Total Posts:17|Showing Posts:1-17
Jump to topic:

DNA question

Danb6177
Posts: 433
Add as Friend
Challenge to a Debate
Send a Message
4/28/2016 5:58:50 PM
Posted: 7 months ago
Just had a quick question

How far back can science accurately examine dna when determining gene relations?

Thanx
Mhykiel
Posts: 5,987
Add as Friend
Challenge to a Debate
Send a Message
4/28/2016 10:51:21 PM
Posted: 7 months ago
At 4/28/2016 5:58:50 PM, Danb6177 wrote:
Just had a quick question

How far back can science accurately examine dna when determining gene relations?

Thanx

Hey Dan, I'm sure Ram has some 3 page description of the science but I'll just get you started with a few points that you can then use to google more info.

Like most answers, depends.

Most accurate DNA comparisons between species doesn't determine time. It determines relationship. Helps scientist create whats called a phylogenetic tree, you seen the tree of life with all the species branching off each other.
https://en.wikipedia.org...

The process is looking at the different genomes and looking for similar patterns. Say a long long ago ancestor had a mutation that duplicated 300 base pairs. (that's 300 nucleotide pairs on the DNA).. well this mutation, if it goes uncorrected ends up in all the descendants. So between two separate but related species should be this same 300 base pairs.

Now it's not just looking for duplications, there are also techniques that look for subtractions, and others that look for additions. Like Endogenous retro viral additions. Each different technique has a different level of accuracy, that's also adjusted by the amount of base pairs. A 1,000 base pair sequence will be more reliable than a 300 base pair sequence.

Also where these base pairs are located is of interest to accuracy. If it is relatively center of the DNA strands the sequence stays unmodified for longer periods of time, than if at the ends. Also if it is mitochondrial DNA in changes stay around for more generations, because mitochondrial DNA is only from the mother. You don't have crossing with the paternal heritage as well.

This gives the shape of the tree, the proposed ancestry of the species.

However it is not good as a clock. One technique for a genetic clock is to look at extant (present) animal species and see how often their DNA mutates. This is different for each animal. http://www.pnas.org...

So comparing genomes they attempt to determine how many new mutations and different mutations have occurred between separate but related species.
Danb6177
Posts: 433
Add as Friend
Challenge to a Debate
Send a Message
4/29/2016 6:42:12 PM
Posted: 7 months ago
At 4/28/2016 10:51:21 PM, Mhykiel wrote:
At 4/28/2016 5:58:50 PM, Danb6177 wrote:
Just had a quick question

How far back can science accurately examine dna when determining gene relations?

Thanx

Hey Dan, I'm sure Ram has some 3 page description of the science but I'll just get you started with a few points that you can then use to google more info.

Like most answers, depends.

Most accurate DNA comparisons between species doesn't determine time. It determines relationship. Helps scientist create whats called a phylogenetic tree, you seen the tree of life with all the species branching off each other.
https://en.wikipedia.org...

The process is looking at the different genomes and looking for similar patterns. Say a long long ago ancestor had a mutation that duplicated 300 base pairs. (that's 300 nucleotide pairs on the DNA).. well this mutation, if it goes uncorrected ends up in all the descendants. So between two separate but related species should be this same 300 base pairs.

Now it's not just looking for duplications, there are also techniques that look for subtractions, and others that look for additions. Like Endogenous retro viral additions. Each different technique has a different level of accuracy, that's also adjusted by the amount of base pairs. A 1,000 base pair sequence will be more reliable than a 300 base pair sequence.

Also where these base pairs are located is of interest to accuracy. If it is relatively center of the DNA strands the sequence stays unmodified for longer periods of time, than if at the ends. Also if it is mitochondrial DNA in changes stay around for more generations, because mitochondrial DNA is only from the mother. You don't have crossing with the paternal heritage as well.

This gives the shape of the tree, the proposed ancestry of the species.

However it is not good as a clock. One technique for a genetic clock is to look at extant (present) animal species and see how often their DNA mutates. This is different for each animal. http://www.pnas.org...

So comparing genomes they attempt to determine how many new mutations and different mutations have occurred between separate but related species.

Thank you for the reply. I assume that biologists scrape bone to get dna off of very old specimens because bone is all that they have to work with. But how old can they be before accuracy is lost? Can bones from 4 million years ago give good dna to classify species on the phylogenetic tree.
I know that they look at similarities in species and use that to classify also but not sure about the genetics part.
Ramshutu
Posts: 4,063
Add as Friend
Challenge to a Debate
Send a Message
4/29/2016 6:46:19 PM
Posted: 7 months ago
At 4/28/2016 5:58:50 PM, Danb6177 wrote:
Just had a quick question

How far back can science accurately examine dna when determining gene relations?

