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Author Topic:   Question concerning evolution
GDR
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Message 1 of 21 (834772)
06-10-2018 6:06 PM


I'm posting this just to see what those of you who have knowledge of this subject have to say about it. My knowledge isn't just minimal but non-existent. It was sent to me in an email. Is there anything to it?

quote:
Massive Genetic Study Reveals 90 Percent Of Earth’s Animals Appeared At The Same Time

The latest research is debunking current knowledge about evolution. After studying 5 million genetic barcodes, scientists found 90 percent of species on Earth may have emerged around the same time as humans. ( Lars Plougmann | Flickr )
Landmark new research that involves analyzing millions of DNA barcodes has debunked much about what we know today about the evolution of species.
In a massive genetic study, senior research associate at the Program for the Human Environment at Rockefeller University Mark Stoeckle and University of Basel geneticist David Thaler discovered that virtually 90 percent of all animals on Earth appeared at right around the same time.
More specifically, they found out that 9 out of 10 animal species on the planet came to being at the same time as humans did some 100,000 to 200,000 years ago.
"This conclusion is very surprising," says Thaler, "and I fought against it as hard as I could."
What Is DNA Barcoding?
Over the last decade, hundreds of scientists collected around 5 million DNA barcodes from 100,000 animal species in different parts of the globe. Stoeckle and Thaler looked through these 5 million genetic imprints to find one of the most surprising discoveries about evolution to date.
There are two types of DNA. Most people know nuclear DNA. This is the DNA containing the genetic blueprint for each single individual. It is passed down from the parents to the offspring. The genome is made from kinds types of molecules arranged in pairs. There are 3 billion of these pairs, which are then used to form thousands of genes.
The other, less familiar type of DNA is one found in the mitochondria of cells. The mitochondria generate energy for the cell and contains 37 genes. One of these is the COI gene, which is used to create DNA barcodes. All species have a very similar mitochondrial DNA, but their DNA is also different enough so we can distinguish between species.
Paul Hebert, biologist and director of the Biodiversity Institute of Ontario, developed a new way to identify species by studying the COI gene.
Born Around The Same Time
In analyzing the COI of 100,000 species, Stoeckle and Thaler arrived at the conclusion that most animals appeared simultaneously. They found that the neutral mutation across species were not as varied as expected. Neutral mutation refers to the slight DNA changes that occur across generations. They can be compared to tree rings because they can tell how old a certain specie or individual is.
As to how that could have happened, it's unclear. A likely possibility is the occurrence of a sudden event that caused large-scale environmental trauma and wiped out majority of the Earth's species.
"Viruses, ice ages, successful new competitors, loss of prey — all these may cause periods when the population of an animal drops sharply," explains Jesse Ausubel, director of the Program for the Human Environment.
Such times give rise to sweeping genetic changes across the planet, causing new species to appear. However, the last time such an occurrence took place was 65 million years ago, when an asteroid hit the Earth and killed off the dinosaurs and half of all other species on the planet.
The study is published in the journal Human Evolution.


Added by edit by Adminnemooseus: http://www.techtimes.com/...ls-appeared-at-the-same-time.htm is the apparent source of the above quoted.

Edited by Adminnemooseus, : Added by edit by Adminnemooseus.


He has told you, O man, what is good ; And what does the LORD require of you But to do justice, to love kindness, And to walk humbly with your God.

Micah 6:8


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AdminModulous
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Message 2 of 21 (834774)
06-11-2018 8:11 PM


Thread Copied from Proposed New Topics Forum
Thread copied here from the Question concerning evolution thread in the Proposed New Topics forum.
    
Faith
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Message 3 of 21 (834775)
06-11-2018 8:29 PM
Reply to: Message 1 by GDR
06-10-2018 6:06 PM


I hope Taq or another geneticist will explain this. What I'd like explained among other things is how they get the 100,000 years by looking at DNA. Also what a DNA barcode is..
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JonF
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Message 4 of 21 (834776)
06-11-2018 9:01 PM
Reply to: Message 1 by GDR
06-10-2018 6:06 PM


I'm not an expert and no doubt one will come along. In other discussions I've found that the paper is published in an obscure vanity journal (i.e. you pay them to publish anything and they don't ask questions). They are immensely ignorant of genetics. They used mitochondrial markers, which don't mark speciation.
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AZPaul3
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Message 5 of 21 (834777)
06-11-2018 9:06 PM
Reply to: Message 1 by GDR
06-10-2018 6:06 PM


Ignorant Reporting
Is there anything to it?

Yes, but, unfortunately for creationists, not what the reporter led on.

From Dr PZ Myers blog:

quote:
This is not saying that there was a single instant in the last 200,000 years from which all modern species arose simultaneously. It’s a statement about the process of speciation: species arise from isolation of a limited subset of an existing population, which is why they have limited variation in their DNA barcodes, followed by an expansion of the new species’ population, during which the DNA barcodes accumulate variation slowly.

