Rosa Rubicondior: Refuting Creationism - How New Genetic Information Arises

Saturday, 29 March 2025

Refuting Creationism

How New Genetic Information Arises
Naturally

Scientists uncover key mechanism in evolution: Whole-genome duplication drives long-term adaptation | Research

Evolved macroscopic "snowflake" yeast from the MuLTEE experiment. The large size of the nuclei (yellow) and cells (cyan) are results of whole-genome duplication and aneuploidy.

Credit: Ratcliff Lab

It is a common claim in creationist circles, despite clear evidence to the contrary, that information theory prevents the creation of new genetic information. They argue incorrectly that Shannon Information Theory dictates that the total amount of information in the universe is fixed. According to this flawed view, creating new genetic information would violate the First Law of Thermodynamics, which states that energy can neither be created nor destroyed.

However, this interpretation demonstrates a misunderstanding of both thermodynamics and Shannon Information Theory, as well as how these concepts relate to genetic information. In reality, the creation of new genetic information can be readily observed each time cells replicate, as the total genetic content effectively doubles, The elements the 'information' is composed of are neither created nor destroyed in the process and, as the result of chemical processes, there is less energy in the system, so the laws of thermodynamics are conserved.

Gene duplication and entire genome duplication (polyploidy) are common occurrences in biology, particularly within the plant kingdom, where tetraploidy — possessing twice the usual diploid number of chromosomes — frequently arises. It is also sometime seen in arthropods, amphibians and reptiles.

Tetraploidy often appears spontaneously in laboratory populations of various organisms. Typically, without selective pressures favouring polyploid states, these conditions tend to revert to diploidy after several generations. However, recent studies by scientists at Georgia Tech, conducting multicellular long-term evolution (MuLTEE) research with 'snowflake yeast', Saccharomyces cerevisiae, have demonstrated that under specific selective pressures, polyploidy can become stable and confer advantageous survival traits to the organism.

The selection pressure in this case was selecting the largest yeast cells from which to produce the next generation. The researchers discovered that polyploidy had arisen early on in the experiment, after about 10 generations, and polyploid cells tended to be the largest cells, so a polyploid strain quickly arose and remained polyploid over thousands of generations - far longer than would be expected if selection had been random or unrelated to cell size.

Understanding Polyploidy: A Beginner's Guide

Polyploidy is a genetic phenomenon that occurs when an organism inherits extra sets of chromosomes.

To understand this, it's helpful to know that chromosomes are structures within cells that carry genetic information (DNA). Most animals, including humans, typically have two sets of chromosomes—one inherited from each parent—making them diploid.

However, polyploid organisms possess more than two complete sets of chromosomes. For example, a tetraploid organism has four complete sets. Polyploidy is quite common in plants and can sometimes occur in animals, though less frequently.

This increase in genetic material can lead to significant changes in an organism, such as larger size, greater robustness, and enhanced ability to adapt to new or challenging environments. Polyploidy has played a vital role in evolution, particularly within the plant kingdom, allowing species to diversify and adapt effectively.

Glossary of Technical Terms

Chromosomes: Structures within cells containing genetic information (DNA).
Diploid: An organism or cell containing two complete sets of chromosomes, one set from each parent.
Polyploidy: A genetic condition in which an organism has more than two complete sets of chromosomes.
Tetraploidy: A specific type of polyploidy involving four complete sets of chromosomes.
Genome: The entire set of genetic material in an organism.
Gene Duplication: A process where a gene is copied, potentially allowing new functions to evolve.

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Information Continually updated

The Georgia Tech team have published their findings in Science where, sadly, only the Abstract is freely available. However, their work is explained in a Georgia Tech News Item:

Scientists uncover key mechanism in evolution: Whole-genome duplication drives long-term adaptation
Sometimes, the most significant scientific discoveries happen by accident.

Scientists have long known that whole-genome duplication (WGD) — the process by which organisms copy all their genetic material — plays an important role in evolution. But understanding just how WGD arises, persists, and drives adaptation has remained poorly understood.
In an unexpected turn, scientists at Georgia Tech not only uncovered how WGD occurs, but also how it stays stable over thousands of generations of evolution in the lab.

The new study was led by William Ratcliff, professor in the School of Biological Sciences, and Kai Tong, a former Ph.D. student in Ratcliff's lab who is now a postdoctoral fellow at Boston University.

Their paper, “Genome duplication in a long-term multicellularity evolution experiment,” was published in Nature as the journal’s cover story in March.

We set out to explore how organisms make the transition to multicellularity, but discovering the role of WGD in this process was completely serendipitous. This research provides new insights into how WGD can emerge, persist over long periods, and fuel evolutionary innovation. That’s truly exciting.

Professor William C. Ratliffe, senior author
School of Biological Sciences
Georgia Institute of Technology, Atlanta, GA, USA.
A secret hidden in the data

In 2018, Ratcliff’s lab launched an experiment to explore open-ended multicellular evolution. The Multicellular Long-Term Evolution Experiment (MuLTEE) uses “snowflake” yeast (Saccharomyces cerevisiae) as a medium, evolving it from a single cell to increasingly complex multicellular organisms. The researchers do this by selecting yeast cells for larger size on a daily basis.
These long-term evolution studies help us answer big questions about how organisms adapt and evolve. They often reveal the unexpected and expand our understanding of evolutionary processes.

Kai Tong, co-first author.
School of Biological Sciences
Georgia Institute of Technology, Atlanta, GA, USA.

