Rosa Rubicondior: Creationism Refuted - The Simple Mutation That Made Grasses So Successful

Sunday, 23 August 2026

Creationism Refuted - The Simple Mutation That Made Grasses So Successful - 100 Million Years Before 'Creation Week'

Maeda and his collaborators sequenced the slow-growing Joinvillea ascendans plant, a close relative of grasses, to compare genomes and learn what makes grass plants unique.

Photo: Sarah Friedrich.

Molecular “bypasses” improve grass plants’ synthesis of lignin and starch, laying the early groundwork for evolutionary success – Department of Biology – UW–Madison

Creationists routinely claim that mutations can only damage genetic “information” and can never produce anything genuinely new. The claim depends partly upon leaving information conveniently undefined and partly upon ignoring the many well-understood processes by which genomes acquire new functions. Gene duplication, mutation and natural selection can preserve an existing function while a spare copy accumulates changes, sometimes enabling it to perform an additional task or participate in a new biochemical pathway.

A new study published in Science provides an unusually clear example. Rather than merely showing that related organisms possess different enzymes, Yuri Takeda-Kimura and colleagues reconstructed how two important metabolic innovations arose during the ancestry of grasses: additional routes for producing starch and lignin. They did this by comparing the genomes of grasses with those of several of their closest non-grass relatives, including Joinvillea, Ecdeiocolea, Pharus and Typha.

Grasses are now among the most ecologically and economically important plants on Earth. The family Poaceae includes wheat, rice, maize, barley, oats, rye, millet and sugarcane, as well as the grasses that dominate vast areas of grassland and support grazing ecosystems. Part of their success lies in their ability efficiently to direct carbon into starch, which stores energy, and lignin, which strengthens cell walls and permits stems and leaves to remain upright while transporting water.

Most plants manufacture lignin through a pathway beginning with the amino acid phenylalanine. Grasses and their closest relatives possess an additional route that can begin with tyrosine and bypass one of the reactions in the older pathway. The researchers traced this biochemical shortcut to an ancient tandem duplication of the gene for phenylalanine ammonia-lyase, or PAL. One copy retained the ancestral function, while the other evolved into the bifunctional enzyme phenylalanine/tyrosine ammonia-lyase, or PTAL.

Crucially, biochemical and structural experiments showed how little genetic change was required. Two amino-acid substitutions—F140H and S112I—were sufficient to convert the ancestral-type PAL enzyme into one with PTAL activity. The altered enzyme could therefore use tyrosine as well as phenylalanine, opening an additional route into lignin production. The duplicated gene had not merely been damaged: mutations had expanded what its protein product could do and helped create a new metabolic pathway.

The second innovation had a different history. A whole-genome duplication known as the rho duplication occurred in the lineage leading to the common ancestor of all living grasses. The extra gene copies produced by this event subsequently contributed to an additional cytosolic pathway for starch synthesis. The lignin shortcut had therefore evolved earlier, before grasses themselves appeared, whereas the duplicated starch pathway arose later in their common ancestor.

That order matters. Comparative genomics places each innovation on a particular branch of the evolutionary family tree. The features did not appear simultaneously as part of a fully formed and immutable grass “kind”. They accumulated successively: duplication supplied additional genetic material, mutations modified enzyme activity, and descendants inherited the resulting biochemical machinery.

Nor does evolution require an entirely unprecedented enzyme to appear from nowhere. It works with what already exists, copying, modifying and redeploying components. In this case, an ancestral enzyme was duplicated and only two substitutions were needed to broaden the activity of one copy. If creationists wish to insist that mutation cannot create new information, they must explain why mutations that gave an enzyme a new substrate and created an additional route to an important biological product should not count.

The research is described in the open-access paper, Genomes of Poaceae relatives reveal key metabolic innovations preceding the evolution of grasses. Together, the genomic, biochemical and structural evidence documents precisely the sort of incremental, mutation-driven innovation that creationist apologetics says cannot happen.

How Gene Duplication and Mutation Produce New Functions. Genes can be copied accidentally during DNA replication, chromosome rearrangement or the duplication of an entire genome. Initially, both copies contain the same genetic instructions. Because one copy can continue performing the original function, mutations in the other may accumulate without depriving the organism of an essential enzyme.

