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Author Topic:   Allele Propagation Prediction
TheoMorphic
Inactive Member


Message 1 of 18 (70198)
12-01-2003 1:41 AM


has science made any predictions/verifications as to what alleles are more likely to propagate through out a species?

i did some searches, but i couldn't find any examples, or really attention to this question. maybe i was searching for the wrong thing.

are there any prediction/verification examples, or is deciding what alleles copy themselves the most in a species and environment just ad hoc reasoning?


Replies to this message:
 Message 2 by NosyNed, posted 12-01-2003 2:01 AM TheoMorphic has responded
 Message 3 by Rrhain, posted 12-01-2003 2:31 AM TheoMorphic has responded

  
NosyNed
Member
Posts: 8838
From: Canada
Joined: 04-04-2003


Message 2 of 18 (70199)
12-01-2003 2:01 AM
Reply to: Message 1 by TheoMorphic
12-01-2003 1:41 AM


What do you mean by "ad hoc" reasoning?
This message is a reply to:
 Message 1 by TheoMorphic, posted 12-01-2003 1:41 AM TheoMorphic has responded

Replies to this message:
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Rrhain
Member
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 3 of 18 (70202)
12-01-2003 2:31 AM
Reply to: Message 1 by TheoMorphic
12-01-2003 1:41 AM


TheoMorphic writes:

quote:
has science made any predictions/verifications as to what alleles are more likely to propagate through out a species?

How can it?

Question: Which is better to call, heads or tails?

Until you know what the scenario is and the specifics of environment in which the allele exists, how can you possibly make a prediction as to its survival benefits?

This is the part that many creationists have a hard time comprehending and it comes up with their continual fallacy that "most mutations are delterious." Most mutations are neutral and of those that do have a noticeable effect, we have no idea if it is beneficial or deleterious until we actually see what it does and how it behaves in the context of the rest of the environmental landscape in which it finds itself.

Which is better: A short, squat body that retains body fat easily or a long, lean body that sheds body fat quickly?

That really depends upon the environment in which you find yourself, now doesn't it?

quote:
are there any prediction/verification examples, or is deciding what alleles copy themselves the most in a species and environment just ad hoc reasoning?

Neither.

------------------
Rrhain
WWJD? JWRTFM!


This message is a reply to:
 Message 1 by TheoMorphic, posted 12-01-2003 1:41 AM TheoMorphic has responded

Replies to this message:
 Message 4 by TheoMorphic, posted 12-01-2003 8:22 AM Rrhain has responded

    
TheoMorphic
Inactive Member


Message 4 of 18 (70232)
12-01-2003 8:22 AM
Reply to: Message 3 by Rrhain
12-01-2003 2:31 AM


Rrhain writes:

Question: Which is better to call, heads or tails?

you make it sound like it's totally luck. given your squat/fat body vs. long lean body, you can examine the makeup of the body and make guesses as to which body type will be better in a given environment.

Rrhain writes:

Until you know what the scenario is and the specifics of environment in which the allele exists, how can you possibly make a prediction as to its survival benefits?

Pretend we already know what differences there are between 2 animals (preferably one small mutation). given the knowledge of what that mutation does to the organism's body, and what environment it will be set in, we should be able to predict if that organism will do better or worse than other animals with out its mutation.

finally, i don't see any other options in this choice. either science has made predictions about "fitness" (surviving to adulthood and producing successful offspring) or it hasn't. if no predictions have been made, then fitness is based on how well an allele propagates throughout a species, and the propagation is dependent on the fitness.


This message is a reply to:
 Message 3 by Rrhain, posted 12-01-2003 2:31 AM Rrhain has responded

Replies to this message:
 Message 13 by Rrhain, posted 12-01-2003 4:56 PM TheoMorphic has responded

  
crashfrog
Inactive Member


Message 5 of 18 (70235)
12-01-2003 8:35 AM


Maybe you were looking for something like this:

quote:
Evolutionary predictions of binding surfaces and interactions.

Lichtarge O, Sowa ME.

Department of Molecular and Human Genetics, 1 Baylor Plaza, Baylor College of Medicine, Houston, Texas 77030, USA. lichtarge@bcm.tmc.edu

Rapid progress in structural biology and whole-genome sequencing technology means that, for many protein families, structural and evolutionary information are readily available. Recent developments demonstrate how this information can be integrated to identify canonical determinants of protein structure and function. Among these determinants, those residues that are on protein surfaces are especially likely to form binding sites and are the logical choice for further mutational analysis and drug targeting.

