partner is ignorant about that location than when he is knowledgeable.

L.A. Townrow, & C. Krupenye
Bonobos point more for ignorant than knowledgeable social partners Proc. Natl. Acad. Sci. U.S.A. 122 (6) e2412450122, DOI; 10.1073/pnas.2412450122 (2025).

Copyright: © 2025 The authors.
Published by National Academy of Science of the USA. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Once again, something proclaimed by creationists as proof of the special creation of humans turns out to be evidence for our common ancestry with the other African apes. This is how you can tell that creationists claims are not based on evidence so are not worth paying attention to.

Unintelligent Design - Sex Determination in Octopuses - For 480 Million Years

Californian two-spot octopus, Octopus bimaculoides

Californian two-spot octopus, Octopus bimaculoides

Octopuses have some of the oldest known sex chromosomes | OregonNews

Although few of them will know enough to understand why, the genetic basis for sex determination in different organisms is a problem for intelligent design advocates because it illustrates a few embarrassing things which can't be explained as the design of an intelligent designer.

Firstly, there are several ways in which gender is determines, rather than the single method a single intelligent designer of all living things would have settled for (see the AI information panel). Secondly, the actual basis is consistent within major clades such as mammals, birds and orders of insects such as Hymenoptera (Bees, wasps and ants), and thirdly, because the methods are unstable over evolutionary time, since the sex chromosomes are unpaired in the heterozygous gender, so the unpaired chromosome tends to acquire mutations, which are not corrected by cross over during meiosis, and the non-sex-determining genes tend to be conserved on the chromosome which is paired in the homozygous gender.

In mammals, this means that the Y-chromosome tends to degenerate; in some species of rodents, which have a short generation time and large litters, so evolution can progress faster than in most other mammals, the Y-chromosome has disappeared, to be replaced by an alternative sex-determining system. No intelligent designer worthy of the name would design a process that degenerates and need to be replaced every few million years.

Malevolent Design - How Zika Is Designed to Spread Maximum Suffering.

Zika manipulates the skin to make it more attractive to mosquitoes

Illustration of Zika virus in blood

Kateryna Kon/Science Photo Library

Zika uses human skin as ‘mosquito magnet’ to spread virus further | LSTM

January was something of a joyous month for devotees of creationism's divine malevolence. Following closely behind the news of how it brilliantly designed HIV to use our cells defences against us so making it better at infecting and killing us, we have news of another breathtakingly brilliant design of a nasty little pathogen - the zika virus that causes microcephaly in children if their mothers become infected during pregnancy.

This news is that it turns our skin into a living 'magnet' to attract the vector that spreads it - mosquitos - so ensuring it gets transmitted to as many victims as possible. It does it by altering a gene and protein expression in dermal fibroblasts, causing the skin to produce odours that are attractive to mosquitoes. In effect, calling them to come and feed.

Before creationists start bleating unscientific and biologically non-sensical nonsense about 'genetic entropy' and devolution allowed by 'sin' I should point out that no mutation that conveys a benefit on an organism can be regarded as 'devolutionary'. It is classic evolution by natural selection. And, as per William Dembski's gibberish about 'specified complexity', any complex DNA or RNA sequence that codes for a specific function must be regarded as 'specified complexity', using his argument, so must have been specified by a magic designer, according to his misuse of statistics and probability. Or perhaps a creationist could explain why such a highly specific function of converting a human gene to make special mosquito-attracting scents, is not an example of Dembski's 'specified complexity'.

So, how was this, in creationist terms, intelligently designed virus, discovered to have this touch of brilliance in its design? That was the result if a new study by an international team led by Liverpool School of Tropical Medicine. Their findings are published, open access, in Communications Biology.

Tell me all about the zika virus, its evolution and recent spread, please. Zika virus (ZIKV) is a mosquito-borne flavivirus primarily transmitted by Aedes mosquitoes, particularly Aedes aegypti. First identified in 1947 in a rhesus monkey in Uganda's Zika Forest, it was subsequently detected in humans in 1952 in Uganda and the United Republic of Tanzania. (who.int).

Evolution and Lineages

Zika virus (ZIKV) is an RNA virus. Specifically, it is a positive-sense, single-stranded RNA virus belonging to the Flavivirus genus within the Flaviviridae family. Other notable flaviviruses include dengue, yellow fever, and West Nile viruses.

Because ZIKV has an RNA genome, it mutates and evolves more rapidly than DNA viruses, which may have contributed to its recent spread and ability to cause large outbreaks.

Phylogenetic studies have identified two main lineages of ZIKV: African and Asian. The virus remained relatively obscure for decades, causing only sporadic human infections in Africa and Asia. However, in 2007, a significant outbreak occurred on Yap Island in Micronesia, marking ZIKV's first major emergence outside its traditional endemic areas. (academic.oup.com)

The Asian lineage is particularly notable for its role in the outbreaks in the Pacific and the Americas. Genetic analyses suggest that mutations in the virus may have enhanced its ability to infect humans and spread more efficiently, contributing to its rapid dissemination. (frontiersin.org).

Global Spread and Recent Developments

Following the Yap Island outbreak, ZIKV caused significant epidemics in the Pacific, including in French Polynesia in 2013. In 2015, Brazil reported its first case, leading to a large outbreak associated with severe birth defects, such as microcephaly, and neurological disorders like Guillain-Barré syndrome. The virus then spread throughout the Americas, prompting the World Health Organization to declare it a Public Health Emergency of International Concern in 2016. (who.int).

As of May 2024, ZIKV transmission persists in several countries, though generally at low levels since 2018. Recent data indicate that three additional countries have reported autochthonous mosquito-borne transmission, and two more have established *Aedes aegypti* populations without documented ZIKV transmission. (who.int).

In January 2025, new research revealed that ZIKV can manipulate human skin to emit chemical signals attracting more mosquitoes, potentially facilitating further spread of the virus. (sciencedaily.com).

Prevention and Control

Preventing ZIKV infection primarily involves controlling mosquito populations and minimizing exposure to mosquito bites. This includes using insect repellent, wearing protective clothing, and eliminating standing water where mosquitoes breed. Given the association between ZIKV infection during pregnancy and birth defects, pregnant women are advised to avoid travel to areas with active ZIKV transmission. (who.int).