The study did not find "that 9 out of 10 animal species on the planet came to being at the same time as humans did some 100,000 to 200,000 years ago."
Bad reporting of an interesting but not an evolution-busting result. The actual result, without the reporting hype, is not outside evolutionary expectations.

Myers blog on the subject: https://freethoughtblogs.com/...-of-science-articles-is-hard

Myers blog site: https://freethoughtblogs.com/pharyngula/


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Chiroptera
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Message 6 of 21 (834778)
06-11-2018 9:14 PM


I quickly glanced at the paper. What they seem to be claiming is that there is a lack of genetic variation in the set of DNA they examined that indicates a lot of species went through population bottlenecks a couple hundred thousand years ago.

Not as fantastical as species suddenly appearing, but still incredible enough that JonF's post makes me doubt the paper.

Added by edit:

Oops. Now AZPaul added a more relevant post than mine. Never mind.

Edited by Chiroptera, : No reason given.



Progress is not an illusion, it happens, but it is slow and invariably disappointing. - George Orwell

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Pollux
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Message 7 of 21 (834779)
06-11-2018 9:30 PM
Reply to: Message 6 by Chiroptera
06-11-2018 9:14 PM


Toba
The eruption of Toba 74,000 years ago produced some 2800 cubic kilometres of volcanic products with signs of global climate change seen in ice cores, and a change of vegetation in India. It was around 100 times the size of Tambora's eruption in 1816 which had very widespread effects on climate, inducing famines with a year or two without a summer. So it is possible that this paper is showing the effects of Toba.
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PaulK
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Message 8 of 21 (834787)
06-12-2018 2:50 AM
Reply to: Message 1 by GDR
06-10-2018 6:06 PM


There is one important point that needs consideration.

They used mitochondrial DNA instead of nuclear DNA. Nuclear DNA is inherited from both parents through recombination, mitochondrial DNA is inherited only from the mother.

Thus in mitochondrial DNA the diversifying effect of mutation is countered by the homogenising effect of matrilineal lineages dying out (a female who only has male offspring cannot pass on mitochondrial DNA but will pass on nuclear DNA). This is the effect that causes a “mitochondrial Eve”

(Note that this paper is pretty bad news for Faith. All variation in human mitochondrial DNA would have to be mutation since the creation of Eve.)


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Faith
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Message 9 of 21 (834788)
06-12-2018 2:57 AM
Reply to: Message 8 by PaulK
06-12-2018 2:50 AM


Mutations are no problem, I just regard them as errors or a disease process rather than normal. But they can be helpful markers when tracing down genetic lineages.
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PaulK
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Message 10 of 21 (834790)
06-12-2018 3:17 AM
Reply to: Message 9 by Faith
06-12-2018 2:57 AM


So you have no problem with Eve living at LEAST 100,000 years ago ?
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Faith
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From: Nevada, USA
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Message 11 of 21 (834791)
06-12-2018 3:27 AM
Reply to: Message 10 by PaulK
06-12-2018 3:17 AM


Oh you know, I don't pay attention to those huge numbers. I did ask if someone would explain how they get such numbers out of DNA. Perhaps you know.
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Tangle
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Message 12 of 21 (834794)
06-12-2018 3:31 AM


Whilst it's been misreported, the findings are still quite intriguing and appear to change a general understanding - or at least mine. As I read it, 9 out of 10 existing animal species arose in the last 200,000 years. (Note, not at the same time 200,000 years ago.)

That's quite amazing really, but I'm still trying to understand why I think that.

And, btw, it also says quite conclusively that there was no extinction event 4,500 years ago.


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"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
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PaulK
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Message 13 of 21 (834795)
06-12-2018 3:33 AM
Reply to: Message 11 by Faith
06-12-2018 3:27 AM


That’s simple enough. The more variation the more mutations must have occurred. Are you proposing that mutations to this section of DNA occurred at 10 times the expected rate ? At an absolute minimum ?
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caffeine
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(5)
Message 14 of 21 (834796)
06-12-2018 5:03 AM
Reply to: Message 12 by Tangle
06-12-2018 3:31 AM


The paper is here

Whilst it's been misreported, the findings are still quite intriguing and appear to change a general understanding - or at least mine. As I read it, 9 out of 10 existing animal species arose in the last 200,000 years. (Note, not at the same time 200,000 years ago.)

That's a better summary that the one in OP, but it's not quite right as I read it.

What I'd like explained among other things is how they get the 100,000 years by looking at DNA. Also what a DNA barcode is..

A DNA barcode is just a short stretch of DNA from one specific mitochondrial gene. Why is it called a barcode? This is a gene that's shared by all animals; and varies enough that it can be used to distinguish different species from one another. For this reason it's long been used in species identification, and scientists have gathered sequence data for about 5 million individual animals.

Because we have so many samples to work with, the authors thought this bit of DNA would be useful to study variation in a comparative way across species. They've previously tried to argue that the level of variation in the barcode region is a good proxy for genetic variation as a whole - using examples where we have the data to compare like humans and other other primates. While they accept that this is not firmly established, they take the attitude that this is the best measure we have until someone has sequenced millions of genomes of us to look in more detail.

