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Experimental evidence for evolution

Discussion of everything related to the Theory of Evolution.

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Re: Experimental evidence for evolution

Postby canalon » Thu Sep 02, 2010 3:54 pm

jevg wrote:canolan

Canalon,
I am not rapeseed ;) although I guess you could probably get quite some oil if you were to press me... More seriously:

jevg wrote:
True randomness as a mathematical abstraction and life do not completely intersects…

May I correct you, randomness is not a mathematical abstraction.

If a sequence is unpredictable, we call it "random". Stated another way, outcomes which lack discernible patterns are said to be "random".
We don't define randomness by what it is, but by what it isn't. Of course an apparently "random" sequence may have an underlying order that we just haven’t yet understood.
[...snipped for brevity...]
If they are random as you seem to wish to assert then the onus must be on you to show how it is so.
With respect all you have done is to provide another hypothesis to support the first one of randomness. This is not evidence.


You are right, I only provided hypothesis to explain how apparent order could emerge from randomness. And I did not elaborate because I do not ave either the space or even the competences to do that here. However there are quite a few patterns by better than me that have demonstrated that simple conditions and randomness can lead to apparent order.
I could refer you to all the chaos theory, or more appropriately to Conway's game of life.

So taking randomness in generation as a null hypothesis is far from being unreasonable. You are of course free to refute that, but in that case you have to at least offer an underlying explanation to the non-randomness. "It converges, so it cannot be random" is not enough. See that ties very nicely with the second part of the argument:

jevg wrote:
…So my point is that the appearance of non randomness can be created by the accumulation of random events and that this appearance cannot be taken as a proof of design.


Occam's razor is a logical principal, it states that one should not make more assumptions than the minimum needed. It underpins all scientific modelling and theory. It admonishes us to choose from a set of otherwise equivalent models of a given phenomenon, the simplest one.

In any given model, Occam's razor helps us to "shave off" those concepts, variables or constructs that are not really needed to explain the phenomenon. By doing that, developing the model will become much easier, and there is less chance of introducing inconsistencies, ambiguities and redundancies.

I am not providing proof of design.
I have been providing data that shows the non-random sequences that falsify the Darwinian concept of randomness. An essential requisite of any scientific theory is that it must be falsifiable.

So may I raise the question again
Non-randomness does explain the data quite easily, does it not?
Why therefore is this not acceptable?


Non-randomness might explain the data quite easily, but it is not enough. If you want to argue non-randomness you have to provide an explanation or a source or something that direct this order. That would falsify the theory that mutation are randomly generated.
On the other hand, there are quite a lot of models that use random events to generate apparent order by using plausible and/or simple laws. So the simplicity of the model might be very relative, but you have to compare that to the implicit pre-requisites of non randomness and then use the razor adequately.
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any proof. (Ashley Montague)
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Re: Experimental evidence for evolution

Postby jevg » Fri Sep 03, 2010 10:44 pm

My sincere apologies, thank you for being so light hearted about it. I promise I will try not to press too hard. :)

… there are quite a few patterns by better than me that have demonstrated that simple conditions and randomness can lead to apparent order.
I could refer you to all the chaos theory, or more appropriately to Conway's game of life.


This is where a lot of confusion enters. May I explain
Chaos theory deals with the spontaneously forming of forms and order. All we have to do to observe spontaneous self-ordering is to pull the plug out of our bathtub drain (the flow of water as you have illustrated). Water molecules quickly self-order into a swirl (a vortex) from purely albeit complex physico-dynamic causes. This is mistakenly called self-organization. The vortex is not organized. It is only self-ordered. Now what is the difference?
This

No decision nodes are required for a bathtub swirl, or a candle flame to self-order out of a seemingly random Brownian movement. Proficient programming choices are not required for the heat agitation of water molecules to self-order into a vortex. No configurable switches have to be purposefully set, each in a certain way, to achieve self-ordering. No pursuit of a goal is involved. No algorithmic optimization is required.

This is totally different to the utility in functional Genetic Algorithms that contain all the above features. Cellular behavior cannot be accounted for in simply physical/chemical processes.

Sadly, for those of us who have not studied chaos or complexity theory in any depth, are fed with some rather sloppy definitions by those who should know better. Clear definitions in any scientific endeavor are an essential pre requisite to good communication.
All too often these or equivalent expressions “self ordering and self organization” are used synonymously, with all the resulting confusion.

