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Author Topic:   The Common Ancestor?
barbara
Member (Idle past 3029 days)
Posts: 167
Joined: 07-19-2010


Message 136 of 341 (586113)
10-11-2010 9:45 AM
Reply to: Message 135 by Dr Jack
10-11-2010 6:43 AM


Re: Time Tree : : Timescale of Life
The Time Tree gives a split date for eukaryotes and bacteria of a nucleotide date of 2622.0 mya. Can someone please explain this to me?

What formula is used for the molecular clock model? Is carbon dating of bones used in the model?


This message is a reply to:
 Message 135 by Dr Jack, posted 10-11-2010 6:43 AM Dr Jack has responded

Replies to this message:
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Coyote
Member (Idle past 333 days)
Posts: 6117
Joined: 01-12-2008


Message 137 of 341 (586118)
10-11-2010 10:20 AM
Reply to: Message 136 by barbara
10-11-2010 9:45 AM


Re: Time Tree : : Timescale of Life
Is carbon dating of bones used in the model?

No, not even close.

They use the increasing differences (mutations) between two groups of organisms as shown in different parts of the DNA.

I could explain how C14 dating works, but I'll let someone else explain the details of DNA dating.


Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
This message is a reply to:
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Dr Jack
Member (Idle past 332 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 138 of 341 (586125)
10-11-2010 11:07 AM
Reply to: Message 136 by barbara
10-11-2010 9:45 AM


Re: Time Tree : : Timescale of Life
The Time Tree gives a split date for eukaryotes and bacteria of a nucleotide date of 2622.0 mya. Can someone please explain this to me?

What do you need explained?

What formula is used for the molecular clock model?

You look at a gene or bit of genome in a bunch of organisms (in this particular case it is almost certainly rRNA). Then you work out the rate of divergence between the particular bits of genome you are looking at by plotting the degree of divergence against the time the organisms split based on other evidence. By taking the gradient of this line you can then use it to estimate the time at which other organisms diverged by looking at the level of divergence they have.

You can test the internal validity of your estimate by testing multiple organisms that should have the same divergence time and seeing if your estimates are similar. You can also check that your original plot follows a roughly straight line.

Is carbon dating of bones used in the model?

It won't be for molecular clocks on that scale, but other radiodating methods will have been. It is possible that the calibration of the clock(s) used may have involved using shorter period data derived in part from radiocarbon dating.


This message is a reply to:
 Message 136 by barbara, posted 10-11-2010 9:45 AM barbara has responded

Replies to this message:
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barbara
Member (Idle past 3029 days)
Posts: 167
Joined: 07-19-2010


Message 139 of 341 (586767)
10-14-2010 5:07 PM
Reply to: Message 138 by Dr Jack
10-11-2010 11:07 AM


Re: Time Tree : : Timescale of Life
rRNA is the location where the protein is made correct?

The protein meaning what it makes such as bone, tissue, organs, etc. right?

So looking at a bunch of organisms to build a tree based on rRNA is still the same method that as used prior to genetics based on morphology likeness and differences.


This message is a reply to:
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Wounded King
Member (Idle past 2322 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 140 of 341 (586772)
10-14-2010 5:39 PM
Reply to: Message 139 by barbara
10-14-2010 5:07 PM


Re: Time Tree : : Timescale of Life
rRNA means ribosomal RNA, ribosomes are what synthesise proteins based on sequences of messenger RNA (mRNA). Ribosomes are unusual in that they are a mixture of protein and RNA molecules.

Ribosomes are an essential part of protein synthesis and the RNA sequences which are incorporated in them are highly conserved. In prokaryotes they are well conserved across the Archaea and Bacterial kingdoms. This conservation makes them a good subject for deep time phylogenetic studies.

