Grand tree of life study shows a clock-like trend in new species emergence and diversity

March 3, 2015, Oxford University Press
The tree of life compiled by Temple University researchers is depicted in a new way -- a cosmologically inspired galaxy of life view -- and contains more than 50,000 species in a tapestry spiraling out from the origin of life. Credit: Temple University

Temple University researchers have assembled the largest and most accurate tree of life calibrated to time, and surprisingly, it reveals that life has been expanding at a constant rate.

"The constant rate of diversification that we have found indicates that the ecological niches of are not being filled up and saturated," said Temple professor S. Blair Hedges, a member of the research team's study, published in the early online edition of the journal Molecular Biology and Evolution. "This is contrary to the popular alternative model which predicts a slowing down of diversification as niches fill up with ."

The tree of life compiled by the Temple team is depicted in a new way —- a cosmologically-inspired galaxy of life view —- and contains more than 50,000 species in a tapestry spiraling out from the origin of life.

For the massive meta-study effort, researchers painstakingly assembled data from 2,274 molecular studies, with 96 percent published in the last decade. They built new computer algorithms and tools to synthesize this largest collection of evolutionary peer-reviewed species diversity timelines published to date to produce this Time Tree of Life.

The study also challenges the conventional view of adaptation being the principal force driving species diversification, but rather, underscores the importance of random genetic events and geographic isolation in speciation, taking about 2 million years on average for a new species to emerge onto the scene.

"This finding shows that speciation is more clock-like than people have thought," said Hedges. "Taken together, this indicates that speciation and are separate processes from adaptation, responding more to isolation and time. Adaptation is definitely occurring, so this does not disagree with Darwinism. But it goes against the popular idea that adaptation drives speciation, and against the related concept of punctuated equilibrium which associates adaptive change with speciation."

Besides the new evolutionary insights gained in this study, their Timetree of Life will provide opportunities for researchers to make other discoveries across disciplines, wherever an evolutionary perspective is needed, including, for example, studies of disease and medicine, and the effect of climate change on future .

Researchers around the world utilize molecular clocks to estimate species divergence times, calculating DNA mutational rates with species divergence times from gene and genomic sequences, that together with the fossil record and geological history, provide a constantly improving view of Darwin's "grandeur of life."

These new results add to the decade-long efforts of the Timetree of Life initiative (TTOL), which includes internet tools and a book, led by team members Hedges and Sudhir Kumar. "The ultimate goal of the TTOL is to chart the timescale of life—to discover when each species and all their ancestors originated, all the way back to the origin of life some four billion years ago," said Hedges.

As an ongoing service to the scientific community, Hedges and Kumar plan to continue adding new data to TTOL from future peer-reviewed studies. They also will improve their current tools, such as web and smartphone apps, and develop new tools, that will make it easier to access the information and to explore the TTOL, and for scientists to update the growing tree with their new data.

Explore further: Reproductive isolation driving evolution of species

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Whydening Gyre
4.3 / 5 (12) Mar 03, 2015
AAhhh.... The widening gyre of evolving - everything...:-)
Vietvet
4.1 / 5 (17) Mar 03, 2015
Hear that explosion?

It was @JVK's head.
Uncle Ira
3.9 / 5 (15) Mar 03, 2015
Hear that explosion?

It was @JVK's head.


Yeah, he's pecking away right this very minute working on something about how this has to do with his sticky love potions. Maybe he'll have him ready to postum in about three or two minutes.
Whydening Gyre
4.4 / 5 (13) Mar 03, 2015
Hear that explosion?

It was @JVK's head.

That was great. VV...:-)
Just like the guy in the movie "Scanners"...:-)
JVK
1 / 5 (13) Mar 03, 2015
http://www.scienc...20.short
"A flurry of other presentations compared different classes of molecules—respiratory proteins, microRNAs, and the heat shock proteins produced in response to stress—in insects and standard crustaceans. For example, hemocyanins, oxygen-carrying molecules once known to exist only in shrimp, lobsters, and other so-called malacostracans, are also made by some insects, including the embryos of cockroaches and grasshoppers. The hemocyanin in insect embryos closely resembles the version Burmester discovered in remipedes, further strengthening the close tie between that group and insects. As land insects evolved more efficient breathing, hemocyanin became superfluous and disappeared in many groups, he hypothesizes."

