From abiogenesis to evolution

[Eric H]

I think the theory of evolution is a valid theory that has stood the test of time, it is a way of ensuring that the best characteristics in a population are carried on from one generation to the next.

How long has evolution been working for, would it be about a billion years?

What about abio genesis when very simple life is formed due to certain conditions being right for the first time on Earth. As I understand the theory, a simple life form grew rapidly in numbers and also in complexity. Presumably the forces of evolution would not be working in this early life on Earth.

Life was past on from one generation to the next at a microscopic size; for the first couple of billion years or so. Which implies there were some very successful laws that governed this.

At some point in time some of these micro organisms must have carried a huge amount of complex information. They would have to grow vastly in size to realize their full potential as an adult, so they could pass on their genes to the next generation.

What I would be interested in trying to find out is, how far advanced would this life formed through abio genesis have to reach, before the forces of evolution take over.

Peace

Eric

[Dr.GH]

"What I would be interested in trying to find out is, how far advanced would this life formed through abio genesis have to reach, before the forces of evolution take over."

This is one of the hot topics in abiogenesis research. There are basicaly two points of view. One is the "molecular evolution" one that basically states that evolutionary forces act on prebiotic molecular systems, nad that stability and hardiness are important from the very first moment that Earth existed. See Stuart A. Kauffman, 1993 The Origins of Order: Self -Organization and Selection in Evolution Oxford:Oxford University Press, for an example of this perspective. Generally speaking, I'd say that this is the most common view point.

Others would argue for a "pre-Darwinian" kind of evolution that operated prior to the elaborated cellular life. Examples here would be Wose and a few others:

Woese, Carl
1998 “The universal ancestor” PNAS Vol. 95, Issue 12, 6854-6859, June 9

Woese, Carl
2002 “On the evolution of Cells” PNAS Vol. 99 13:8742-8747, June 25

[RRoman]

Evolution occurs as soon as you have imperfect replicators. Thats what the TOE is about: That in a population of imperfect replicators, some will, through mutations, be better adapted to an environment and thus produce more offpring.

For example: Lets say you have an imperfect replicator in a population of other identical replicators.
If it gets a mutation that makes it replicate more often, it will make more offspring than any of the other replicators. The offspring will inherit the mutation, and also have more offspring than the replicators without the mutation. This continues until the replicators with the mutation eventually replace the replicators without the mutation.

I am sorry if I am not clear. It is 3:30 am here and I am rather tired.

I just want to say, that abiogenesis is just simple molecules being formed from non-living things. Once imperfect self-replicating molecules are formed, evolution takes over.




Life doesn't need to "realized its potential" to evolve or pass on its genes. It hust happens automatically. Think of bacteria: Imagine that a population consists of bactria that have an antibody-resistance gene and those that dont. If antibiotics are applied to them, only the ones with the resistance survive, and pass on the mutation to their offspring.

i repeat my apology that I am incoherent due to sleep. sorry if i don't make sense.

[Eric H]

Thank you Dr. GH, two very useful names Woese and Kauffman, while I don’t pretend to understand them fully, I did find them interesting. I will try and read more and come back later with comments.

After reading summaries of these guys work, a question on complexity is forming in my mind.

If you were to look at the amount of change in complexity that happens at a micro organism size during the early stages of life on Earth, and before evolution started.

Then you compared it with the amount of change in complexity that is attributed to evolution when the first dinosaurs came about.

Is it possible to say roughly what percentage of change in complexity happened at micro size?

And roughly what percentage of change happens through evolution?

Peace

Eric

[Eric H]

Rroman quote
Life doesn't need to "realized its potential" to evolve or pass on its genes. It hust happens automatically. Think of bacteria: Imagine that a population consists of bactria that have an antibody-resistance gene and those that dont. If antibiotics are applied to them, only the ones with the resistance survive, and pass on the mutation to their offspring.
------------------------------------


Looking back I don’t think I explained myself very well.

When life started on Earth it was about the size of a seed, and each subsequent generation remained about the size of a seed for a couple of billion years or so.
Although they remained at a micro size it seems they grew in complexity during this time.

At some point in time other laws of change kicked in and these seeds then grew to adult size like a dinosaur, and competed against each other in some way as an adult, before they could pass their genes on to the next generation.

Evolution is a good explanation of how life adapted over the last billion years or so, but to me, the more interesting questions to be answered concerns the pre evolution period.

To my way of thinking the theory or laws of evolution can only account for a limited amount of change.

