Scientists develop new theory of molecular evolution

October 23, 2017, CU Anschutz Medical Campus
Evolution

Researchers from the University of Colorado Anschutz Medical Campus and the University College London have developed a new theory of molecular evolution, offering insights into how genes function, how the rates of evolutionary divergence can be predicted, and how harmful mutations arise at a basic level.

"Molecules are the basis of all life and we wanted to find out why molecules evolve the way they do," said study co-author David Pollock, PhD, professor of biochemistry and molecular genetics at the CU School of Medicine.

Pollock and fellow author Richard Goldstein, Ph.D., professor of infection and immunity at University College London, published the study October 23, 2017 in the journal Nature Ecology and Evolution.

Their theory of evolutionary mechanics transforms evolving molecular systems into a framework where the tools of can be applied, opening a novel window into how evolution works.

"The approach rests on understanding proteins as integrated systems," said Goldstein. "Too often we ignore interactions between different parts of a protein, but we know that changes in one part of the protein affect subsequent changes in other parts. It turns out this is really important for understanding why these molecules evolve the way they do."

Proteins constantly change as mutations become fixed or eliminated depending on the protein structure, function and stability. This depends on amino acid interactions throughout the protein that cause evolution at one site to alter the chance of evolution at other sites.

The scientists discovered that they could predict rates of based on their biochemical properties.

"This was a real surprise," Pollock said. "Our theory accounts for well-known population genetics effects such as strength of selection and effective population size, but they drop out of the final equations that predict the rate of molecular evolution."

For years, researchers have run up against problems with standard models of used in studying the evolutionary relationships among species. This led to difficulties in reconstructing important evolutionary events in ancestral organisms.

These patterns of molecular convergence were found to change regularly over evolutionary time in ways that indicated continually fluctuating constraints in different parts of proteins.

"This flips around the usual idea that the amino acids will adjust to the requirements of the rest of the protein," Goldstein said. "But we couldn't explain exactly why this happened, or whether there was any regularity to the process."

But once the system was placed into a statistical mechanics framework, the magnitude of amino acid entrenchment was seen as central to understanding rates of evolutionary divergence.

The researchers said that the strength of selection in protein is balanced by the sequence entropy of folding, the number of sequences that provide a protein with a given degree of stability.

"We like to think of the other as a bunch of kids jumping down on a memory foam mattress while you try to walk on it," Pollock said. "Most of the time your feet are sunk into the mattress and you can't step forward, but every so often the kids will create a dent in the mattress that allows you to step ahead."

Explore further: New discovery challenges long-held evolutionary theory

More information: Richard A. Goldstein et al. Sequence entropy of folding and the absolute rate of amino acid substitutions, Nature Ecology & Evolution (2017). DOI: 10.1038/s41559-017-0338-9

Related Stories

New discovery challenges long-held evolutionary theory

October 19, 2017

Monash scientists involved in one of the world's longest evolution experiments have debunked an established theory with a study that provides a 'high-resolution' view of the molecular details of adaptation.

Ancient proteins studied in detail

May 8, 2017

How did protein interactions arise and how have they developed? In a new study, researchers have looked at two proteins which began co-evolving between 400 and 600 million years ago. What did they look like? How did they ...

A new tool to decipher evolutionary biology

May 9, 2017

Understanding evolution is one of the cornerstones of biology—evolution is, in fact, the sole explanation for life's diversity on Earth. Based on the evolution of proteins, researchers may explain the emergence of new species ...

Folding biomolecule model shows how form dictates function

September 13, 2017

Proteins are fundamental macromolecules for life, with a diversity of functions, like acting as channels through cellular walls, catalysers, DNA benders, etc. When it comes to these functions, what matters is the layout of ...

Researchers probe protein diversity

July 10, 2017

Proteins make up a wildly diverse class of molecule, with key roles in everything from catalyzing reactions to helping fight off infection to transporting oxygen through the body. Now, Harvard scientists are beginning to ...

Recommended for you

Using machine learning to design peptides

December 10, 2018

Scientists and engineers have long been interested in synthesizing peptides—chains of amino acids responsible for conducting many functions within cells—to both mimic nature and to perform new activities. A designed peptide, ...