Despite ongoing research, there is currently no specific antiviral treatment or vaccine for ZIKV. Efforts to develop a vaccine have faced challenges, including fluctuating transmission rates and limited funding.

Zika is still spreading. Why don’t we have a vaccine yet?

Zika uses human skin as ‘mosquito magnet’ to spread virus further

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Zika virus hijacks the skin of its human host to send out chemical signals that lure more mosquitoes to infect and spread the disease further, new research shows.

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Zika transmission has been reported more than 90 countries as the spread of the Aedes aegypti mosquito that carries the virus, as well as dengue and chikungunya, has increased over recent years as an effect of climate change and urbanisation. Yet surprisingly little is known about the factors that drive Zika transmission success.

A new study led by Liverpool School of Tropical Medicine and published in Communications Biology shows that Zika causes metabolic changes in human skin that essentially transforms it from a protective barrier to a magnet for mosquitoes.

Their research shows that the Zika virus alters gene and protein expression in dermal fibroblasts, the cell type responsible for maintaining structural integrity in the skin. These metabolic changes increase the production of certain chemicals emitted through the skin, known as volatile organic compounds (VOCs), that are attractive to mosquitoes and encourage them to bite. Their findings are supported by an extensive meta-proteome analysis, a technique that examines the overall effect of the interaction of different types of gene and protein within an organism.

Our findings show that Zika virus isn’t just passively transmitted, but it actively manipulates human biology to ensure its survival. As Zika cases rise and Aedes mosquitoes expand their range, understanding the mechanisms by which they gain a transmission advantage could unlock new strategies for combating arboviruses. This could include developing genetic interventions that disrupt the signal transmitted through the skin which seems to be so attractive to mosquitoes. The possibilities are as intriguing as they are urgent.

Dr Noushin Emami, co-corresponding author Department of Molecular Bioscience
Wenner-Gren Institute
Stockholm University, Stockholm, Sweden
And Vector Biology Department (VBD)
Liverpool School of Tropical Medicine (LSTM)
Liverpool, UK.

Most Zika infections do not lead to disease, and those that do generally cause mild symptoms that last for 2-7 days.

Zika can occasionally cause more serious complications and can harm a developing baby if contracted by a pregnant woman.

This study was conducted in collaboration with Emami Lab at Stockholm University, alongside researchers from the Nature Research Centre in Vilnius, the University of Veterinary Medicine in Hanover, Molecular Attraction AB, Umeå University, Leibniz University Hannover, and the University of Greenwich.

Abstract
Transmission of Zika virus (ZIKV) has been reported in 92 countries and the geographical spread of invasive virus-borne vectors has increased in recent years. Arboviruses naturally survive between vertebrate hosts and arthropod vectors. Transmission success requires the mosquito to feed on viraemic hosts. There is little specific understanding of factors that may promote ZIKV transmission-success. Here we show that mosquito host-seeking behaviour is impacted by viral infection of the vertebrae host and may be essential for the effective transmission of arboviruses like ZIKV. Human skin fibroblasts produce a variety of metabolites, and we show that ZIKV immediately alters gene/protein expression patterns in infected-dermal fibroblasts, altering their metabolism to increase the release of mosquito-attractive volatile organic compounds (VOCs), which improves its transmission success. We demonstrate that at the invasion stage, ZIKV differentially altered the emission of VOCs by significantly increasing or decreasing their amounts, while at the transmission stage of the virus, all VOCs are significantly increased. The findings are complemented by an extensive meta-proteome analysis. Overall, we demonstrate a multifaceted role of virus-host interaction and shed light on how arboviruses may influence the behaviour of their vectors as an evolved means of improving transmission-success

Introduction
The human body comprises around 40 trillion (3.7 × 10¹³) cells¹, which produce an enormous variety of metabolites including volatile organic compounds (VOCs). The qualitative and quantitative changes in VOC profiles reflect the optimum status of healthy cells. The skin is the body’s largest organ, serving multiple essential functions, including acting as a physical barrier for protection, a site for sensory perception, and a centre for vitamin synthesis. The release of VOCs through the skin, which contributes to the distinct odours of the human body, is a familiar part of our daily experience². These VOCs include a large number of volatiles that can be listed as carboxylic acids, aldehydes, alcohols or ketones³. Dermal fibroblasts are the main cell type present in skin connective tissue (dermis)⁴. These mesenchymal/stromal cells derived from the embryonic mesoderm, reside in the dermal layer of skin. They produce extracellular matrix proteins to strengthen the dermal compartment and interact with epidermal cells⁵.

Zika virus (ZIKV) had not been widely known until a series of outbreaks occurred with severe clinical complications that made it a matter of global public health concern. The emergence of ZIKV followed a typical pattern of a vector-borne disease being introduced into a new ecosystem and host population and spreading rapidly with severe implications for human health. ZIKV is a mosquito-borne virus belonging to the genus Flavivirus and is transmitted to humans by mosquitoes of the genus Aedes. Both Aedes aegypti and Aedes albopictus are the primary vectors for ZIKV transmission in nature⁶. Vector-mediated transmission of ZIKV is initiated when a blood-feeding female Aedes mosquito injects the virus into the skin of its mammalian host, followed by infection of a wide range of permissive cells. Indeed, skin cells, including dermal fibroblasts were found to be permissive to ZIKV infection. Infection of skin fibroblasts rapidly resulted in the presence of high RNA copy numbers and a gradual increase in the production of ZIKV particles over time, indicating an active viral replication stage. In humans, the incubation period from mosquito bite to symptom onset is ≈3–12 days⁷. Accumulating data indicate that ZIKV alters the biochemical processes of the infected cells by modifying glucose^8,9 and fatty acid¹⁰ metabolism. However, no published data has yet revealed any changes in the composition of infected cell volatome. While Zhang and colleagues¹¹ demonstrated that flaviviruses can manipulate host skin microbiota to produce an odour that attracts mosquitoes, the specific role of infected human skin cells in manipulating mosquitoes’ behaviour remains unclear.

