Refuting Creationism - Evolution of Cultivated Cotton - No Magic Required

Wild cotton, on left, has short, brown, and coarse fibers, while modern domesticated cotton has white, fine and abundant fibers. A new study led by Iowa State University scientists identified the northwestern Yucatan Peninsula in Mexico as the original source of domesticated cotton.

Photo: Corrinne Grover/Iowa State University.

Cotton’s roots trace to Yucatan Peninsula, where wild gene pool runs deepest - News Service

My last blog post looked at the evolution of the strawberry and how the evidence of multiple whole-genome duplications and speciation by hybridisation refutes several basic creationist, counter-evidential myths and articles of faith.

This post deals with the evolution and cultivation of the cotton plant, which again refutes the childish notion of divine creation, perfectly suited for use by the creator god's favourite creation, humankind, as well as the creationist article of faith that no new genetic information can arise without the direct intervention of a designer god, because this would supposedly violate the laws of thermodynamics.

As a recent paper in Proceedings of the National Academy of Sciences of the USA (PNAS), by a team of researchers including Professor Jonathan Wendel of Iowa State University, has shown, modern upland cotton, Gossypium hirsutum, is the result of thousands of years of human selection acting on naturally occurring genetic variation. The team traced its domestication to the Yucatán Peninsula in Mexico, probably to the north-western Yucatán, where wild populations still retain the deepest gene pool. Cotton was first domesticated there about 5,000 years ago, which, if creationist chronology were taken seriously, places it before the supposed genocidal global flood, which it appears to have survived along with the people who cultivated it.

The researchers found that domestication transformed a wild, perennial shrub with small bolls and short, coarse, brown fibres into the modern crop with abundant, long, fine, white fibres. This was not the result of a single act of magical design, nor of a sudden, miraculous improvement, but of long-term selection acting on many mutations of relatively small effect, accumulated and filtered over many generations.

The team also showed that, while human selection produced fibres more useful to people, it did so at a cost. Useful traits present in wild populations, such as disease resistance and salt tolerance, were left behind as farmers selected repeatedly from a restricted subset of the original wild gene pool. Each generation of selection narrowed the genetic base still further, pushing cultivated cotton through a genetic bottleneck.

The researchers reached these conclusions by comparing the genomes of cultivated cotton with those of specimens collected from wild populations across the plant's native range. Their analyses showed that domesticated cotton is most closely related to wild cotton from north-western Yucatán, where two random wild plants still show, on average, about twice as much genetic difference as two random modern cultivars.

After cultivated upland cotton spread out of the Yucatán, it eventually became the dominant cotton crop worldwide, displacing or overshadowing other cotton species that had been independently domesticated in South America, Africa and India. Today, Gossypium hirsutum, or upland cotton, accounts for about 90% of the world's cotton crop.

Refuting Creationism - How The Strawberry Evolved - No Magic Needed

Wild starwberry, Fragaria vesca

By Jörg Hempel, CC BY-SA 3.0 de, Link

A genomic time machine traces how the modern strawberry came to be | EurekAlert!

Doubtless God could have made a better berry, but doubtless God never did

Dr. William Butler, Physician - (1535–29 January 1618)
Talking of the strawberry.

This and my next blog post deal with essentially the same refutations of creationist mythology and pseudo-science. The mythology is the Bible’s unambiguous claim that a creator god made everything for its favourite creation, humankind; the pseudo-science is the creationist claim that no new genetic information can arise without the direct intervention of that creator god, because, so they tell us, new genetic information can only be produced by magic, otherwise it would violate the laws of thermodynamics [sic]. Both claims are demonstrable nonsense, of course.

The first example concerns a fruit now ripening in UK gardens and fields — the strawberry. If strawberries had been specially created for humans, we might expect them to have arrived fully formed, already perfect for our tastes and purposes. Instead, like other cultivated crops, they bear the marks of a long evolutionary history followed by recent human selection, breeding and improvement.

