Fossil origin based on DNA testing

[artis]

I often read that whenever a new fossil is found (like a bone fragment or skull fragment etc) they trace it back to either some animal or human , now mostly (and before DNA testing was possible) this was done I suppose by visual inspection and "radiocarbon" dating to put the fossil in a historical context which would help determine it's origin, now for some 2 decades we have DNA testing and I see writings that say that "such and such bone" belonged to a neanderthal or other species living "such and such " years ago,
I also read that humans in general share some 95% or DNA with other animals , here I get the conclusion that genetically we are far more similar than different , so here is my question

How can those researchers be certain that the bone they have found is human or human ancestor instead of maybe from a chimp by DNA?
Or how do they know it's from a human subspecies (Denisovan hominoid) instead of being from a Homo sapiens just long ago?

Is it true that one cannot tell the age of a specimen purely from DNA but has to use other information to factor the age of the sample? Like for example once the DNA is know then it is compared to the known fossils of same DNA structure and either radiocarbon or other methods are used to tell the sample age like molecular clock?

 

[jim mcnamara]

You are really asking 'How do we date fossils and rocks we find the fossils in?'. And then how do we identify them?

This is way more than is reasonable in a forum answer.

Q1. Answer: Biotratigraphy and Chronostratigraphy (layer of rock the fossil is found in), plus isotope ratios (example Carbon 14 to Carbon 12)
https://en.wikipedia.org/wiki/Biostratigraphy
https://en.wikipedia.org/wiki/Chronostratigraphy
https://en.wikipedia.org/wiki/Radiocarbon_dating has limits, other isotopes of other elements and complex lab tests can be used.
Cubic Zirconia for dating meteor impact craters >2 billion ya:
https://www.nature.com/articles/s41467-019-13985-7

Q2. There is a time limit to using DNA samples in teeth and other bones. DNA is NOT necessarily used in identification. DNA "falls apart" over very long periods of time.

Human family tree: https://genetics.thetech.org/ask-a-geneticist/how-far-back-can-ancestry-test-go
https://phys.org/news/2015-06-bank-global-access-ancient-dna.html

This NPR link gives you an idea about the care and time required to ID and date ancient remains.
https://www.npr.org/sections/thetwo...ike-species-lived-more-recently-than-expected

And lastly, nobody wants a repeat of Piltdown Man which is what is actually motivating your question, a bogus ID and/or date:
https://en.wikipedia.org/wiki/Piltdown_Man

 

[jim mcnamara]

Probably more useful: PBS EONS 8 minute video on DNA in fossils
https://www.pbs.org/video/can-we-get-dna-from-fossils-zjwrun/

 

[BillTre]

95% of the human genome size (~3 billion base pairs) is 150,000,000 base pairs.
This provides a lot of information to discriminate between humans and other species.
Similar relationships are found between other species pairs.

Not all bones are going to contain usable DNA.

DNA sequence differences can provide approximate ages of when two evolutionary lines separated (based on approximations of how fast sequences change in those organisms).
Fossils (whose age can be well estimated) can provide more exact limitations of the divergence time of a lineage and the rate of DNA change in those organisms being studied.

 

[artis]

Thank you guys so far, from the given multitude of links I got the impression that all in all DNA testing is not straight forward and can be complicated even for relatively young samples and gets harder for older samples and also a lot is dependent on the preservation of the sample as for many samples no real useful info can be obtained due to degradation. (I guess one could say entropy doing it's job)

@jim mcnamara the link you gave to pbs doesn't work for me , but I think I found the same video just in youtube and watched it , tell me is this the one ?


Another takeaway from the DNA testing that I sort of think I got is that still a lot of "final" info about a certain sample must be taken from the environment the sample has been in not just the DNA itself as that most of the time would be insufficient to tell the tale, info like what sort of rock layer or if it's a newer sample radiocarbon etc right?
Could we say that in dating fossils and rocks the system works similarly to how we define measurement units in the SI system where we take one unit that we are certain of and then define other constants in relation to that unit , so here in geology and samples we have few defined (or approximately defined) constants like radiocarbon, half life and DNA and then we take those and define the ages and possible living environments according to those?I want to go further and ask some more questions , I am not accusing anyone here I just wanted to point out that often times questions about the validity of evolutionary models are looked at with skepticism because of long known heated debates between people in the subject with different religious/personal biases , I myself hold no such biases and am only interested in what is truthful , that being said I did some googling and saw some interesting articles with respect to DNA evolution and the theory of evolution, namely that

it seems that on average (over long time spans) there are more negative mutations happening within the human genome than positive ,
It was rather hard to find any relevant info on the subject matter but I found an article from a scientist Alexey Kondrashov
https://www.ncbi.nlm.nih.gov/pubmed/7475094
this paper also exists in other places.

