13 replies to this topic

[prabhubct]

Hello,
What is your opinion about Lab mutations of any kind. Is they distorting Evolution? If somebody start studying evolution from scratch. would these mutants bother that person in studying originals?

Edited by prabhubct, 04 September 2012 - 04:50 AM.

[ascacioc]

I do not understand your question:

what are lab mutants in your comprehension? like mutants I make by site-directed mutagenesis, epPCR in a specific targeted gene or mutants more like E. coli strains B that were isolated in repeated cycles of exposure to UV?

prabhubct, on 04 September 2012 - 04:49 AM, said:

would these mutants bother that person in studying originals?

I am totally lost here: how would mutants bother a person unless the person lost the WT. I.e. what is the original E. coli strain? Well in this case we lost the original a long time ago like in the 40s

Andreea

[prabhubct]

If sequences of all organisms (e.g. bacteria) are available including Wild type and mutant. How one is supposed to predict Evolution? wouldn't mutant might be considered in drawing Evolution for Original ( i.e. Wildt type). If that is the case what will be point of studying it then?

[ascacioc]

Yeah...we do not have all the bacteria and at least for the lab bacteria, I do not know of anybody having the original E. coli strain isolated in the 40s. These bacteria that we work in the lab with are mutants that have nothing to do with nature....for example, B strains, the protease deficient ones were selected for this property (not available in nature and not a natural selection) in the meantime they have lost the originals. I mean...I am not aware of no case in which we have the original bird of a species or any original organism to compare it with the evolved one. The best case is still the physical observations of Darwin in these birds in these islands (I am a molecular biologist so names escape me now:P) that had different beaks.

[bob1]

ascacioc, on 04 September 2012 - 01:13 PM, said:

I am not aware of no case in which we have the original bird of a species or any original organism to compare it with the evolved one. The best case is still the physical observations of Darwin in these birds in these islands (I am a molecular biologist so names escape me now:P) that had different beaks.

Darwin's Finches (Galapagos Finches) are the ones you are thinking of. Apparently they evolve very rapidly - changes in beak shape over a couple of years depending on the conditions to which they are exposed.  

Type specimens are the original collected specimen of any species, there is supposed to be one for any plant or animal (not sure about fungi, bacteria, and unicellular eukaryotes) that has been scientifically described.  Of course, these are not living, so it is hard to compare behavioural changes, and I doubt that there would be many people allowed to take samples for DNA/protein analysis, if these have survived the preservation processes intact.

@Prabhubct:
Evolution is evolution, it doesn't matter what the selective pressure is or where it is coming from.  Predicting exactly what will happen may be simple or difficult, depending on the level of detail you are looking at.  For instance you could easily select for optimal growth of E. coli at 15 deg C rather than 37, morphologically the bacteria would probably look the same.  Doing detailed genetic or proteomic analysis would undoubtably show changes from the parent line, but predicting what those changes (e.g. which genes, when, how) would be exactly would be very difficult.

Lab based evolution is a big problem for mammalian cell cultures, where people rely on a cell line to behave in the same manner in different labs, for scientific reproducibility.  A number of journals are now requesting that your cell lines be validated for behaviour, morphology and gene expression before they will accept papers for publication -this is mostly to ensure that the cell lines haven't been contaminated with another line though.

[Trof]

I think there is no problem in obtaining "the original" E.coli. You know, E.coli are like assholes... oh wait..

However I think this is the second? prabhubct's topic aboutmutations and evolution  and I still don't get what is he asking..

[ascacioc]

I think he is just bored and wants a philosophical discussion. Last time we learned that we have to be cautious about calling any king of evolution, especially lab evolution, evolution (a lot of evolution here:P) Pito got angry when I suggested that we do evolution in the lab But I still believe that the original E coli isolated by Escherich in 1886 is still there somewhere. (\ref:{wikipedia}) (not the 40s as I stated above, I think the 40s was the time of K strains and B strains getting separated; sorry they don't teach us this history in school). But I might be wrong since that one was pathogenic and I am definitely not going above S1 level and maybe the pathogenic ones are still frozen somewhere and are for sale as the mammalian cells in the ATCC. But considering that bacteria are more prone to mutations....I really believe that the original is lost.

