Visualizing Genetic Geometry

Genes are physical transmissions of data that make up DNA. They act as instructions to make molecules called proteins. In a human the size of these genes can range from a few hundred DNA bases, to a few million. The Human Genome Project estimates that humans have between 20-25,000 types of genes to make up our DNA.

Every human being has two copies of each gene. One from each of their parents. Most of our genes are the same person to person. In genes there is something called Alleles. Alleles are forms of the same gene but with very small differences in their DNA bases.Alleles are responsible for creating your own individual personal features.

Scientists track genes by naming them. Gene names are usually represented by symbols. Which can be short combinations of letters and/or numbers.

What are Genes?
DNA

DNA (deoxyribonucleic acid) is the material that makes up every organism on Earth. In humans, almost every cell in our bodies contains the same DNA. DNA located in the cell nucleus is called nuclear DNA. DNA found in the mitochondria is called mitochondrial DNA or mtDNA. Mitochondria are the powerhouses of the cell. They convert food into energy.

DNA is made up of four chemical bases. These are adenine (A), guanine (G), cytosine (C), and thymine (T).Human DNA contains 3 billion bases. The way these bases are ordered/stacked together determines how the animal is built and how the creature will operate.

Generally the bases A and T will group together, and the same goes for C and G. These groups are called base pairs. Each base then attaches to a sugar molecule and phosphate molecule. Together, these three things are called a nucleotide. Nucleotides arrange themselves into spiral, double helix shaped strands. This becomes the familiar shape we know as a DNA strand. They usually stay together in pairs.

DNA strands can and will replicate themselves until they are physically unable to. Each new cell in a body needs an exact copy of the old cell’s DNA in order to split correctly. Both of these DNA strands store the same biological information. About 98% of our DNA is non-coding. This means that it does not contain patterns for protein sequence.

Alongside DNA there is something called RNA. (Ribonucleic Acid) RNA is sort of the opposite of DNA. It is one stranded, and specifies the sequences of amino acids in proteins. RNA is created with DNA in a process called transcription. Transcription is when DNA bases (A, G, C, but not T), are swapped between each other.

Within human cells, DNA is organized into long structures called chromosomes. Chromosomes duplicate in the process of DNA replication. Human cells fit into a category of cells called eukaryotic cells. Organisms that have these cells are plants, fungi,protists, and other animals. Eukaryotic cells are cells that store most of their DNA inside their nucleus, and the rest inside their mitochondria. In plants, DNA stored inside chloroplasts is chloroplast DNA.

Bacterial organisms only store their DNA in their cytoplasm, in circular chromosomes.

Human chromosomes contain sequences that make sure the end regions of DNA are not harmed when the cell replicates. It makes sure the replication origins, telomeres and the centromere are all copied properly. Replication origins are the sequence regions where DNA is copied to make new copies of the chromosome.


Genomes

Genomes are the total group of genes in an organism or cell. These are usually stored in chromosomes. Chromosomes are one single DNA strand, on which thousands of genes exist. The region within a chromosome on which a single gene is located is called a locus.

The majority of genes in humans are stored in linear shaped chromosomes packed inside a nucleus. They are then surrounded by storage proteins (histones), and together they form something called a nucleosome. DNA packed inside a nucleosome is called a chromatin.

The way these histones are arranged regulates with part of the DNA that can spread its genes.

Prokaryotes (bacteria and archaea), store their genomes on a large singular chromosome. Bacteria sometimes supply their chromosomes with DNA bits called plasmids. These plasmids encode a few genes when they are traveling around the cells.

Structures and Functions

Genes are essentially patterns that are repeated over and over again. These patterns can then duplicate over and over with different outcomes based on how they pair up with each other. So what do these patterns look like?

There isn’t much understood science on how gene patterns are established when animals are born or created. There also isn’t a lot understood about how these patterns affect the shape of biological shapes overall.But there are a few promising studies.

There is some science to say that biological patterns, such as fractals in plants are caused by lack of cell movement. Growth and shape in plants is mainly controlled by four things. Growth rate,anisotropy, direction, and rotation. These traits are controlled by the actions of genes.

In 2003, a few scientists in the USA were able to create a few functioning simulations that proved that you can control gene expressions through playing with the regional identities, regionalizing morphogens, and polarizing morphogens of genes.

Link to study: https://www.pnas.org/content/101/14/4728/tab-article-info

Their simulation proved that patterns in plants are controlled by specific gene expression patterns. As well as cell mutations. They specifically simulated snapdragon petal growth to see how the genes and cells of the plant would affect it’s form.

One way of describing the growth of any structure is by the velocities at which it’s points move in relation to its fixed position. In a 3D software these velocities can be represented through vectors or vector fields.

Tracking the velocities of a growth pattern is important to do when you are attempting to map how individual leaves grow, or parts of a plant branch outwards. In a 3D sense it allows you to track cell movement, or where those points (cells) are traveling to.

Physically, you can also track cell movement in plants by marking a leaf or part of the plant with a pen.

Another way you can track cell movement is by representing and showcasing the regions of plants that have local growth characteristics. Every section of a plant has its own unique branching pattern, and the key is to figure out where the pattern starts, ends, and continues.