Just as a matter of interest the UK recorded the hottest day since records started of 37.9c.

peace

Eric

[Happy Wonderer]

I think that you may be assuming that 'larger' means 'more complex'. You need to get yourself a microscope and a bucket of sea water. (I'm sincere about that.) You will find quite complex organisms that are much smaller than the average seed.

Thought experiment: what is the difference in complexity between a flea and a swimming pool full of distilled water?

hw

[Eric H]

Hello hw

I can remember going to the dentist a couple of years back, she took a tiny scrapping of something from my teeth and put it under the microscope. The picture came up on a computer monitor to show a complete self-contained eco-system going on, and it seemed highly complex. I thought I had cleaned my teeth properly only half an hour previously.

As to your question, I have no idea what the difference in complexity might be between a flea, and distilled water.

I find the search for the origins and the history of life fascinating, although I am largely ignorant about the details.

Einstein came up with a theory of how the universe has been expanding for the past fifteen billion years or so.

Darwin has the theory of how life has adapted over the last billion years or so.

What seems to be missing is laws that govern how life adapts and changes pre evolution.

If you where to take a male sperm, and a female egg; between them they carry the full information to make an early dinosaur.

Is there any way to try and ascertain how much of this information was gathered due to the forces of evolution? And also how much of this information in the early egg and sperm could have come about by other laws of change pre evolution?

Peace

Eric

[Doubting Didymus]

How are you defining 'forces of evolution'?

[Azathoth]

I just thought I'd point out something that you've mentioned,that might not be exactly correct.

If you where to take a male sperm, and a female egg; between them they carry the full information to make an early dinosaur.

The only way,I'm afraid,that you would,or could,get an early dinosaur from an egg and sperm,is if the egg and sperm came from two early dinosaurs.

If you meant it in a different way,would it be possible for you to elaborate on this statement?

[RRoman]

mmmm...are you perhaps asking whether there is a set of laws regarding early life, which cause it to change and increase in complexity, different from evolution?
If so, then I don't think that there is any such mechanism. Evolution starts right away once you get imperfect replicators.

[Data]

Originally posted by Azathoth
The only way,I'm afraid,that you would,or could,get an early dinosaur from an egg and sperm,is if the egg and sperm came from two early dinosaurs.

If you meant it in a different way,would it be possible for you to elaborate on this statement?
I think he means that if we evolved from dinosaurs we should have all the DNA required to make a dinosaur.
The first big problem is that we didn't evolve from dinosaurs ;)

Sorry if I read that wrong though.

[Oolon Colluphid]

Hi Eric!
Originally posted by Eric H

As to your question, I have no idea what the difference in complexity might be between a flea, and distilled water.
Think of it this way: if you randomly rearrange the components of the water, what have you got? And if you do the same to a flea, is the result still a flea? I would suggest that what you’d get in the latter case is ‘a mess’ :).

What it amounts to is that, of all the ways of arranging the parts -- the chemical constituents, say -- of a flea, only a vanishingly small number of them actually are a flea. So that’s where the complexity comes in -- specifically, the organised complexity that makes a flea, and makes it able to make more fleas. Whatever ‘it’ is, a flea has it and water doesn’t.
I find the search for the origins and the history of life fascinating, although I am largely ignorant about the details.
Well you’ve come to the right place! Ask away!
Darwin has the theory of how life has adapted over the last billion years or so.
Life has been around on earth for about three-and-a-half billion years, not ‘merely’ one. And the neo-Darwinian ‘random-mutation-plus-natural-selection’ is only part, though a major part, of the Theory of Evolution as it presently stands, but I get your meaning.
What seems to be missing is laws that govern how life adapts and changes pre evolution.
How life adapts and changes is via evolution. Evolution is what you get, automatically and inevitably, once you have self-replication and the consequent competition for resources. It is evolution, all the way back to the first self-replicating molecules. At which point the question becomes ‘where did the very first replicators come from?’ And at that point, it becomes a question of ‘abiogenesis’ -- and a question for chemists and biochemists. There is no life pre evolution, because the crucial thing about life is its tendency to make copies of itself, which leads to competition, which leads to natural selection, which leads to evolution.
If you where to take a male sperm, and a female egg; between them they carry the full information to make an early dinosaur.
You’ve lost me. Sure, an early dinosaur sperm and egg had the necessary ‘information’ for making an early dinosaur... because they came from an early dinosaur that had lived long enough -- thanks to the ‘information’ in its parents’ DNA -- to get to reproduce in its environment.