Mosquitoes have made themselves at home in new geographical regions throughout recent years, bringing with them some historically exotic diseases. Epidemiologic and laboratory studies have implicated various Aedes spp. mosquitoes as ZIKV vectors¹¹. In mosquitoes, it appears that the viral load is initially high on the day of feeding, but then decreases to undetectable levels for about ten days. After this incubation period, the viral content increases again by day 15 and remains high from days 20 to 60. This is important because it suggests that it takes about 10 days for the virus to reach the salivary glands of the mosquito where it can potentially be transmitted to humans⁷. There is currently no specific treatment or vaccine available to mitigate or prevent ZIKV infection. Prevention measures, particularly conventional vector control, are currently the priority while we await these and other advances in control of the substantial harm caused by this virus. The World Health Organization has issued recommendations on this matter¹².

To further understand this complex issue, this study aims to demonstrate how ZIKV manipulate vector behaviour by altering gene/protein expression in human dermal fibroblasts at different stages of infection. These changes lead to an increased release of mosquito-attractive VOCs, ultimately enhancing transmission success. Here, we describe how ZIKV infection of human host cells provoked the modified feeding behaviour of its tiger mosquito vector in a manner that plausibly results in enhanced transmission success.

Obviously, to creationism's intelligent designer who designed mosquitoes to drink human blood and so spread several nasty parasites and viruses, and gave them the ability to detect and home in on the scents we give off, it was a simple matter to design the zika virus to enhance those scents to attract more mosquitoes and have the virus spread as widely as possible, to maximise the number of children born with microcephaly. At least, since that is about all the zika virus does, we have to assume that wehoever designed it, designed it with that specific function in mind.

And William Dembski insists that whatever a DNA/RNA sequence produces it must have been intelligently specified to produce that outcome. The malice of this designer knows no bounds apparently. That's if you believe what creationists claim.

If you believe what science says, it's easy to see how genes mutating and being selected for when they convey an advantage can produce this sort of host-parasite arms race over time, especially if it only takes a few tweaks of the RNA sequence to manipulate one of our genes, and suddenly, lots more mosquitoes are homing in and spreading the new variant far and wide.

Refuting Creationism - Humans Have Been Selectively Breeding Sheep Since 1000 Years Before 'Creation Week'

Scottish Blackface from Applecross, Scotland - a common sheep breed of the British Isles. This breed is represented in the panel of modern reference genomes.

Photo by J. Peters

Sheep in arid landscape, southeastern Morocco.

Photo by J. Peters, LMU_SNSB

Ancient DNA history of sheep and humans - News & Events | Trinity College Dublin

Domesticated animals are an embarrassment for creationists who believe that their god created all the animals for the convenience of mankind, because just about every domesticated animal (or plant for that matter) has been highly modified by selective breeding to make it suitable for whatever purpose it was domesticated for.

An intelligent god could have made them fit for purpose in the first place, if it had really created them for mankind's convenience. This shows that either the creation myth is wrong, or the creator god lacked the foresight to know what humans would be using the animals for. So, we've had to modify them, in some cases. almost beyond recognition as the descendants of their wild ancestors, to make them fit for purpose.

And it gets worse when we discover that the domestication process began long before the same creation myth says all the animals were created in the same week as humans.

Sheep, for example, according to a study by an international and interdisciplinary team of researchers led by geneticists from Trinity College Dublin, and zooarchaeologists from Ludwig Maximilian University Munich and the Bavarian State Collections of Natural History (SNSB) were first domesticated over 11,000 years ago. An analysis of their genome also reflects patterns of migration in the human population, with whom sheep have been intertwined for over 11,000 years.

Unintelligent Design - Vestigial 'Fossil' Ear Muscles Still Try to Function

Muscles of the head

AI-generated image (with AI spelling)

Muscles of the ear

Image by BioDigital, edited by Lecturio

‘A neural fossil’: human ears try to move when listening, scientists say | Biology | The Guardian

In my book, The Body Of Evidence: How the Human Body Refutes Intelligent Design I list very many examples of the sort of design only a fool would produce - examples of sub-optimal compromises in structures and processes that could have been less error-prone and more efficient in terms of resource use or function.

These also included vestigial structures and system that still exist, sometime causing problems such as appendicitis when the functionless appendix becomes infected, and the wasted metabolism in making all the tiny hairs on your body stand up in cold weather using the tiny arrector pili muscles and the autonomic nerves that supply them.

Now we have another example, involving the superior and posterior auricular muscles that once moved the ears in a remote simian ancestor, but now only serve as party tricks for the few of us that can wiggle our ears.

Refuting Creationism - How Horseshoe Crabs Have Evolved And Diversified

Indo-pacific horseshoe crab, Tachypleus gigas

By Shubham Chatterjee - Own work,
CC BY-SA 3.0, Link

Indo-Pacific Horseshoe Crab, Tachypleus tridentatus

Photo: Dr Tang Qian

Preserving Asian horseshoe crab populations through targeted conservation strategies

In creationist mythology, horseshoe crabs have remained unchanged for 400 million years, so they prove there is no such thing as evolution and Earth is only 6-0,000 years old. Apart from the typical lack of joined-up thinking in that non sequitur, there are a couple of fallacy at work here.

Firstly, evolution does not necessarily involve major changes in the phenotype because it happens at the genetic level, so the genome is where we need to look to find evidence of it (or lack of it); secondly there is no requirement for a species that is already adapted to its environment to change unless its environment changes in a way that requires adaptation. This might include increased predation, depletion of food resource, major changes in temperature or oxygenation, increased competition from another species, etc.

With their child-like understanding of evolution, creationists assume a species must change into something else for evolution to happen.

In fact, as a team a research team led by Associate Professor Frank Rheindt from the Department of Biological Sciences at the National University of Singapore (NUS) Faculty of Science have now shown, there are four different species of horseshoe crab which have all diversified from a common ancestor.

Tell me about the evolution and distribution of the horseshoe crabs, please. Horseshoe crabs (order Xiphosura, class Merostomata) are marine arthropods that have existed for over 450 million years, making them one of the oldest living groups of animals. They are often called "living fossils" because their body plan has remained largely unchanged since the Ordovician period.

Evolutionary History

Horseshoe crabs belong to the subphylum Chelicerata, making them more closely related to arachnids (such as spiders and scorpions) than to true crabs or other crustaceans. Their evolutionary history includes several now-extinct relatives, such as Eurypterids (sea scorpions), which were once dominant marine predators.