TTFN,

WK


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Dr Jack
Member (Idle past 332 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 141 of 341 (586849)
10-15-2010 5:29 AM
Reply to: Message 140 by Wounded King
10-14-2010 5:39 PM


Re: Time Tree : : Timescale of Life
Minor point: Archaea and Bacteria are different domains (aka empires) not different kingdoms.
This message is a reply to:
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Dr Jack
Member (Idle past 332 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 142 of 341 (586850)
10-15-2010 5:38 AM
Reply to: Message 139 by barbara
10-14-2010 5:07 PM


Re: Time Tree : : Timescale of Life
Wounded King has already dealt with what rRNA is.

The protein meaning what it makes such as bone, tissue, organs, etc. right?

Those things are composed to varying degrees of proteins, yes, but proteins are much important for their other roles. Nearly all enzymes are proteins, and enzymes control which reactions happen when and where in the body; receptors are proteins so the way that cells respond to signals is controlled by proteins, and a lot of those signals are themselves proteins.

So looking at a bunch of organisms to build a tree based on rRNA is still the same method that as used prior to genetics based on morphology likeness and differences.

Firstly, we were talking about molecular clocks, not constructing trees. Molecular clocks are used to date splits not construct trees.

Secondly, yes, there's some similarities in the way that trees are constructed based on morphology and genetics but the genetic approach is much better because (a) genes contain much more information than morphology; (b) the identification of different characters in morphology is subjective and arbitrary whereas the identification of differences in genes is objective and consistent and (c) genes can still be reliably compared even when there is almost no morphological similarity between two organisms.

A morphological comparison of Archaea, Bacteria and Eukarya would suggest Archaea and Bacteria are closer to each other than either is to Eukarya; but the genetics of rRNA revealed that Archaea are closer to Eukarya than they are to Bacteria. As our knowledge of the cell physiology of Archaea has increased this finding has been widely supported.


This message is a reply to:
 Message 139 by barbara, posted 10-14-2010 5:07 PM barbara has responded

Replies to this message:
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barbara
Member (Idle past 3029 days)
Posts: 167
Joined: 07-19-2010


Message 143 of 341 (586943)
10-15-2010 4:29 PM
Reply to: Message 142 by Dr Jack
10-15-2010 5:38 AM


Re: Time Tree : : Timescale of Life
What information is genes telling you? Some people here do not agree that genes actually carry information. My understanding is you are only able to see what the protein makes in the form of bone, tissue etc.
Considering that most species do share the same proteins because we share the same parts, wouldn't this make the connection between them harder to determine?
This message is a reply to:
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Taq
Member
Posts: 7997
Joined: 03-06-2009
Member Rating: 3.8


Message 144 of 341 (586949)
10-15-2010 5:02 PM
Reply to: Message 143 by barbara
10-15-2010 4:29 PM


Re: Time Tree : : Timescale of Life
What information is genes telling you?

The same information that everything in the universe has. Humans look at stuff and extract information from them in order to determine their state and their origin. This is true of rocks, clouds, and life. Same type of information in all of them.

My understanding is you are only able to see what the protein makes in the form of bone, tissue etc.

We are able to determine the DNA sequence which tells us how long it has been since two species shared a common ancestor. The more distant that common ancestor the more the DNA sequences for a shared gene will differ.

Considering that most species do share the same proteins because we share the same parts, wouldn't this make the connection between them harder to determine?

It would be harder if they DIDN'T share any parts.


This message is a reply to:
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Wounded King
Member (Idle past 2322 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 145 of 341 (586954)
10-15-2010 5:45 PM
Reply to: Message 143 by barbara
10-15-2010 4:29 PM


Re: Time Tree : : Timescale of Life
Some people here do not agree that genes actually carry information.

What people do you mean here? I'd ask what you mean by information as well, but that traditionally sends us off down a rabbit hole.

My understanding is you are only able to see what the protein makes in the form of bone, tissue etc.

