All eyes evolved from a common ancestor!

Originally posted by KellyJay
When you look at a race, is getting out of the starting block part of
the race, or is it only when the runners are on the track running?
Kelly

Do you need to know the conductivity of a piece of iron to account for its gravitational acceleration?

Originally posted by KellyJay
When you look at a race, is getting out of the starting block part of
the race, or is it only when the runners are on the track running?
Kelly

I assume that the analogue of a typical human race with the process of evolution is wrong because I assume that usually one of the defining feature of such a human race is humans lining up at the starting block the moment before the race begins but there is nothing analogous to that in the process of evolution because the process of evolution is always a PROCESS throughout its history rather than a static situation.

For this reason, a only very slightly better analogy (not much better) would be the running steps the human racers take during the race (and NOT the race itself) because this is a PROCESS and not static. But there are several things very wrong even with this analogue with evolution. Obviously evolution must have a starting point but, even right at the start, evolution is always a PROCESS rather than something that is static.

A better although far from perfect analogue of evolution would be a avalanche.
-and, like evolution, you don’t need to know what started it to observe its effects.

Originally posted by Andrew Hamilton
[b]….However for natural selection (*) to be a theory of the origin of all life
..…

Perhaps you didn’t mean the above statement literally but it is incorrect to say natural selection is a theory of the “origin” of all life because it isn’t. It is correct to say that the theory of evolution (and not just natural selection) is a theory of the ...[text shortened]... ll life).
-this seems to repeatedly be a source of constant confusion throughout these threads.[/b]

Actually I can construct an argument for it as for abiogenesis to occur you need non alive (*) auto-catalysing molecules to evolve into something recognisably living (a cell) - if natural selection predates the origin of life (which isn´t that unreasonable) then it is a theory of the origin of all life.

(*) Definitions of alive are a sticking point - the current standard definition is ¨has a cell membrane¨. If you start claiming auto-catalysing molecules are alive then my argument collapses.

Originally posted by Andrew Hamilton
….the probability that the 'right' mutation will occur and spread through the population is very close to 1? A near certainty.
..…

Correct (assuming that what you mean by the ‘right way’ is the way that leads to better adaptation)
And for those who don’t see why; a beneficial mutation would be selected by natural selection so to spread to t ...[text shortened]... would STILL make only the few beneficial ones become predominant in the population as a whole.[/b]

No this is nonsense. If a beneficial gene is swamped by deleterious ones to the extent you stated then it will become extinct along with the rest of the species. There are some problems with what you´ve said, one is that genes can be both good and bad.

Take the example of sickle cell anemia. This is caused by a mutation which causes blood cells to form into a sickle shape and they become metabolically useless. If you have two copies of the gene you are in real trouble as it happens spontaneously. If you have one copy then you are at a slight disadvantage to a non-carrier as you can still get anemia, but not very frequently and then it´s much milder than in people with two copies of the gene, However if you happen to live in a malaria affected area you have a definite advantage as your blood cells form into sickle shapes when infected and trap the bug. You get resistance to malaria.

A gene is not in itself ¨good¨ or ¨bad¨ - assuming you get a more-or-less viable individual then what matters is the phenotypic expression and how that interacts with the environment. The selection process is not as strong as you are giving it credit for - you have two copies of each chromosome and a number of the genes you carry are definitely bad - this doesn´t matter as you have good ones on the other chromosome to do what you need them to do.

This means that you may pass on the bad gene rather than the good one to your offspring. As long as they get a good gene off the other parent that´s fine.

Natural selection works over many generations - ¨bad¨ genes are compensated for - they are less likely to be passed on only because when you get two copies the individual dies. What happens is that deleterious genes go into the background - they can survive provided there are enough ¨good¨ genes floating around in the population to allow them to piggy back. This is a lot more of a marginal effect than you are giving it credit for.