So, we know that humans have lower than average genetic diversity for a big species. What Stoecke and Thaler discovered by comparing genetic diversity in this one region across many species is that human diversity is probably not as low as believed, comparitvely.

The average pairwise difference between humans in the DNA barcode region is about 0.1%. 90% of the species looked at have an average distance of 0.5% or less. In our closest relatives, chimps and bonobos, you're looking at about 1%. It's often assumed that humans are the outliers because of our unusual recent history; but if this work is correct it seems that it's actually the high diversity among chimps that's more unusual.

So what do they conclude from this? In simple terms, the unusual recent history of humans as a species may not be that unusual. Humans experienced a massive expansion in the recent geological past, in which they spread rapidly across the planet and the genes from one African population largely replaced that of other populations around the world.

This is where the number of years you were asking about comes from. It's nothing directly calculated from the DNA; and the authors don't put any number on it. All they're saying is that humans have a similar pattern of diversity to other species, implying a similarity in population history. Journalists are then looking up estimates for the origins of Homo sapiens (50,000, 100,000, 200,000 years) and extrapolating that most species are as old as whichever estimate they picked.

But, important here is that we're not looking at exactly the same pattern of variation for all species, which is one of the main reasons the OP's 'simultaneous appearance' is silly. As mentioned, the range of average pairwise difference is between 0% and 0.5% for 90% of species. Humans are still towards the lower end of this range so are probably still 'younger' than most other species looked at.

I put 'younger' in inverted commas since the idea that what we're measuring here is the age of a species seems really stupid to me - not so much wrong as meaningless.

What are we actually looking at? We're looking at how long the mitochondrial genome has had to accumulate neutral variations - the more neutral variations, the longer it is since we can trace a populations mitochondrial diversity back to a small group of individuals. Is that the origin of a species?

Things that could cause reduced mitochondrial diversity would be population bottlenecks, rapid population expansions (like with humans) or selective sweeps.

This last one seems to me particularly important. Mitochondrial DNA is all inherited as a unit; so if any positively selected variant arises and spreads quickly through a population, it by necessity eliminates all neutral variation. You can't inherit the gene being selected for without also inheriting the other genes it happens to share a mitochondrion with.

Is that the origin of a species? If we have an existing population, and a new mutation appears in mitochondrial DNA which rapidly spreads in the population, did it just become a new species? That strikes me as an absurd thing to say. And the same thing applies for demographic models, for that matter. Cheetahs are going through a population bottleneck at the moment. Assuming the species survives into the future, there should be clear evidence there of reduced diversity at this point in the past; but would that mean that the cheetah species traces its origin to the 20th century? Were cheetahs in the medieval era a different species then?

This is why I think it makes no sense to say anything about origins of species in connection with this work. What they have actually demonstrated is that animal species seem to regularly (on geological timescales) go through phases of greatly reduced genetic diversity; which means either population bottlenecks, rapid expansions or selective sweeps. And it should be made clear that we're only talking about mitochondrial DNA here - it's not established that the same pattern will hold in the nuclear genome. This means the whole pattern could be explained simply by adaptive selection of mtDNA being more common than is usually assumed (a point argued by some geneticists already).

-----------------
ABE: To be clear, I'm not calling the paper's claims absurd, but the way this has sometimes been reported in the press. The actual conclusion in the paper is worded much more sensibly:

quote:
Similar neutral variation of humans and other animals implies that the extant
populations of most animal species have, like modern humans, recently passed
through mitochondrial uniformity.

This seems to be the actual quote to the press from one of the authors which has been twisted into what you see in the OP (via phys.org):

quote:
Our work suggests that most species of animals alive today are like humans, descendants of ancestors who emerged from small populations possibly with near-extinction events within the last few hundred thousand years."

Edited by caffeine, : No reason given.

Edited by Adminnemooseus, : Fix link.


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Faith
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From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.2


Message 15 of 21 (834872)
06-14-2018 9:15 AM
Reply to: Message 14 by caffeine
06-12-2018 5:03 AM


This is where the number of years you were asking about comes from. It's nothing directly calculated from the DNA; and the authors don't put any number on it. All they're saying is that humans have a similar pattern of diversity to other species, implying a similarity in population history. Journalists are then looking up estimates for the origins of Homo sapiens (50,000, 100,000, 200,000 years) and extrapolating that most species are as old as whichever estimate they picked.

Thanks, that's what I wanted to know.

What are we actually looking at? We're looking at how long the mitochondrial genome has had to accumulate neutral variations - the more neutral variations, the longer it is since we can trace a populations mitochondrial diversity back to a small group of individuals. Is that the origin of a species?

You'd have to have a very reliable rate of accumulation of those "neutral variations," by which I suppose you mean mutations, right? But how reliable could such a number be?

I think I get the general point you're making: can't really tell anything about origins from the mitochondrial information?


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