Publication Types:
Review
Review, Tutorial

PMID: 11839485 [PubMed - indexed for MEDLINE]


Here they seem to be predicting what proteins (and therefore, what alleles) are most likely to lend themselves to useful mutations. Or so I read it. (Not a biologist.)

I had read somewhere that they knew enough about the metabolism of E. coli to make accurate predictions about what environments E. coli could mutate to survive in.


  
TheoMorphic
Inactive Member


Message 6 of 18 (70236)
12-01-2003 8:38 AM
Reply to: Message 2 by NosyNed
12-01-2003 2:01 AM


with out general rules about how well various alleles will do in various environments with various other alleles it means nothing to talk about beneficial or detrimental mutations.

with science it's not enough to just look at the current evidence and explain it. predictions have to be made. it's not enough to say "this structure of an atom can explain these elements". you have to add "and we are guessing that someday we will find this, this and this element."

it's not enough to say "well, since these alleles have propagated throughout this species, they are better at propagating themselves". you have to add "but this same allele won't propagate as well in this environment, however it will if it is combined with this other allele."


This message is a reply to:
 Message 2 by NosyNed, posted 12-01-2003 2:01 AM NosyNed has not yet responded

Replies to this message:
 Message 7 by crashfrog, posted 12-01-2003 8:46 AM TheoMorphic has responded
 Message 8 by Quetzal, posted 12-01-2003 2:40 PM TheoMorphic has responded

  
crashfrog
Inactive Member


Message 7 of 18 (70240)
12-01-2003 8:46 AM
Reply to: Message 6 by TheoMorphic
12-01-2003 8:38 AM


with science it's not enough to just look at the current evidence and explain it. predictions have to be made.

I'm not sure this is true in the sense that you seem to imply. Most people draw a distiction between science that attempts to explain ongoing phenomenon and science that explains phenomenon that occured in the past. Of course all models have a bit of both, but what kind of predictions would you expect from paleontology? "We predict we'll find more fossils?"

Evolution does make some predictions. It predicts that mutations will continue, and that the majority will decrease an organism's chance of survival, but every so often one will do the opposite, and that mutation will tend to replace other copies of the allele in the gene pool.

What else do you expect? You're asking finite minds to make predictions about how nature, which operates in a radically different method than intelligent action, is going to solve a particular problem. Does that seem fruitful or even possible to you?


This message is a reply to:
 Message 6 by TheoMorphic, posted 12-01-2003 8:38 AM TheoMorphic has responded

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 Message 9 by TheoMorphic, posted 12-01-2003 2:49 PM crashfrog has not yet responded

  
Quetzal
Member (Idle past 3947 days)
Posts: 3228
Joined: 01-09-2002


Message 8 of 18 (70317)
12-01-2003 2:40 PM
Reply to: Message 6 by TheoMorphic
12-01-2003 8:38 AM


with out general rules about how well various alleles will do in various environments with various other alleles it means nothing to talk about beneficial or detrimental mutations.

I guess you have a problem then. A mutation can be considered beneficial if a) it has a phenotypical effect and b) that effect has relevance for the overall adaptation of the individual organism in its particular environment - or allows the individual carrier to exploit a new environment or niche. That's all. There are no really universal, general rules - although a lot of ink has been expended trying to find and justify some. Most of the rules in biology are generalizations, and like most generalizations have lots and lots exceptions.

it's not enough to say "well, since these alleles have propagated throughout this species, they are better at propagating themselves". you have to add "but this same allele won't propagate as well in this environment, however it will if it is combined with this other allele."

Why not? Nearly the totality of the science of population genetics does just that - provides a theoretical framework and description for how and why allele frequencies change in a population over time. In addition, it's very rare that you can point to a single allele and say "this one's a good'un" even if you take in the environmental context in which it manifests - at least in vertebrates. Occasionally you can point to a specific trait that places an individual organism further up the adaptive peak of its particular environment. However, in general relative fitness relies on a suite of phenotypical traits rather than a single allele, many of which are covariant (IOW, change one trait implies changes in others). Basically, in one sense you are correct: the analysis is a posteriori rather than predictive, except in very generic terms.

Of course, no biologist ever said it was, so I don't understand your argument. Maybe you can explain what implication you think this has for evolutionary theory.