But sperm and eggs come a looong way after life’s origins. Are you suggesting here that the first life had the information (whatever that is) to make a dinosaur, a dinoflagellate, a dragonfly or Charles Darwin? Cos it didn’t. What it had -- what it passed on -- was the necessary instructions for making more of itself, instructions that had been successful enough in the past to reach the present. Change those instructions, and it may be better, worse or indifferent, relative to the environment. Change the environment, and those instructions may no longer be as effective.

So it wasn’t all there from the start. But genetics shows us many ways to ‘add information’.

At which point I suggest you have a read of The Information Challenge (http://www.skeptics.com.au/journal/dawkins1.htm). And pop along to your library and browse in the genetics textbooks :).
Is there any way to try and ascertain how much of this information was gathered due to the forces of evolution?
The forces? All of them? All of it. The reason it was ‘gathered’ was due to evolution -- to natural selection. It was the filtering of natural selection that got them to where they were, when the slightly different instructions in many ancestors’ contemporaries didn’t.
And also how much of this information in the early egg and sperm could have come about by other laws of change pre evolution?
Covered above, I hope!

Incidentally Eric, where abouts in Hampshire are you? :)

Cheers, Oolon

[Happy Wonderer]

Hi Eric, I'm not quite sure that I'm understanding you. If I'm off track in my reply let me know.

What is confusing me is that you are interested in "how life adapts and changes pre-evolution" which could be a good question, but then you bring up Dinosaurs. If evolution had a beginning subsequent to 'life', then it was surely long before dinos, sea sponges, or the bacteria came into being.

If you accept the broad scope of evolution then there is no real puzzle here. The evolutionary explanation is that early dinos had great(x100)-grandparents who looked almost completely like dinos and great(x1000)-grandparents who were recognizably dinos.

Of course the line between 'dino' and 'non-dino' is simply an artifact of our relentless human urge to classify things. Note that even with living species there are controversies over whether two groups of salmon (or birds, or Orcas) are different species or are 'just' geographically isolated. From a layman's perspective, just try to tell the difference between a large crow and a small raven to get an idea of what I'm talking about.

The basic idea of evolution is put well by other posters and fits well for everything we recognize easily as life, from bacteria to elephants. If the question is that you think there is a fundamental reason that something as large as an elephant couldn't have eventually evolved from something as small as a bacteria, then just consider that humans begin life as just one cell. (I'm pretty sure that even a fertilized egg is a single cell.)

The interesting question is how well do evolutionary principles apply to things that are not as obviously 'life', such as viri and prions. The answer seems to be that it applies here just as well (if not moreso because viri are very imperfect replicators) which leads to the interesting proposition that evolution may not be dependent upon 'life.' Anyway that is where I think the conversation could get interesting but let's see how it goes.

Happiness

hw

[Eric H]

Thank you all for your patience and tolerance with your replies, as I am asking questions mainly in ignorance. Sorry I am really stuck for time at the moment just a quick reply.

To my way of thinking there must be other laws that govern the progress of life between abiogenesis and the first replicators.

Also evolution only works in populations, so would that mean there are other laws that govern the way life progressed from abiogenesis to the first populations?

Would the time between abiogenesis and the first replicators and the first population of a species be about two billion years or so?

DR. GH gave the name of Stuart A Kauffman at the beginning of this thread, and here is a short quote.


Quote Kauffman

After pointing out the grounds to suppose that no general law is likely to govern all possible non-equilibrium systems, the central aim of the first lecture is to discuss the general conditions that allow evolution and coevolution to assemble complex systems. Not all complex systems can be assembled by an evolutionary process.

--------------------------------------


My thoughts are in line with Kauffmans last sentence.

I will try and make more individual comments latter tonight

Peace

Eric

[Oolon Colluphid]

Originally posted by Eric H
To my way of thinking there must be other laws that govern the progress of life between abiogenesis and the first replicators.
Well, there's chemistry... ;) But once you have replicators, it won't be long before they've significally dented their resources. So then, the ones that are better at getting the resources start to out-compete the others. almost at once, you have evolution.

And re-reading, you've lost me a little. Abiogenesis is how you get the first replicators... so how can there be anything in between?
Also evolution only works in populations,
And thereby you demonstrate anything but ignorance! Congrats, you're well ahead of the vast majority of people at large!:cool:
so would that mean there are other laws that govern the way life progressed from abiogenesis to the first populations?
Abiogenesis -- basically, chemistry -- produces a replicator. This, well, replicates. Those ones replicate. Hey presto -- a population! What other laws are required?
Would the time between abiogenesis and the first replicators and the first population of a species be about two billion years or so?
Nope, because as I've said, abiogenesis is how you go from chemistry to replicators. The term 'species' is fairly useless in the context of replicators. They were just lineages... and if modern bacteria and viruses are anything to go by at all, there was heaps of genetic swapsies going on. So I suppose the question is, what are you getting at by saying 'species'?
Kauffman: Not all complex systems can be assembled by an evolutionary process.