Similarities and differences across species are clearly due to the balance of viral microRNAs and anti-entropic nutrient-dependent microRNAs. https://www.youtu...NcMR_-RU
JVK
1.1 / 5 (12) Mar 03, 2015
Combating Evolution to Fight Disease http://www.scienc...88.short

"Nutrient-dependent changes in glucose- and glucose dehydrogenase-dependent hydrogen bonds of base pairs might alter the hydrogen bonds of miRNAs. Altered hydrogen bonds in miRNAs could alter the miRNA/mRNA balance. The cascade of nutrient-dependent, epigenetically-effected, pheromone-controlled, receptor-mediated ecological adaptations might result in alternative splicings of pre-mRNA and amino acid substitutions that determine cell types in individuals of different species. Nutrient-dependent pheromone-controlled amino acid substitutions and host specialization probably led to evolutionary divergence via reciprocal miRNA/mRNA interactions that differentiate the cell types of individuals in different species." http://figshare.c...s/994281
JVK
1 / 5 (13) Mar 03, 2015
Re: "...life has been expanding at a constant rate."
See for comparison to an accurate representation of biologically based cause and effect:
Non-Adaptive Amino Acid Convergence Rates Decrease over Time
http://mbe.oxford...abstract

Conclusion: "The inclusion of variation in the substitution process across sites and
over time – details that standard models currently lack – should be included in future
evolutionary models to obtain more accurate descriptions of protein evolution."

The amino acid substitution process is nutrient-dependent and controlled by RNA-directed DNA methylation and fixation of the amino acid substitutions via the metabolism of nutrients to species-specific pheromones that control the nutrient-dependent physiology of reproduction in species from microbes to man. See for examples: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353
JVK
1 / 5 (13) Mar 03, 2015
In 2002 S. Blair Hedges wrote: ".. the tree of life provides direction for finding genes and mutations of interest in close relatives, and the timescale of life is crucial for determining rates of substitution in genes and associations with environmental change. A focus on model organisms will continue to be productive, but the future is likely to see fusions of fields, cross-cutting initiatives and greater interdisciplinary exchange as a by-product of this renewed emphasis on comparative biology." Hedges, S. B. 2002. The origin and evolution of model organisms. Nature Reviews Genetics 3:838-849.

Rarely do we see anyone who is so dedicated to touting pseudoscientific nonsense about mutations that they continue to do so while others have learned how to link physics and the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding to cell type differentiation in all cells of all individuals of all species via conserved molecular mechanisms.
JVK
1 / 5 (13) Mar 03, 2015
See also: Quantum Criticality at the Origin of Life http://arxiv.org/...02.06880
"Our results also suggest that quantum transport played a distinguished role in evolution and selection."

See also: A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution http://www.ncbi.n...23206328

Quantum transport is linked to quantum theory via natural selection for nutrient uptake, which suggests that all organisms must eat and that none mutate into another species before or after they starve to death. Simply put, ecological variation leads to ecological adaptation, not to mutation-driven evolution. Indeed, ideas about mutations and evolution are nothing more than pseudoscientific nonsense.

The fact that ridiculous theories have been accepted instead of biologically-based facts attests only to the ignorance of the biologically uninformed masses and most phys.org participants.
cgsperling
4.4 / 5 (17) Mar 03, 2015
You know, JVK, intelligent people realize that scientists who really know their subject don't spend huge amounts of their time posting comments on popular science websites.
Vietvet
4.4 / 5 (14) Mar 03, 2015
@verkle

There is only one problem with this Grand Chart. The underlying basis of evolution has never been seen nor replicated. And it is a mathematical impossiblity.

Some built on a non-existant foundation will collapse.
No matter how hard atheist evolutionists try.



Are you suggesting it is "a mathematical impossibility" because a book of fairy tales tells you the Earth is only 6,000 years old?
Steve 200mph Cruiz
5 / 5 (13) Mar 04, 2015
They observe it in real time everyday Verkle.