In each cell, in every organism, there is a liquid crystal layer in its membrane. Inside this membrane are receptors and effectors of the cell. A receptor is the part of the cell that receives information, and an effector produces a response to the information. Depending on how these two parts of the cell operate will determine how thick the cell is and overall awareness and evolution of a creature. The more receptors a cell has, the more that orgasim will evolve and change shape.

Visualizing Genes

There are some wonderful scientific visualizations of genetic geometry out there. Alot of them prove that mapping the shape of something can help diagnose diseases and trace genetic lineage.

A few scientists at the Center for Translational Imaging and Precision Medicine at UC San Diego, were able to create a model of the Human Cerebral Cortex based on genetic mapping.They were able to find patterns in anesterial DNA, and then based on those patterns generate a model that would predict how someone's cortex would look.

They also found no correlation between a brain’s shape and intelligence. ( Which side note reminds me of a story in Bill Bryson’s The Body. Bill recounts a story where a man went to go participate in a scientific study, and in the process learned most of his brain didn’t exist and that the rest of his material in his skull was a tumour. But he had a perfectly normal intelligence level. (It’s a good read and I highly recommend it.) Back to the study :) )

They used four continental populations as ancestral references: European, West African, East Asian and Native American. Then they visualized each to try and better understand how each group’s brain formed. They also looked at children's brains, as human cortices finish developing after 12 years.

They determined that there are subtle differences between the groups when it comes to brain development. As well as shape. So depending on where your family is from, your brain shape will be dependent on those factors.

This same team is also responsible for developing the open source software called FreeSurfer in 1993. This software is a brain imaging analysis software suite. It is now widely used at several universities.

Visualizing these structures also plays a huge role in how we design architecture. Often, load bearing structures and large buildings are hard to build if they have complex surfaces. Or if their design involves several curves.So how would one build a structure efficiently with curves? By using genetic algorithms. Researchers at the West Pomeranian University of Technology have developed a system that gives them freedom of design using this algorithm. As we know, genes contain patterns, and these patterns repeat and are uniformly packed together. So following their algorithms will give you an optimal way to stack a structure.

These algorithms are also being applied to the use and design of nanoparticles. Nanoparticles are used in nanomaterials, carbon nanotubes in aircraft wings, nanowires in solar cells, and much more.

Genetic Geometry in Houdini

Visualizing genes in Houdini isn’t something a lot of people do for fun. It’s even harder to find its use in gene visualizations. However, there is one person online who is having a lot of fun sharing his Houdini gene knowledge.

Stuart at Making Biocienimaics is that person. Currently, he runs a Youtube channel where he talks about how to use Houdini for modeling chromosomes, and other filaments. As well as his life journey as an artist.

You can check out his channel here: https://www.youtube.com/c/MakingBiocinematics/videos

Entagma and Вячеслав Великоредчанин on Youtube also have some interesting modeling tutorials for DNA strands.

New in Houdini 18.5 Pt. 6: Chain SOP - Building A DNA Strand: https://www.youtube.com/watch?v=KvY82q8Salk

Houdini - DNA Infection (Rus): https://www.youtube.com/watch?v=HIaQoXiWZDs

References



The genetics of geometry
https://www.pnas.org/content/101/14/4728

The geometry and genetics of hybridization
https://pubmed.ncbi.nlm.nih.gov/33150956/

Genetic Geometry Takes Shape
https://www.quantamagazine.org/genome-architecture-in-twists-of-dna-20150225/

Genetic Geometry
https://www.labroots.com/trending/genetics-and-genomics/1361/genetic-geometry

A New Wrinkle: Geometry of Brain’s Outer Surface Correlates With Genetic Heritage
https://health.ucsd.edu/news/releases/pages/2015-07-09-shape-of-brain-correlates-with-heritage.aspx

The geometry and genetics of hybridization
https://www.biorxiv.org/content/10.1101/862235v2

Expressing geometry
https://www.nature.com/articles/nphys3656

Modeling the 3D Geometry of the Cortical Surface with Genetic Ancestry
https://www.cell.com/current-biology/comments/S0960-9822(15)00671-5

Application of the Genetic Algorithm for a Geometry Rationalisation of a Load-bearing Structure for Free-form Roof
https://www.sciencedirect.com/science/article/pii/S1877705816328818

Nutritional geometry of mitochondrial genetic effects on male fertility
https://royalsocietypublishing.org/doi/10.1098/rsbl.2019.0891

Geometry for a selfish foraging group: a genetic algorithm approach
https://royalsocietypublishing.org/doi/10.1098/rspb.1997.0170

Genetic Algorithms in Application to the Geometry Optimization of Nanoparticles
https://www.mdpi.com/1999-4893/2/1/410/htm

Did Sequence Dependent Geometry Influence the Evolution of the Genetic Code?
https://arxiv.org/abs/2003.01553

Zeolite structure determination using genetic algorithms and geometry optimisation
https://pubs.rsc.org/en/content/articlelanding/2018/fd/c8fd00035b#!divAbstract

How old is the genetic code? Statistical geometry of tRNA provides an answer
https://science.sciencemag.org/content/244/4905/673

DNA
https://en.wikipedia.org/wiki/DNA

What is a gene?
https://medlineplus.gov/genetics/understanding/basics/gene/

Gene
https://en.wikipedia.org/wiki/Gene

​Gene
https://www.genome.gov/genetics-glossary/Gene