A May 2025 paper published in the journal Horticulture Research by researchers from the U.S. Department of Agriculture and collaborating institutions, describes a new way to reconstruct the deep evolutionary history of the cultivated strawberry, Fragaria × ananassa. Their work helps explain how the modern strawberry acquired its complex octoploid genome — not by magic, but by ordinary, natural processes of genome duplication, hybridisation and subsequent evolutionary divergence.

Cultivated strawberries, like many crop plants, are polyploids. Humans are normally diploid, with two sets of chromosomes; cultivated strawberries are octoploid, with eight sets. In the notation used by geneticists, humans are 2n, while the cultivated strawberry is 2n = 8x = 56. This genomic complexity is the outcome of a series of ancient whole-genome duplication and hybridisation events in which entire chromosome sets from different ancestral lineages were brought together in one organism.

Whole-genome duplication does not require supernatural intervention. It is a well-known natural process, especially common in plant evolution. Initially, it duplicates existing genetic material, but those extra gene copies then provide raw material for mutation, altered regulation, divergence, subfunctionalisation and neofunctionalisation. In other words, duplicated genes can be retained, modified, silenced, repurposed or combined in new ways. Hybridisation adds another layer of novelty by bringing together different genomes, producing new combinations of genes and regulatory networks in a single evolutionary lineage.

The research team disentangled the strawberry’s complex polyploid genome by exploiting the evolutionary signatures left by long terminal repeat retrotransposons, or LTR-RTs. These mobile genetic elements accumulate in genomes over time and can act rather like molecular time stamps. By comparing patterns of similarity between these elements across chromosomes, the researchers were able to reconstruct the strawberry’s subgenome architecture and infer the timing of major genome-merging events.

Using this serial similarity matrix method, the researchers found evidence for three successive allopolyploidisation events in the evolutionary history of the cultivated strawberry genome: first between about 3.1 and 4.2 million years ago, then between about 1.9 and 3.1 million years ago, and finally between about 0.8 and 1.9 million years ago. The result is a genome composed of multiple subgenomes with different ancestry, interacting and evolving together over time.

What is perfectly clear from this research is that new genetic variation and genomic complexity can arise through entirely natural mechanisms. Polyploidy, hybridisation, mutation, transposable elements and selection are not gaps in biology into which a magic creator needs to be inserted; they are part of the normal machinery of evolution. The cultivated strawberry is not evidence of special creation, but of a long, traceable evolutionary history later shaped by human cultivation.

Refuting Creationism - The Unintelligently Designed Ancestral Potato and How Humans Improved It

S. jamesii tubers in a ceremonial basket.

Credit: Alastair Bístoí

S. jamseii flowers

Credit: Tim Lee/NHMU

This wild potato may change the agricultural story in the American Southwest – @theU

Anthropologists at the University of Utah and the Natural History Museum of Utah have traced the anthropogenic spread and cultivation of a relative of the potato, Solanum jamesii (the Four Corners potato). Their findings are published in PLOS ONE. This plant has been a culinary, medicinally and culturally important food crop across the Colorado Plateau for millennia.

Until now, despite its long history, the extent to which indigenous people domesticated S. jamesii has been unknown. Genetic evidence has shown that it had been transported and cultivated far from its natural range and had acquired frost resistance, longer dormancy and sprouting resilience, all of which made it more suitable for cultivation in its anthropogenic range. The Utah team have now shown how it arrived on the Colorado Plateau from its origins in the south-west USA, probably through a trading network.

A problem which I have found impossible to get a creationist to address without them running for the bolt-hole of ‘mysterious ways’ is the fact that, with only a very few exceptions, every domesticated animal and cultivated plant has been considerably improved on the wild stock and is always the result of a human-mediated evolutionary process. The result is often almost unrecognisable as the same species as their wild ancestor.

Yet according to the Bible, all animals and plants were created for the sole benefit of humankind by a supposedly omnipotent, omniscient god. Had that been so, we could expect them to have been created fit for purpose and perfectly suited to the uses to which we put them. The fact that we have had to adapt them and change them so drastically to make them fit for purpose gives the lie to claims of intelligent design by an omniscient designer.