Most duplicated genes are eventually lost or disabled, but occasionally a copy acquires a useful additional activity. Natural selection can then preserve and refine it. This is one of the principal ways in which evolution produces new genes, protein functions and biochemical pathways from existing biological components.

From PAL to PTAL

Most vascular plants begin lignin production using the amino acid phenylalanine. The enzyme phenylalanine ammonia-lyase, or PAL, converts phenylalanine into cinnamic acid. Another enzyme must then convert that into p-coumaric acid, an important precursor of lignin and other phenylpropanoid compounds.

Before grasses evolved, the ancestral PAL gene underwent a tandem duplication, meaning that an additional copy was created alongside the original gene. One copy retained the ancestral PAL function. The other evolved into phenylalanine/tyrosine ammonia-lyase, or PTAL, which could also convert tyrosine directly into p-coumaric acid. This provided an alternative, shorter entry route into lignin production.

The researchers identified two amino-acid substitutions that were sufficient to produce this expanded activity:

F140H: phenylalanine at position 140 in the enzyme was replaced by histidine.

S112I: serine at position 112 was replaced by isoleucine.

Introducing both substitutions into an ancestral-type PAL enzyme enabled it to use tyrosine much more effectively. The mutations therefore did not merely damage or remove an existing function: they broadened the enzyme’s range of substrates and made an additional biochemical route possible.

Is This “New Genetic Information”?

Creationists frequently assert that mutation cannot create new genetic information, but they rarely provide a measurable scientific definition of “information” that could be tested or falsified. In this example, evolutionary change produced:

additional inherited DNA through gene duplication;

a modified protein sequence;

an enzyme able to act efficiently upon an additional substrate;

a new reaction available to the plant’s metabolism; and

an alternative route towards an important biological product.

If additional DNA, an expanded enzyme function and an additional metabolic route are all excluded from the definition of “new information”, the creationist assertion has been protected by wordplay rather than supported by evidence. Scientifically, this study demonstrates exactly how mutation and duplication can expand the functional capabilities encoded by a genome.

The paper was accompanied by University of Wisconsin–Madison news release:

Molecular “bypasses” improve grass plants’ synthesis of lignin and starch, laying the early groundwork for evolutionary success
One hundred million years ago, long before human intervention, ancestors of grasses, like wheat, rice and maize generated “bypasses” of chemical pathways that are used to create two critical compounds: lignin and starch. These more efficient pathways could explain why grass plants are so successful in nature and agriculture, according to a new paper recently published in Science by researchers from the University of Wisconsin–Madison and their collaborators.
Like a beltway that creates a more flexible traffic flow in a city, these metabolic bypasses led to efficient and robust synthesis of both lignin and starch, chemical compounds that are critical for plants.

Grasses and cereal grains make up the majority of global human caloric intake. However, it remains a mystery how these grasses became dominant and successful in both nature and later in agriculture. The lab of Hiroshi Maeda, a professor of botany at UW–Madison, teamed up with researchers from around the world to address this question.

The team was particularly interested in the metabolism of grasses, focusing on genes that are needed to make starch and lignin. Grasses are rich in starch, a complex carbohydrate that acts as the plant’s energy storage, and their rapid growth requires the efficient production of lignin, a major component of plant biomass.

Just as scientists use the chimpanzee’s genome as a comparison tool to study how humans evolved, Maeda’s group and their collaborators including James Leebens-Mack from University of Georgia, turned to one of the closest relatives of grasses, Joinvillea ascendens.

This long-leafed plant is found in wet forests of the South Pacific islands and grows much more slowly than many grasses.

Only two out of over 100 seeds obtained from the National Tropical Botanical Garden in Hawaii germinated initially. It took another two years for these plants to grow large enough to be harvested for genomic sequencing. Then, they were finally able to sequence the genomes of Joinvillea, along with three related species.

Comparing thousands of genes found in these genomes, they revealed that Joinvillea has only one pathway to create starch. All grasses though, have two.

Joinvillea ascendans, a close relative of grass plants.

Photo: Sarah Friedrich.

This means that an additional starch synthesis pathway, or a bypass route, emerged at the common ancestor of all grasses and now allows grasses to produce double the amount of energy than Joinvillea and other non-grass plants.

In the natural world, a seed with more energy packed inside can germinate, sprout out of the ground, and begin the process of photosynthesis sooner. That allows the plant to grow taller quickly, outcompeting surrounding slower growing plants.

