Genomes uncover life's early history

Genomes uncover life's early history
The tree of life

A University of Manchester scientist is part of a team which has carried out one of the biggest ever analyses of genomes on life of all forms.

This has allowed them to map the of eukaryotic genes in unprecedented detail - giving insight into the mechanisms of evolution in the very earliest forms of life.

Their paper, which is published in Nature, builds upon the work of famous palaeontologist Stephen Jay Gould who suggested that even though evolution is usually a slow process, it can sometimes take great jumps forward in a relatively short space of time. This theory was called 'punctuated equilibrium'.

The team, including the Faculty of Life Sciences' Professor James McInerney, wanted to look at the different ways in which eukaryotic and prokaryotic life evolved to see if there were any clues to how evolution could do these great leaps forward. Traditional models had shown that lateral gene transfer (LGT) (the flow and swapping of genes between two individuals) happened in prokaryotes and thus helped explain the enormous diversity they have compared to . The team therefore asked: could LGT in eukaryotes explain these great leaps forward?

The project lead, Professor Bill Martin of the University of Dusseldorf explained the results:

"The big surprise of the study was that eukaryotes, don't engage in this kind of continuous gene swapping nearly as much [as prokaryotes] – though when they do, it's a really, really important event and in early evolution, it corresponded to the origin of organelles. These events were huge evolutionary leaps."

Organelles are parts of the cell that scientists can use to help differentiate between eukaryotic and . Eukaryotes crucially have structures like mitochondria and chloroplasts, mini-factories that work in the cell to provide energy for the organism. Research has shown that both mitochondria and chloroplasts evolved from two cells coming together to share genes and form a 'hybrid' organism.

Importantly the team's computer model has shown that after this initial hybrid-forming stage, the organism starts to lose some of its newly acquired genetic information. Professor McInerney explains: "It's like in a game of chess. The cells starts out with two full sets of genes, one from each symbiotic partner, all lined up at either end of the board.

"But during evolution, the pieces are removed from the board one by one, so that at the end of the game almost no pieces are left, and from those that are left one tries to reconstruct how the game went, retracing the moves back in time."

The team's research has therefore shown that these evolutionary great leaps forward can take place when prokaryotes and eukaryotes mix their genes together in an endosymbiotic event. This evidence gives strong support to the theory of punctuated and can explain the origins of complex life here on Earth.


Explore further

Sex among eukaryotes is far more common than once believed

More information: "Endosymbiotic origin and differential loss of eukaryotic genes." Nature (2015) DOI: 10.1038/nature14963
Journal information: Nature

Citation: Genomes uncover life's early history (2015, August 24) retrieved 16 October 2019 from https://phys.org/news/2015-08-genomes-uncover-life-early-history.html
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Aug 24, 2015
The science to back it up: "The team's research has therefore shown that these evolutionary great leaps forward can take place when prokaryotes and eukaryotes mix their genes together in an endosymbiotic event."

The science of not only observation: "Organisms are only rarely preserved as fossils in the best of circumstances, and only a fraction of such fossils have been discovered. This is illustrated by the fact that the number of species known through the fossil record is less than 5% of the number of known living species, suggesting that the number of species known through fossils must be far less than 1% of all the species that have ever lived.[24] Because of the specialized and rare circumstances required for a biological structure to fossilize, only a small percentage of life-forms can be expected to be represented in discoveries, and each discovery represents only a snapshot of the process of evolution."

[ https://en.wikipe...itations ]

Aug 24, 2015
The scientific support for evolution:

"Evolution is a cornerstone of modern science, accepted as one of the most reliably established of all facts and theories of science, based on evidence not just from the biological sciences, but also from anthropology, psychology, astrophysics, chemistry, geology, physics, mathematics, and other scientific disciplines, as well as behavioral and social sciences." [ http://phys.org/n...ory.html ]

The scientific support for its critics and for alternate theories:

-.