• Ordovician Period (~450 mya): Early xiphosurans appear in shallow marine environments.
• Paleozoic Era (~300 mya): More advanced forms develop but remain morphologically similar to modern species.
• Mesozoic Era (~150 mya): Horseshoe crabs survive mass extinctions, adapting to various shallow marine environments.
• Cenozoic Era (Present day): Four extant species remain, showing remarkable evolutionary stability.

Modern Distribution

Today, only four species of horseshoe crabs survive, all found in coastal and estuarine environments:

1. Limulus polyphemus (Atlantic Horseshoe Crab) – Found along the eastern coast of North America, from the Gulf of Mexico to the northeastern United States.
2. Tachypleus tridentatus (Tri-spine Horseshoe Crab) – Found in coastal waters of China, Japan, and Southeast Asia.
3. Tachypleus gigas (Indo-Pacific Horseshoe Crab) – Inhabits the waters of the Bay of Bengal and Southeast Asia.
4. Carcinoscorpius rotundicauda (Mangrove Horseshoe Crab) – Found in shallow waters and estuaries from India to Indonesia.

Ecological Role & Conservation

Horseshoe crabs play a crucial ecological role. Their eggs provide an important food source for migratory shorebirds, and they contribute to benthic (seafloor) ecosystems. They are also vital to biomedical research because their blue blood contains limulus amebocyte lysate (LAL), used to detect bacterial contamination in medical applications.

However, populations are declining due to:

• Overharvesting (for bait and biomedical use)
• Habitat loss (coastal development)
• Climate change (affecting spawning conditions)

Conservation efforts focus on protecting nesting beaches, regulating harvesting, and exploring synthetic alternatives to LAL for medical testing.

Fossil Record of Horseshoe Crabs (Order Xiphosura)

Horseshoe crabs have an extensive fossil record dating back to the Ordovician period (~450 million years ago). Their morphology has remained remarkably stable, making them classic examples of "living fossils." The fossil record reveals several extinct relatives and a gradual adaptation to different marine environments over geological time.

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Key Fossil Discoveries and Evolutionary Timeline

1. Ordovician Period (485–443 mya) – Oldest Known Horseshoe Crab Ancestors
   • The earliest xiphosurans appeared in shallow marine environments.
   • Fossils of Tetraspidella from the Upper Ordovician suggest primitive horseshoe crab-like arthropods already existed.
2. Silurian Period (443–419 mya) – Emergence of True Xiphosurans
   • More recognizable horseshoe crab relatives evolved.
   • Kasibelinurus (Late Silurian) is considered one of the earliest known xiphosurans.
3. Devonian Period (419–359 mya) – Diversification and Expansion
   • This period saw the emergence of several marine genera with more developed carapaces and feeding structures.
   • Bellinurus and Euproops are well-known genera from the Devonian.
4. Carboniferous Period (359–299 mya) – Peak Diversity
   • This was the golden age of xiphosurans, with numerous species thriving in marine, brackish, and even freshwater environments.
   • Genera like Euproops, Bellinurus, and Paleolimulus flourished, some resembling modern horseshoe crabs.
   • Some species, such as Euproops danae, had spines and unique adaptations to different ecological niches.
5. Permian Period (299–252 mya) – Decline and Extinctions
   • The Permian saw a decline in diversity, possibly due to changing environments and competition with other arthropods.
   • Many species perished during the Permian-Triassic mass extinction (~252 mya), the most severe extinction event in Earth's history.
6. Mesozoic Era (252–66 mya) – Survival and Adaptation
   • Xiphosurans survived the mass extinction but were less diverse than in the Carboniferous.
   • Fossil genera like Mesolimulus (Jurassic) and Limulitella (Cretaceous) were similar to modern horseshoe crabs.
   • Some species adapted to shallow coastal waters, much like their modern counterparts.
7. Cenozoic Era (66 mya–Present) – Modern Horseshoe Crabs
   • Fossil records show that Limulus polyphemus, the modern Atlantic horseshoe crab, has remained almost unchanged for at least 20 million years.
   • Their ability to survive drastic environmental changes has made them one of the longest-surviving arthropod groups.

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Key Fossil Finds

1. Kasibelinurus (Silurian) – One of the earliest known true xiphosurans.
2. Euproops (Carboniferous) – Small, with a reinforced carapace and spines for protection.
3. Mesolimulus (Jurassic) – Nearly identical to modern Limulus, showing little evolutionary change.
4. Paleolimulus (Permian) – A transitional form between early and modern horseshoe crabs.

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Why Have Horseshoe Crabs Changed so Little?

• Stable ecological niche: They have occupied similar coastal and estuarine environments for hundreds of millions of years.
• Efficient body plan: Their tough exoskeleton, simple yet effective feeding structures, and ability to tolerate low-oxygen conditions have helped them persist.
• Survivors of mass extinctions: They have outlived dinosaurs and many other ancient marine species due to their resilience and adaptability.

The results of their study are published open access in the journal Conservation Letters and is the subject of a news item from NUS>

Preserving Asian horseshoe crab populations through targeted conservation strategies

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NUS biologists conduct the first comprehensive population study of all three Asian horseshoe crab species, mapping their population distribution, evolutionary histories and vulnerabilities to climate change to propose customised conservation strategies

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The photo shows the moult of a young tri-spine horseshoe crab, Tachypleus tridentatus – an endangered species – found on the beach at Beihai, China. The genomic data gathered by NUS researchers on this species provides a launchpad for conservation strategies.

Photo: Dr Tang Qian.

Horseshoe crabs are often referred to as the “living fossils” of our planet — the four known species, including three in Asia and one in North America, remain nearly identical to their ancient relatives from hundreds of millions of years ago. These arthropods are a fundamental building block of coastal marine ecosystems. Their eggs, for example, serve as a major food source for shorebirds, some of which have evolved to time their migrations to coincide with peak horseshoe crab spawning activity. In addition to their ecological role, horseshoe crabs are also used in biomedicine to test for harmful toxins in vaccines.