Thanx

"How far back" in terms of time, or how far back a relationship goes?
Mhykiel
Posts: 5,987
Add as Friend
Challenge to a Debate
Send a Message
4/29/2016 6:57:42 PM
Posted: 7 months ago
At 4/29/2016 6:42:12 PM, Danb6177 wrote:
At 4/28/2016 10:51:21 PM, Mhykiel wrote:
At 4/28/2016 5:58:50 PM, Danb6177 wrote:
Just had a quick question

How far back can science accurately examine dna when determining gene relations?

Thanx

Hey Dan, I'm sure Ram has some 3 page description of the science but I'll just get you started with a few points that you can then use to google more info.

Like most answers, depends.

Most accurate DNA comparisons between species doesn't determine time. It determines relationship. Helps scientist create whats called a phylogenetic tree, you seen the tree of life with all the species branching off each other.
https://en.wikipedia.org...

The process is looking at the different genomes and looking for similar patterns. Say a long long ago ancestor had a mutation that duplicated 300 base pairs. (that's 300 nucleotide pairs on the DNA).. well this mutation, if it goes uncorrected ends up in all the descendants. So between two separate but related species should be this same 300 base pairs.

Now it's not just looking for duplications, there are also techniques that look for subtractions, and others that look for additions. Like Endogenous retro viral additions. Each different technique has a different level of accuracy, that's also adjusted by the amount of base pairs. A 1,000 base pair sequence will be more reliable than a 300 base pair sequence.

Also where these base pairs are located is of interest to accuracy. If it is relatively center of the DNA strands the sequence stays unmodified for longer periods of time, than if at the ends. Also if it is mitochondrial DNA in changes stay around for more generations, because mitochondrial DNA is only from the mother. You don't have crossing with the paternal heritage as well.

This gives the shape of the tree, the proposed ancestry of the species.

However it is not good as a clock. One technique for a genetic clock is to look at extant (present) animal species and see how often their DNA mutates. This is different for each animal. http://www.pnas.org...

So comparing genomes they attempt to determine how many new mutations and different mutations have occurred between separate but related species.

Thank you for the reply. I assume that biologists scrape bone to get dna off of very old specimens because bone is all that they have to work with. But how old can they be before accuracy is lost? Can bones from 4 million years ago give good dna to classify species on the phylogenetic tree.
I know that they look at similarities in species and use that to classify also but not sure about the genetics part.

Fossils are mineralized bone. They don't have DNA in them. DNA analysis is done between extant species
Danb6177
Posts: 433
Add as Friend
Challenge to a Debate
Send a Message
4/30/2016 5:21:13 PM
Posted: 7 months ago
At 4/29/2016 6:46:19 PM, Ramshutu wrote:
At 4/28/2016 5:58:50 PM, Danb6177 wrote:
Just had a quick question

How far back can science accurately examine dna when determining gene relations?

Thanx

"How far back" in terms of time, or how far back a relationship goes?

I guess I would need clarifying. To me if we cannot get dna samples after a period of time then dna would not aid in relationships after that time. Something else would have to be used like comparisons, inference etc..
Danb6177
Posts: 433
Add as Friend
Challenge to a Debate
Send a Message
4/30/2016 5:21:53 PM
Posted: 7 months ago
At 4/29/2016 6:57:42 PM, Mhykiel wrote:
At 4/29/2016 6:42:12 PM, Danb6177 wrote:
At 4/28/2016 10:51:21 PM, Mhykiel wrote:
At 4/28/2016 5:58:50 PM, Danb6177 wrote:
Just had a quick question

How far back can science accurately examine dna when determining gene relations?

Thanx

Hey Dan, I'm sure Ram has some 3 page description of the science but I'll just get you started with a few points that you can then use to google more info.

Like most answers, depends.

Most accurate DNA comparisons between species doesn't determine time. It determines relationship. Helps scientist create whats called a phylogenetic tree, you seen the tree of life with all the species branching off each other.
https://en.wikipedia.org...

The process is looking at the different genomes and looking for similar patterns. Say a long long ago ancestor had a mutation that duplicated 300 base pairs. (that's 300 nucleotide pairs on the DNA).. well this mutation, if it goes uncorrected ends up in all the descendants. So between two separate but related species should be this same 300 base pairs.

Now it's not just looking for duplications, there are also techniques that look for subtractions, and others that look for additions. Like Endogenous retro viral additions. Each different technique has a different level of accuracy, that's also adjusted by the amount of base pairs. A 1,000 base pair sequence will be more reliable than a 300 base pair sequence.