I fully endorse that randomness, as a null hypothesis, is a perfectly reasonable and scientific position to take.
Darwin certainly put this whole subject on to a solid scientific footing and of course it was the null hypothesis for his day. Science has often progressed through the formulation of null hypotheses. Falsification though allows for the elimination of plausible hypotheses.

It is here where I disagree with your comment

Non-randomness might explain the data quite easily, but it is not enough. If you want to argue non-randomness you have to provide an explanation or a source or something that direct this order. That would falsify the theory that mutation are randomly generated.


First just to be clear, I am not and have not stated that mutations are not randomly generated.
Mutations are randomly generated from different sources both internal and external.
What I am arguing is that these random mutations do not account for, or indeed are, the source of the functional utility that is observed in cellular processes and I have provided evidence to that effect.

I know of nothing in the scientific method that requires a theory can only be falsified if another was put in place, or that the source of any function must be known or explained in order for a theory to be validated, which if I understand correctly, you are suggesting.

You appear to be trying to shift the goalposts in this regard. However I would caution against that, because if what you say, is to be regarded as a criteria for a theory to be scientifically acceptable then you had better start re-evaluating, for instance, the theory of gravity.

Here is a theory of a force, who source we do not know, it violates the most fundamental law in physics, the law of conservation of energy, there is no explanation except that there is a manifestation that can be measured, and yet it is accepted, quite rightly, as a scientific theory.
(trust me I do know what I am talking about here, and would be happy to explain, but perhaps on another thread)

Alan Guth’s inflation theory, a fundamental part of the so called Big Bang theory, has no identifiable source or even explanation and yet it is regarded as a valid scientific theory and in many quarters as a fact.

So methinks it would be safer to put the goalposts back. :)

What I am trying to say is this non-randomness cannot be addressed by any law that we are aware of, or if it is even possible to have such a biological law.

Of course I could say that it is the Flying Spaghetti Monster wot did it.:)

The creationists would regard me as some manifestation from hell.
The Idists would not even touch me with a bargepole and you would probably pat me on the head, give me a lump of sugar and let me dribble away in a corner, while sending for the men in white coats. :)

There is though a serious point behind this little piece of nonsense.

If the evidence repeatedly shows any theory to be wrong, then still sticking to it would only echo the words of what Darwins brother Erasmus is reported to have said just before Darwin released his publication Origin of species.
"In fact the a priori reasoning is so entirely satisfactory to me that if the facts won't fit in, why so much the worse for the facts."

Science is the victim when scientists ignore evidence in favour of some philosophical bias
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Re: Experimental evidence for evolution

Postby Geokinkladze » Fri Sep 03, 2010 11:18 pm

My understanding of the driver behind evolution is change in the environment. This could be changes in predators of a species, prey or the species itself, and of course the habitat, weather conditions etc. In fact I could be here as long as the Lensky experiment listing all the possible drivers for evolutionary change.

As I understand it Darwin believed this too.

Does that make Darwin a gradualist or a punctured wotsitface?

In my book it makes him neither as well as both. He certainly believed in single step mutation which can redily explain the terms which were hijacked by a few scientists who wanted some publicity. Forgive my apparent insincerity above but it is wearisome reading people trying to stir up a controversy that doesn't really exist.
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Postby Geokinkladze » Fri Sep 03, 2010 11:44 pm

Could those of you who say "Darwin was a Gradualist not a Punctualist" explain what he meant when he said this:

"the periods during which species have undergone modification, though long as measured in years, have probably been short in comparison with the periods during which they retain the same form".
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Re: Experimental evidence for evolution

Postby Geokinkladze » Sat Sep 04, 2010 1:15 am

jevg wrote:.
What I am arguing is that these random mutations do not account for, or indeed are, the source of the functional utility that is observed in cellular processes and I have provided evidence to that effect.


I read a lot of what you say, and have even followed some of the links you posted but I have to say I don't agree with many of your claims (such as the "Darwin was a gradualist not a punctuated equilibriumist...")

So can you AS CONCISELY AS POSSIBLE point out where you have provided evidence to support your claim above. If you think you have lots of sources, please just provide what you believe to be your most convincing ONE and we can discuss it's merits.
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Re: Experimental evidence for evolution

Postby Geokinkladze » Sat Sep 04, 2010 12:59 pm

jevg wrote:Science is the victim when scientists ignore evidence in favour of some philosophical bias


Absolutely, so how do you explain ignoring the approx 3.5 million single step genetic mutations that lead to benefitial improvements in the Lenski experiment up to the 20,000th generation.