Among the four species, only the Atlantic horseshoe crab (Limulus polyphemus), found along the Atlantic coast of the United States and the Gulf of Mexico, has been extensively studied. In contrast, scientific information about the three Asian species is so scant and scattered that the IUCN Red List, which tracks the extinction risk of species around the world, listed two of them (the mangrove horseshoe crab and the coastal horseshoe crab) as “data deficient”. This designation indicates insufficient data to assess their extinction risk. On the other hand, the tri-spine horseshoe crab is considered endangered.

Understanding our planet’s living fossils

to help fill in these knowledge gaps, a research team led by Associate Professor Frank Rheindt from the Department of Biological Sciences at the NUS Faculty of Science conducted the first comprehensive population genomic study of all three Asian horseshoe crab species: the mangrove horseshoe crab (Carcinoscorpius rotundicauda), coastal horseshoe crab (Tachypleus gigas), and tri-spine horseshoe crab (Tachypleus tridentatus).

The study underscores the importance of Southeast Asia’s Sunda Shelf, a shallow-marine region, as a critical coastal marine habitat. Importantly, this region has sustained the survival of these ancient arthropods for millennia and could continue to act as a refuge for Asian horseshoe crabs amid accelerating anthropogenic climate change.

The researchers have also established the first-ever genomic baseline dataset for these species, which lay the groundwork for targeted conservation planning. Their findings, which propose different conservation strategies for each species, were published in Conservation Letters on 16 December 2024.

Back to the basics: Filling data gaps to advance conservation efforts

To protect and conserve these species, it is crucial that we first cover the basics — understanding their population structure, evolutionary histories and climate-change-driven vulnerabilities. This foundational knowledge will enable us to develop targeted conservation strategies and prioritise habitats critical for their survival.

Associate Professor Frank E. Rheindt, co-corresponding author
Department of Biological Sciences
National University of Singapore, Singapore.

Tracking and monitoring Asian horseshoe crabs is in and of itself a challenging feat. They spend most of their lives on the seabed, making them difficult to observe, and they take 14 years to mature — too long to assess population changes effectively through traditional surveys. To overcome these challenges, the researchers turned to population genomic approaches, where they analysed DNA from 251 horseshoe crabs collected across 52 sites in 11 countries.

Using this data, NUS researchers created the first genomic baseline dataset for Asian horseshoe crabs. This dataset enabled the team to map population structures and delineate genetic boundaries among the three species.

Such distinctions are important, as they highlight populations that harbour unique genetic traits essential for adapting to specific local environments. Genomic data also helps us pinpoint coastal hotspots that should be prioritised for conservation.

Dr Tang Qian, first author.
Department of Biological Sciences
National University of Singapore, Singapore.

The study also revealed how horseshoe crabs have responded to environmental fluctuations over time. The Sunda Shelf emerged as a vital refuge for horseshoe crabs during periods of past climate change. By reconstructing the species’ evolutionary histories, the researchers found that the region has not only preserved genetic diversity but also served as a migratory corridor, which allowed populations to remain connected despite environmental changes.

Tailored conservation strategies needed

The study highlighted that future climate change poses varying levels of risk to the three species of Asian horseshoe crabs. While all are vulnerable, their ability to adapt differs. For instance, the mangrove horseshoe crab, with its limited dispersal capacity, faces higher threats of local extinction compared to the more mobile coastal and tri-spine horseshoe crabs.

Based on these findings, the researchers have proposed tailored conservation strategies to support each species in adapting to climate change:

Mangrove horseshoe crabs

• Protect and restore mangrove habitats, which are essential for the species’ survival and ability to migrate southward in response to rising temperatures.
• Prioritise the conservation of populations in the Gulf of Tonkin and South China as they face the highest evolutionary pressures from climate change.

Coastal horseshoe crabs

• Protect the Sunda Shelf region, which serves as a critical refugial habitat, particularly around the Bay of Bengal, the Malacca Strait and Southern Vietnam.
• Maintain connectivity between populations by safeguarding coastal corridors to mitigate the species’ vulnerability to habitat fragmentation.

Tri-spine horseshoe crabs

• Implement sustainable fishery regulations and restore coastal habitats, especially in areas with a history of intensive development, such as Japan, Taiwan and China.
• Focus conservation efforts on reducing human-driven threats like harvesting and habitat loss as these currently pose greater risks than climate change.

Next steps

Our study provides an important impetus and the necessary baseline data for the preservation of key habitats for horseshoe crabs’ future survival. As an important caveat, however, our work is only based on environmental factors and does not take into account future human activities that may directly alter habitats, such as coastal development. The survival of horseshoe crabs will therefore critically depend on interventions based on local contexts.

Dr Tang Qian.

Looking ahead, the researchers plan to further explore the evolutionary potential of Asian horseshoe crabs. This includes studying how specific functional genes contribute to their ability to adapt to local environments and changing climates.

We have established the Horseshoe Crab Global Biorepository, with its physical collection located at the Lee Kong Chian Natural History Museum at NUS, to support ongoing and future research. Through this resource, we hope to foster collaborations and secure funding to advance genomic research on horseshoe crabs. We are currently working with the Chinese University of Hong Kong on genomic research specifically focused on the tri-spine horseshoe crab.

Associate Professor Frank E. Rheindt.

ABSTRACT
Horseshoe crabs are unique living fossils that have remained almost unaltered through 400 million years of global change. They face rapid worldwide declines under increasing anthropogenic pressure. Using comprehensive geographic and genomic sampling combined with approaches that integrate DNA with environmental and climatic datasets, we assessed the population genetic structure, demographic histories, and vulnerability to future climate change in three out of four extant horseshoe crab species, all centered in Asia. Our study highlights that the Sunda Shelf, a complex and dynamic shallow-marine landscape, has been the sole repository of most genetic diversity among all three Asian species, and therefore crucial to the long-term survival of horseshoe crabs. Our study not only provides the first genomic baseline data for the evaluation of Asian horseshoe crabs’ conservation status but also identifies core habitats that potentially act as refugia and corridors for Asian horseshoe crab populations with impending anthropogenic global warming.