Originally posted by KellyJay
What you are suggesting occurs is that through time with changes
occurring everywhere at once without a plan, purpose, and design not
only keeps life going, it allows it to through time become more and
more complex. This is the game in place, get it wrong dead end
results occur, change the environment drastically you can get dead
end results, the amoun ...[text shortened]... if any of them go wrong in so many differnt ways those
number dwarf what must be right.
Kelly

I can't tell from your response whether or not you have understood my explanation.
Do you agree with me that:
1. Most of the 'dead ends' you refer to would be single individuals.
2. All life forms die eventually.
3. A large percentage of life forms die before reproducing (dead ends).
4. A life form is only a 'dead end' if it fails to reproduce.
5. There are a vast array of genes in all species that do not result in dead ends ie the number of 'right' genes in humans is significant.
6. The statistical calculation of 'right' to 'wrong' should include the total number of offspring of an individual whether or not they reach reproducing age and whether or not they even pass the two cell stage ie count every fertilized egg as an offspring.

Originally posted by DeepThought
Actually I can construct an argument for it as for abiogenesis to occur you need non alive (*) auto-catalysing molecules to evolve into something recognisably living (a cell) - if natural selection predates the origin of life (which isn´t that unreasonable) then it [b]is a theory of the origin of all life.

(*) Definitions of alive are a sticking p ...[text shortened]... embrane¨. If you start claiming auto-catalysing molecules are alive then my argument collapses.[/b]

….- if natural selection predates the origin of life (which isn’t that unreasonable) then it is a theory of the origin of all life.
..…

I would agree that is true IF you are taking a non-standard more general meaning for the words “natural selection” (nothing wrong with using a non-standard meaning of a term providing you make CLEAR that that is what you are doing) but what is normally meant by “natural selection” in the context of life normally ONLY refers to selection of LIVING reproducing organisms:

http://en.wikipedia.org/wiki/Natural_selection

“….Natural selection is the process by which favourable heritable traits become more common in successive generations of a population of reproducing ORGANISMS,…”(my emphasis)

-and for that reason that statement of yours in your original post is misleading because you didn’t make clear that you where representing a non-standard meaning with the term “natural selection” that is a quite meaning from what is normally meant by “natural selection” in normal scientific terminology.

Originally posted by DeepThought
No this is nonsense. If a beneficial gene is swamped by deleterious ones to the extent you stated then it will become extinct along with the rest of the species. There are some problems with what you´ve said, one is that genes can be both good and bad.

Take the example of sickle cell anemia. This is caused by a mutation which causes blood cells to ...[text shortened]... them to piggy back. This is a lot more of a marginal effect than you are giving it credit for.

….If a beneficial gene is swamped by deleterious ones to the extent you stated then it will become extinct along with the rest of the species.
..…

What do you mean by “swamped” by the deleterious ones (mutations)? How would the fact that the deleterious ones vastly outnumber the beneficial ones prevent natural selection selecting for only the beneficial ones and selecting out the deleterious ones?
After all, deleterious ones DO vastly outnumber the beneficial ones in all species! And yet this doesn’t cause them to “go extended” -right?

….There are some problems with what you´ve said, one is that genes can be both good and bad.

Take the example of sickle cell anemia…
…
…

A gene is not in itself ¨good¨ or ¨bad¨
..…

Yes, I know all that. That’s why I have been trying to avoid the words “good” and “bad”.
-so your point is?:

…assuming you get a more-or-less viable individual then what matters is the phenotypic expression and how that interacts with the environment. The selection process is not as strong as you are giving it credit for - you have two copies of each chromosome and a number of the genes you carry are definitely bad - this doesn´t matter as you have good ones on the other chromosome to do what you need them to do.
..…

So what? -that just means that natural selection would simply select specifically for individuals with one copy but also specifically against individuals with two copies -I fail to see how this makes the selection process for each “less strong”.
I am well aware that sometimes natural selection doesn’t always just simply selects for or against a particular gene but RATHER for or against a particular NUMBER of copies of the gene or, sometimes, a particular EXPRESSION of a gene etc. -so your point is?