Eric: My thoughts are in line with Kauffmans last sentence.
Hmmm. We're not in for another 'irreducible complexity' discussion, I hope...?

Sure, 'not all complex systems can be assembled by an evolutionary process'. But there's no evidence, or reason to think, that what we have on earth is the result of anything but evolutionary processes.

Cheers, Oolon

[pz]

Originally posted by Oolon Colluphid
Sure, 'not all complex systems can be assembled by an evolutionary process'. But there's no evidence, or reason to think, that what we have on earth is the result of anything but evolutionary processes.Of course there is. Kauffman is a structuralist, and makes a good case that there are universal laws of growth and form that are independent of historical constraints and are uniformly applied to all organisms at all times. Because they are universal and we take them for granted does not mean that they don't contribute to the patterns of life on earth.

For instance, lipid vesicles tend to spontaneously self-organize into hollow spheres. There's nothing evolutionary or even biological about it, but that's a property that has had important consequences for what we have on earth.

[Oolon Colluphid]

Thanks pz, quite right. That's what happens when one knocks out a quickie reply before running for the bus home! I was thinking too anti-creationist again, anticipating the next line: 'if it's not assembled by evolutionary forces, it must be god'. Whatever Eric's actual position, the Kauffman quote looked just enough out-of-context to set off my finely-tuned creationist-argument detector... especially given Eric's agreement with the most cretinist-friendly line in it.

So for the record, there is of course plenty of organised complexity around that doesn't require evolution: salt crystals, snowflakes, the way proteins fold, the lipids you mention... none of which requires evolution, but which is instead explained by other natural forces. For the position of Complexity Former, no gods need apply.

Cheers, Oolon

[Eric H]

Hello Oolon,

If you don’t want to dance that little old irreducibly complex dance sequence that’s fine, although I believe in God, I had not intended to bring God into this discussion.

However I sense another God creeping into this discussion, which is evolution.

No other explanations is needed, evolution did it all.

From a science point of view can there be any other laws that could govern the progression of life, apart from evolution?

By the way I live just down the road from you, in Eastleigh.

Peace

Eric

[Doubting Didymus]

Originally posted by Eric H
From a science point of view can there be any other laws that could govern the progression of life, apart from evolution?

Well, I don't think I really understand what you're asking. PZ has mentioned the easily overlooked fact that there are laws related to form that influence the structure of lifeforms, and I'm sure that certain processes that follow from physics and chemistry can be said to be "responsible" for the origin of the first replicator. Come to think of it, isn't Kauffman the guy who reckons that there are non-evolutionary principles at work that might allow the first replicator to be much more complex than most people are willing to allow? Is that the kind of thing you mean?

[pz]

Originally posted by Doubting Didymus
Come to think of it, isn't Kauffman the guy who reckons that there are non-evolutionary principles at work that might allow the first replicator to be much more complex than most people are willing to allow? That's right. Kauffman argues that there are properties inherent to pools of molecules that can spontaneously bootstrap them into increasing order. There isn't a hint of the supernatural or intelligent design behind it, though -- he models these things on computers, and there's no more magic to it than there is to cellular automata -- so it's a mystery why the ID crowd seems so enamored of the guy. I suspect it's yet another example of IDists completely failing to comprehend something, or confusing novel, non-darwinian ideas with anti-evolutionism.

[Doubting Didymus]

Originally posted by pz
it's a mystery why the ID crowd seems so enamored of the guy.

Perhaps the idea is that the presence of laws that facilitate the spontaneous origin of life contribute to the fine tuning argument?

[pz]

Originally posted by Doubting Didymus
Perhaps the idea is that the presence of laws that facilitate the spontaneous origin of life contribute to the fine tuning argument?
Maybe. But I don't see the point of that argument, either -- it doesn't impinge on evolution at all, since all the super-duper constants would have been set in place 14 or 15 billion years ago, before the earth even existed. If all that was what the IDists were proposing, they'd be leaving us biologists alone and annoying the physicists instead.

[Dr.GH]

Dembski is fond of Kauffman, I think, because he claims that there is a connection between Kauffman's use of "complexity" and his notion of "specified complexity." I don't see it myself. Also, a few years ago Kauffman made the comment that Dembski's work was legitimate math. At the same time, Kauffman's remarks led me to think that Kauffman had not actually read much about Dembski's "math."