Also how do you explain ignoring the fact that the Lenski experiment showed the historic contingency could not be reproduced before the 20,000th generation.

Seems to me you have a philisophical bias of your own that you're trying to convince yourself of.
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Postby JackBean » Sat Sep 04, 2010 1:52 pm

jevg:

Can you say in ONE sentence, WHAT is your point? Because you're writing such long posts, I'm all tired about reading that (and apparently I'm not the only one) and it actually seems, that you agree with canalon...
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Re: Experimental evidence for evolution

Postby jevg » Sun Sep 05, 2010 8:54 pm

by Geokinkladze » Fri Sep 03, 2010 11:44 pm
Could those of you who say "Darwin was a Gradualist not a Punctualist" explain what he meant when he said this:

"the periods during which species have undergone modification, though long as measured in years, have probably been short in comparison with the periods during which they retain the same form".



Darwin saw change not in terms of years but in terms of small modifications that gradually changed species. That is what your quote means.

There is no controversy that Darwin believed that evolution was driven by random mutations that gradually accumulated producing species change.

Just about every biologist I am aware of understands that, including ones on this forum. eg

by canalon » Fri Jun 25, 2010 3:43 pm (post no 20 I believe) 2nd page
…. I do not think that Darwin was anything but gradualist.

So there is no reason for you to become wearisome.

Perhaps before I respond to your other comments, this little bit of confusion can be cleared up.
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Re: Experimental evidence for evolution

Postby jevg » Sun Sep 05, 2010 8:58 pm

JackBean

jevg:

Can you say in ONE sentence, WHAT is your point? Because you're writing such long posts, I'm all tired about reading that (and apparently I'm not the only one) and it actually seems, that you agree with canalon...



My point in this regard is simply this.
Random mutations do not cause one species to change into another.

I don’t know what canalon believes so I don’t know if we are in agreement.
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Re: Experimental evidence for evolution

Postby Geokinkladze » Mon Sep 06, 2010 12:01 am

jevg wrote:Darwin saw change not in terms of years but in terms of small modifications that gradually changed species. That is what your quote means.


It seems you missunderstood so I'll quote Darwin again and this time add some emphasis for you:

""the periods during which species have undergone modification, though long as measured in years, have probably been short in comparison with the periods during which they retain the same form".


If you read the bits underlined as if one sentence, and ignore the "though long as measure in years", you will realise that Darwin was saying that species go through short periods of modification and long periods of stability.

The point is that gradualist is not mutually exclusive to punctuated equilibrium, in fact punctuated equilibrium embodies gradualism. However some advocates of punctuated equilibrium can also allow for other methods that drive change such as saltation, which is mutually exclusive to gradualist.

Also I'll quote Stephen J Gould for you

"the process of speciation takes thousands or tens of thousands of years. This amount of time, so long when measured against our lives, is a geological microsecond. It represents much less than 1 per cent of the average life-span for a fossil invertebrate species—more than ten million years"

Read those two quotes by Gould and Darwin again and compare how similar they are.


jevg wrote:If you research the history of Gould’s and Eldridge’s theory of Punctuated Equilibrium you will appreciate why they are so controversial among some prominent evolutionary scientists.


Oh yes I know that one, wikipedia can be such an easy reference sometimes:

"As a result, many non-specialists sometimes inferred from his early writings that Darwinian explanations had been proven to be unscientific (which Gould never tried to imply). Along with many other researchers in the field, Gould's works were sometimes deliberately taken out of context by creationists as a "proof" that scientists no longer understood how organisms evolved. Gould himself corrected some of these misinterpretations and distortions of his writings in later works"


Seems I'm getting closer to where your coming from now.

How about we rephrase your quote above and substitute "evolutionary scientists" for "Scientific creationists"?


jevg wrote: Punctuated Equilibrium is a theory that does not agree with Darwinian explanation


But hold on.. the quotes from Gould and Darwin above.. and the other one from origin of species, you know, that famous one about the molluscs.

"Species of different genera and classes have not changed at the same rate, or in the same degree. In the oldest tertiary beds a few living shells may still be found in the midst of a multitude of extinct forms. Falconer has given a striking instance of a similar fact, in an existing crocodile associated with many strange and lost mammals and reptiles in the sub-Himalayan deposits. The Silurian Lingula differs but little from the living species of this genus; whereas most of the other Silurian Molluscs and all the Crustaceans have changed greatly


So how is it you think that Darwin's Gradualism is mutually exclusive with Gould's Punctuated Equilibrium.

wikipedia wrote: Gould's greatest contribution to science was the theory of punctuated equilibrium which he developed with Niles Eldredge in 1972. The theory proposes that most evolution is marked by long periods of evolutionary stability, which is punctuated by rare instances of branching evolution. The theory was contrasted against phyletic gradualism, the popular idea that evolutionary change is marked by a pattern of smooth and continuous change in the fossil record.