…This means that you may pass on the bad gene rather than the good one to your offspring.
..…

-don’t see how this could potentially stop natural selection from working (if that is what you are implying?)

….Natural selection works over many generations - ¨bad¨ genes are compensated for - they are less likely to be passed on only because when you get two copies the individual dies. What happens is that deleterious genes go into the background - they can survive provided there are enough ¨good¨ genes floating around in the population to allow them to piggy back. This is a lot more of a marginal effect than you are giving it credit for.
.…

And yet the survival of the human race is not threatened by sickle cell anaemia nor any other similar disease caused by two copies of a gene and there is no evidence that the very survival of any species is threatened by other similar disease caused by two copies of a gene apart from in those populations of living things that have become so small as to suffer from inbreeding depression. -and the reason for this -natural selection prevents each of these genes becoming too common.

Originally posted by Andrew Hamilton
[b]….- if natural selection predates the origin of life (which isn’t that unreasonable) then it is a theory of the origin of all life.
..…

I would agree that is true IF you are taking a non-standard more general meaning for the words “natural selection” (nothing wrong with using a non-standard meaning of a term providing you make CLEAR that ...[text shortened]... ite meaning from what is normally meant by “natural selection” in normal scientific terminology.[/b]

It was obvious what I meant in the original post - all currently alive life. At worst it was an abuse of notation, and I´m probably entirely entitled to use the term natural selection to mean that.

You need to be wary of Wikipedia - the quality control mechanism is kind of anarchic, Having said that I´m going to refer to Wikipedia - it´s main advantage is that it is a mutually available reference. If you look at the pages on Evolutionary history of life and Abiogenesis you will see the words natural selection applied to the kinds of molecular ¨life¨ I was talking about, without the kind of qualification you are asking for. Although I agree that the process then was probably rather different to now.

There is a real danger in this thread that people get hung up on semantics and pick on tiny parts of posts without responding to the overall points. Which I have a tendency of interpreting as an attack on the overall argument whether it is or is not.

On a totally different note; this page is interesting - its relevance is to my earlier question about how complete the theory of natural selection actually is, and not something I´d heard of until I checked your claim that natural selection only applies to life as per the biology definition:
http://en.wikipedia.org/wiki/Neutral_theory_of_molecular_evolution

Originally posted by Andrew Hamilton
[b]….If a beneficial gene is swamped by deleterious ones to the extent you stated then it will become extinct along with the rest of the species.
..…

What do you mean by “swamped” by the deleterious ones (mutations)? How would the fact that the deleterious ones vastly outnumber the beneficial ones prevent natural selection selecting for only ...[text shortened]... . -and the reason for this -natural selection prevents each of these genes becoming too common.[/b]

In the post I was quoting you wrote: thus even if the debilitating mutations outnumber the beneficial mutation 1000,000,000,000,000,000 to one, natural selection would STILL make only the few beneficial ones become predominant in the population as a whole.

You have a population of 1 quintillion individuals versus one with the beneficial gene - this just isn´t a meaningful number outside astronomy. If you are thinking of bacteria then there is a problem because they are capable of horizontal gene transfer - and the model of natural selection appropriate to animals isn´t appropriate to them. (second sentence is later edit)

It´s not clear what you mean by deleterious and beneficial mutations if you don´t mean good or bad from an individual´s point of view. In fact it´s not clear what you mean by that at all. Do you mean that there are two alleles, the standard one and a better one, or do you mean there are three, an ancestral one, an advantageous mutation and a deleterious one?

The processes we are talking about take thousands of generations, and depend on gene diffusion rates. The way you wrote your post makes it sound like it´s over in a couple of weeks. What I am trying to get away from is the level of evolutionary determinism which seems to be taking over the non-design side of the debate.