Also where these base pairs are located is of interest to accuracy. If it is relatively center of the DNA strands the sequence stays unmodified for longer periods of time, than if at the ends. Also if it is mitochondrial DNA in changes stay around for more generations, because mitochondrial DNA is only from the mother. You don't have crossing with the paternal heritage as well.

This gives the shape of the tree, the proposed ancestry of the species.

However it is not good as a clock. One technique for a genetic clock is to look at extant (present) animal species and see how often their DNA mutates. This is different for each animal. http://www.pnas.org...

So comparing genomes they attempt to determine how many new mutations and different mutations have occurred between separate but related species.

Thank you for the reply. I assume that biologists scrape bone to get dna off of very old specimens because bone is all that they have to work with. But how old can they be before accuracy is lost? Can bones from 4 million years ago give good dna to classify species on the phylogenetic tree.
I know that they look at similarities in species and use that to classify also but not sure about the genetics part.

Fossils are mineralized bone. They don't have DNA in them. DNA analysis is done between extant species

So how does genetics fit into the fossil record?
janesix
Posts: 3,467
Add as Friend
Challenge to a Debate
Send a Message
4/30/2016 7:24:55 PM
Posted: 7 months ago
At 4/28/2016 5:58:50 PM, Danb6177 wrote:
Just had a quick question

How far back can science accurately examine dna when determining gene relations?

Thanx

About 50,000 years.
Mhykiel
Posts: 5,987
Add as Friend
Challenge to a Debate
Send a Message
4/30/2016 10:42:34 PM
Posted: 7 months ago
At 4/30/2016 5:21:53 PM, Danb6177 wrote:
At 4/29/2016 6:57:42 PM, Mhykiel wrote:
At 4/29/2016 6:42:12 PM, Danb6177 wrote:
At 4/28/2016 10:51:21 PM, Mhykiel wrote:
At 4/28/2016 5:58:50 PM, Danb6177 wrote:
Just had a quick question

How far back can science accurately examine dna when determining gene relations?

Thanx

Hey Dan, I'm sure Ram has some 3 page description of the science but I'll just get you started with a few points that you can then use to google more info.

Like most answers, depends.

Most accurate DNA comparisons between species doesn't determine time. It determines relationship. Helps scientist create whats called a phylogenetic tree, you seen the tree of life with all the species branching off each other.
https://en.wikipedia.org...

The process is looking at the different genomes and looking for similar patterns. Say a long long ago ancestor had a mutation that duplicated 300 base pairs. (that's 300 nucleotide pairs on the DNA).. well this mutation, if it goes uncorrected ends up in all the descendants. So between two separate but related species should be this same 300 base pairs.

Now it's not just looking for duplications, there are also techniques that look for subtractions, and others that look for additions. Like Endogenous retro viral additions. Each different technique has a different level of accuracy, that's also adjusted by the amount of base pairs. A 1,000 base pair sequence will be more reliable than a 300 base pair sequence.

Also where these base pairs are located is of interest to accuracy. If it is relatively center of the DNA strands the sequence stays unmodified for longer periods of time, than if at the ends. Also if it is mitochondrial DNA in changes stay around for more generations, because mitochondrial DNA is only from the mother. You don't have crossing with the paternal heritage as well.

This gives the shape of the tree, the proposed ancestry of the species.

However it is not good as a clock. One technique for a genetic clock is to look at extant (present) animal species and see how often their DNA mutates. This is different for each animal. http://www.pnas.org...

So comparing genomes they attempt to determine how many new mutations and different mutations have occurred between separate but related species.

Thank you for the reply. I assume that biologists scrape bone to get dna off of very old specimens because bone is all that they have to work with. But how old can they be before accuracy is lost? Can bones from 4 million years ago give good dna to classify species on the phylogenetic tree.
I know that they look at similarities in species and use that to classify also but not sure about the genetics part.

Fossils are mineralized bone. They don't have DNA in them. DNA analysis is done between extant species

So how does genetics fit into the fossil record?

(scenario and numbers are made up for illustration purposes only))

Scientist take DNA from a dog and DNA from a cat. They use their models (the formulations of looking for similar base pairs ect...) to conjecture that 15 million years ago Dog and Cats were related.

Then they look to fossils they have collected and at those that are estimated to be 15 million years ago. They were dated by rock layer and radiometric dating.

They look for body plans, taxonomy that has features similar to cats and dogs.

Then they say this is the link between cats and dogs. and here is the genetic proof.