So before I go in and ask about the broader consequences of this I want to double check and ask you guys is this correct and is it true that indeed over time we develop more harmful mutations than beneficial?PS. from a personal point of view I would tend to agree to this as it seems that there are so many fatal diseases within our genome , like for example I personally know a lot of people that have cancer in every generation or other serious and fatal defects, also I find interesting the fact that our population was only able to expand longevity and reach increasing population numbers with the help of advances in science and better living conditions which mostly have happened over the last few centuries, but evolution gives us timescales that are thousands of times longer than that and from what we know the living conditions should have been extremely harsh back then

 

[jim mcnamara]

Hmm. I'll try to fix the link - and yes you got the right one. But you now see about DNA half life in natural preservation of fossil materials. And now you see the limits on testing Mr Weevil in the image above. The original research had many problems with contamination.

Almost all mutations are termed deleterious. So yes. Example: You can think of cancer initiation as a kind of bad mutation. It may be due to existing inherited genetic problems, or new damage to DNA. This is overly general but you get the idea. Example -- The BRCA1 and BRCA2 inherited gene mutations affect breast cancer rates:
https://www.nationalbreastcancer.org/what-is-brca

You can ask questions to clear things up if you want. But Natural Selection is as close as existing Biological science has to a law right now. It is explanatory, for example.

This is very important to get past what scientists mean for words like "theory" which has completely different meaning to a scientist:
https://ned.ipac.caltech.edu/level5/March07/Quinn/Quinn.html

Yes, that is how we assemble corroborating elements to fine tune dating tool results. In fact most Geological science works that way once you get past naming types of things like rock formations, crystals, and minerals. Interpreating new data in light of what we leanered earlier. That is why I put the zircon link in there for the Australian crater, 2.2 billion years ±error. I think you are on the correct track here

 

[Vanadium 50]

How can those researchers be certain that the bone they have found is human or human ancestor instead of maybe from a chimp by DNA?

Are you seriously suggesting they can't tell the species a bone came from?

 

[BillTre]

Are you seriously suggesting they can't tell the species a bone came from?

There are many fossils that might not be identifiable to the species level by morphology alone.
An important example is the the bone that the first Denisovan DNA was isolated from.

Scientists from the Institute of Archaeology and Ethnology of Novosibirsk have investigated the cave. Among the artifacts which had been left about 30,000 to 48,000 years ago (strata 9–11), bones were identified. One of these bones was a piece of phalanx of a child found in layer 11.2 of the East Gallery. The fossil element was analyzed by Svante Pääbo and coworkers from the Max Planck Institute for Evolutionary Anthropology in Leipzig; its [URL="https://www.physicsforums.com/insights/when-did-mitochondria-evolve/"]mitochondrial DNA[/URL] revealed a structure that differs from known human patterns and has been ascribed to "Denisova hominin", apparently an extinct hominin species or subspecies.[11] Further analysis revealed the Denisovans were related to the Neanderthals and interbred with the ancestors of modern Melanesians.[15]

 

[jim mcnamara]

@Vanadium 50 that is why I mentioned Piltdown Man - Because people think competent scientists are still fooled by such things as they were fooled by 100 years ago. Or they have a special agenda, not science.

 

[pinball1970]

Are you seriously suggesting they can't tell the species a bone came from?

There has been a lot of heated debate regarding naming specimens and assigning a species with respect to human origins.
Bones of contention by Roger Lewin goes into this.

 

[Vanadium 50]

But we're not talking about Piltdown man, or any of several closely related species living in the same place and time - the contention was that an expert in the field could not distinguish Homo Sapiens from Pan Troglodytes.

 

[pinball1970]

But we're not talking about Piltdown man, or any of several closely related species living in the same place and time - the contention was that an expert in the field could not distinguish Homo Sapiens from Pan Troglodytes.