This message is a reply to:
 Message 6 by TheoMorphic, posted 12-01-2003 8:38 AM TheoMorphic has responded

Replies to this message:
 Message 11 by TheoMorphic, posted 12-01-2003 3:00 PM Quetzal has responded

  
TheoMorphic
Inactive Member


Message 9 of 18 (70320)
12-01-2003 2:49 PM
Reply to: Message 7 by crashfrog
12-01-2003 8:46 AM


how about an analogy. pretend someone asserts that cars that have bad breaks are more likely to get into car crashes. when a car crash occurs the person says "well that car probably had bad breaks". when a car crash doesn't occur the person says "that car probably didn't have bad breaks." However if you give this person a set of breaks he is not able to tell you if they are bad or good. so maybe such a thing as "bad breaks" doesn't even really exist. at least not in a quantifiable and predictable manner. it's just another way of saying whether a car is more likely to get in a crash or not.

a similar analogy. pretend you have someone that says "luck causes people to win at craps". when you show him a person who won some money at craps they say "that person was lucky". when you show him someone who lost they say "that person was not lucky". but you can't show them a person and expect them to tell you if they are lucky or not. so in this sense luck is simply an extension of whether they won at craps or not.

so there's no such thing as luck, and no such thing as bad breaks... at least not in any significant sense.

yes deciding what these predictions are would be very difficult. the environment, genetic code, and the code's effect on the organisms body would have to be taken into account. maybe we're really far away from knowing enough about any animals body to make a prediction like this. but can you at least see the need for these kinds of predictions?


This message is a reply to:
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NosyNed
Member
Posts: 8838
From: Canada
Joined: 04-04-2003


Message 10 of 18 (70323)
12-01-2003 2:55 PM
Reply to: Message 9 by TheoMorphic
12-01-2003 2:49 PM


I'll have to do a little digging and don't have time now but I think there are mathematical predictions made about the spread of alleles and the balance they get to under certain conditions. If I'm remembering correctly the percentages are born out when examined. But I just have the most fuzzy idea of this.

Is there a geneticist in the house?
This one seems to hint at something like you want:
http://ocw.mit.edu/NR/rdonlyres/Biology/7-03GeneticsFall2001/F371B270-F2DE-407D-A8E4-D2FAC1A6F521/0/fa01lec26.pdf

[This message has been edited by NosyNed, 12-01-2003]


This message is a reply to:
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TheoMorphic
Inactive Member


Message 11 of 18 (70325)
12-01-2003 3:00 PM
Reply to: Message 8 by Quetzal
12-01-2003 2:40 PM


until predictions can be made about alleles (even if the predictions are very very complex with lots of conditions with regards to environment and other genes) there is no driving force behind evolution. genes are heritable, and can mutate a bit when they are passed on. but a given set of genes is no better or worse than any other set.

so either evolution has to predict which alleles in which environments will push evolution, or a new engine has to be found. until predictions can be made about the effects of alleles on survival chances, the relationship may as well not exist.


This message is a reply to:
 Message 8 by Quetzal, posted 12-01-2003 2:40 PM Quetzal has responded

Replies to this message:
 Message 12 by Quetzal, posted 12-01-2003 4:15 PM TheoMorphic has responded

  
Quetzal
Member (Idle past 3947 days)
Posts: 3228
Joined: 01-09-2002


Message 12 of 18 (70341)
12-01-2003 4:15 PM
Reply to: Message 11 by TheoMorphic
12-01-2003 3:00 PM


There are actually quite a few mathematical formulae to calculate the relative fitness of new alleles (or the effect of allele changes in hypothetical populations). However, none of them have been really well confirmed in the field, and I don't know how to copy weird symbols into a post anyway. IOW, there are plenty of "rules" if I'm understanding how you're using the term, but few confirmations from actual observations. Sort of like the difference between theoretical and practical physics. In truth, physics is easier, because all you need to do is spend a couple gazillion dollars on a supercollider and see the reactions when you blow things up. Without a time machine, evo biologists are unable to do this.

However,

until predictions can be made about alleles (even if the predictions are very very complex with lots of conditions with regards to environment and other genes) there is no driving force behind evolution. genes are heritable, and can mutate a bit when they are passed on. but a given set of genes is no better or worse than any other set.