JVK
Aug 25, 2015
Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system http://www.scienc...abstract

Sulfur-cycling fossil bacteria from the 1.8-Ga Duck Creek Formation provide promising evidence of evolution's null hypothesis http://www.pnas.o...abstract

Evolution is a cornerstone of modern science...


Riding the Evolution Paradigm Shift With Eugene Koonin http://www.huffin...216.html
Excerpt: "The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis..."

What type of evolution should we attempt to discuss here? Which type is the cornerstone of your religious beliefs? Is it the type that left out the first ~2 billion years of symbiosis on earth?

JVK
Aug 25, 2015
...each discovery represents only a snapshot of the process of evolution.


The "snapshot" of the re-evolved flagellum in 4 days can be compared to the abstract art painted by evolutionary theorists, which is unsupported (no change in ~2 billion years).

Why hasn't any evolutionary theorist explained the difference between the experimental evidence used to develop the "snapshot" and the development of the ridiculous theory that led to claims about ~2 billion years of no change -- attributed to no evolution because the organisms did not NEED to evolve?

Let's trace the ~2 billion year gap in the pictures to the origins of neo-Darwinism.

Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. invented it, based on de Vries' definition of mutation:

Excerpt: " The accumulation of genetic mutations was touted to be enough to change one species to another....." See:
http://www.huffin...211.html

JVK
Aug 25, 2015
RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon.
http://www.ncbi.n.../2427930

Biophysically constrained nutrient-dependent RNA-mediated gene duplication is the cornerstone of evidence-based claims that support all other claims that link ecological variation to ecological adaptation.

Adaptation occurs via fixation of amino acid substitutions in the context of reproduction. The physiology of reproduction links nutrient-dependent cell type differentiation in all cell types of all individuals of all living genera.

Early life history was linked to the sun's biological energy by Schrodinger in "What is Life?" The missing ~2 billion years of life's history has been attributed to "Peptide synthesis triggered by comet impacts" See: http://phys.org/n...and.html

The first amino acid came from somewhere. Let's compare what's known about UV light and creation to theories about comets.

Aug 26, 2015
neo-Darwinism.
jk believes that the world still follows neo-Darwinism in it's modern Evolution Theory
Neo-Darwinism is the "modern synthesis" of Darwinian evolution through natural selection with Mendelian genetics
https://en.wikipe...arwinism
Yet anyone with the reading ability of a 9th grade dropout can continue down and actually find the TRUTH
"the term neo-Darwinism for the synthetic theory is wrong, because the term neo-Darwinism was coined by Romanes in 1895 as a designation of Weismann's theory."
https://en.wikipe...arwinism#Modern_evolutionary_synthesis
so- despite the term being a specific reference to what we can SEE above as being a reference to something very particular that IS NOT A REPRESENTATION OF THE MODERN THEORY OF EVOLUTION...
2bcont'd

Aug 26, 2015
cont'd
jk continues to insist that it IS a true representation because he doesn't believe in definitions
here are some ACTUAL quotes of his
Only pseudoscientists try to do that with definitions
&
Medical laboratory scientists are not taught to believe in definitions or in theories about evolution
http://phys.org/n...ists.htm

The Scientific method follows the evidence but ALL science requires a lexicon to establish rules of clear, concise communication, otherwise people would be confused as the term for one thing would alter based upon the people discussing the topic

There is a common lexicon for biology/medicine normally taught in 1st year college (jk failed out)
this lexicon defines terms for communication (jk has a 100% fail rate to date)
it is the definitions which jk argues most, which he doesn't believe in anyway (so why argue it?)

REAL SCIENTISTS use definitions to communicate

Aug 26, 2015
one last point
Medical laboratory scientists are not taught to believe in definitions or in theories about evolution
http://phys.org/n...ory.html

http://phys.org/n...ists.htm

This comment is what is known as a BLATANT LIE in an attempt to push a known fallacy that is tied to a religious dogma for the sake of proselytizing

This is called PSEUDOSCIENCE as it pushes a dogma that is supported by circular argument and semantics rather than physical evidence

this is the tactic of religions and [other] pseudoscience

the evidence speaks for itself, from Dr. Extavour and Drosophila to Lenski and e.coli... even your attempt to use Beacon failed miserably

what it boils down to is that your mensa brain apparently cannot comprehend how to read and understand basic english, science and reality
this is apparent in your epic FAIL rate of 100% to date on PO regarding studies

JVK
Aug 26, 2015
"the term neo-Darwinism for the synthetic theory is wrong
When was it changed? Why?