Originally posted by DeepThought
You have a population of 1 quintillion individuals versus one with the beneficial gene - this just isn´t a meaningful number outside astronomy.

Though I don't dispute your argument, I would like to point out that the total population is not the number that is important.
Suppose we are talking about a fairly important gene that in all current individuals is identical. Now suppose that there are 1 thousand possible mutations that can happen to that gene, and only one of those results in a viable embryo. But the mutations only happen once out of every 100 times an embryo is formed.
If we have a population of 100 individuals it is quite possible in the space of a number of generations for the beneficial mutation to occur. All the other mutations that occur will happen, result in non-viable embryos and have almost no effect on the population whatsoever (depending on the typical number of embryos per parent). For example it could be insects which lay thousands of eggs of which only some make it to adult hood, or pigs which may have 8 per breeding cycle or humans which only have one a month. But even with humans the number of non-viable embryos that go unnoticed each generation is much greater than the human population.

Originally posted by DeepThought
In the post I was quoting you wrote: [b]thus even if the debilitating mutations outnumber the beneficial mutation 1000,000,000,000,000,000 to one, natural selection would STILL make only the few beneficial ones become predominant in the population as a whole.

You have a population of 1 quintillion individuals versus one with the beneficial gene - ...[text shortened]... vel of evolutionary determinism which seems to be taking over the non-design side of the debate.[/b]

….You have a population of 1 quintillion individuals versus one with the beneficial gene - this just isn’t a meaningful number outside astronomy.
..…

I don’t understand at all what you mean here by “not meaningful“; why isn’t 1 quintillion not a “meaningful” number outside astronomy? -can you clarify what you mean by not “meaningful” in this context?
-are you disputing that this number can exist outside astronomy?

….If you are thinking of bacteria then there is a problem because they are capable of horizontal gene transfer -
..…

http://en.wikipedia.org/wiki/Horizontal_gene_transfer

Again, I don’t understand what you mean by this;
In exactly what way does horizontal gene transfer make “1 quintillion individuals versus one with the beneficial gene” a “problem”?

…and the model of natural selection appropriate to animals isn´t appropriate to them (second sentence is later edit) ...…

What?

…It´s not clear what you mean by deleterious and beneficial mutations if you don´t mean good or bad from an individual´s point of view. In fact it´s not clear what you mean by that at all. Do you mean that there are two alleles, the standard one and a better one, or do you mean there are three, an ancestral one, an advantageous mutation and a deleterious one?
..…

In this extremely narrow context of evolution, I would say that what I generally mean by ‘deleterious mutations’ are ones that, for whatever reason, reduces the chances of an individual passing its genes on to the next generation and what I generally mean by the ‘beneficial mutations’ are ones that, for whatever reason, increases the chances of an individual passing its genes on to the next generation.

However, in this very narrow context, even this way of defining it is too simplistic because, for example, if a mutation increases the chances of an individual passing its genes on to the next generation BUT results in all those offspring being sterile so that THOSE offspring will not in turn pass on that mutation onto the next generation then, in this very narrow context, I would call that a ‘deleterious mutation’ because natural selection will select against it in the longer run.

So perhaps a better way of defining what I mean is;
‘deleterious mutations’ are ones that, for whatever reason, natural selection tends to select against in the long run.
‘beneficial mutations’ are ones that, for whatever reason, natural selection tends to select for in the long run.

-and perhaps it is better to talk about “inheritable characteristics” here rather than “mutations” -the two are not necessarily always identical.

….The processes we are talking about take thousands of generations, and depend on gene diffusion rates..…

What do you mean by “gene diffusion rates”?
-I did a goggle search for “gene diffusion rate” and got nothing and this is certainly not a term I have ever heard of.

….The way you wrote your post makes it sound like it´s over in a couple of weeks.
…

In what way?
-I fail to see how.