1 Introduction
Horseshoe crabs are one of the planet's foremost “living fossils”. They are known for their high morphological conservatism and a consistently slow evolutionary rate over hundreds of millions of years (Bicknell and Pates 2020). Although they are a fundamental building block of coastal marine ecosystems where they occur (Botton 2009), only four geographically restricted species remain today (Sekiguchi and Shuster 2009.1): the Atlantic horseshoe crab (Limulus polyphemus) along the Atlantic coast of the United States and the Gulf of Mexico, and three Asian horseshoe crabs, the mangrove horseshoe crab (Carcinoscorpius rotundicauda), coastal horseshoe crab (Tachypleus gigas), and tri-spine horseshoe crab (Tachypleus tridentatus), in coastal East, Southeast, and South Asia (Figure 1). Although anecdotal reports suggest declines of horseshoe crabs worldwide (John et al. 2018; Wang et al. 2020.1), important baseline population data remain scant and are mostly only available in economically advanced regions. Hence, the Atlantic horseshoe crab is more intensively studied compared with its Asian cousins (Luo et al. 2020.2), two of which (C. rotundicauda and T. gigas) are currently classified as data deficient in the IUCN Red List, whereas T. tridentatus is considered endangered.

FIGURE 1

Distribution and genetic divergence of Asian horseshoe crabs. Top left: map of the sampling localities; colored coastal lines (see legend) highlight the natural range of the three Asian horseshoe crab species; dotted lines delimit seven geographical regions (A–G) identified in genetic analysis; sampling localities are color coded according to each of the seven geographical regions. Top right: Principal component analysis (PCA) plots of horseshoe crab individuals (based on SNP dataset with 10% missing data and linked loci filtered). Colors in PCA plots correspond to colors of sampling localities on the map. Bottom: consensus population assignments (thick lines above the bar plots) and individual population assignments using ADMIXTURE (bar plots based on SNP dataset with 10% missing data and linked loci filtered) and discriminant analysis of principal components (membership assignments across SNP datasets displayed as lines under the bar plots). The consensus populations’ pairwise F_st and D_xy values (calculated based on the SNP dataset with 10% missing data and linked loci filtered) are depicted on the right of the corresponding population assignments.

The biology of all four extant horseshoe crab species has been tightly adapted to ephemeral coastline habitat and shallow-marine conditions since the late Paleozoic (Blażejowski et al. 2017; Bicknell and Pates 2020). The three Asian species’ ranges broadly overlap across the Southeast Asian Sunda Shelf, which is known as one of world's biodiversity hotspots for terrestrial (Myers et al. 2000), freshwater (He et al. 2018.1), and coastal marine (Hoeksema 2007; Schumm et al. 2019) flora and fauna. Owing to accelerated diversification rates fueled by habitat dynamics across glacial cycles, the Sunda Shelf has become a cradle of terrestrial and freshwater endemism following its first submergence at ∼400 ka (Cros et al. 2020.3; Husson et al. 2020.4; Salles et al. 2021; Sholihah et al. 2021.1; Garg et al. 2022). The region also exhibits high marine biodiversity but relatively low endemism (Costello et al. 2017.1), suggesting niche filling by dispersion (Ludt and Rocha 2015; Pinheiro et al. 2017.2), which may have turned the Sunda Shelf into a sanctuary for coastal marine biodiversity during interglacial periods.

To understand population structure, evolutionary histories, and climate change-driven vulnerability, we comprehensively sampled the three Asian horseshoe crab species across their natural range. Our results provide baseline data for conservation action geared toward the continued existence of a species group that has survived global change almost unaltered since before the age of the dinosaurs.

Far from being the 'living fossils' that 'prove evolution never happened', these four species of horseshoe crab turn out to be evidence that it has happened, driven by environmental changes that produced the present distribution and diversity, and then stabilised, resulting in a prolonged period of evolutionary equilibrium because the species were optimally adapted to their environments in warm, shallow seas with sandy beaches on which to spawn.

To anyone with the courage to lean about evolution and what causes it, which of course excludes creationists, the horseshoe crabs are not a problem for the Theory of Evolution but a vindication of it.

Refuting Creationism - How The Common Barn Swallow Shows Evolution In Progress

Hirundo rustica rustica (left) and Hirundo rustica tytleri (right) have different sexually selected traits. For example, one has a red chest and the other has a pale chest.

A pair of Hirundo rustica erythrogaster.

Credit: Matt Wilkins.

A front-row seat to evolution: What common barn swallows can teach us about how new species form | CU Boulder Today | University of Colorado Boulder

This paper in Science passed me by last December but it's too good to ignore because it is an example of something that creationists insist has never been seen because it doesn't happen - evolution in progress. And, to annoy creationists even more, it's an example of something Charles Darwin proposed as a mechanism for speciation - mate selection - as the isolating mechanism.

Barn swallows are one of the species that has formed a commensal relationship with humans that does not, like many other commensal species, involve it in consuming our crops either in the fields or in storage, from when we began building permanent or semi-permanent buildings. They are now dependent on our barns and out-houses as nesting places.

What can you tell me about the subspecies of barn swallow, Hirundo rustica, their commensal relationship with humans and their evolution into different subspecies? The barn swallow (Hirundo rustica) is a widely distributed passerine bird with several recognized subspecies that have evolved in different geographic regions. Their evolution and divergence into subspecies have been shaped by geographical isolation, ecological adaptation, and their long-standing commensal relationship with humans.

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Subspecies of the Barn Swallow (Hirundo rustica)
There are six generally recognized subspecies, each adapted to different regions:

1. H. r. rustica – Nominate subspecies
   • Breeds in Europe and Asia (west of the Urals) and winters in Africa and South Asia.
   • Characterized by a long, deeply forked tail and a reddish forehead and throat.
2. H. r. transitiva
   • Found in the Levant (Middle East, particularly Israel and Palestine).
   • Slightly darker underparts and a shorter tail compared to H. r. rustica.
3. H. r. savignii
   • Endemic to Egypt.
   • Has shorter tail streamers and a darker, more intense red coloration on the throat and forehead.
4. H. r. gutturalis
   • Breeds in East Asia (Japan, China, Korea, and parts of Russia) and winters in Southeast Asia.
   • Has a paler underbelly and slightly shorter tail than H. r. rustica.
5. H. r. tytleri
   • Breeds in central Asia (from the Altai Mountains to Mongolia and northeast China) and winters in South Asia.
   • Larger body size, darker plumage, and a more pronounced reddish throat.
6. H. r. erythrogaster
   • Found in North America, migrating to Central and South America in winter.
   • Has a deeper red or orange belly and a more robust body compared to Old World subspecies.