JVK,
Just go do something else with your life, go read Tom Sawyer or something, I always forget what a fun a read it is and its a way better way to spend your time
mooster75
4.7 / 5 (12) Mar 04, 2015
They observe it in real time everyday Verkle.

JVK,
Just go do something else with your life

He can't; snake oil won't sell itself.
jsdarkdestruction
5 / 5 (14) Mar 04, 2015
There is only one problem with this Grand Chart. The underlying basis of evolution has never been seen nor replicated. And it is a mathematical impossiblity.

Some built on a non-existant foundation will collapse.
No matter how hard atheist evolutionists try.


Again, where does this leave christian and other religion scientists?
No matter how hard you creationists try your athiest conspiracy theories will not stand up.
Moebius
5 / 5 (5) Mar 04, 2015
Geographical isolation, a survival strategy. A strategy that we have been busily subverting on every front both for us and every other plant and animal. Yet no one sees the inevitable outcome. It isn't called a survival strategy for nothing.
JVK
1 / 5 (11) Mar 04, 2015
intelligent people realize that scientists who really know their subject don't spend huge amounts of their time posting comments on popular science websites.


Agreed. They see what happens when someone like me posts comments that challenge the pseudoscientific nonsense that others have been taught to believe in. When an article like this is published at the same time as one that directly contradicts the findings, however, intelligent people begin to realize that the biologically uninformed have spread their ignorance across all internet context, and that science idiots will continue to do so.

It's worth a little effort on my part to let others know what serious scientists are reporting -- if only to show what science idiots are continuing to ignore.

The full text of the article on amino acid substitutions is free:
http://mbe.oxford...abstract

I can't find the article mentioned here.
JVK
1 / 5 (10) Mar 04, 2015
No matter how hard you creationists try your athiest conspiracy theories will not stand up.


The atheistic nonsense does not stand up in yet another detailed report on amino acid substitutions that differentiate cell types.

First published online: March 3, 2015 http://mbe.oxford...abstract

Creationist claims made in Dobzhansky (1973) are again fully supported by experimental evidence. He wrote "...the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla." http://www.jstor..../4444260

The conserved molecular mechanisms of biologically-based cause and effect have repeatedly been detailed. See also:

MicroRNA-Based Single-Gene Circuits Buffer Protein Synthesis Rates against Perturbations
http://pubs.acs.o...b4001867
Whydening Gyre
4.7 / 5 (13) Mar 04, 2015
There is only one problem with this Grand Chart. The underlying basis of evolution has never been seen nor replicated. And it is a mathematical impossiblity.

Some built on a non-existant foundation will collapse.
No matter how hard atheist evolutionists try.

Unfortunately, Verkle, you just described any number of religions with that statement...

At least, evolution theory is an honest, reasoned and logical attempt to document the Universe, NOT just an emotionally imagined one...
JVK
1 / 5 (11) Mar 04, 2015
"...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world." Mutation-Driven Evolution http://www.amazon...99661731

...evolution theory is an honest, reasoned and logical attempt...


Combating Evolution to Fight Disease http://www.scienc...88.short

Of Cells and Limits http://www.the-sc...-Limits/

Re: Mathematical impossibility: "Both the number of known small molecules and proteins is about 108 and the number of chemically feasible small (< 500Da) organic compounds is astronomical, estimated[52] to be 10~60. The number of proteins grows exponentially with the number n of amino acids as 20n, and the largest known has about n 26000. This shows that chemical and biological evolution selected only a tiny fraction p 10" http://arxiv.org/...02.06880
Whydening Gyre
4.6 / 5 (9) Mar 04, 2015
So.... what, exactly, was your point with that last post, Kohl? It looks like you were supporting mutational evolution...
Captain Stumpy
4.1 / 5 (9) Mar 04, 2015
Creationist claims made in Dobzhansky (1973) are again fully supported by experimental evidence
NOT
1- creationists simply stole the delusional ramblings of the head prophetess of the 7th day adventist ( as proven by science and talked about here: https://www.youtu...jWkVKyRo ) because they needed attention
creationists have NO BASIS in science, and even the court system can see that: https://en.wikipe...Arkansas