That likely gave a competitive advantage to grasses to grow in open habitat, where a lot of plants would love to grow because of all the sun. That’s one potential reason why grasses ended up maintaining this highly efficient starch pathway. That same metabolic trait was also very beneficial to agriculture.

Professor Hiroshi Maeda, senior author.
Department of Botany
University of Wisconsin–Madison
Madison, WI, USA.

The researchers, including Maeda’s postdoctoral researcher, Yuri Takeda-Kimura, were also interested in how grasses and Joinvillea produced lignin, a chemical compound that gives strong structural support to plants. Plants with high lignin content, like woody plants, tend to grow slowly. Grasses, however, are an exception; they can grow rapidly despite having relatively high lignin contents.

Tracing back the history of lignin synthesis pathways, the team found that both grasses and Joinvillea had two pathways for lignin synthesis.

It turned out, this unique feature of grasses being capable of synthesizing lignin by two routes, evolved even before grasses existed.

Professor Hiroshi Maeda.

Knowing when this critical change happened, the team further discovered how the dual lignin pathways were generated.

We found two mutations in their DNA that are critical and sufficient to create this new bypass pathway. So, that means, we can actually introduce similar mutations in other plants to create this second lignin pathway.

Professor Hiroshi Maeda.

Maeda says that understanding what makes grasses unique opens doors for future improvements to cereal and bioenergy crops and other plants, whether it be augmented energy stores through additional starch synthesis pathways or improved structure strength and resilience through increased production of lignin and other related compounds. Maeda and his collaborators are using this basic science knowledge for potential applications in plant biotechnology to improve sustainable production of beneficial nutrients and other useful chemicals in agricultural and bioenergy crops.

Publication:
Yuri Takeda-Kimura et al.
Genomes of Poaceae relatives reveal key metabolic innovations preceding the evolution of grasses. Science 393, eadv0443 (2026). DOI:10.1126/science.adv0443

Structured Abstract

INTRODUCTION
The grass family (Poaceae) includes foundational primary producers in global ecosystems and economically important crops. Rice, wheat, and maize account for more than 40% of caloric intake for humans, and sugarcane, sorghum, and bamboo make abundant sugars and lignocellulosic biomass for renewable bioenergy and biomaterial production. Their genome assemblies have advanced our understanding of critical traits in agriculturally and ecologically important grass species. However, we still lack chromosomal assemblies for their closest relatives, which diverged from grass progenitors more than 100 million years ago, before the rho whole-genome duplication (ρWGD) in the ancestor of all grasses. This gap limits our understanding of how gene and genome duplications contributed to evolutionary innovations that define the grass lineage.

RATIONALE
This study generated reference-quality genomes for Joinvillea ascendens and Ecdeiocolea monostachya, which represent the sister lineage to all grasses, along with Pharus latifolius and Typha latifolia, which represent sister lineages to core grasses and all other members of the order Poales, respectively. Using these new genomic resources, we traced the evolutionary history of two distinctive metabolic traits of grasses: dual starch and lignin biosynthetic pathways. These grass-specific metabolic innovations contribute to the starch-rich endosperm of cereals and substantial lignin deposition in the vasculatures and fibers of grasses.

RESULTS
In this study, the new high-quality genome assemblies and annotations enabled comparative genomic analyses to place the timing of the ρWGD event just after the divergence of ancestral lineages leading to the grasses and their sister clade, including Joinvilleaceae and Ecdeiocoleaceae. Phylogenetic and molecular evolutionary analyses of more than 20 gene families involved in starch biosynthesis across many Poaceae and Poales species revealed that ρWGD contributed to the duplication of several of these genes, which now support cytosolic starch biosynthesis in grass endosperms. By contrast, genome comparisons and biochemical analyses of the lignin biosynthesis pathway revealed that an earlier tandem duplication of phenylalanine ammonia lyase (PAL) gave rise to phenylalanine/tyrosine ammonia lyase (PTAL) before the ρWGD and the origin of grasses, enabling grasses to synthesize lignin and other phenylpropanoid compounds from two aromatic amino acid precursors, phenylalanine and tyrosine. Precise determination of the timing of the plant PTAL evolution, combined with site-directed mutagenesis and x-ray crystal structural analyses, further identified two key residues, Ile¹¹² and His¹⁴⁰, that are responsible for the neofunctionalization of plant PAL into PTAL, providing a promising gene-editing strategy to enhance diverse phenylpropanoid production in plants.