Also, the "No Free Lunch" equasions by Wolpert and Macready (1997) that Demski recently mis-applied came out of Kauffman's Santa Fe Institute. Wolpert wrote a critique of Dembski's book "No Free Lunch," which is (I think) where Wolpert points out the the NFL theorems cannot apply to co-evolutionary systems. That said, Wolpert merely disagrees with Dembski's math, and is personally antagonistic toward the ID movement. (Note, I didn't say that Wolpert agreed with the IDCs.)



Wolpert, David H. 2002. “William Dembski’s Treatment of the No Free Lunch Theorems is Written in Jello.” www.talkreason.org/articles/jello.cfm , accessed on Aug 15, 2003.

Wolpert, David H and William G. Macready. 1997. “The No Free Lunch Theorems For Optimization.” IEEE Trans. Evol. Comp. v.1, no 1, 67-82.

[Oolon Colluphid]

Hi EricOriginally posted by Eric H
Hello Oolon,

If you don’t want to dance that little old irreducibly complex dance sequence that’s fine, although I believe in God, I had not intended to bring God into this discussion. I’d rather not either. It’s be done to death here: basically, there’s no irreducible complexity -- nothing that requires God -- in biology. It just sounded like you were leading that way, as so many before you have... ;) And God does tend to get mentioned too, from time to time....However I sense another God creeping into this discussion, which is evolution. Come again? Sorry for letting evolution creep into a discussion of... erm... now what’s this forum’s title...? ;):pNo other explanations is needed, evolution did it all. Did all what? Evolution is a pretty big subject. Yes, everything we see alive has evolved. So? Evolution does not, repeat not, explain everything. It just explains a hell of a lot. For instance, it does not explain mass extinctions; it does explain radiations after them. It may not explain why certain theropods took to the air, it explains how they did it.From a science point of view can there be any other laws that could govern the progression of life, apart from evolution? For what seems like the umpteenth time, yes. Meteorite impacts. Plate tectonics. The properties of elements and molecules. Historical constraint, perhaps. What are you looking for?By the way I live just down the road from you, in Eastleigh. Even nearer than you think. Though I work in Winchester, I live in Chandler’s Ford!

Is this the point when one of us says, ‘say, do you know so-and-so?’ :D

Cheers, Oolon

[Eric H]

Quote Doubting Didymus
Come to think of it, isn't Kauffman the guy who reckons that there are non-evolutionary principles at work that might allow the first replicator to be much more complex than most people are willing to allow? Is that the kind of thing you mean?
----------------------------------------------------

Yes something along these lines, somehow I think there needs to be a number of processes that accelerate the rate of change. The reason Being there seems to be a vast amount of change needed to go from chemicals on Earth to the life we see today.

A Kauffman quote again,
In later lectures I return to the concept of the adjacent possible, for it appears to be an expression of a very general feature of the Universe: Since the number of possible large molecules, say with several tens of thousands of atoms per molecule, is vast, the Universe has not had sufficient time to make each such molecule at least once since the Big Bang. Thus, there are 10 raised to the 260 kinds of proteins length 200. If the universe has 10 to the 80th particles, and if a "reaction" required only a femtosecond, then the universe can have "tried" only 10 to the 193 pairwise "reactions" among the particles - a vast number, but vastly smaller than the number of proteins length 200. Thus, it is an essential feature of the universe that it is necessarily non-ergodic with respect to the generation of complex structures such as complex molecules, let alone species, legal systems and so forth.


peace

Eric

[Eric H]

Hello Oolon

Quote Oolon
For what seems like the umpteenth time, yes. Meteorite impacts. Plate tectonics. The properties of elements and molecules. Historical constraint, perhaps. What are you looking for?


:) Would any of these things accelerate the rate of change through evolution?

The reason I ask is if you take a population of any one species they must be surviving fairly well as they are. If one of this species introduced another advantageous trait to that population, would it normally be a case of fine tuning?

The examples often given are introducing camouflage, beak size and shape, a better hunting or defensive strategy.