Never mind that body plan, ie form changes to match environment. never mind there is no Genetic evidence connecting the fossil to the living species.

Sometimes these similarities in the genetic code are endoretro viruses. They are virus that have added the genes into the species. And related species should have the same additions in the same spots.

But sometimes to creatures Scientist don't want related have the same ERV's and so they are said to have been separate independent but similar additions.

Same happens with the taxonomy. when the fossils look the same as an extant species but would mess up the tree of life scientist are working on they then say it is a similar feature that formed for the same environment but not related.

Some of these rejections are understandable. For instance they have one ERV in common but no other genetic material.

Just like when evolution was created the basis for a relationship is similar body plan. ((even though body plans adapt to environment)). To back up this connection Evolutionist use DNA similarities between living animals with similar body plans to the fossilized one.

BUT the error and faulty science is too obvious. What says this fossil of this extinct animal is genetically related to the living samples taken?

Nothing. there is no physical connection affirming the assumption.
Ramshutu
Posts: 4,063
Add as Friend
Challenge to a Debate
Send a Message
5/1/2016 12:34:01 AM
Posted: 7 months ago
At 4/30/2016 5:21:53 PM, Danb6177 wrote:
So how does genetics fit into the fossil record?

To answer this question (and the one you asked before), it's not a case of "genetics fitting into the fossil record", but that the fossil record, taxonomy in general, and genetics all say the same thing.

It's pretty clear that humans are more similar to dogs than we are to fish; and more similar to other forms of apes than we are to everything else.

The first person to posit a formal explanation of this, was Darwin who proposed his theory of evolution. Without going into a staggering amount of detail, he proposed that the same mechanics that allows us to produce different types of dog, plant or pigeon breeds from a single common ancestor operates in nature, and if that operates over long periods of time, then all life forms could share a single common ancestor, with the process that generates new forms, operating continually to change everything. He got a lot of the processes and details of this theory wrong, but this is really the part that hasn't changed a great deal.

At that point, it was merely a hypothesis, so he proposed a few tests of his theory; the biggest prediction was the existence of transitional forms. Because if multiple species originated from a single one; then species will exist that are similar to one, or more species aside from their specialised features. His famous example, was that if birds (with fused arms) evolved from dinosaurs (without fused arms), then one should find a primitive bird without fused arms; and that was found in his life time.

Now, obviously there are hundreds of discovered forms; and while one could expect different species to now to exist in non-evolutionary explanations; what is critical is that when species are found with a mix of two lineages; we only find them at levels consistent with evolution; we don't find mixes of creatures outside of that; for example bat-dogs, or ape-fish.

Remember at the time, paleontology and geology were both in their infancy; and this was before any sort of radiometric or decent dating mechanisms were discovered (all of which corroborate the timelines, when they didn't have to at all).

Most importantly, Darwin made his proposition before the discovery of DNA, and far before anyone understood the detail of the mechanics of it; I believe at this time people were aware of DNA as a substance, but didn't know what it was, how it was structured nor how it operated if they understood it's purpose as genetic material at all.

When proteins, genetics and a basic understanding of the fundamentals of DNA starting coming about, it was possible to make predictions.

Remember, if two species share a common ancestor, at one point in both their ancestry, they shared their DNA sequence too. If you have a tree of organisms, then they all share ancestors at different periods of times, and different levels; meaning they have all been separate species from that common DNA sequence at different points, with different numbers of generations since the split.

Given also that we know that proteins sequences, genes, etc can exist in multiple species, and that they often have functional redundancy (they can do the same thing even though they have some differences) a prediction can be built on that.

Specifically, that genes that do the same thing in multiple organisms alive today will have more differences between species that are closely related than those that are not. For example a chicken and turkey, chimps and humans, dogs and foxes should have near identical copies of their genes, with bigger differences between those groups.

Importantly, while a genome could theoretically hold the same level of differences between two organisms as they show physical differences because of those physical differences, this genetic approach is separate from what the creature looks like and can't be caused by it.

IE: it's a different way of measuring how related two creatures are independent of their taxonomic relationship; and if evolution were true, should pretty much match the taxonomic relationship.

Even more importantly, what the differences are, is as important as how many; for example, a dog and a cat could have 2 differences between them lets say Amino Acid 4 and 17 of the gene are different between them, and both have 4 differences compared to, say, a rat; if the cat differs from a rat by AA 4, 12, 93, and 113, and a dog differs by AA 17, 32, 84 and 89, that blows evolution out of the water. the differences between the cat and the rat and the dog and the rat has to be the same (excluding the differences between the dog and the cat):

IE: the dog and cat differ by 17 and 4, and the dog AND the cat differ from the rat by AA 55 and 83.