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Commensal Relationship with Humans
Barn swallows have one of the most well-documented commensal relationships with humans among birds. Unlike many species that avoid human settlements, barn swallows have thrived in human-altered environments, particularly in agricultural landscapes.

How They Benefit from Humans:

• Nesting Sites: They originally nested in caves and rocky outcrops but now prefer human-made structures such as barns, bridges, and eaves of houses. This shift has expanded their range and allowed for increased breeding success.
• Foraging Opportunities: Agricultural areas provide open fields where they can hunt flying insects more efficiently.
• Predator Protection: Nesting near human settlements reduces predation by natural enemies such as corvids and raptors.

Human Benefits:

• Pest Control: Barn swallows consume vast numbers of flying insects, including mosquitoes and agricultural pests, making them beneficial to farmers.
• Aesthetic and Cultural Value: Many cultures associate barn swallows with good luck and the arrival of spring.

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Evolution and Subspecies Divergence
The divergence of barn swallow subspecies is a classic example of allopatric speciation (geographical isolation) and ecological adaptation:

1. Glacial and Post-Glacial Expansion:
   • During the last Ice Age, populations were likely confined to refugia in warmer regions. As glaciers receded, they expanded into new territories, leading to genetic divergence.
2. Geographical Barriers:
   • Mountain ranges (e.g., the Himalayas), deserts, and oceans have limited gene flow between populations, leading to the formation of distinct subspecies.
3. Adaptation to Local Environments:
   • Differences in climate, insect availability, and nesting opportunities have influenced morphological and behavioral traits.
   • For example, H. r. erythrogaster in North America has evolved a more vibrant belly color, possibly due to sexual selection pressures differing from those in Europe.
4. Human Influence:
   • Their close association with human settlements has likely accelerated their spread and may have contributed to gene flow between some subspecies.

While the different subspecies show clear distinctions in plumage, size, and migratory behavior, they still interbreed where their ranges overlap, maintaining them as a single species rather than diverging into separate species.

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Conclusion
The barn swallow is a remarkable example of how a species can adapt to human presence and expand its range globally. Their subspecies have evolved due to historical climatic events, geographical isolation, and ecological pressures, yet they remain a single, highly mobile species with a complex migratory and commensal relationship with humans.

News of how they are in the process of speciating comes in the form of a paper in Science by a team led by Professor Rebecca Safran, the paper’s senior author and professor in the Department of Ecology and Evolutionary Biology at the University of Colorado Boulder, and an article in CU Boulder Today by Yvaine Ye:

A front-row seat to evolution: What common barn swallows can teach us about how new species form

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Beauty is in the eye of the beholder—even if that beholder is a barn swallow.

Depending on where the birds live, some of them may favor mates with a paler chest color while others find a redder chest more attractive. The difference in what these birds prefer when it comes to choosing a mate is helping scientists unlock one of biology’s greatest mysteries: How do new species originate?

In a new CU Boulder-led study, biologists used genetic sequencing from barn swallows around the globe to provide real-time evidence that sexual selection, in which organisms choose mates based on traits they find attractive, drives the emergence of new species.

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The study was published Dec 12 in the journal Science.

This is one of the very first papers to comprehensively show the role of mate selection decisions in the evolution of new species.

Professor Rebecca Safran, senior author
Department of Ecology and Evolutionary Biology
Colorado University Boulder
Boulder, Colorado, USA.

The new findings shed light on how new species form, a fundamental but elusive process for all life on Earth.

Proving Darwin right

Charles Darwin proposed the theory of sexual selection in 1875. It suggests that organisms evolve showy traits, like extravagant plumage or eye-catching dance moves, to attract mates. When organisms of the same species develop preferences for different traits and no longer breed with each other, new species could emerge over time, a process known as speciation.

For the past 150 years, researchers of sexual selection have primarily studied organisms that already diverged into distinct species. For example, orchids, which now encompass more than 25,000 species, originated from a common ancestor. Their remarkable diversity often leads to the assumption that they evolved different looks to attract different pollinators, said Drew Schield, the paper’s first author and assistant professor at the University of Virginia.

It’s logical to think this way and it could totally be the case, but with speciation already having occurred, it’s impossible to know for certain.

Assistant Professor Drew Schield, first author
Department of Ecology and Evolutionary Biology
University of Colorado, Boulder, CO, USA. Now at the Department of Biology
University of Virginia, Charlottesville, VA, USA.

As a result, it has been difficult to find direct evidence that sexual selection drives the emergence of new species.

Barn swallows provide a unique opportunity to explore the speciation process as it unfolds.

These birds are one of the most common and widespread species on our planet. Currently, there are six subspecies of barn swallow each looking slightly different in some traits critical to the mate choice decisions depending on where they are.

For example, the East Asian group, Hirundo rustica gutturalis, has a pale chest and shorter tail streamers—the elongated outer tail feathers. Hirundo rustica tytleri, found in Siberia, has long tail streamers and red chest feathers. The subspecies in Europe and western Asia, Hirundo rustica rustica, has a pale chest and long tail streamers.

Reuniting after isolation

Evidence suggests that the bird’s ancestors left the Nile River valley in northern Africa about 11,000 years ago and spread out across the Northern Hemisphere. For thousands of years, different populations barely interacted and developed diverse traits, forming subspecies.

Some 800 to 2000 years ago, certain subspecies expanded their territories, and habitats began to overlap. In some parts of the world, subspecies now interact with each other, producing hybrid offspring.

Safran and her team set out to investigate whether sexual selection in these birds was driving the speciation process.

The team, including Elizabeth Scordato, associate professor at the California State Polytechnic University, sequenced the genomes of 336 barn swallows from around the globe, encompassing all subspecies and three hybrid zones, where subspecies interbreed, in Eurasia.

The researchers found a dozen regions in the barn swallow genome associated with the birds’ two sexually selected traits: Ventral coloration—the plumage color of their chest and belly— and tail streamer length.

When individuals reproduce, the genes from both parents reshuffle and combine to form the genes of their offspring. When two populations encounter one another, the flow of genetic material from one to another is a marker of how similar the populations are. If the rate of gene flow is low, it means the two populations are breeding with each other at a lower rate than they would if they are the same species.