CONCLUSION
Our integrated genomic, biochemical, and structural analyses, supported by robust phylogenetic resolution of grasses and their relatives, have unveiled the evolutionary history and molecular basis of key metabolic innovations predating the emergence of grasses. Our findings highlight critical roles for both WGDs and tandem gene duplications as drivers of evolutionary innovation. The nonmodel, noncrop Poales reference genomes generated for this study now offer valuable resources for dissecting the diverse and complex traits that contribute to the ecological and economic importance of grasses. The evolutionary basis of grass-specific traits will inform efforts to conserve grass-dominated ecosystems and accelerate breeding and engineering of cereals and other grass crops for sustainable production of food, feed, bioenergy, and biomaterials.

Metabolic innovations that predate the origin of grasses.
This study sequenced genomes of four Poales species—one grass and three grass relatives (encircled photos)—and revealed key metabolic innovations that took place before the ρWGD and the emergence of the grass (Poaceae) family. Our integrated phylogenomic, biochemical, and structural analyses further identified two amino acid substitutions (His¹⁴⁰ from Phe and Ile¹¹² from Ser) underlying the neofunctionalization of the enzyme PAL into PTAL.

Abstract
The grass family (Poaceae) has immense economic and ecological importance and exhibits distinctive metabolic traits, including dual starch and lignin biosynthetic pathways. We sequenced the genomes of Pharus, Joinvillea, Ecdeiocolea, and Typha species to investigate when and how these metabolic innovations evolved relative to the origin of the grass family. The rho whole-genome duplication (ρWGD) within the lineage that led to the last common ancestor of all grasses contributed to the gene family expansions underlying cytosolic starch biosynthesis, whereas an earlier tandem duplication of phenylalanine ammonia lyase (PAL) gave rise to phenylalanine/tyrosine ammonia lyase (PTAL), which is responsible for the dual lignin biosynthesis. Integrated biochemical, functional, and structural studies, guided by phylogenomic analyses, further revealed the molecular basis of key metabolic innovations predating the evolution of grasses.

Yuri Takeda-Kimura et al.
Genomes of Poaceae relatives reveal key metabolic innovations preceding the evolution of grasses. Science 393, eadv0443 (2026). DOI:10.1126/science.adv0443

© 2026 American Association for the advancement of Science.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

There is no room in this history for a young Earth or for grasses appearing suddenly as part of a collection of separately created “kinds”. The alternative lignin pathway arose before the grass family itself, while the duplicated starch pathway appeared later in the common ancestor of all grasses. These successive innovations were inherited, modified and retained across immense spans of evolutionary time—long before the few thousand years permitted by creationist mythology.

The genetic evidence is equally inconvenient. Gene duplication created additional DNA; mutations altered the resulting protein; and two amino-acid substitutions enabled an enzyme to use an additional substrate, thereby opening another route into lignin production. This was new inherited capability produced by mutation—new genetic information in every biologically meaningful sense of the term. Declaring that it does not count simply makes the creationist claim immune to evidence and therefore scientifically worthless.

These molecular changes eventually contributed to one of the most consequential developments in the history of terrestrial life. Grasses came to dominate enormous areas of the planet, reshaping landscapes, fire regimes, carbon cycling and food webs. Their spread influenced the evolution of grazing mammals and the predators that followed them; much later, cereal grasses such as wheat, rice, maize, barley and millet became foundations of agriculture and human civilisation.

Yet none of this was planned in anticipation of grasslands, grazing animals or future human farmers. Genome duplications occurred without foresight, mutations arose without regard to what organisms might need, and their consequences depended upon the environments in which their possessors lived. Natural selection preserved changes that happened to confer an advantage, while countless others disappeared. The eventual ecological dominance of grasses was not a destination towards which evolution had been directed but the contingent outcome of inherited variation filtered over deep time.

From two substitutions in an enzyme to grasslands covering continents, the history is one of cumulative, fortuitous opportunity rather than intelligent planning. No supernatural designer needed to foresee the result, manufacture a completed biochemical system or introduce a fully formed grass “kind”. Ordinary mutation, duplication, inheritance and selection were sufficient—and the genomes of living plants still contain the evidence.

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