See there's what you did, you confused Darwin's Gradualism with Phyletic Gradualism. Don't worry it happens all the time.




jevg wrote:
Just about every biologist I am aware of understands that, including ones on this forum. eg

by canalon » Fri Jun 25, 2010 3:43 pm (post no 20 I believe) 2nd page
…. I do not think that Darwin was anything but gradualist.

So there is no reason for you to become wearisome.

Perhaps before I respond to your other comments, this little bit of confusion can be cleared up.


Canlon is indeed correct, Darwin was a gradualist, but as you can see from Darwins own words above, he was also a punctured equilibriumist, however he did not believe in Saltationism or Phyletic Gradualism.

jevg wrote: Stephen Jay Gould suggested that sometimes mutations happen that have no immediate benefit; but those mutations remain in the gene pool because they are not harmful .

Darwin believed this too.

jevg wrote:Gould’s opponents say that the environment drives evolution to a particular solution, so it doesn’t depend on past accidents. Furthermore, a mutation that has no immediate benefit will likely disappear from the gene pool before it is eventually needed


Who are these opponents of Gould who say this? I know of many evolutionary scientists who believe natural selection drives out "bad" mutations and that a mutation that has no immediate benefit will likely disappear, but not always disappear, such scientists aren't opponents of Gould. In fact most evolutionary scientists understand that many benefitial mutations will likely disappear too, just not as likely as a neutral mutation.

jevg wrote: Perhaps before I respond to your other comments, this little bit of confusion can be cleared up.


Lets hope so, I can't wait to move on to this bit:

jevg wrote: What I am arguing is that these random mutations do not account for, or indeed are, the source of the functional utility that is observed in cellular processes and I have provided evidence to that effect.
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Re: Experimental evidence for evolution

Postby jevg » Mon Sep 06, 2010 4:35 pm

Origin of species – Chapter 6 Difficulties on Theory
http://embryology.med.unsw.edu.au/pdf/O ... pecies.pdf
Darwin argues some of the difficulties experienced by his hypothesis. In this case the lack of transition fossils.

“These difficulties and objections may be classed under the following heads:-Firstly, why, if species have descended from other species by insensibly fine gradations, do we not everywhere see innumerable transitional forms? Why is not all nature in confusion instead of the species being, as we see them, well defined?…”

“Insensibly fine gradations” Does that sound like punctuated equilibrium or gradualism?

Chapter 4 (Natural selection)

“Natural selection will modify the structure of the young in relation to the parent, and of the parent in relation to the young. In social animals it will adapt the structure of each individual for the benefit of the community; if each in consequence profits by the selected change…”

Does this sound like he was advocating punctuated equilibrium?

Chapter 9 On the Imperfection of the Geological Record

“Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely graduated organic chain; and this, perhaps, is the most obvious and gravest objection which can be urged against my theory. The explanation lies, as I believe, in the extreme imperfection of the geological record.”

If Darwin was advocating punctuated equilibrium why would he argue on the “extreme imperfection of the geological record”.

Gould and Eldridge argue that it is the geological record that supports their hypothesis.

Oh and by the way I don’t use wikipedia so please don’t attribute sources to me that I don’t use. Now when I use the expression “evolutionary scientists” I mean precisely that. You know ones like Gould,EldridgeShapiro,Dawkins,Coyne,Orr,Fordyke, Collins, Lenski etc. I could of course go on.

What I don’t use is the expression “Scientific creationists" so you see you would be no good as a spokesman for me. :)

Who are these opponents of Gould who say this?


Well if you read Lenski’s own paper you need go no further than read the first three paragraphs after the Abstract to have your question answered.

Now as far as the evidence I have provided this forum with,may I will refer you to the following.
This particular thread from post 11 Thu Jun 17, 2010 11:32 pm
Also about17587-12.html from post 16 on Tue Aug 17, 2010 4:25 pm
Also about18849.html from post 6 Fri Jul 02, 2010 12:42 pm
Also about19377.html from post 4Mon Aug 30, 2010 6:47 pm

Happy reading :)
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Re: Experimental evidence for evolution

Postby Geokinkladze » Mon Sep 06, 2010 8:09 pm

jevg wrote:“Insensibly fine gradations” Does that sound like punctuated equilibrium or gradualism?