This is incorrect. The "driving forces behind evolution" (as you put it) are the known and observed mechanisms that alter the frequency of specific traits in populations over the generations. Whether those changes will be beneficial or not is only possible to determine by actually observing their effects on the organism in its environment. The fact that we can observe beneficial and deleterious mutations in short-lived organisms like Drosophila and observe similar "mutants" in wild drosophilid populations bears out the validity of the evolutionary mechanisms. We DO see the mechanisms operating in the wild - just that the patterns observed are much much smaller than would possible if we could observe them over millions of years.

I'm still unclear why you think evolution has to predict anything about which alleles in which environments "push evolution", since that's not what evolution is. Natural selection and all the other mechanisms are what "push evolution". Changes in allele frequency are the results.


This message is a reply to:
 Message 11 by TheoMorphic, posted 12-01-2003 3:00 PM TheoMorphic has responded

Replies to this message:
 Message 15 by TheoMorphic, posted 12-02-2003 1:40 AM Quetzal has responded

  
Rrhain
Member
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 13 of 18 (70344)
12-01-2003 4:56 PM
Reply to: Message 4 by TheoMorphic
12-01-2003 8:22 AM


TheoMorphic responds to me:

quote:
quote:
Question: Which is better to call, heads or tails?

you make it sound like it's totally luck.


Well, in many cases it is.

quote:
quote:
Until you know what the scenario is and the specifics of environment in which the allele exists, how can you possibly make a prediction as to its survival benefits?

Pretend we already know what differences there are between 2 animals (preferably one small mutation). given the knowledge of what that mutation does to the organism's body, and what environment it will be set in, we should be able to predict if that organism will do better or worse than other animals with out its mutation.


No, not really because we have no idea how that mutation will connect with the morphology already present. That is, knowing that changing X has a direct effect on Y, that doesn't tell us how it will have an indirect effect on Z. You can boost the power output of your engine, but that doesn't mean the fuselage can withstand the increased velocity that comes with it. There are also questions of scale and how it will behave within a population of organisms that have it. As an analogy, a beehive needs only one queen. A beehive that contains many queens may not function as well as those with only one so even though the individual queen is "better" because she will be more likely to have offspring and thus her genes will go on to the next generation, the whole hive as a result may suffer due to the split on resources.

quote:
if no predictions have been made, then fitness is based on how well an allele propagates throughout a species, and the propagation is dependent on the fitness.

And?

------------------
Rrhain
WWJD? JWRTFM!


This message is a reply to:
 Message 4 by TheoMorphic, posted 12-01-2003 8:22 AM TheoMorphic has responded

Replies to this message:
 Message 14 by TheoMorphic, posted 12-02-2003 1:23 AM Rrhain has responded

    
TheoMorphic
Inactive Member


Message 14 of 18 (70499)
12-02-2003 1:23 AM
Reply to: Message 13 by Rrhain
12-01-2003 4:56 PM


Rrhain writes:

No, not really because we have no idea how that mutation will connect with the morphology already present...

er, well i didn't explicitly state this, but i thought i implied it. basically pretend we know everything EXCEPT how the organism will actually perform in an environment (including the effects of a single mutation on all other parts of the organism). Will we actually be able to predict its relative success in terms of survival, and reproduction?

if the answer is yes, then are there any examples, if there are no examples, what do we need before we can make these predictions. if the answer is no then we need to find some other reason as to why allele frequencies change.


This message is a reply to:
 Message 13 by Rrhain, posted 12-01-2003 4:56 PM Rrhain has responded

Replies to this message:
 Message 16 by Rrhain, posted 12-02-2003 2:05 AM TheoMorphic has responded

  
TheoMorphic
Inactive Member


Message 15 of 18 (70500)
12-02-2003 1:40 AM
Reply to: Message 12 by Quetzal
12-01-2003 4:15 PM


if chance of survival and reproductivity (I think I just made this word upů it means ability to reproduce) have no discernable (predictable) influence as to which alleles propagate throughout a species, then it can not be said that fitness (read: relative survival/reproductivity ability) has any influence on allele frequencies.

so (without predictions and verifications) there is no connection between "fitness" and alleles, and in turn there is no connection between natural selection and allele frequencies.

actually any of the "driving forces" (sexual selection, natural selection etc.) become irrelevant unless predictions can be made that connect those driving forces and allele frequencies.


This message is a reply to:
 Message 12 by Quetzal, posted 12-01-2003 4:15 PM Quetzal has responded

Replies to this message:
 Message 18 by Quetzal, posted 12-02-2003 4:21 PM TheoMorphic has not yet responded

  
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