It's a VERY specific pattern and isn't just about "differences" but what the differences actually are.

As these proteins all do the same thing, if there was no heredity involved, it is highly unlikely that all organisms happen to have such differences that "just so happen" to match the predictions of heredity, and even less likely that these differences could be so specifically tied to heredity in the way I've described, rather than simply random.

Since this, all manner of "conserved proteins" (proteins that all organisms share) have matched this pattern to a high degree. There has been 15 years since the human genome was first sequenced in 2001, and even less time since it was cheap and easy enough for this to have proceeded rapidly.

There are other methods of tracing heredity using other genes, and general changes; such as duplications, deletions; but these build up a broad picture of differences, and because they can happen quickly, and can happen under selective pressures, it's not possible to say whether a creature that differs by 10 deletions is more closely related than one with 20.

But in a broad sense, we can confirm the predictions of evolution here, by showing not just similarity, but a pattern of similarity between organisms matching descent. Much like you can tell whether two documents were copied from another one vs independently written. (Interestingly, the same software used to compare genomes can be used to detect plagurism!)

Every way that you can tell using genetics, indicates this pattern exists in all manner of ways.

The problem is, these patterns between organisms is so significant, so profound, and so low level; both in terms of genetics and taxonomy; that they can't just be shrugged off.

Thus far, no Creationist, ID, or non-evolutionary source has provided any potential, possible or logical explanations about why such patterns can meaningfully exist in a system of non heredity.

Most do what Mhyk does above; try to pretend they don't show anything, or don't matter.
distraff
Posts: 1,005
Add as Friend
Challenge to a Debate
Send a Message
5/1/2016 1:07:12 AM
Posted: 7 months ago
At 4/28/2016 5:58:50 PM, Danb6177 wrote:
Just had a quick question

How far back can science accurately examine dna when determining gene relations?

Thanx

About a few hundred thousand years. We have Neanderthal DNA but DNA from older species is not in any shape to tell us anything useful.
Danb6177
Posts: 433
Add as Friend
Challenge to a Debate
Send a Message
5/8/2016 12:10:17 AM
Posted: 7 months ago
At 5/1/2016 12:34:01 AM, Ramshutu wrote:
At 4/30/2016 5:21:53 PM, Danb6177 wrote:
So how does genetics fit into the fossil record?

To answer this question (and the one you asked before), it's not a case of "genetics fitting into the fossil record", but that the fossil record, taxonomy in general, and genetics all say the same thing.

It's pretty clear that humans are more similar to dogs than we are to fish; and more similar to other forms of apes than we are to everything else.

The first person to posit a formal explanation of this, was Darwin who proposed his theory of evolution. Without going into a staggering amount of detail, he proposed that the same mechanics that allows us to produce different types of dog, plant or pigeon breeds from a single common ancestor operates in nature, and if that operates over long periods of time, then all life forms could share a single common ancestor, with the process that generates new forms, operating continually to change everything. He got a lot of the processes and details of this theory wrong, but this is really the part that hasn't changed a great deal.

At that point, it was merely a hypothesis, so he proposed a few tests of his theory; the biggest prediction was the existence of transitional forms. Because if multiple species originated from a single one; then species will exist that are similar to one, or more species aside from their specialised features. His famous example, was that if birds (with fused arms) evolved from dinosaurs (without fused arms), then one should find a primitive bird without fused arms; and that was found in his life time.

Now, obviously there are hundreds of discovered forms; and while one could expect different species to now to exist in non-evolutionary explanations; what is critical is that when species are found with a mix of two lineages; we only find them at levels consistent with evolution; we don't find mixes of creatures outside of that; for example bat-dogs, or ape-fish.

Remember at the time, paleontology and geology were both in their infancy; and this was before any sort of radiometric or decent dating mechanisms were discovered (all of which corroborate the timelines, when they didn't have to at all).

Most importantly, Darwin made his proposition before the discovery of DNA, and far before anyone understood the detail of the mechanics of it; I believe at this time people were aware of DNA as a substance, but didn't know what it was, how it was structured nor how it operated if they understood it's purpose as genetic material at all.

When proteins, genetics and a basic understanding of the fundamentals of DNA starting coming about, it was possible to make predictions.

Remember, if two species share a common ancestor, at one point in both their ancestry, they shared their DNA sequence too. If you have a tree of organisms, then they all share ancestors at different periods of times, and different levels; meaning they have all been separate species from that common DNA sequence at different points, with different numbers of generations since the split.

Given also that we know that proteins sequences, genes, etc can exist in multiple species, and that they often have functional redundancy (they can do the same thing even though they have some differences) a prediction can be built on that.