1) Replace the Modern Synthesis (Neo-Darwinism): An Interview With Denis Noble
[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent.... Evolution was defined as "changes in gene frequencies in natural populations." The accumulation of genetic mutations was touted to be enough to change one species to another.... Assumptions, made but not verified, were taught as fact.

2) Riding the Evolution Paradigm Shift With Eugene Koonin
The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis...

3) Mae-Wan Ho: No Boundary Really Between Genetic and Epigenetic
...evolutionary science has now "moved on to such an extent" that she and Peter Saunders don't really care anymore about "trying to convince the neo-Darwinists."

JVK
Aug 26, 2015
http://www.scienc...abstract Excerpt: "Single-molecule and single-cell studies reveal behaviors that are hidden in bulk measurements (1, 2). In a human cell, the genetic information is encoded in 46 chromosomes. The variations occurring in these chromosomes, such as single-nucleotide variations (SNVs) and copy-number variations (CNVs) (3), are the driving forces in biological processes such as evolution and cancer. Such dynamic variations are reflected in the genomic heterogeneity among a population of cells, which demands characterization of genomes at the single-cell level (4–6)."

Evolutionary theorists think the same biological processes are linked to cancer and evolution. They based their theories on assumptions that incorporated de Vries turn of the 20th century definition of "mutation." They assumed that accumulated mutations, which lead to cancer, also lead to evolution. Their assumptions have not changed in more than 100 years.

JVK
Aug 26, 2015
No experimental evidence of biologically-based cause and effect has supported the assumptions of evolutionary theorists who have not changed their ridiculous opinions about mutations and evolution.

All experimental evidence of cause and effect links physics to chemistry and the conserved molecular mechanisms of epigenetically-effected cell type differentiation in all cells of all individuals of all living genera.

See, for example, Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity http://dx.doi.org.../ncb3227 reported as Reprogramming Cancer Cells Back to Normal Cells http://neuroscien...ng-2491/

Excerpt: "The investigators discovered that PLEKHA7 maintains the normal state of the cells, via a set of miRNAs, by tethering the microprocessor to E-cadherin and p120. In this state, E-cadherin and p120 exert their good tumor suppressor sides."

JVK
Aug 26, 2015
Re: No experimental evidence of biologically-based cause and effect has supported the assumptions of evolutionary theorists....

See for comparison to everything known about cell type differentiation, which has been accurately represented during the past 100 years:

Evidence for Retromutagenesis as a Mechanism for Adaptive Mutation in Escherichia coli http://journals.p....1005477

Excerpt: "Retromutagenesis is apt to be a universal method of evolutionary adaptation, which enables the emergence of new mutants from mutations acquired during counterselection rather than beforehand, and it may have roles in processes as diverse as the development of antibiotic resistance and neoplasia"

This claim could be predicted based on the collective ignorance of all evolutionary theorists who refuse to accept the fact that ecological adaptations are nutrient-dependent and controlled by the physiology of reproduction.

Aug 26, 2015
The biggest jump that evolution made is when all life forms suddenly emerged on the planet Earth. Since this remarkable event to present days evolution is on vacation.

If one organism has a semi functioning organs or systems this organism is not fully operational. The more complex an organism Is, the more complicated task is adding new functionality to it. This requires correction of all old functionality to enable all organs and systems to function properly with new added functionality. This task is very difficult for intelligent approach and impossible for random events. Random event is incomparable more likely to damage the old functionality than to contribute to its complication and optimization. This is the reason why all material things lose their integrity and functionality with time. When probability for damage is Many times more than probability for positive effect this leads to unconditional degradation.