@bob1: even though the originals are morphologically described, we are referring here (if I am not mistaken, prabhubct??) to point mutations in the genome, which of course we cannot assess since nobody will sequence the, e.g. old mammoths frozen in Siberia (one of my bio profs was in the team that discovered that one a few years back; the one with the frozen flesh and they wondered how it tasted and after all the teams collected their lab samples, they decided that anyhow it is going to waste so they tasted a bit; it tasted like mud; story I've heard in my first year bio class; just to let you know how much they actually take care of the rare samples) or nobody will give us a bit of the samples to do our own analysis or... clone it to get a bit more for bigger experiments (yeah, I know, I am going against so many ethics rules by only thinking the previous sentence)

I believe that what prabhubct is pointing towards is: we have the technology to compare sequences of different things and predict evolution, why don't we do it? weeeell, the people who have the possibilities/the samples/the data, hoard it and do not share it because they will publish more articles like this and they can take their time with the data. There is no competitor that has the same data. If this annoys you: welcome to the open science movement

[prabhubct]

Trof, on 04 September 2012 - 02:11 PM, said:

However I think this is the second? prabhubct's topic aboutmutations and evolution  and I still don't get what is he asking..

Hello Trof,
         I mean if I have originals A,B,C,D sequences and they evolved in same sequence as per current evolutionary analysis as A->B-> C-> D


and if we have e,f,g as mutant sequences.

If By mistake or lack of awareness about original and mutant , I took A,B,C,D,e,f,g all together and do evolutionary analysis is there chance that I get it like
e->B-> D->f-> A->g-> C

[Trof]

I usually percive evolution as the mechanism of creating new lifeforms by the means of selection by enviroment from avalable variation.
Mutations are one of the sources of this variations. If I create mutation in a lab, it's just a mutation. If this appear to be an advantage and the mutation would spread, then you can call it microevolution or something I guess.

Our evolutionary analysis is only a tool to analyse the evolution happening through history. It's simplified and inaccurate. So I wouldn't care at all about what it may say about mutants created in a lab. Who cares? It's like you took a tool designed for something else and use it different way. What value such results could have?

And if we're thinking about mutants escaping the lab and dividing in the enviroment, because of the advantage, so it will actually in time maybe become a step in evolution, why talk about distorting anything? What, are we breaking any evolution rules? There aren't any. Nature doesn't care how the mutation was created, there isn't any "natural" way anyway, there are replication mistakes, recombination mistakes, pathogen effect, whatever other things, enviromental damage... and from some time in past a direct human actions. So what?
Humans are breeding domestic animals for ages, it's not mutation, right, but it's a serious effect on variation. How many wild pigs, wild dogs and wild (small) cats you have on the Earth compared with the domestic couterparts. We flooded this planet with animals of our design. So what, we are part of evolution, they are part of evolution, your modified E.coli is part of evolution.

So in philosophical disscusion about human created mutants and evolution, there is nothing really to deal with.
Practical problems arising from that are other thing, but that is the part I don't understand much, first I would say it may distort our analyses right, not the evolution. And for second, I can't much imagine this actually happening, if you do evolution analysis, you go out and catch something in the wild. You don't usually look into single mutations, because in case of microorganisms for example there would be huge mess of them, their mutate so often. So for long scale evolutionary analysis I think conserved genes or regions are analysed. Besides, you think it's really possible to create a single point mutation in a lab, that no microbe in the wild doesn't ever had? I don't think so. If it was any use, it would be preserved any many wild-types would have it, if not, it would disappear, but that implies we can't really change anything seriously by a single point mutation in microorganisms. It's so easy to create.

Complex changes like gene switches between species are different thing, here you jump over many small steps that would be needed in normal evolutionary steps and maybe not even possible, but you will surely find something odd if you find wild-type E.coli with GFP, so that shouldn't screw any analysis either. IMHO.

[bob1]

@Prabhubcut: I presume you are talking about the evolutionary changes predicted by such things as parsimony analysis - this is just a liklihood, analysis, meaning that it is looking for the minimum number of changes to get the tree - it makes NO statement about the order of these events, or that it is the true evolutionary path, just that this is the minimum number of changes needed to get the end result.  