It sounds like what it is, insensibly fine gradations, i.e. small changes from one generation to the next. Which as I have pointed out previously is incorporated into punctuated equilibrium, or do you disagree?

In other words do you believe that punctuated equilibrium is mutually exclusive to gradualism? In fact I don't need to ask this because you have already said as much but I'm asking anyway. So question for you:

Q. Do you believe that Puntured Equilibrium is mutually exclusive to Gradualism?

jevg wrote:“Natural selection will modify the structure of the young in relation to the parent, and of the parent in relation to the young. In social animals it will adapt the structure of each individual for the benefit of the community; if each in consequence profits by the selected change…”

Does this sound like he was advocating punctuated equilibrium?


This paragraph was a set up for the next line which you so skillfully missed out so I've added it, and then if you read all together I'm sure you will agree (actually you probably won't) that Darwin was really emphasizing that species do not adapt for the benefit of other species as was being argued by some people at the time ie the reason bees exist is to benefit flowers.

“Natural selection will modify the structure of the young in relation to the parent, and of the parent in relation to the young. In social animals it will adapt the structure of each individual for the benefit of the community; if each in consequence profits by the selected change. What natural
selection cannot do, is to modify the structure of one species, without giving it any advantage, for
the good of another species;


This then begs a further question:

Q Do you believe that natural selection does not modify the structure of the young in relation to the parent, and of the parent in relation to the young?

jevg wrote:If Darwin was advocating punctuated equilibrium why would he argue on the “extreme imperfection of the geological record”.


Hold on, are you saying that because Darwin observed that the fossil record is extremely imperfect that he is not a punctured equilibriumist? Well there's the next question then:

Q. Do you believe that the fossil record is extremely imperfect?


jevg wrote:Oh and by the way I don’t use wikipedia so please don’t attribute sources to me that I don’t use.

I wouldn't and I didn't, I was in fact pointing out where I had used wikipedia.

jevg wrote:What I don’t use is the expression “Scientific creationists" so you see you would be no good as a spokesman for me.

I'm not trying to be your spokesman, just trying to uncover your true philosphophical viewpoint.

jevg wrote:
Who are these opponents of Gould who say this?


Well if you read Lenski’s own paper you need go no further than read the first three paragraphs after the Abstract to have your question answered.


I had done and I couldn't find anybody who said

jevg wrote: so it doesn’t depend on past accidents


but I could find the following:

Simon Conway Morris countered that natural selection constrains organisms to a relatively few highly adaptive options, so that ‘‘the evolutionary routes are many, but the destinations are limited’’. He and others point to numerous examples of convergent evolution as evidence that selection finds
the same adaptations despite the vagaries of history


I think the translation of Morris and others towards the Lenski experiment is this:

Run the experiment long enough and a new species of bacteria will eventually start using Citrate.


Anyway while were on the subject of Lenski, could we clear up a few more of your errors?

jevg wrote: They fed them glucose and citrate

Actually they didn't feed them Citrate, the glucose was there as the sole source of carbon and energy.

jevg wrote: The goal of the experiment was to try to force the E. coli to evolve in such a way that they could digest citrate, like some other bacteria can.

No that was not the goal of the experiment at all. You really haven't actually read Lenski have you? What you have been reading is someone elses version of it. Either that or your making your own interpretation up. I hope it's the former.

jevg wrote: The expectation was that if the E. coli did evolve into a form that could digest citrate, that new variety would flourish in the citrate-rich environment and drive the old variation to extinction.


There you go again, making stuff up. The appearance of the Citrate using bacteria was a complete surprise to Lenski's team. They weren't trying to breed a citrate using bacteria, but once it happened they went back and re-ran the experiments. Here's what they found (you would know this if you actually followed the experiments and understood them);

    The neutral mutation (which allowed for a historical contingency) came about around 20,000 generations (ok I acknowledge you've spotted this).
    The neutral mutation has to fix itself within the population, after this the next (random single step mutation) when it happened did so within 750-3700 generations.

jevg wrote: However, repeating the final stages of this experiment on samples preserved from earlier generations of the original population, before it developed the citrate-feeding capability, resulted in identical citrate-feeding populations, all of which emerged after the same total number of generations.


What !?! I don't like accusing people of blatantly lying so I'll say this to you Jevg, you have been badly misinformed.
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