JVK
Aug 26, 2015
Only theorists seem to consistently link virus-driven entropic elasticity to the accumulation of viral microRNAs that perturb nutrient-dependent RNA-mediated protein folding chemistry and link the viruses from mutations to evolution.

Serious scientists have been trying to find experimental evidence of an anti-entropic force that could link ecological variation to ecological adaptations. But most of them are embarrassed to admit that top-down causation starts with the sun's anti-entropic energy, because Schrodinger proposed that in 1943.

Dobzhansky confirmed it in 1973 with the reporting of the single amino acid substitution that differentiates the cell types of gorillas from those of chimpanzees and humans via their nutrient-dependent pheromone-controlled physiology of reproduction.

Aug 27, 2015
When was it changed? Why?
@jk
1- i've linked the data to you before

2- Kutschera U, Niklas KJ (2004). "The modern theory of biological evolution: an expanded synthesis"
Pigliucci, M. (2007). "Do We Need An Extended Evolutionary Synthesis?"
Reif W-E. Junker T. Hoßfeld U. (2000). "The synthetic theory of evolution: general problems and the German contribution to the synthesis"

3- you are using the term wrong, and also don't specify which definition is in play when you rant... maybe this is because you never learned definitions? (YOUR WORDS, not mine)
No experimental evidence of biologically-based cause and effect has supported the assumptions of evolutionary theorists
WRONG
Lenski, Extavour, Whittaker ALL prove you wrong with this comment
shall i link their work to you AGAIN? after all, every link you used of theirs to try and support your own claims FAILED to date!

try to keep up, Mensa boy... i thought you smart folk could read!

Aug 27, 2015
They based their theories on assumptions that incorporated de Vries turn of the 20th century definition of "mutation."
@jk
no, they don't
the modern definition is published in various college texts as well as on-line at various points, from NIH to Research papers... in fact, if you read the definition, all of which i've linked to you many times in the past, you would learn that your own model requires mutations
but i have already told you THAT as well
They assumed that
a hypothesis assumes, a THEORY [like Evolution] is based upon EMPIRICAL EVIDENCE, you know... that stuff that keeps proving you an idiot!
Their assumptions have not changed in more than 100 years
WRONG
medicine and biology are vastly different than 100yrs ago... but you wouldn't know that because you failed out of college [self admitted]

QUIT SPREADING LIES and try posting fact!
maybe you will learn something

that is, if you can get around your religion

JVK
Aug 27, 2015
At the same time neo-Darwinian theorists are trying to tweak their pseudoscientific theories and regain the minimal credibility required to continue in academia, serious scientist are reporting this:

http://phys.org/n...lls.html

Unfortunately, this claim -- "...viral entry, cytoskeletal remodeling, interactions with the extracellular matrix, and the evolution of lipid rafts" -- must be placed into the context of "DNA methylation pathways and their crosstalk with histone methylation" http://dx.doi.org.../nrm4043

The facts about RNA-directed DNA methylation and the nutrient-dependent de novo creation of olfactory receptor genes link virus-perturbed protein folding to loss of function in genes that are no longer required for organism-level thermoregulation.

No matter what theorists attempt to do, they cannot make revisions of neo-Darwinian nonsense fit what is known to serious scientists.


JVK
Aug 27, 2015
See:

The extended evolutionary synthesis: its structure, assumptions and predictions
http://rspb.royal...20151019]http://rspb.royal...20151019[/url]

reported as: http://rspb.royal...20151019]http://rspb.royal...20151019[/url]

Also: Mae-Wan Ho: No Boundary Really Between Genetic and Epigenetic http://www.huffin...450.html

"...evolutionary science has now "moved on to such an extent" that she and Peter Saunders don't really care anymore about "trying to convince the neo-Darwinists."

No one cares about trying to convince the neo-Darwinists, and their only care is expressed in the hopes that they can get people to believe in the ridiculous extended evolutionary synthesis now that neo-Darwinian beliefs have been ridiculed by all intelligent researchers.

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