Biomimetic strategy leads to strong, recyclable rubber

December 10, 2018

Inspired by nature, Chinese scientists have produced a synthetic analogue to vulcanized natural rubber. Their material is just as tough and durable as the original. In the journal Angewandte Chemie, they reveal the secret ...

Custom-made artificial mother-of-pearl

December 10, 2018

Natural mother-of-pearl, such as mussels, is one of the hardest, most stable and stiff natural materials. Researchers have always been fascinated by it. The structure of mother-of-pearl is exquisite under the electron microscope; ...

21 comments

Adjust slider to filter visible comments by rank

Display comments: newest first

Bart_A
1 / 5 (9) Oct 24, 2017
Evolutionary scientists will continue to try to find new theories, but they constantly find that the current ones just don't make sense. Everything we see around us is just made too perfectly that it is hard to believe this arose by chance and time. Life is just too complex. And all these complex parts have to come together at the exact same time, or else life just won't happen.

Time to throw away this unfounded theory.

humy
5 / 5 (10) Oct 24, 2017
Evolutionary scientists will continue to try to find new theories, but they constantly find that the current ones just don't make sense.

That's simply not true.
And the basic underlining theory of evolution does not only make perfect sense but is proven to be true by a vast mountain of irrefutable evidence. So much so that anyone that denies it, just like any member of the flat-Earth society, is either extremely ignorant or extremely delusional or both.
434a
5 / 5 (7) Oct 24, 2017
Everything we see around us is just made too perfectly that it is hard to believe this arose by chance and time.


There are around 5,000 known human genetic disorders (illnesses).
~4.5% of all children born have some form of genetic illness. That's 600,000 children born, globally each year.
50% of pregnancies end in miscarriage and there are ~131 million live births per year presently, so 65.5 million miscarriages each year.

Surely you have cogent explanation for that level of error, how does your perfect world account for that?
TheGhostofOtto1923
4.8 / 5 (5) Oct 24, 2017
Surely you have cogent explanation for that level of error, how does your perfect world account for that?
Sure he does. Original sin. Ie we'd all be perfect if eve hadn't eaten the apple/pomegranate.

Ie genetic disorders are our own fault. Don't you feel guilty?

You've got to remember, religions have had millenia to develop clever ways of covering their ass. And as they evolved, innovations from lessons learned were constantly incorporated so that we are left with the highly polished and refined bullshit machines we see today.

This is true intelligent design.
434a
5 / 5 (4) Oct 24, 2017
Surely you have cogent explanation for that level of error, how does your perfect world account for that?
Sure he does. Original sin. Ie we'd all be perfect if eve hadn't eaten the apple/pomegranate.

Ie genetic disorders are our own fault. Don't you feel guilty?

You've got to remember, religions have had millenia to develop clever ways of covering their ass. And as they evolved, innovations from lessons learned were constantly incorporated so that we are left with the highly polished and refined bullshit machines we see today.

This is true intelligent design.


Cogent being the operative word ;)
Hyperfuzzy
1 / 5 (2) Oct 24, 2017
huh? LOL a prediction of randomness; better, a result based upon what set of parameters, oh, there is so much we must learn before exposing to even wear the PhD!

TheGhostofOtto1923
5 / 5 (1) Oct 24, 2017
Cogent being the operative word ;)
Yah well (yahweh?) To a believer god is the ultimate cogent.
Hyperfuzzy
not rated yet Oct 24, 2017
Cogent being the operative word ;)
Yah well (yahweh?) To a believer god is the ultimate cogent.

Belief in God is a connotation to the Living God before money. Are the one's the Christians murdered, the scientist, the philosophers? Reflect upon an Ancient Hieroglyphic "The Declaration of Human Rights". Note the posting. Well, we are here, being disrespectful. Not that world, with focus upon respect, cooperation, logic. No try a fantasy God, pay for your sins(everything) with the gold we stole.
Hyperfuzzy
1 / 5 (1) Oct 24, 2017
We have randomly changed the human genome with the reward of money. So what PhD has defined this?
Hyperfuzzy
1 / 5 (1) Oct 24, 2017
Please, reflect upon the life of Hypatia and think about where we are, i.e. The World Socially, Infrastructure, Common Plans ... With our world defined as the Freedom to Disrespect! Respect cannot be earned. Respect does not demand your subjective measure. Disrespect is inhumane!
Hyperfuzzy
1 / 5 (1) Oct 24, 2017
Obtain wealth, maybe good, maybe pompous, instead of rewarding ourselves with the wealth of the world without damage, a group of intelligent men, motive?
Da Schneib
4.5 / 5 (2) Oct 24, 2017
The thing about science is that it advances. Old theories get modified or replaced when new information is found by observation or experiment, or when new techniques are tried and give better results than old techniques.

