Mutual Divorce - tree of life (Jan/18/2006 )

There are enough lazy people around. May be people are taking advances is technology for granted. I cant imagine an ancient lab without internet connection,PCR nad Restriction Enzymes. Though all these things are meant to decrease the burden and fasten the research definitely they are making people > and > lazy.

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when I was doing my undergrad work, it was soooo different; I barely knew anything about computers and learned a lot on the job as new software became available ...as well as the techniques. at that time, PCR and the 'net were only a couple years old and so much that we take for granted was new then

I can barely imagine working without the internet now; I have become so dependent...but I could do it if I had to

it does seem as though today's college students just find all the answers online. how many of them actually study???? I tutor a young gal in college algebra and she has the hardest time just taking notes properly in class...does her homework next to the computer with an online tutorial that does most of the work...then she struggles when she gets to the test. lazy lazy lazy

some of these things you actually have to KNOW if you want to go into science

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CLARIFICATION : all the qs were numbered in a way that the addition of the 1st and second no. in that no. is 1 ... i tried to explain it. I thought that my numerology is good... but it was not that true because nobody answered them.
ONe BIGGEST CLARIFICATION: this things aren't included in my syllabus I'm not a university student yet. ANd still i'm thinking about this and these are qs that i got into my mind and was trying to solve them for myself... I think that these qs are too easy for u all as you don't appear that curious to answer...



shrei

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So all the best... when u r able to solve them do post the answers here may be with better numerology...

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So all the best... when u r able to solve them do post the answers here may be with better numerology...
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Thanks if u really intend to wish me.Hope i improve upon both my numero and bio,chem,phy...

Shrei

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Dear 743430, if you genuinly are unable to find the questions, then you can post your doubts here on the forum. Try getting the answers on google.com, browse through pubmed-bookshelf etc. After all attempts doesnt yield anything then ask your question one by one without random numbering. Try to keep ur question simple and straight.

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he's over on the BioTechniques website and asking the same questions. at least this time he eft the odd numbering system out.......hehe

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Thanks for such a relief... I've searched through and have mentioned what i got below-

When we are examining a specefic prot or a specefic DNA sequence[ DNA sequence complimentary to the probe we use], we should comment just about the evolution of that specefic prot. or DNA. We can , still , get a constriant like -as the prot lines/DNA lines got separate T years ago, the organism-lines must have separated [ not a reproductive separation i mean] Tyrs ago or Before.
For correct judgement of time of separation we have to compare many prots and DNAs of the two organisms.A rigorousssest thing!!!

Am I correct??? Please help...

One more thing-
1.What makes some sequce conserved??? What is the mechanism behind it???
-I'm reading ncbi biochem for it.

2.We must use conserved sequences of DNA or Proteins as if the rate is faster then nearly correct no. of mutations is not obtained due to overlapping of mutations.I think if we divide the whole DNA into longer units this error may be reduced .But still we can't use fastly changing proteins eg. fibrinogen in human. So, this reduses our resolution. -Is my thinking correct???

3. In the eqn, we get a constant 1/2 in the expression of the rate constant [ ''the fraction of changed amino acids per unit time''].Why is it there??? how could we determine it??? How to get the rate constant? Is it by comparing C-14 / U-235 dating of available fossils and their protein/DNA sequences of those fossilized organisms??? -ncbi, and oxford chem.evolution book didn't contain any explanation of this constant [ 1/2],

We can use this to find out how prot families may be linked...same way we can use this for judging the evolution DNA sequences. Is it being done??? -Hehe offcourse !!!



Hrushikesh
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First of all not an evolutionary biologist, but this first part makes sense, some proteins tolerate more changes than others so if you look at only one protein then the capability of that protein to change will affect the rate you get for evolutionary distance



Some proteins have to be more conserved because their structure or amino acid sequence is very highly important for their funciton, in this case maybe the protein is used to say bind a specific ligand and any changes in this structure or amino acid sequence prevent the ligand binding then assuming this ligand binding is essential to survival any changes lead to no survival of the organism and therefore only organsisms that carefully conserve this protien survive...as a result the sequence is very well conserved throughout evolution..(hope that description is making sense for you...)



ok you lost me here a little, I was just arguing that the rate of mutation for conserved genes would be SLOWER not Faster....

nearly correct number not obtained due to overlapping mutations??? not getting that statement either....

Longer units would potentially reduce error--this makes sense as does the whole fibrinogen thing, you can't use the whole genome....