Getting late for me, probably rambling again


peace

Eric

[pz]

Originally posted by Eric H
A Kauffman quote again,
In later lectures I return to the concept of the adjacent possible, for it appears to be an expression of a very general feature of the Universe: Since the number of possible large molecules, say with several tens of thousands of atoms per molecule, is vast, the Universe has not had sufficient time to make each such molecule at least once since the Big Bang. Thus, there are 10 raised to the 260 kinds of proteins length 200. If the universe has 10 to the 80th particles, and if a "reaction" required only a femtosecond, then the universe can have "tried" only 10 to the 193 pairwise "reactions" among the particles - a vast number, but vastly smaller than the number of proteins length 200. Thus, it is an essential feature of the universe that it is necessarily non-ergodic with respect to the generation of complex structures such as complex molecules, let alone species, legal systems and so forth. I would like to see you state, in your own words, what you think Kauffman means here, and what conclusion he draws from this observation.

I've found that Kauffman is the second most egregiously misinterpreted author of popular evolutionary literature, right after SJ Gould.

[Dr.GH]

Originally posted by Dr.GH
That said, Wolpert merely disagrees with Dembski's math, and is personally antagonistic toward the ID movement. (Note, I didn't say that Wolpert agreed with the IDCs.)

I found that I had made an error that I can not edit. Wolpert is NOT personally antagonistic towards ID. He is, if one may say so, agnostic.

BTW, when did this time limited editing deal happen. I must have missed the memo on this.

[RufusAtticus]

Originally posted by Dr.GH
BTW, when did this time limited editing deal happen. I must have missed the memo on this.

When we switched to the new software. It's 120 mins if I recall.

[Happy Wonderer]

Although I agree with his conclusion, I think that there is a flaw in his logic.


Thus, there are 10 raised to the 260 kinds of proteins length 200. If the universe has 10 to the 80th particles, and if a "reaction" required only a femtosecond, then the universe can have "tried" only 10 to the 193 pairwise "reactions" among the particles - a vast number, but vastly smaller than the number of proteins length 200.


The reactions do not have to be tried in sequence, they can (and are) tried in parallel. The time that it takes to do a reaction is not relevant; I can halve that time by doing two reactions at once. I will not run out of space in an infinite universe, though I may run out of particles to try at once if I take his assumptions.

However, then consider the fact that any protein of length N is composed of two smaller protiens, which can be rearranged to form a different protein of length N and the search space seems a lot smaller. (IOW, although it takes 200 reactions to make protein ABC, it is only a few more to make protein CAB.) Thus, I can cover the search space with far fewer particles.

(Yes, this is not how any observed physics is known to work, but if you are making a pure-reason argument like this you are open to such a line of counter-reasoning.)

The creationist probability arguments fail for the same reason. Drawing two perfect bridge hands is incredibly unlikely for an individual. They like to talk about how long one would have to play bridge to get two perfect hands. It doesn't take long at all when you have an infinite number of players for one of them to get two perfect hands...

Despite this objection, there seem to be good structural reasons that some proteins are more 'likely' than others.

hw

[Doubting Didymus]

Yes something along these lines, somehow I think there needs to be a number of processes that accelerate the rate of change. The reason Being there seems to be a vast amount of change needed to go from chemicals on Earth to the life we see today.

Hmm.... Because there isn't enough time for evolution to produce all this change, something else must have done it?

That doesn't hold water I'm afraid. There has been plenty of time, far more than evolution "needs". Just as an example, see this article (http://www.world-of-dawkins.com/Dawkins/Work/Articles/1995-06-16peepers.htm), by Dawkins, extracted from River Out of Eden. Evolution can work at breakneck speed, and is capable of producing an eye from scratch in just half a million years. That's peanuts.

[Eric H]

Hello pz, and Happy Wonderer
The trouble with statistics and probabilities is they can be read in many ways. And as HW says you can halve the reaction time just by starting of with 2 reactions.

On the downside there is a probability that many reactions will be duplicated rather than produce new variations, or they may produce useless variations or they could even produce a virus causing death.

Possibly Kauffmans probabilities amount to little more than a party game; using very large numbers, ultimately they prove nothing.

However they do have a use, they can challenge the mind to think, and if they provoke thought, then they are very useful.

peace

Eric

[Eric H]

Hello Doubting Didymus,

I read Dawkins evolution of the eye, and he quotes a very conservative estimate of 400, 000 generations to go from skin to a working eye.

I have tried to read Dawkins account of the computer programme for the evolution of the eye, as honestly as possible. Maybe I am not reading all the information correctly or maybe I am jumping to wrong conclusions, but the programme seemed biased so it would only create an eye.



---------------------------------------------------------
Quote Dawkins, They then let the model deform itself at random, ‘’constrained’’ only by the requirement that ‘’’’’any change must be small and must be an improvement on what went before’’’’’’
----------------------------------------------------------





It seems to imply that the end result of this programme could not produce an unwanted growth, or any other type of body part other than an eye, because each change was restricted to making a small improvement.