Think of it as evolution in action.
Hyperfuzzy
1 / 5 (1) Oct 24, 2017
The thing about science is that it advances. Old theories get modified or replaced when new information is found by observation or experiment, or when new techniques are tried and give better results than old techniques.

Think of it as evolution in action.

Only obvious truths are ignored; else, you are able to define technique, method, control, ... not this nonsense. Hence, we are not scientist, we are money grubbing idiots.
Whydening Gyre
5 / 5 (1) Oct 24, 2017
Just a little food for thought -
Perhaps Bart is struggling with the enormity of "experiments" nature is performing at any given moment with any given number of atom, molecules, environments, etc.
It's WAY more than the number of atoms we've calculated to be in the Universe...
Whydening Gyre
5 / 5 (1) Oct 24, 2017
Cogent being the operative word ;)
Yah well (yahweh?) To a believer god is the ultimate cogent.

Yes way, Ted...
Hyperfuzzy
1 / 5 (1) Oct 24, 2017
Simple, sort it all by stability, define your sort as fuzzy sets. Show control of the stability and of the instability based also upon a fuzzy gradient. Are clear, measure the attributes of each set, let that define the set, also define reference to you human controls, based upon human rights and Maxwell! Done. Think by experimenting without the ability to predict makes any sense? That phase is discovery, but not as the science.
Whydening Gyre
5 / 5 (1) Oct 24, 2017
Simple, sort it all by stability, define your sort as fuzzy sets. Show control of the stability and of the instability based also upon a fuzzy gradient. Are clear, measure the attributes of each set, let that define the set, also define reference to you human controls, based upon human rights and Maxwell! Done. Think by experimenting without the ability to predict makes any sense? That phase is discovery, but not as the science.

HF,
Your comment indicates you are a fan of Heisenberg...:-)
georgi_gladyshev
5 / 5 (1) Oct 25, 2017
The driving force of evolution is hierarchical thermodynamics (the near to equilibrium thermodynamics).
Have a look at please:
1. On General Physical Principles of Biological Evolution https://www.resea...volution
2. Hierarchical Thermodynamics: Foundation of Extended Darwinism
Imperial Journal of Interdisciplinary Research (IJIR) • February 2017
https://www.resea...arwinism
3. Life - A Complex Spontaneous Process Takes Place against the Background of Non-Spontaneous Processes Initiated by the Environment
https://www.omics...0188.pdf
Da Schneib
not rated yet Oct 25, 2017
The thermodynamic hypothesis is very interesting. There is some pretty good evidence for it, but it is still controversial. The use of statistical mechanics in this new methodology tends to support it, since thermodynamics is based on statistical mechanics.
Hyperfuzzy
1 / 5 (1) Oct 25, 2017
Simple, sort it all by stability, define your sort as fuzzy sets. Show control of the stability and of the instability based also upon a fuzzy gradient. Are clear, measure the attributes of each set, let that define the set, also define reference to you human controls, based upon human rights and Maxwell! Done. Think by experimenting without the ability to predict makes any sense? That phase is discovery, but not as the science.

HF,
Your comment indicates you are a fan of Heisenberg...:-)

Heisenberg used methods defined by QM. QM or the wave equation, potential and kinetics has an error, mass. Unresolvable. The particles being measured do not exist; however, the momentum and position of the charge centers added to your solutions will produce correct effects but the interpretation and causality? Heisenberg did not have our tools. So no cat in the box.
Hyperfuzzy
1 / 5 (1) Oct 25, 2017
The thermodynamic hypothesis is very interesting. There is some pretty good evidence for it, but it is still controversial. The use of statistical mechanics in this new methodology tends to support it, since thermodynamics is based on statistical mechanics.

So, using unverifiable methods, eh?

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.