2- the ONLY "science idiots" here are the ones who refuse to accept the known science for their religion, like kohl and ren

jk, you admitted to failing out of college and not being able to comprehend the BASICS when you finally admitted you stupidly don't comprehend MUTATIONS or how your own model causes them (which i can quote for you if you want)

even your own LINKS call you stupid
like this one
http://www.scienc...014.full

epic FAIL again for creationists/7th day adventists
Captain Stumpy
4.5 / 5 (8) Mar 04, 2015
"...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world." Mutation-Driven Evolution http://www.amazon...99661731
@Wyde
He IS SUPPORTING IT!
that is what he can't understand in his delusion... even his own model supports mutational evolution!
more epic failure fo jk:
https://www.youtu...1zni_AxE

https://www.youtu...5uqzlwsU

https://www.youtu...NWwk7LIg

https://www.youtu...Z6MrBl9E

one big reason that jk cannot comprehend basic science?
because he is trying to cherry pick and support his delusional religion... NOT follow the evidence and learn about biology

but that is to be expected from a liar who claims to have "decades of experience in Diagnostic Medicine" in violation of state and federal law as well as showing his lack of scientific knowledge

Vietvet
4.2 / 5 (10) Mar 04, 2015
I thought JVK's head would explode with this article. Look for the fireworks this article will bring.

http://medicalxpr...l#ajTabs
Torbjorn_Larsson_OM
5 / 5 (10) Mar 04, 2015
@WG: "evolution theory is an honest, reasoned and logical attempt to document the Universe".

Even better, it is tested science.

And, if you use the observations, as Noor notes in his hugely popular MOOC on Genetic & Evolution, it is a mathematical inevitability.

Noor uses a gedanken experiment of squirrels that have acquire an allele from variation that makes them scared of cars. Then over time, the population of his driveway (or more generally around roads) will see an increase in that allele. Say A makes you scared and an AA squire will make 4 squirrels, but aa will go splat 3 times out of 4. Then a will hang on, but A will dominate. Because squirrels that go "splat" won't do as well...

Evolution. Creationists won't know what hit them. (Because they can't do the math.)
JVK
1 / 5 (9) Mar 04, 2015
can't do the math


What math? Did you not see: Quantum Criticality at the Origin of Life http://arxiv.org/...02.06880

"...the number of known small molecules and proteins is about 108 and the number of chemically feasible small (< 500Da) organic compounds is astronomical, estimated[52] to be 10~60. The number of proteins grows exponentially with the number n of amino acids as 20n, and the largest known has about n 26000. This shows that chemical and biological evolution selected only a tiny fraction p 10"

Anyone who does the math understand the need for selection of nutrients and mates that ensures reproduction. What most can't understand is the magic of evolution that you just attested to because you think the molecular mechanisms can be observed.
JVK
1 / 5 (9) Mar 04, 2015
UCLA researchers devise new method to identify disease markers
http://www.eureka...0315.php

Even the biologically uniformed science idiots who participate on phys.org may begin to understand the difference between RNA-mediated amino acid substitutions that stabilize the DNA in organized genomes and mutations that perturb protein folding and DNA stabiity.

See, for instance: "RNA editing is different from mutations. A mutation is written incorrectly in our genes. In RNA editing, our genetic material is normal, but modifications occur later when a gene is expressed."

The modifications linked from RNA-directed DNA methylation and RNA-mediated amino acid substitutions to cell types are fixed in the context of the nutrient-dependent pheromone-controlled physiology of reproduction, which links them from ecological variation to ecological adaptations manifested in the morphological and behavioral diversity of species from microbes to man.
jsdarkdestruction
5 / 5 (9) Mar 05, 2015
No matter how hard you creationists try your athiest conspiracy theories will not stand up.


The atheistic nonsense does not stand up in yet another detailed report on amino acid substitutions that differentiate cell types.