The study found that in barn swallow hybrid zones much of their genes flows freely across groups. But the genetic regions coding for ventral coloration and tail streamer length hardly transfer to other populations.

A pair of Hirundo rustica rustica in Turkey.

Credit: Matt Wilkins.

It suggests that among the hybrid individuals with parents from different subspecies, a small number of lucky birds that inherit a favorable combination of tail streamer and ventral color genes are able to attract mates. Hybrids that receive less favorable combinations tend to be less successful in reproduction.

These genes are hitting a boundary due to divergent sexual selection, and they stop moving from one population to the other.

Assistant Professor Drew Schield.

The different preferences for tail feather length and chest color across subspecies make barn swallows more likely to mate within their own group, Schield added. If the trend continues, these groups could no longer interbreed or produce offspring, markers for the formation of separate species.

Next, the team plans to sample more birds and study whether being a hybrid affects reproductive success.

It’s very cool that we could capture a real-time evolutionary portrait of this common animal and understand how and why the populations are diverging. Our understanding of the process is fundamentally important for addressing a wide range of questions related to biodiversity, evolution and conservation.

Professor Rebecca Safran.

Structured Abstract

INTRODUCTION
Assessing how sexual traits and their genetic basis contribute barriers to gene flow in secondary contact due to effects on hybrid fitness remains critical to establishing a causal role of sexual selection in in speciation. Leveraging natural systems with intraspecific variation in sexual traits at early stages of the speciation process holds promise for identifying links between patterns of phenotypic and genomic variation and the evolution of reproductive isolation.

RATIONALE
Observational and experimental studies indicate that barn swallows (Hirundo rustica) are a robust empirical model of divergent sexual selection and that the presence of multiple hybrid zones between populations in Eurasia enables investigation of barriers to gene flow. We investigate genotypic and phenotypic variation in barn swallows to (i) map the genetic basis of plumage traits used in sexual signaling, (ii) test whether loci underlying sexual traits have experienced divergent sexual selection in allopatry and present barriers to gene flow in secondary contact, and (iii) test the prediction that sexual selection has maintained linkage disequilibrium (LD) between barrier loci in secondary contact as a result of their effects on hybrid fitness.

RESULTS
We sequenced the genomes of 336 barn swallows sampled across the breeding distribution of the species and quantified variation in ventral coloration and tail streamer length, two signal traits used in mate choice. Populations differ in these traits and hybrids between the subspecies rustica, tytleri, and gutturalis exhibit phenotypes that are intermediate between or similar to parental populations. The genetic architecture of ventral color is concentrated on chromosome 1A and the Z chromosome whereas phenotypic variation is largely explained by genotypic variation at 10 loci, including the melanogenesis genes KITLG, SLC45A2, and BNC2. Variation in tail streamer length is explained by loci on chromosome 2. Sexual trait loci—ventral color loci in particular—exhibit peaks of high differentiation between populations and signatures of divergent positive selection in allopatry. We further investigated whether loci under divergent sexual selection contribute barriers to gene flow in secondary contact using geographic and genomic cline analyses across hybrid zone transects, finding that sexual trait loci constitute barriers in the rustica-tytleri and rustica-gutturalis hybrid zones whereas gene flow is less constrained across the remainder of the genome. Clines for sexual trait loci in these hybrid zones also show a high degree of concordance, consistent with selection for specific combinations of alleles from parental populations in hybrids. Finally, we tested whether selection has generated ongoing coupling of barrier loci by investigating LD patterns in hybrid zones. These tests reveal elevated LD among sexual trait barrier loci in hybrids beyond what is expected under admixture alone, consistent with the genetic coupling of barriers being an emergent property of divergent sexual selection.

CONCLUSION
Our findings demonstrate an important role for sexual selection in speciation through the analysis of the genomic basis of sexual signal traits in barn swallows, evidence for divergent selection in geographic isolation, and evidence that loci underlying traits involved in prezygotic isolation represent barriers to gene flow. Our results further support the conclusion that the genetic coupling of sexual trait loci generated by selection promotes reproductive isolation upon secondary contact.

Sexual signal traits form barriers to gene flow upon secondary contact. Barn swallows breed across nearly the entire North Hemisphere and exhibit variation in sexual signal traits across populations. Hybrid zones between these populations enable the identification of the genetic basis of sexual traits and tests of the hypothesis that divergent sexual selection promotes reproductive isolation. Genetic loci underlying sexual traits show signatures of divergent selection between allopatric populations and are barriers to gene flow in secondary contact, whereas gene flow is less constrained across the rest of the genome.

Abstract
Despite the well-known effects of sexual selection on phenotypes, links between this evolutionary process and reproductive isolation, genomic divergence, and speciation have been difficult to establish. We unravel the genetic basis of sexually selected plumage traits to investigate their effects on reproductive isolation in barn swallows. The genetic architecture of sexual traits is characterized by 12 loci on two autosomes and the Z chromosome. Sexual trait loci exhibit signatures of divergent selection in geographic isolation and barriers to gene flow in secondary contact. Linkage disequilibrium between these genes has been maintained by selection in hybrid zones beyond what would be expected under admixture alone. Our findings reveal that selection on coupled sexual trait loci promotes reproductive isolation, providing key empirical evidence for the role of sexual selection in speciation.

Schield, Drew R.; Carter, Javan K.; Scordato, Elizabeth S. C.; Levin, Iris I.; Wilkins, Matthew R.; Mueller, Sarah A.; Gompert, Zachariah; Nosil, Patrik; Wolf, Jochen B. W.; Safran, Rebecca J. (2024)
Sexual selection promotes reproductive isolation in barn swallows
Science; 386(6727) eadj8766; DOI: 10.1126/science.adj8766

Copyright: © 2024 The authors.
Published by American Association for the Advancement of Science. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

So, there we are; as good an example as any creationist would wish to ignore, of observed evolution in progress as the barn swallow diversifies into species which then become species as barriers to geneflow evolve to ensure complete genetic isolation. And an example of how, as the process of speciation progresses, interbreeding is still possible when the process is sympatric, in other words, where the two gene pools are not physically isolated. This is pretty much how human speciation occurred both in Africa and in Eurasia when Homo erectus followed by H. sapiens migrated there.