Over a period of 400, 000 generations I would expect error, if only one percent of the generations had errors that would give 4,000 generations with error. Would it also be reasonable to expect these errors to compound in some way if they occurred?

It seems we both read the same article and draw different conclussions

Peace

Eric









.

[Wounded King]

Surely thats where the natural selection comes in Eric? To weed out the errors that make it less fit.

[Eric H]

Hello Wounded King, Whoops, I could have worded that better.

The computer model for the evolution of the eye by Nilsson and Pelger did not show how it was programmed.

They start of with a photo sensitive cell, which on its own would be useless, unless it is connected to some sort of brain that can interpret what this cell can sense. For this photo cell to be of any benefit, this brain would also have to direct movement based on the information received from this cell.

It could be like grafting a perfectly good eye on to the back of a human head, how would it work?

The computer programme does not show,
How many successive changes would be needed to make an eye?

Were only eye making advantages programmed into the computer? (yes; but that is only my interpretation of Dawkins words)

Were realistic alternative mutations programmed, which may not end up as an eye? ( no; my interpretation again)

Could there be any negative biological or other forces working against the evolution of the eye at each successive change, and what might they be?

Many of you could find better questions, but Dawkins account does not lay out fully how the computer was programmed, so that the reader may make an informed conclusion for themselves. I have now read this piece several times, and each time something else jumps out. Dawkins sees nothing negative, no alternatives, he seems to jump from one positive step to the next all seemingly based on assumptions. (only my interpretation)

How much of Dawkins computer eye is based on science facts?

Peace

Eric

[Doubting Didymus]

How much of Dawkins computer eye is based on science facts?

The entire article is based on a published peer reveiwed journal article. So, all of it really.

Here is the ref: A Pessimistic Estimate Of The Time Required For An Eye To Evolve, D.-E. Nilsson and S. Pelger, Proceedings of the Royal Society London B, 1994, 256, pp. 53-58.

Here is the pubmed abstract. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8008757&dopt=Abstract)

Were only eye making advantages programmed into the computer? (yes)

Were realistic alternative mutations programmed, which may not end up as an eye? (no)

This is not meant to be a simuilation of how evolution works. The purpose of the research was to estimate the amount of time evolution would need under an assumed selection pressure favouring an increase in the amount of detectable spatial information. If you remember, the amount of time needed was your objection in the first place.

Your objection about wiring the first photocell into the brain is not relevant to this point, but as several others on this forum as well as myself only recently finished explaining this question to somone else, I'll link you to that discussion.

... one moment, while I wrestle with the search function.

[Doubting Didymus]

Here is the thread. (http://www.iidb.org/vbb/showthread.php?s=&threadid=53023&perpage=25&pagenumber=3)

I've linked to page three, where I start spouting off about basic cell biology in an effort to explain how the first photocell might usefully come into being. I'll reproduce that first post here now. See the above thread for an extended exchange on the topic.


__________________________________________________
Originally posted by luvluv
Doubting Didymus:

It's probably best to assume I know nothing. Give me or reference me to as quick a guide to this as possible, if you would be so kind.

You don't like making my job easy do you? ;)

Right, Have a look at This diagram (http://www.emc.maricopa.edu/faculty/farabee/BIOBK/cellmemb_1.gif) from about the middle of this page (http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBooktransp.html). The copyright is mentioned under every picture. "Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com)". I don’t think I can actually display it here.

The page itself isn't the best place to go for a simple run down, however. Most of the information we are talking about is at the undergraduate first year level, which is fairly deep as a starting point. I'll explain it myself as best I can.

On the diagram, you'll notice that the membrane isn’t “made of” protein, but that proteins are intricately folded molecules embedded IN the membrane, which is made of molecules called phospholipids. Those are the little round things with two tails you can see in two layers. The phospholipid part is the bit that peez is talking about when he says that the membrane is highly specific about what it will and wont allow to cross it. Whenever the cell needs to import something other than water, charged hydrogen ions, molecules that are hydrophobic (lit. water hating), and a few things like that, it needs to employ the proteins that traverse the membrane to do it. There is a protein for practically everything.

This is universal to extant organisms, because it is the (more or less) direct result of DNA. Ultra-swiftly: DNA builds an RNA template, the RNA moves to a ribosome, which translates the code into a chain of amino acids, which is a protein. The folding of the protein is determined largely by the order of amino acids in it. Thus, when a mutation occurs in the DNA, it sometimes has an effect on the folding of the protein that that part of the DNA codes for.