Specifically, that genes that do the same thing in multiple organisms alive today will have more differences between species that are closely related than those that are not. For example a chicken and turkey, chimps and humans, dogs and foxes should have near identical copies of their genes, with bigger differences between those groups.

Importantly, while a genome could theoretically hold the same level of differences between two organisms as they show physical differences because of those physical differences, this genetic approach is separate from what the creature looks like and can't be caused by it.

IE: it's a different way of measuring how related two creatures are independent of their taxonomic relationship; and if evolution were true, should pretty much match the taxonomic relationship.

Even more importantly, what the differences are, is as important as how many; for example, a dog and a cat could have 2 differences between them lets say Amino Acid 4 and 17 of the gene are different between them, and both have 4 differences compared to, say, a rat; if the cat differs from a rat by AA 4, 12, 93, and 113, and a dog differs by AA 17, 32, 84 and 89, that blows evolution out of the water. the differences between the cat and the rat and the dog and the rat has to be the same (excluding the differences between the dog and the cat):

IE: the dog and cat differ by 17 and 4, and the dog AND the cat differ from the rat by AA 55 and 83.

It's a VERY specific pattern and isn't just about "differences" but what the differences actually are.

As these proteins all do the same thing, if there was no heredity involved, it is highly unlikely that all organisms happen to have such differences that "just so happen" to match the predictions of heredity, and even less likely that these differences could be so specifically tied to heredity in the way I've described, rather than simply random.

Since this, all manner of "conserved proteins" (proteins that all organisms share) have matched this pattern to a high degree. There has been 15 years since the human genome was first sequenced in 2001, and even less time since it was cheap and easy enough for this to have proceeded rapidly.

There are other methods of tracing heredity using other genes, and general changes; such as duplications, deletions; but these build up a broad picture of differences, and because they can happen quickly, and can happen under selective pressures, it's not possible to say whether a creature that differs by 10 deletions is more closely related than one with 20.

But in a broad sense, we can confirm the predictions of evolution here, by showing not just similarity, but a pattern of similarity between organisms matching descent. Much like you can tell whether two documents were copied from another one vs independently written. (Interestingly, the same software used to compare genomes can be used to detect plagurism!)

Every way that you can tell using genetics, indicates this pattern exists in all manner of ways.


The problem is, these patterns between organisms is so significant, so profound, and so low level; both in terms of genetics and taxonomy; that they can't just be shrugged off.


Thus far, no Creationist, ID, or non-evolutionary source has provided any potential, possible or logical explanations about why such patterns can meaningfully exist in a system of non heredity.

Most do what Mhyk does above; try to pretend they don't show anything, or don't matter.

I appreciate the extensive answer. I was viewing some lectures and it would seem from the professor that dna was being taken from old fossils. I get now what he was saying and why he says it in a factual way.
Ramshutu
Posts: 4,063
Add as Friend
Challenge to a Debate
Send a Message
5/8/2016 1:57:27 AM
Posted: 7 months ago
At 5/8/2016 12:10:17 AM, Danb6177 wrote:
At 5/1/2016 12:34:01 AM, Ramshutu wrote:
At 4/30/2016 5:21:53 PM, Danb6177 wrote:
So how does genetics fit into the fossil record?

To answer this question (and the one you asked before), it's not a case of "genetics fitting into the fossil record", but that the fossil record, taxonomy in general, and genetics all say the same thing.

It's pretty clear that humans are more similar to dogs than we are to fish; and more similar to other forms of apes than we are to everything else.

The first person to posit a formal explanation of this, was Darwin who proposed his theory of evolution. Without going into a staggering amount of detail, he proposed that the same mechanics that allows us to produce different types of dog, plant or pigeon breeds from a single common ancestor operates in nature, and if that operates over long periods of time, then all life forms could share a single common ancestor, with the process that generates new forms, operating continually to change everything. He got a lot of the processes and details of this theory wrong, but this is really the part that hasn't changed a great deal.

At that point, it was merely a hypothesis, so he proposed a few tests of his theory; the biggest prediction was the existence of transitional forms. Because if multiple species originated from a single one; then species will exist that are similar to one, or more species aside from their specialised features. His famous example, was that if birds (with fused arms) evolved from dinosaurs (without fused arms), then one should find a primitive bird without fused arms; and that was found in his life time.

Now, obviously there are hundreds of discovered forms; and while one could expect different species to now to exist in non-evolutionary explanations; what is critical is that when species are found with a mix of two lineages; we only find them at levels consistent with evolution; we don't find mixes of creatures outside of that; for example bat-dogs, or ape-fish.