Perhaps you would like to address the fact its not only athiest scientists who support evolution and how they fit into evolution being an athiest conspiracy.
FainAvis
5 / 5 (7) Mar 05, 2015
@ JVK tl;dr
JVK
1 / 5 (9) Mar 05, 2015
Perhaps someone should address the experimental evidence that links RNA-mediated events to cell type differentiation in all cells of all individuals of all species via the biophysically constrained chemistry of nutrient-dependent protein folding.

The experimental evidence clearly shows the involvement of amino acid substitutions and eliminates any pseudoscientific nonsense about biodiversity when claims are made that it arises outside the context of the pheromone-controlled physiology of reproduction and fixation of the amino acid substitutions.
yacp
3 / 5 (2) Mar 07, 2015
This is certainly a difficult chart to understand. I understand that each colored line segment represents a species. The length of the segment represents how many million years ago that species has existed based on a logarithmic scale. But I don't understand the placement of the species on the spiral. I think there's a general left-to-right trend regarding time within a species, because the segments get shorter, but not sure about that. My first thought was, "where are the dinosaurs", but maybe it's only documenting extant families.
Whydening Gyre
4 / 5 (8) Mar 08, 2015
Amazing what these delusional atheists can come up with their astrology evolution religion. It gets more and more complicatedly new age silly as it goes on.

What's amazing is the amount of time religious zealots spend on a site dedicated to disseminating info they discredit, in the first place...
Prostitution isn't the oldest profession - proselytizing and fear mongering are...
JVK
1 / 5 (6) Mar 08, 2015
Amazing what these delusional atheists can come up...


Agreed. They do not seem capable of addressing any aspect of experimental evidence about cell type differentiation or extending what is currently known to differences in species via the evolution of morphological or behavioral phenotypes that are clearly nutrient-dependent and pheromone-controlled during their development in species from microbes to man.

For example, they have failed to learn anything about the role of viruses in cell type differentiation, which must be controlled to link entropic elasticity to anti-entropic epistasis. Instead, the biologically uniformed theorists seem to think that mutations somehow automagically cause dinosaurs to evolve into birds -- and that fits into the context of other pseudoscientific nonsense.

Viruses--Architects of the Brain? http://www.icr.or...cle/8639
Steve 200mph Cruiz
5 / 5 (9) Mar 08, 2015
Verkle JVK

If you are going to reduce your argument down to whether or not God interacts with the world in the way that you expect him too why do you guys think this argument is going to be settled?

I mean when in history has a debate been settled this way. When Galileo first ascertained that the earth was just another planet orbiting the sun people just like you guys told him he was wrong because that didn't agree with their particular interpretation of the bible at the time.
They even "proved" he was wrong by showing all these convoluted orbits of planets to try and match observations, just like your theories JVK. Evolution is the nice elliptical orbits of planets around the sun, your guys theories are the wild direction shifting orbits that only revolve around your preconceived notions of how the world should be. Galileo discovered that the universe doesn't revolve around you.
jsdarkdestruction
5 / 5 (6) Mar 09, 2015
Jvk, danieljknight, creationist,
I will ask you once again - Perhaps you would like to address the fact its not only athiest scientists who support evolution and explain how they fit into your claim of evolution being an athiest conspiracy. 
Torbjorn_Larsson_OM
5 / 5 (5) Mar 09, 2015
@JVK: "What math?"

JVK: 'Evolution - TL;DR.'

So will you stop posting inanities that have nothing to do with actual biology as it is understood and researched, since you admit you haven't studied it?

I won't hold my breath, since that doesn't sell your stinky potions (or your stinky anti-science). =D
greenfish66
1 / 5 (1) Mar 31, 2015
What is Time ? ; If not a Measure of Change? Everything, including Evolution, Changes, with/in Time...;)
JVK
1 / 5 (2) Apr 01, 2015
...will you stop posting inanities that have nothing to do with actual biology as it is understood and researched...


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

This news links the viral microRNA / nutrient-dependent microRNA balance from the microRNA/messenger RNA balance to RNA-mediated amino acid substitutions and cell type differentiation in all genera via the biophysically constrained chemistry of their nutrient-dependent RNA-mediated protein folding.

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