…. What I am trying to get away from is the level of evolutionary determinism which seems to be taking over the non-design side of the debate.…

http://www.encyclopedia.com/doc/1O8-evolutionarydeterminism.html

“evolutionary determinism” means:
“…Change in gene frequencies by directed or deterministic processes, in contrast with change due to random or stochastic processes. The relative importance of the two kinds of change in evolutionary development is uncertain.…”

This is honestly the first time I have heard of “evolutionary determinism”
I assume that what it means by “directed or deterministic processes” part in the above statement “…Change in gene frequencies by directed or deterministic processes…” is normally natural selection? (and please can somebody correct me if I have misinterpreted this) -assuming this is so, then GIVEN the fact that natural selection is generally non-random (or at most only partly random) then surely there is no logical alternative to “evolutionary determinism”? -I mean, you can’t say that natural selection is totally random because, clearly, it is not. -not sure why you would think that this is wrong or a bad thing to believe.

Originally posted by twhitehead
Though I don't dispute your argument, I would like to point out that the total population is not the number that is important.
Suppose we are talking about a fairly important gene that in all current individuals is identical. Now suppose that there are 1 thousand possible mutations that can happen to that gene, and only one of those results in a viable e ...[text shortened]... non-viable embryos that go unnoticed each generation is much greater than the human population.

Well ok., but it´s fairly reasonable to restrict members of a species to the ones that get to the point where it´s the environment that kills them and not internal biochemistry - if the gene is that bad then it´s really not going to affect the species.

What I´m trying to do is stop the plethora of partially thought out hypothetical examples (my peacock one falls into this category as I don´t know how big the costs are but I put a strong disclaimer at the end). If a professional evolutionist (or whatever they call biologists who study this stuff) does it then that´s ok., they understand the theory a lot better than we do and understand its limitations better - so an example from one of them is likely to provide a simple case which doesn´t introduce a whole bunch of problems. I just picked on Andrew Hamilton´s because of that number.

Originally posted by Andrew Hamilton
[b]….You have a population of 1 quintillion individuals versus one with the beneficial gene - this just isn’t a meaningful number outside astronomy.
..…

I don’t understand at all what you mean here by “not meaningful“; why isn’t 1 quintillion not a “meaningful” number outside astronomy? -can you clarify what you mean by not “meaningful” in t ...[text shortened]... clearly, it is not. -not sure why you would think that this is wrong or a bad thing to believe.[/b]

Sorry it´s the middle of the night and I can´t sleep for the second night running 🙁 so don´t expect me to answer everything completely. I´ve put headings in bold to indicate what point I´m replying to.

1.0E15
The astronomy reference was hyperbole - if you can name a terrestrial vertebrate species with that many individuals in it then I´ll take it back. Also see my response to twhitehead above.

Horizontal gene transfer
No, the point there was that it occurred to me after I´d posted that you probably can have a unicellular species that has that many members. As a way out for myself I invoked horizontal gene transfer to point out that the selection rules for prokaryotes are different - species are not well separated in the way that happens with eukaryotes - and there is evidence for gene transfer between domains (Archeans and bacteria). Essentially I just wanted to avoid you having an easy counterexample.

What you meant by deleterious/advantageous mutations:
Biology has a nice catchphrase for this - it´s called fitness. It doesn´t mean strong or even necessarily healthy - you can live half as long but if you have twice as many viable offspring you are twice as fit in the evolutionary sense (example straight from the wikipedia page on fitness). By the way, the offspring are required to be viable. Having lots of sterile offspring is unfitness.

Gene diffusion rates
I made this term up by analogy with physics. There is a term gene flow but that means the transfer of genes between separate populations (well not totally separate obviously...). What I meant was the way you start of with a mutation in one individual (although it can happen multiple times, e,g, see the Wiki page on sickle cell anemia) and it spreads out through the entire population. The problem with the analogy is that this involves replacement of the individuals in the population, which e.g. heat diffusion does not.