Remember at the time, paleontology and geology were both in their infancy; and this was before any sort of radiometric or decent dating mechanisms were discovered (all of which corroborate the timelines, when they didn't have to at all).

Most importantly, Darwin made his proposition before the discovery of DNA, and far before anyone understood the detail of the mechanics of it; I believe at this time people were aware of DNA as a substance, but didn't know what it was, how it was structured nor how it operated if they understood it's purpose as genetic material at all.

When proteins, genetics and a basic understanding of the fundamentals of DNA starting coming about, it was possible to make predictions.

Remember, if two species share a common ancestor, at one point in both their ancestry, they shared their DNA sequence too. If you have a tree of organisms, then they all share ancestors at different periods of times, and different levels; meaning they have all been separate species from that common DNA sequence at different points, with different numbers of generations since the split.

Given also that we know that proteins sequences, genes, etc can exist in multiple species, and that they often have functional redundancy (they can do the same thing even though they have some differences) a prediction can be built on that.

Specifically, that genes that do the same thing in multiple organisms alive today will have more differences between species that are closely related than those that are not. For example a chicken and turkey, chimps and humans, dogs and foxes should have near identical copies of their genes, with bigger differences between those groups.

Importantly, while a genome could theoretically hold the same level of differences between two organisms as they show physical differences because of those physical differences, this genetic approach is separate from what the creature looks like and can't be caused by it.

IE: it's a different way of measuring how related two creatures are independent of their taxonomic relationship; and if evolution were true, should pretty much match the taxonomic relationship.

Even more importantly, what the differences are, is as important as how many; for example, a dog and a cat could have 2 differences between them lets say Amino Acid 4 and 17 of the gene are different between them, and both have 4 differences compared to, say, a rat; if the cat differs from a rat by AA 4, 12, 93, and 113, and a dog differs by AA 17, 32, 84 and 89, that blows evolution out of the water. the differences between the cat and the rat and the dog and the rat has to be the same (excluding the differences between the dog and the cat):

IE: the dog and cat differ by 17 and 4, and the dog AND the cat differ from the rat by AA 55 and 83.

It's a VERY specific pattern and isn't just about "differences" but what the differences actually are.

As these proteins all do the same thing, if there was no heredity involved, it is highly unlikely that all organisms happen to have such differences that "just so happen" to match the predictions of heredity, and even less likely that these differences could be so specifically tied to heredity in the way I've described, rather than simply random.

Since this, all manner of "conserved proteins" (proteins that all organisms share) have matched this pattern to a high degree. There has been 15 years since the human genome was first sequenced in 2001, and even less time since it was cheap and easy enough for this to have proceeded rapidly.

There are other methods of tracing heredity using other genes, and general changes; such as duplications, deletions; but these build up a broad picture of differences, and because they can happen quickly, and can happen under selective pressures, it's not possible to say whether a creature that differs by 10 deletions is more closely related than one with 20.

But in a broad sense, we can confirm the predictions of evolution here, by showing not just similarity, but a pattern of similarity between organisms matching descent. Much like you can tell whether two documents were copied from another one vs independently written. (Interestingly, the same software used to compare genomes can be used to detect plagurism!)

Every way that you can tell using genetics, indicates this pattern exists in all manner of ways.


The problem is, these patterns between organisms is so significant, so profound, and so low level; both in terms of genetics and taxonomy; that they can't just be shrugged off.


Thus far, no Creationist, ID, or non-evolutionary source has provided any potential, possible or logical explanations about why such patterns can meaningfully exist in a system of non heredity.

Most do what Mhyk does above; try to pretend they don't show anything, or don't matter.

I appreciate the extensive answer. I was viewing some lectures and it would seem from the professor that dna was being taken from old fossils. I get now what he was saying and why he says it in a factual way.

It's no problem, I'm happy to answer any other questions or queries you have on the subject; this is probably one of my biggest area's of interest.
Danb6177
Posts: 433
Add as Friend
Challenge to a Debate
Send a Message
5/8/2016 3:26:08 AM
Posted: 7 months ago
At 5/1/2016 1:07:12 AM, distraff wrote:
At 4/28/2016 5:58:50 PM, Danb6177 wrote:
Just had a quick question

How far back can science accurately examine dna when determining gene relations?

Thanx

About a few hundred thousand years. We have Neanderthal DNA but DNA from older species is not in any shape to tell us anything useful.