If it's a complete pelvis, skull or femur then no problem.
If it's a single ancient fossil of one small bone then I suppose it becomes more difficult.
Do we have any paleontologists on here?

 

[chemisttree]

Radiocarbon dating only goes back to 50,000 years at best. For pristine samples. Fossils are much much older.

 

[artis]

@jim mcnamara sure I learned some time ago that theory in science in most cases is as close to 2+2=4 as one can get like with gravity and relativity and speed of light etc, although I am more reserved towards some evolution theory cases , I don't doubt cell mutation or virus formation as those are all real time observables , but when it comes to these very long timescales and some fossils that are found I do sometimes have my "questions" especially in the light of what I am reading and what you yourself presented here which states that as the samples get older due to biological degradation of the encoded information the possibility of determining the accurate age becomes less likely,

and correct me if this is wrong but for such old samples where all the common methods are out of reach like radiocarbon and accurate DNA, and given the sample s not radioactive by nature then the age determining is more or less just determined by the place and surrounding of where the specimen was found , in other words the age is determined by the "background" which then itself in many cases is determined by other larger factors like theories of rock formation etc, right?

I think I would want to agree with what @pinball1970 said that if the fossil is a complete skeleton or if it has some very definitive features like a dinosaur skull etc then one can be rather certain even without the sophisticated dating needed but in cases where one finds just say a piece of a leg bone or arm bone then I would believe it becomes rather difficult to determine the original "owner".

Please tell me is this acceptable reasoning within the current information in the field or am I way off here ?
Also another factor I have thought about , to the best of my knowledge we haven't found any "transitional fossils" with respect to humans right? What we have done is found differently shaped human like fossils which we attribute to the lesser developed humans that all came after we split from the so called "common ancestor" which was still an ape at that point , correct?

As for the negative mutations I will have to read up on the subject to know more, it seems interesting to me, so from what we know can we say that in long term aka multiple generations over the effect to our genome is more negative than positive , in other words is our genome getting weaker and more prone to harmful mutations instead of getting stronger ?

I am asking this partly because it is not easy to find a "clear cut" answer on this subject but I found some papers and the paper from the Russian geneticist Kondrashov where he asked rhetorically "why aren't we dead 100 times over" supposedly to to the slow but steady degradation of the human genome over time due to harmful mutations which take root more frequently than good ones, so I guess I might as well ask the same question , but as I said parallel to your answers here I will look into this myself, just kind of short on time at the moment.

 

[BillTre]

old samples where all the common methods are out of reach like radiocarbon and accurate DNA

Contrary at was implied above, there are many radioactive methods (other than C14) for dating fossils of a variety of ages. This Wikipedia article lists a lot of them.

Also another factor I have thought about , to the best of my knowledge we haven't found any "transitional fossils" with respect to humans right? What we have done is found differently shaped human like fossils which we attribute to the lesser developed humans that all came after we split from the so called "common ancestor" which was still an ape at that point , correct?

Frequently when someone finds a transitional fossil between two organisms, it gets a name (loses it aura of transitionalness) and then someone else wants to see a transition between it and another form.

Proving a fossil is directly in the evolutionary lineage between two forms is not easy, but is occasionally done.
Within the human lineage, one might argue that Neanderthals and Denisovans are ancestors to humans since they have been shown to contribute DNA sequence to modern humans, presumably by interbreeding. This seems a pretty direct proof to me, but one that would be more difficult to demonstrate for older species for which DNA sequence recovery is not possible.
Australopithecine species (or which there are many) might all be species that diverged from the lineage leading directly to modern humans (thus not being a direct ancestor), but they could well be closely related to the line that did lead to humans and therefor represent a fairly close representation to what that evolutionary line looked like.

Making sense of relationships and occurances in the past like these is the difficult burden of historical sciences such as biology, geology (earth and non-earth), and astronomy/cosmology.

 

[pinball1970]

Radiocarbon dating only goes back to 50,000 years at best. For pristine samples. Fossils are much much older.

There are direct/indirect methods to date fossils that Jim/Bill have outlined.

I certainly recommend one of the many books on the subject, they are not very technical but certainly give some insight.

'Origin of our species,' by Chris Stringer is a fantastic book. It goes through the technology used to date fossils and also outlines advances in the science since the 80s.