That’s exactly what happened when Ozan Bozdag, a research faculty member in Ratcliff’s lab, noticed something unusual in the snowflake yeast. Bozdag observed the yeast when it was 1,000 days old and saw characteristics suggesting it might have gone from diploidy (having two sets of chromosomes) to tetraploidy (having four).

Decades of lab experiments show that tetraploidy is characteristically unstable, reverting back to diploidy within a few hundred generations. For this reason, Tong was skeptical that WGD had occurred and persisted for thousands of generations in the MuLTEE. If true, it would be the first time a WGD arose spontaneously and persisted in the lab.

After taking measurements of the evolved yeast, Tong found that they had duplicated their genomes very early — within the first 50 days of the MuLTEE. Strikingly, these tetraploid genomes persisted for more than 1,000 days, continuing to thrive despite the usual instability of WGD in laboratory conditions.

The team discovered that WGD arose and stuck around because it gave the yeast an immediate advantage in growing larger, longer cells and forming bigger multicellular clusters, which are favored under the size selection in the MuLTEE.

Further experiments showed that while WGD in snowflake yeast is normally unstable, it persisted in the MuLTEE because the larger, multicellular clusters had a survival advantage. This stability allowed the yeast to undergo genetic changes, with aneuploidy (the condition of having an abnormal number of chromosomes) playing a key role in the development of multicellularity. As a result, MuLTEE became the longest-running polyploidy evolution experiment, offering new insights into how genome duplication contributes to biological complexity.

A MuLTEE-talented team

Ratcliff emphasized that rigorous undergraduate research played a critical role in their unexpected breakthrough. Four undergraduate students were integral to the success of the experiment, joining the research early in their education at Georgia Tech.

This kind of authentic research experience is life-changing and career-altering for our students. You can’t get this level of learning in a classroom.

Professor William C. Ratliffe.

Vivian Cheng, who joined Ratcliff’s lab as a first-year and graduated in 2022, took on the challenge of genetically engineering diploid and tetraploid yeast strains along with another student. Ratcliff and Tong ended up using these same strains as a major part of their analysis.

This work is another step toward understanding the various factors that contribute to the evolution of multicellularity. It's super cool to see how this single factor of ploidy level affects selection in these yeast cells.

Vivian Cheng, co-author
School of Biological Sciences
Georgia Institute of Technology, Atlanta, GA, USA

Ratcliff notes that some of his team’s most significant findings could never have been anticipated when they started MuLTEE. But that’s the whole point, he says.

The most far-reaching results from these experiments are often the ones we weren’t aiming to study, but that emerge unexpectedly. They push the boundaries of what we think is possible.

Professor William C. Ratliffe.

[Professor Ratcliffe] and assistant professor James Stroud expanded upon this theme in a review of long-term experiments in evolutionary biology, published in the same issue of Nature.

This discovery sheds new light on the evolutionary dynamics of whole-genome duplication and provides a unique opportunity to explore the consequences of such genetic events. With its potential to fuel future discoveries in evolutionary biology, this work represents an important step in understanding how life evolves on both a short-term and long-term scale.

Scientific progress is seldom a straightforward journey. Instead, it unfolds along various interconnected paths, frequently coming together in surprising ways. It's at these crossroads that the most thrilling discoveries are made.

Kai Tong.
Note: Ozan Bozdag, Sayantan Datta, Daniella Haas, Saranya Gourisetti, Harley Yopp, Thomas Day, Dung Lac, Peter Conlin, and Ahmad Khalil also played major roles in this experiment.

Abstract
Whole-genome duplication (WGD) is widespread across eukaryotes and can promote adaptive evolution^1,2,3,4. However, given the instability of newly formed polyploid genomes^5,6,7, understanding how WGDs arise in a population, persist, and underpin adaptations remains a challenge. Here, using our ongoing Multicellularity Long Term Evolution Experiment (MuLTEE)⁸, we show that diploid snowflake yeast (Saccharomyces cerevisiae) under selection for larger multicellular size rapidly evolve to be tetraploid. From their origin within the first 50 days of the experiment, tetraploids persisted for the next 950 days (nearly 5,000 generations, the current leading edge of our experiment) in 10 replicate populations, despite being genomically unstable. Using synthetic reconstruction, biophysical modelling and counter-selection, we found that tetraploidy evolved because it confers immediate fitness benefits under this selection, by producing larger, longer cells that yield larger clusters. The same selective benefit also maintained tetraploidy over long evolutionary timescales, inhibiting the reversion to diploidy that is typically seen in laboratory evolution experiments. Once established, tetraploidy facilitated novel genetic routes for adaptation, having a key role in the evolution of macroscopic multicellular size via the origin of evolutionarily conserved aneuploidy. These results provide unique empirical insights into the evolutionary dynamics and impacts of WGD, showing how it can initially arise due to its immediate adaptive benefits, be maintained by selection and fuel long-term innovations by creating additional dimensions of heritable genetic variation.

Not only does whole genome duplication clearly demonstrate the creation of new genetic information capable of placing organisms on novel evolutionary pathways, but it also directly challenges creationist assertions. Researchers consistently interpret their findings through the well-established framework of evolutionary biology, with no need for supernatural intervention, assumptions of original perfection, or appeals to supposed genetic deterioration caused by 'Sin' or 'genetic entropy'.

Contrary to claims made by William A. Dembski, the advantageous genetic information observed in evolving organisms does not require an intelligent designer introducing mysterious 'specified information' at each step. Instead, these findings are simply and effectively explained by evolutionary mechanisms — natural processes thoroughly supported by empirical evidence, without recourse to magic or unexplained supernatural intervention.

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