Evolutionary determinism
Ouch - didn´t realise that existed in biology - what I meant was that some of the points raised by the natural selection advocates read as if evolutionary outcomes are somehow inevitable (this may not be what people mean to say - it´s just how it reads).

My position
Just for clarity I´ll try to explain where I´m coming from. Kelly raised a couple of interesting points - along with a false dichotomy. He is right to point out that there are problems for the theory of natural selection, but I do not agree with his conclusion that there therefore must be a designer. The fact that the theory - as far as I understand it - does not explain everything does not mean that it is impossible for an updated natural selection theory to explain it.

He also raised an interesting epistemological point, which is when we actually decide that the evidence is good enough to validate a theory. Especially one like natural selection where, at first sight, there isn´t a satisfactory alternative (or at least one that doesn´t generate all sorts of other difficulties). Actually I´d say that there are alternatives, as the biology community argue about rival versions of natural selection.

The other point of his about organs is awkward as soft tissues are not well preserved in the fossil record. However, there are more fundamental issues, such as how and why tissues became differentiated in the first place - you can probably get a heart by a series of point mutations. But why select for tissues?

Even more serious, most of the mutations you (seem) to have been talking about are point mutations, where a gene changes and this changes the protein it codes for. However natural selection also has to account for chromosome number differences. Humans have 46 chromosomes, chimps and gorillas our nearest living relatives have 48. As it happens it can - I thought this would be difficult, but apparently not - and I had to dig around for this it´s not easy to find as you have to ask the right question.

See this link: http://en.wikipedia.org/wiki/Karyotype#Observations_on_karyotypes
and this location: http://en.wikipedia.org/wiki/Paleopolyploidy

The first one explains how chromosome number can change (functionality moves between chromosomes). The Paleopolyploidy page is interesting as it describes a mechanism where doubling of the number of chromosomes (from 2 pairs of each to 4 pairs of each), you can get relatively safe mutations which don´t just kill off the organism as there is redundancy when a gene just stops working due to a mutation. Especially the Paleopolyploidy page is nice as it shows how they spot it.

Originally posted by Andrew Hamilton
I assume that the analogue of a typical human race with the process of evolution is wrong because I assume that usually one of the defining feature of such a human race is humans lining up at the starting block the moment before the race begins but there is nothing analogous to that in the process of evolution because the process of evolution is alwa ...[text shortened]... avalanche.
-and, like evolution, you don’t need to know what started it to observe its effects.

My point would be when looking at the race, if you cannot get out
of the starting block you don't get to run.
Kelly

Originally posted by twhitehead
I can't tell from your response whether or not you have understood my explanation.
Do you agree with me that:
1. Most of the 'dead ends' you refer to would be single individuals.
2. All life forms die eventually.
3. A large percentage of life forms die before reproducing (dead ends).
4. A life form is only a 'dead end' if it fails to reproduce.
5. T not they even pass the two cell stage ie count every fertilized egg as an offspring.

1. So you want to suggest that most dead ends are single individuals,
and am I to assume that those that get the good mutations only
are the groups so that those go in the genetic pool can propagate
through the species quickly enough to do some good? I may be
reading something into your post here, are you suggesting that even
the good mutations are also found in just individual life forms as
well?
2. Yes
3. Sure
4. No, they will end up dead over time, but reproducing could still be
taking place before the end.
5. Well since we are looking at life all around us, duh. That simply
acknowledges where we are, it does not mean your conclusions are justified.
6. You lost me here, step back a minute. The statistical calculation of
‘right’ to ‘wrong’ requires you actually understand all the variables in
play. I don’t think you grasp that at all! You also seem to be under
the illusion that once you get a piece of a building block to make say
bone, that the next round of ‘random’ mutations wouldn’t just take
that away, or start to build it in the wrong spot. Random, if you go by
the normal definition of the word implies that all the mutations would
be without any pattern, plan, system, or anything else that may
produce some favorable result and keep it next time around.
Kelly