Your reply forced me to look that up. I found where they say a dna sample of the Neanderthal could be 170k years. How do they date this stuff. I know its radiometric but what exactly do they date?
Danb6177
Posts: 433
Add as Friend
Challenge to a Debate
Send a Message
5/8/2016 3:28:27 AM
Posted: 7 months ago
At 4/30/2016 10:42:34 PM, Mhykiel wrote:
At 4/30/2016 5:21:53 PM, Danb6177 wrote:
At 4/29/2016 6:57:42 PM, Mhykiel wrote:
At 4/29/2016 6:42:12 PM, Danb6177 wrote:
At 4/28/2016 10:51:21 PM, Mhykiel wrote:
At 4/28/2016 5:58:50 PM, Danb6177 wrote:
Just had a quick question

How far back can science accurately examine dna when determining gene relations?

Thanx

Hey Dan, I'm sure Ram has some 3 page description of the science but I'll just get you started with a few points that you can then use to google more info.

Like most answers, depends.

Most accurate DNA comparisons between species doesn't determine time. It determines relationship. Helps scientist create whats called a phylogenetic tree, you seen the tree of life with all the species branching off each other.
https://en.wikipedia.org...

The process is looking at the different genomes and looking for similar patterns. Say a long long ago ancestor had a mutation that duplicated 300 base pairs. (that's 300 nucleotide pairs on the DNA).. well this mutation, if it goes uncorrected ends up in all the descendants. So between two separate but related species should be this same 300 base pairs.

Now it's not just looking for duplications, there are also techniques that look for subtractions, and others that look for additions. Like Endogenous retro viral additions. Each different technique has a different level of accuracy, that's also adjusted by the amount of base pairs. A 1,000 base pair sequence will be more reliable than a 300 base pair sequence.

Also where these base pairs are located is of interest to accuracy. If it is relatively center of the DNA strands the sequence stays unmodified for longer periods of time, than if at the ends. Also if it is mitochondrial DNA in changes stay around for more generations, because mitochondrial DNA is only from the mother. You don't have crossing with the paternal heritage as well.

This gives the shape of the tree, the proposed ancestry of the species.

However it is not good as a clock. One technique for a genetic clock is to look at extant (present) animal species and see how often their DNA mutates. This is different for each animal. http://www.pnas.org...

So comparing genomes they attempt to determine how many new mutations and different mutations have occurred between separate but related species.

Thank you for the reply. I assume that biologists scrape bone to get dna off of very old specimens because bone is all that they have to work with. But how old can they be before accuracy is lost? Can bones from 4 million years ago give good dna to classify species on the phylogenetic tree.
I know that they look at similarities in species and use that to classify also but not sure about the genetics part.

Fossils are mineralized bone. They don't have DNA in them. DNA analysis is done between extant species

So how does genetics fit into the fossil record?

(scenario and numbers are made up for illustration purposes only))

Scientist take DNA from a dog and DNA from a cat. They use their models (the formulations of looking for similar base pairs ect...) to conjecture that 15 million years ago Dog and Cats were related.

Then they look to fossils they have collected and at those that are estimated to be 15 million years ago. They were dated by rock layer and radiometric dating.

They look for body plans, taxonomy that has features similar to cats and dogs.

Then they say this is the link between cats and dogs. and here is the genetic proof.

Never mind that body plan, ie form changes to match environment. never mind there is no Genetic evidence connecting the fossil to the living species.

Sometimes these similarities in the genetic code are endoretro viruses. They are virus that have added the genes into the species. And related species should have the same additions in the same spots.

But sometimes to creatures Scientist don't want related have the same ERV's and so they are said to have been separate independent but similar additions.

Same happens with the taxonomy. when the fossils look the same as an extant species but would mess up the tree of life scientist are working on they then say it is a similar feature that formed for the same environment but not related.

Some of these rejections are understandable. For instance they have one ERV in common but no other genetic material.

Just like when evolution was created the basis for a relationship is similar body plan. ((even though body plans adapt to environment)). To back up this connection Evolutionist use DNA similarities between living animals with similar body plans to the fossilized one.

BUT the error and faulty science is too obvious. What says this fossil of this extinct animal is genetically related to the living samples taken?

Nothing. there is no physical connection affirming the assumption.

Thanks Mhykiel for the other side of the coin. This is a topic im highly interested in
Danb6177
Posts: 433
Add as Friend
Challenge to a Debate
Send a Message
5/8/2016 3:33:05 AM
Posted: 7 months ago
At 5/4/2016 7:12:00 AM, creamycreamy wrote:
I know that mitrochondrial DNA which is past down through the mothers side can be used.

I know that mitochondrial dna differs from nuclear dna but is it usable more accurately? or for a longer period of time? I would think it would be the same in that respect.