As I said not evolutionary biologist so the whole math thing is beyond me.... constant is 1 amino acid changed per 2 units of time????? don't know what that means though

I will say it seems to me that only highly conserved proteins may be found in two organisms of very distinct descent ie: humans and fruit flys share alot of proteins, but most of the ones I know about are highly conserved and important for some basic functions like development, cell division etc...

Just a thought to throw out there, but maybe the best thing is to pick one very conserved protien and use it then you cancel out the whole rate of that protein thing b/c you only look at it in all different organisms???

anyway hope that helps you... keep checking those resources and try us back if you come up with anything...

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Thanks alot, for ur support and answers.
beccaf22 -

First of all not an evolutionary biologist, but this first part makes sense, some proteins tolerate more changes than others so if you look at only one protein then the capability of that protein to change will affect the rate you get for evolutionary distance.
Explaining the query-
In this method , we consider that at the point of separation of two lines and before , the sequence of the chosen protein/DNA is identical. And two lines are said to get separated when one difference between the protein/DNA is confirmed. But this point of separation may or may not correspond to reproductive separation [the time of mutual divorce!] [u]as the protein or gene chosen might not be involved in reproduction in a way to block it. To over come this i think we have to examine enough number of reproduction-related [ involved in mutual compatibility] conserved proteins/DNAs...or examine many proteins/DNAs and the short time range, when there is maximum no. of separation times of twolines observed , should be considered as the time-range for reproductitve separation.
I think those proteins/DNAs leading to reproductive compatibility or non-compatibility should change atleast once to have two non-compatible lines [ new species]... so those might not be that conserved.



Some proteins have to be more conserved because their structure or amino acid sequence is very highly important for their funciton, in this case maybe the protein is used to say bind a specific ligand and any changes in this structure or amino acid sequence prevent the ligand binding then assuming this ligand binding is essential to survival any changes lead to no survival of the organism and therefore only organsisms that carefully conserve this protien survive...as a result the sequence is very well conserved throughout evolution..(hope that description is making sense for you...) -Absolutely, thanks for that ligand-bound explanation!



ok you lost me here a little, I was just arguing that the rate of mutation for conserved genes would be SLOWER not Faster.... nearly correct number not obtained due to overlapping mutations??? not getting that statement either....
Q with corrections-
2.We must use conserved sequences of DNA or Proteins b/c If the proteins having faster rate are chosen then even nearly correct no. of mutations is not obtained due to overlapping of mutations [ mutation sites].I think if we divide the whole DNA into longer units this error may be reduced or made predictable.But still we can't use fastly changing proteins eg. fibrinogen in human. So, this reduses our resolution.Means we can't differenciate between closely related individuals that well. -Is my thinking correct???-
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3. the eqn is

2Kt= -ln(1-d/n)...

K=-(1/2).t.ln(1-d/n)

n=no of residues
d=no. of sites having different residues
t=time interval
K= the rate of evolutionary amino acid substitution per site per year.
[ K = -(1/2).t.ln[(n-d)/n]

I thought its derivation is same as that in my radioactivity chapter.
It is similar as (n-d) is similar to no. of unchanged atoms at that instant , n is similar to the original [ birth no.] of atoms, this follows exponential replacement [ 'decay' for atoms] . but-
In the eqn, we get a constant 1/2 in the expression of the rate constant [ ''the fraction of changed amino acids per unit time''].Why is it there??? how could we determine it??? How to get the rate constant? Is it by comparing C-14 / U-235 dating of available fossils and their protein/DNA sequences of those fossilized organisms??? -ncbi, and oxford chem.evolution book didn't contain any explanation of this constant [ 1/2],



I will say it seems to me that only highly conserved proteins may be found in two organisms of very distinct descent ie: humans and fruit flys share alot of proteins, but most of the ones I know about are highly conserved and important for some basic functions like development, cell division etc...

Just a thought to throw out there, but maybe the best thing is to pick one very conserved protien and use it then you cancel out the whole rate of that protein thing b/c you only look at it in all different organisms??? - means same using scale for all? Good idea!!!
But it may or may not give us the reproductive separation time.So, it should be involved in reproduction as an important part of compatibility criterion. But it may not be very conserved one though.

anyway hope that helps you... keep checking those resources and try us back if you come up with anything...
Ofcourse...i like discussions, it helps both people- those asking and those answering.


BY THE WAY - Reading below the LIne [ the scientists' statements], was pleasuresome.

hrushikesh

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