Okay, I may be being redundant here but define "light sensitive"? What would it specifically entail? A change in the proteins shape?

Yes, that’s about right. Let me expound: we are thinking about one of the trans-membrane proteins in (probably) a nerve cell. Imagine it’s a heat sensor. Now this protein has a hole in the middle, which admits, say, calcium (a commonly used molecule for cellular messages). Its usually closed, but it opens when it heats, which allows calcium into the cell, which then does a lot of things, but put simply, it stimulates the nerve cell to send its electric signal, which the brain of the organism translates as heat. What we imagine happening is a mutation, in the DNA, which puts a slightly different order of amino acids in the protein. This might have any number of effects. It might make it permanently open or closed, or otherwise useless. It MIGHT make it slightly less stable. At first, that sounds bad, but it might easily make the protein susceptible to open to things that aren’t heat, but are like it. It might now open not only when heated by air, but when heated by light bombardment. Think about what this simple mutation means for the organism. Their heat sensors are working normally, but they are ALSO reacting to light. Imagine this in some sort of starfish, which normally responds to heat by moving away from it. That starfish will now also instinctively move away from sunlight. In other words, by a single simple mutation (this might be as basic as a point mutation, which happen all the time), making one of its proteins unstable, the lucky starfish is gifted with the ability to hide.

The gene for that protein might be duplicated at some point, and if so, the two proteins might then progress in different directions. One of them might continue to mutate in such a way that it begins to lose its ability to open in response to heat, essentially making it that bit more specific to light stimulus, without having to worry about losing its heat sensing ability, because the original molecule remains unchanged.

At all times, we are talking about minute alterations to protein structures. Nothing drastic ever has to occur.

I hope I’ve explained the basic idea sufficiently in under seven hundred words. Have I left anything too murky?

[Happy Wonderer]

Hi Eric, hope you had a good weekend.

Let's look at one sentence of what Kauffman is saying:


Thus, it is an essential feature of the universe that it is necessarily non-ergodic with respect to the generation of complex structures such as complex molecules, let alone species, legal systems and so forth.

Recall that ergodic (http://www.wikipedia.org/wiki/Ergodic) means a hypothesis for a given system that over time, any two possible states are equally likely. Obviously not all systems are ergodic, and by observation chemical systems are definitely not ergodic. We even know why, as we know why atoms show different preferences for other atoms. So it is quite clear that the universe is non-ergodic with respect to molecules.

Kauffman is arguing that this is an essential property of the Universe. I do not have a longer quote so I don't know the context; I might agree that it is essential to the universe as we know it, but that it is really just a consequence of atomic physics. If basic properties of atomic physics were changed then things would be, well, different. I'm not sure that I would draw any deeper philosophical meaning from that fact.

You say:

On the downside there is a probability that many reactions will be duplicated rather than produce new variations, or they may produce useless variations or they could even produce a virus causing death.


which puzzles me. If the subject is abiogeneisis, which to me is imagining how a self-replicating molecule came about. It seems to me to be jumping the gun to talk about death and viri before you have a self-replicator!

You object that many reactions will be useless in forming self-replictators. That is true, and there were probably a vast number of reactions that almost worked. It is even possible that on some planet somewhere self-replicating chemical lines existed for awhile and then went extinct. It is highly likely that life on earth will go extinct sometime before the earth falls into the sun, and it is pretty certain that it will go extinct after that. (Cheerful thought.)


Life is probably not an inevitable consequence of chemistry, but it is obviously one that has a probability greater than zero.

hw

Probability estimates are only as good as the underlying assumptions.

[Godless Dave]

Eric, the biology experts on this board have given detailed answers to some of your questions, but in the process I think a couple misconceptions have been overlooked.

Originally posted by Eric H
Einstein came up with a theory of how the universe has been expanding for the past fifteen billion years or so.

Einstein didn't actually do this, but his work in physics was part of what allowed astronomers to come up with explanations of the observed expansion of the universe and determine its age.

Originally posted by Eric H
Darwin has the theory of how life has adapted over the last billion years or so.
I've seen you throw out this billion years number twice, but I'm not sure where you're getting it. Darwin's theory explains how life has adapted since the beginning of life. There is no reason to think there is a gap between the first self-replicator and the beginning of evolution. As long as there have been living things, there has been evolution. Darwin didn't have the means to determine how long life had existed on earth, but we now have a pretty good idea that it's been about 3.5 billion years.

I also think it's a mistake to talk of evolution governing changes in populations. IMHO (correct me if I'm wrong, O Wise Ones) it would be more accurate to say evolution describes how populations change.