Long story short: know the limitations of your analysis!

[prabhubct]

bob1, on 05 September 2012 - 01:22 AM, said:

I presume you are talking about the evolutionary changes predicted by such things as parsimony analysis - this is just a liklihood, analysis, meaning that it is looking for the minimum number of changes to get the tree - it makes NO statement about the order of these events, or that it is the true evolutionary path, just that this is the minimum number of changes needed to get the end result.  

Then If one takes a samples(mutated) which one is not supposed to take will they have effect on how parsimony analysis gives tree ( not Evolutionary path). I know that by phylogeny we can not determine age of which organism evolved when it shows based on homology which organism is more closely related with whom?



I mean to ask whether it is possible that we make relations between sequences distorted. As stated if A->B-> C-> D ( I guess it means A-> C too) is tree drawn by parsimony. could e,f,g (mutant) make it go as e->B-> D->f-> A->g-> C ? whether it would mean as B->D->A->C

[bob1]

Absolutely, adding samples to your analysis will often change the trees that are drawn, especially if the sample is not easily related to the ones already in the analysis.

prabhubct, on 05 September 2012 - 02:54 AM, said:

I mean to ask whether it is possible that we make relations between sequences distorted. As stated if A->B-> C-> D ( I guess it means A-> C too) is tree drawn by parsimony. could e,f,g (mutant) make it go as e->B-> D->f-> A->g-> C ? whether it would mean as B->D->A->C

Is it possible that you have making it confusing by how you are explaining this?  Are you talking about efg as mutant forms of A, B and D?  If so, they would be better described as A*, B* and D* or something similar

You can't state whether or not the order of the changes is possible from the analysis; a completely non-related sample where you only have efg,and no ABCD, should form its own clade, joined only at the base (if you are drawing a based tree).  If the efg mutant also contains the ABCD traits, and the ABCD non-mutants, contain basal forms of the efg traits, then it is entirely possible that there will be a change in the tree drawn.

You must, must, must, understand that this is only minimum number of changes analysis - it may have no bearing on what actually happened.  It makes the assumption that the changes proceed by a minimum number of steps, when in fact the traits could have formed several times completely independently.  For instance if you look at the kingdom Animalia - you have three major groups of flying organisms - insects, birds and mammals (bats).  If you did an analysis where you looked at the form of locomotion, trait A could be walking/ running, trait B could be swimming, and trait C could be flying.  Under this analysis, flying insects, flying birds and bats would all group together - yet if you go and look at the actual animals, it is very very obvious that they have evolved the trait independently, whales, dolphins, frogs and fishes would also group together - yet so far as we know, fish have never left the water, whales and dolhins used to inhabit the land, and frogs are somewhere inbetween...

Do you see where this is going?

[prabhubct]

Thanks Bob and all,
I agree that I may be confusing it more, or I have to give it more thought. Right now First option seems right. Good Day.

Edited by prabhubct, 06 September 2012 - 12:02 AM.

[ascacioc]

I've been out of this discussion for a while, but wow!!!

Just a small comment, besides: I totally agree with bob about: know your limitations of your analysis. Half of the things I do are computational blah-blah and I literally pray everytime my predictions are put under experimental challenge by smb (lately I do predictions for other people's project). I pray because I know that anything we have now, in many fields of computational biology/bioinformatics takes into account many assumptions to ease the computational load/substitute for lack of knowledge. However, people rely on these bioinformatic predictions like they are always 100% true. They are not a coin toss (50% true) but let's say 70%.

Now to my small comment/observation: when I was taking the class in which they (physicists with no biology clue) were telling us about the blast algorithm and how you build phylogenetic trees (algorithm), the prof made an observation: no matter what protein/gene you take, the phylogenetic tree over all species for that protein will look the same (more or less) as the phylogenetic tree of any other protein/gene i.e. the yeasts will group together, so will bacteria and so on; more, the yeasts that were closer together in terms of gene A, will be also closer together in terms of gene B. So it is not so random. And more: evolution is really happening over a whole organism in the same manner for all the genes. End observation from professor.

Andreea