Your understanding is wrong, we can analyze specific proteins to determine their amino acid sequence and other modifications, we can also directly examine their structure to find out what form they take in vivo and how they interact with other proteins. As well as this we can study the genes coding for these protein sequences.

Considering that most species do share the same proteins because we share the same parts, wouldn't this make the connection between them harder to determine?

I'm not following your logic here. If your point is that the proteins have to have certain form in order to form tissues and organs then A) There is no reason to believe this is true since there are multiple possible amino acid sequences which can create the same functional folds in proteins, and possibly many totally distinct folds which can perform equivalent functions, the fact of the matter is that we only have a very rudimentary understanding of the functional phase space of proteins. B) We know that even if a protein is 100% conserved in terms of amino acid sequence it can still diverge almost 40%, possibly more in some cases, at the DNA sequence level.

TTFN,

WK


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Dr Jack
Member (Idle past 332 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 146 of 341 (586956)
10-15-2010 5:54 PM
Reply to: Message 143 by barbara
10-15-2010 4:29 PM


Re: Time Tree : : Timescale of Life
Your understanding is wrong.

These dates are established by directly comparing DNA sequences.


This message is a reply to:
 Message 143 by barbara, posted 10-15-2010 4:29 PM barbara has responded

Replies to this message:
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barbara
Member (Idle past 3029 days)
Posts: 167
Joined: 07-19-2010


Message 147 of 341 (586965)
10-15-2010 9:16 PM
Reply to: Message 146 by Dr Jack
10-15-2010 5:54 PM


Re: Time Tree : : Timescale of Life
Then please explain what information do genes give you?
This message is a reply to:
 Message 146 by Dr Jack, posted 10-15-2010 5:54 PM Dr Jack has responded

Replies to this message:
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Dr Jack
Member (Idle past 332 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 148 of 341 (586987)
10-16-2010 2:12 AM
Reply to: Message 147 by barbara
10-15-2010 9:16 PM


Re: Time Tree : : Timescale of Life
The sequence of nucleotides
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Nuggin
Member (Idle past 720 days)
Posts: 2965
From: Los Angeles, CA USA
Joined: 08-09-2005


Message 149 of 341 (586999)
10-16-2010 5:35 AM
Reply to: Message 143 by barbara
10-15-2010 4:29 PM


Re: Time Tree : : Timescale of Life
What information is genes telling you? Some people here do not agree that genes actually carry information. My understanding is you are only able to see what the protein makes in the form of bone, tissue etc.

I'm gonna over simplify this for easy clarity.

There has been a concerted effort by geneticists over the last few decades to record all the genes and figure out what they do.

It's easier for us to locate a gene than to determine it's function.

The way you determine function is by looking at a large number of individuals, recording their gene sequences and looking for abnormalities.

If 99% of a population has Gene A, and 1% of that population has Gene B instead, you look at what the Gene B individuals have in common.

Another way to gather this information is to look for odd traits in a population, examine the individual and see what gene variants they have which is not seen in the rest of the population.

A lot of this science is done with fruit flies - largely because they mature quickly and cost almost nothing to keep alive.


Considering that most species do share the same proteins because we share the same parts, wouldn't this make the connection between them harder to determine?

This is why its useful to look for differences.

For example, an albino rat differs from a normal rat in an obvious way. Locating the difference in the code tells us something about the cause of the condition. Then you can compare the gene in the rat where this happened with a gene in a human with a similar condition and see if it's the same error or not.


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frako
Member
Posts: 2814
From: slovenija
Joined: 09-04-2010


Message 150 of 341 (587000)
10-16-2010 5:47 AM
Reply to: Message 143 by barbara
10-15-2010 4:29 PM


Re: Time Tree : : Timescale of Life
Some people here do not agree that genes actually carry information

If this where true, transfering Jellyfish Genes, the ones that make them glow in the dark, to rats would not make rats glow in the dark. Guess what they made fluorescent rats, so gens hold information.

http://www.wisn.com/health/16166778/detail.html


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