This relative of the potato therefore serves as an illustration of how humans, unwittingly or otherwise, have modified and changed the distribution of cultivated plants by inadvertently mimicking the process of evolution — mutation → selection → reproduction. S. jamesii is native to the Mogollon Rim, a region spanning south-central Arizona and into the Mogollon Mountains of New Mexico. The researchers were able to build a picture of how this plant was transported from there to the Four Corners region of southern Utah, south-west Colorado and north-west New Mexico by extracting the characteristic starch granules embedded in the stone tools used to process the tubers, recovered from 14 archaeological sites within and beyond the tuber’s natural range.

This research adds to the growing body of evidence that indigenous people in the south-western USA actively cultivated crops of their own and did not just acquire them from other peoples. It had previously been believed that they relied primarily on crops domesticated in Mesoamerica, such as maize, beans or squash. It also adds another species to the long list of plants and animals that have had to be modified from their wild type, and for which creationists are at a loss to explain why their supposed omniscient designer god did not do a very good job of it to begin with.

Creationism Refuted - Why Did The 'Creator' Get It So Wrong?

Domestic animals

A sample of cultivated root crops.

The fundamental problem for creationists is their dependence on a book that can so easily shown to be wrong on almost every level. It's rather like taking an imaginative story made up by an uneducated 6-year-old to explain the world as he or she saw it and pointing out the errors in it.

Trivially easy, especially for someone with a little education, especially in the relevant subject like biology, geology, cosmology and history.

One of the more glaring errors is very early on in the Bible narrative which describes how a magic creator created all the animals for human use. It comes mostly from the first version of creation. In this version, the animals were all created before a man and a woman who were both created together, and then the animals and plants were all given to them for 'meat'.

In the second version, a man was created alone, then the animals, then a woman.

Obviously, both can be true, but it is mostly from the first version that creationists get the idea that all the animals and plants in the world were created especially for them. And that's where things begin to fall apart on close inspection of the facts.

Here is how the story goes. The first version:

Creationism in Crisis - Evolution of Wheat Since the Neolithic

Creationism in Crisis

Evolution of Wheat Since the Neolithic

Awned wheat, similar to that grown for 10,000 years since first cultivated in the Neolithic

The cultivation of cereals such as wheat represented a turning point in the progress of human civilisation (cylinder seal from Uruk, 3.200 BCE).

Evolution of wheat spikes since the Neolithic revolution - Universitat de Barcelona

The evolution of cultivated wheat presents challenges most Creationists will avoid if possible. The first and perhaps most obvious challenge is why has wheat needed to be improved by cultivation and human selection if, as Creationists believe, it was created by a perfect, omniscient designer for the benefit of humans? Did the designer not foresee the future needs of humans or anticipate the problem of feeding a large population from a crop with inadequate yields?

The second is that fact that, despite the ludicrous Creationists' insistence that the Theory of Evolution (TOE) is a theory in crisis, and about to be overthrown as a scientific theory by their superstition, including magic and an unproven magical entity, the only viable explanation for the changes which have occurred over time is selection by human agency, in other words a form of accelerated evolution by natural selection and primitive genetic engineering by people who knew nothing of genetics, just like the natural environment.

Awnless wheat, similar to that which first appeared about 2,000 years ago.

Archaeological records show that, for about 10,000 following the first cultivation of wild wheat in Mesopotamia about 12,000 years ago, wheat grains had long awns, then about 2000 years ago, wheat diversified into awned and awnless or very short awned varieties.

Clearly, given the length of time awned whet was grown, there was not strong selection for awnless wheat, so why did the different varieties evolve, apparently suited to different environmental conditions. This was the question a study, published in the journal Trends in Plant Science, co-led by the University of Barcelona, the Agrotecnio centre and the University of Lleida, set out to answer. Creationists might note that nowhere does magic or a magic entity appear in the explanation, which depends in its entirety on the workings of the TOE.

The research and its significance are explained in a University of Barcelona news release: