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Theories - Origin of Life

Discussion of everything related to the Theory of Evolution.

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Postby BDDVM » Fri Apr 22, 2011 7:30 pm

Scottie,
Bad design is not evidence of randomness, it's evidence of design by a non omnicient, non omnipotent designer.Its evidence of a design process that has limits in how perfect it can be because it has to start with designs that are preexisting.
As for randomness not producing the designs we see in the cell. You seem to forget that only part of the process of evolution is random.
The selection process brutally removes all organisms that don't fit into an available niche.
An analogy, Obviously it's impossible for an industrial paint sprayer to paint the greek alphabet in 1'' letters on a wall. ( the sprayer paints only a blast of paint 3ft wide) Unless you first mask off all of the wall that isn't shaped like the greek alphabet. This makes a stencel that removes all the paint that doesn't fit in the niche. Random paint, non random niche. In life the niche tends to be constantly changeing as well as the organisms that are fit in it.
Variation (Random changes to current design) Selection (non random removal of designs that aren't fitting) Reproduction. repeat a few quadrillion times.

Now if you walk into a room and see the greek alphabet on the wall in 1 inch letters you can't say that a random process wasn't involved.
You might say it appears that someone painted it on with a brush or it might have been done with a stensel. To determine which it was just look closely. A brush will leave brush strokes. The sprayer will show stippled paint and overspray.
We are just saying that the often half baked bodged together designs we see in nature look like paint sprayer evidence not masterful brushstrokes.
(awesome metaphore if I do say so myself)
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Re: Theories - Origin of Life

Postby scottie » Wed Apr 27, 2011 11:06 pm

BDDVM
Sorry for the delay. I have been away for a few days.

I think you have misunderstood me.
It’s not me that is suggesting bad design is evidence of randomness.
This idea has been put out by canalon and you appear to agree with him.

I was merely responding to his assertion. He appears not to answer any questions his assertions raise. So they are coming over as statements of doctrine, and I get very suspicious of doctrinaire pronouncements, because they invariably lack evidence or logic.

When you say

“As for randomness not producing the designs we see in the cell. You seem to forget that only part of the process of evolution is random.”


With respect there is nothing random at all about the cell process. I have explained, and any text book or peer reviewed paper will concur that as a fact.

More than that I have also explained that any mistakes in copying are corrected before cell division takes place.

Random mutations cannot produce the feedback processes we see in the cell. If you say they do then surely it is incumbent on you to show evidence of that.

I am arguing that only design accounts for what we observe in the cell. You keep presuming that I am trying to bring religion into science.

Why?

After all my 13 year old grandson studies Design Technology in class and it is not a religious school.
Design is a perfectly valid scientific topic.

Is it your contention that unless the cell arrived by random mutations of the genetic material followed by natural selection, any other explanation must be religiously based.

Could you please clarify your position.
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Postby BDDVM » Thu Apr 28, 2011 12:41 am

First all mutations are not repaired, most are repaired, a few kill the cell and an extremely tiny fraction give the cell something it didn't have before.
It might be your use of the term design that is confusing me. When you say design do you imply a designer that is an entity?
The process of evolution is a design process without an entity guiding it.
This design process has actually been used recently to design robots and some software.
Random processes (Mutation) can result in feedback systems in cells. A well studied system is called the lac operon. It's a bacterial system for regulating when certain DNA segments are expressed and when they aren't. Because it is such a simple system it takes less imagination to see how it evolved.
It is not my contention that designer based explainations are religeously based. It is however consistent with all my previous experience.
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Re: Theories - Origin of Life

Postby scottie » Sat Apr 30, 2011 4:42 pm

First all mutations are not repaired, most are repaired, a few kill the cell


Yes the cell proof reading catches most errors and corrects them. Only rarely, as in such cases as in cancer will a new mutation lead to a phenotype so dramatic that we will realise that something new has happened. Note of course that the new mutation is invariably deleterious. At best these mutations are neutral.

Is there any mutation observed that has resulted in beneficial phenotypic change? If so
Could you please point me to any peer reviewed paper to confirm that.

btw. please think for a moment, do natural laws proof read for errors?

When you say design do you imply a designer that is an entity?


The best way for me to answer that is by referring to the lac operon that you cite
as an example this way
Because it is such a simple system it takes less imagination to see how it evolved.


Firstly to suggest that this is a simple system so that less imagination is required, I find quite astonishing.
May I suggest you review the actual operation of this lac operon. Here is a good visual of what it does and how.

http://highered.mcgraw-hill.com/olc/dl/120080/bio27.swf

If bacteria encounter two sugars, e.g. glucose and lactose, then E. coli cells will keep the lac operon turned down as long as glucose is present. It is not appropriate if glucose is still available, because E. coli cells metabolize glucose more easily than lactose, it would therefore be wasteful in energy for them to activate the lac operon in the presence of glucose.

This operon is therefore described as a combination of switches, and that is exactly what it is.
Now switches are decision nodes that allow a process to go one way or another depending on what the circumstances require.

There is nothing simple about this system. It requires informational signalling from both within and without the cell. That symbolic signalling determines which switch sequence to turn on or off and when, along with energy saving decisions

We see algorithmic commands such as START, STOP, AND, OR, ELSE and so on
in operation. These things are never seen in natural laws.

We still don’t understand how these genes come to grouped in the way they are on the genome except that this grouping is definitely non random, as a clear understanding of the operon shows.

So this is not haphazard design at work. This is clearly design to cater for different energy sources, functioning with a definite purpose in mind.

It is definitely not a simple system

However by way of comparison lets consider the circular settings of the large upright stones at Stonehenge in England. Some of these massive stones have equally massive cross member stones perched on top.

How did this massive configuration come about?
Does anyone believe that is was the result of natural forces?
And why not ?--- after all we have seen for ourselves how in the recent tsunami heavy vehicles being perched on top of buildings in a matter of minutes demonstrating that natural forces do have the capacity to deposit heavy structures on top of others.

But we don’t believe these came about naturally, because we recognise functional design in the configuration. It is simple and it could even be argued that it is not a very good design. Still we attribute it to an outside agency. We don’t know who that outside agency was but yet in the science of archaeology it is carefully studied and accepted that outside agency is definitely involved.

Now can science identify a designer? Well the simple answer is that science cannot.
A historical record can, but that is not a scientific topic.
Also a historical record may or may not be true.

Now

The Churches of Christendom claim that their Triune creator did it.
The Islamic churches claim that their creator did it.
The Hindus claim their creator(s) did it.
The Church of the Flying Spaghetti Monster claims their creator did it, and so on.

These are simply belief systems and therefore cannot be falsifiable in the scientific sense and therefore are not subjects for scientific debate, even though many try to make it so.

However the creator we call decent with modification by random mutations/natural selection claims to be scientific and not a belief system.
Therefore it must be, by it’s very definition, falsifiable.

Please ask yourself this question
Why are there so many different theories about the origin of species i.e. macro evolution?

The answer must be because each theory is simply not fitting the evidence, an essential requirement of any scientific theory.

Just about every facet of evolutionary theory is being falsified time and time again.
This is not a dogmatic statement because the peer-reviewed material is abundant showing this to be so. The interesting point about this material is that most of it is coming from the evolutionary community itself.

I am quite happy to point you to any necessary papers to confirm my argument.
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Postby BDDVM » Sat Apr 30, 2011 11:10 pm

First, falsefiable doesn't mean false. It means a theory that can be tested. If I say, Santa Claus lives at the North Pole. That is falsefiable. You just have to look. Anyone who wants to can look for themselves.
If you say, God just talked to me and told me that I am the new Pope therefore all that cool stuff in the Vatican belongs to me. That isn't falsefiable. God only talks to me, sorry.
You appear to have a common problem among creationists. A very limited imagination. I have little choice but to assume you are in the creationist mindset as you dodged my question about an entity designer.
The lac operon has only a handful of parts, non of which will mean instant death if it's missing. Once the bits of the system finally get together in the same E coli it gives a very nice advantage of not wasting recources on lactose metabolic machinery when it's not needed. It's just a few mutations. No need to get God involved. Just give the little beasties some time.
I've often wondered why God tells his chosen people that they are chosen but neglects to tell everyone else.
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Postby BDDVM » Sat Apr 30, 2011 11:30 pm

As for Origen of species. First you have to realise that the concept of species itself is a human construct. There, I said it, I think it's kind of a red herring. Many will argue with this. That's fine, It doesn't mean that we need a God to explain life. It's another of those detail arguments that some would use to invalidate all of Biology.
As for just about every aspect of evolutionary theory being falsefied, Well to put it cordially, Male Bovid Feces.
If you want to see selection,reproduction, mutation happen in a short period of time. You can do it yourself. Petri dish, bacterial culture, pick an antibiotic, apply it to the plate for a while. What you will see is a large percentage of the initial population die off and are replaced by a new population of bacteria that are more resistant to the antibiotic in question. (unfortunately they will likely also get resistant to several other antibiotics due to how a lot of bacteria share resistance factors).
If you don't believe this happens I would invite you to take good old fashioned penicillin for your next staph infection.
As you appear to have about the average amount of preexisting bias about this experiments outcome I would suggest you team up with someone who will be able to counter your conscious and unconscious biases with appropriate controls. (scientific method)
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Re: Theories - Origin of Life

Postby scottie » Mon May 02, 2011 4:05 pm

Thank you for your two posts
Let me start by responding to the first.

First, falsefiable doesn't mean false. It means a theory that can be tested


You are actually making my point for me.
For a theory to be considered scientific it must be falsifiable and if evidence is produced to rebut the theory then the theory must be abandoned or at least modified.

However when I present valid scientific arguments that the theory does not and indeed cannot explain, you launch into anti-religious rhetoric. You don’t even know what my belief system is or even if I have one. I have no idea what all this "chosen people" rhetoric is all about

So can we just stick to science please.

You stated that the lac operon is a simple example of evolution.

In fairness you have tried to expand upon that by adding

The lac operon has only a handful of parts, non of which will mean instant death if it's missing. Once the bits of the system finally get together in the same E coli it gives a very nice advantage of not wasting recources on lactose metabolic machinery when it's not needed. It's just a few mutations. No need to get God involved. Just give the little beasties some time.


Firstly, and with great respect, that does not even begin to explain how some pre existing structure whatever it may have been, came to be, what is known as the lac operon.

It’s just a few mutations you say. Is that really the best “scientific” explanation you can come up with?
Simply stating that a few mutations did it is frankly no different the “god did it argument”.

Secondly lac operon is evidence of the system's built in redundancy that enables E coli to exist on different energy sources.
Redundancy in any system is evidence of forward planning and which is of course evidence of design.

Random mutation by their very nature cannot forward plan.

Another biological fact you need to appreciate is that mutations invariably are deleterious, at best neutral, to the organism. There has been enough experimental evidence over the past at least 60 or so years, to establish that point.

If you wish I will point you some of the research that has been carried out.
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Postby Darby » Mon May 02, 2011 4:40 pm

Beneficial mutations -

http://www.ncbi.nlm.nih.gov/pubmed/16396175

http://www.csun.edu/~sd51881/readings/E ... l_1996.pdf

http://www.jstor.org/pss/2411188

How duplication and preservation increases the chances of beneficial mutation while preserving original function (something that would look to the uneducated like "forward planning") -

http://www.ncbi.nlm.nih.gov/pmc/article ... 101175.pdf

That took all of 5 minutes searching.
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Re: Theories - Origin of Life

Postby scottie » Mon May 02, 2011 7:10 pm

Thanks Darby

At last someone has decided to engage in some real science.
I was beginning to wonder if the anti-religious flow towards me was ever going to change to genuine science. So once again thanks

Firstly this discussion is in relation to origin of species not the evolution within species which no one that I am aware of disputes.
As I understand it even the creationists recognise this fact.

You claim it took you about 5 minutes to locate these papers, but did it take you 5 minutes to actually read them.

Please point me to any one of them that shows how a new species has emerged.
All these mutations observed did not produce any new species.

Did any of the beneficial mutations produce phenotypic change required for a new species?
I think you already know the answer to that.

Two of these papers includes the very good work of Richard Lenski with some collegues.
http://www.ncbi.nlm.nih.gov/pubmed/16396175
and
http://www.csun.edu/~sd51881/readings/E ... l_1996.pdf

Now the latter is particularly interesting, however you have chosen a more dated paper of Lenski.

This paper from 1996 refers to his experiment with E.coli, but what is pertinent is that the paper in it’s opening paragraph refers to the Stephens Gould / Niles Eldridge theory of punctuated equilibriam to explain the origin of species. They developed this theory in response to the fossil record in Cambrian strata that even Darwin himself acknowledged was a real problem for his theory.

Now I would suggest you read his more recent paper(2008) relating to this experiment that was conducted over more than 22 years and involving some 600,000 generations of E.coli growth in 12 population groups.
http://myxo.css.msu.edu/lenski/pdf/2008 ... t%20al.pdf

And what appears to be his concluding paper on this experiment (2011)
http://www.microbemagazine.org/images/s ... 000030.pdf

In the 2008 paper in his concluding comments he asks the question
“Will the Cit and Cit lineages eventually become distinct species?”

Clearly up to that point the answer was no.

Lets move on to 2011 and his accolade to Darwin
Lets again go to his concluding comments relation to his long experiment to show how Darwin’s theory of the origin Species was being supported by his experoiments.
After all these long years of painstaking experimenting he enters what he terms his midlife crisis.
“From Bacteria to Computers,and Back Again
Perhaps it was a midlife crisis: my bacteria were slowing down, and I was looking for some new action. So I had an affair—one that continues today, though with slightly less feverish intensity—with some artificial creatures. Avidians are computer programs that copy their own genomes, and they live in a virtual world that exists inside a computer.”

No new species then.
So he has given up on the real world and goes to a virtual reality.

Your third citation
http://www.jstor.org/pss/2411188
far from showing that random mutations cause new species attempts to demonstrate that these random mutations tend more to immunise species from extinction.. As I read it therefore stasis rather than evolution in the order of the day.

Finally your last citation is simply a hypothesis.
I don’t see how using one hypothesis to support another can be classed as empirical evidence.
I think you will find that things have moved on since 1998

But thanks for your response.
Much appreciated.
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Postby BDDVM » Mon May 02, 2011 11:01 pm

Scotty,
In order to see new species you must do a few things. First define species, relatively easy for sexually reproducing organisms, very difficult for bacteria. Bacteria would be nice because of the relatively short time per generation but the definition problem makes this a non starter.
The best place to look would likely be African rift lake Cichlids. They have been spinning off new species at a very fast rate. Still it's going to likely take 10's of years.
Another place to look is in a very small system like Darwins finches in the Galopago islands. "The Beak of The Finch" chronicles the Grants' herculean multiyear study of these finches separating into 3 species during bad years and hybridizing back into one big genetic blob during high rainfall years. It's quite readable. They actually captured, measured, and followed every single bird on the Island for many years.
I'm still curious about your version of a designer. Please describe, I can't argue with your beliefs/biases if you won't define them. Are you ashamed of your beliefs? Incidentally, I find that saying your biases out load helps to see alternatives more clearly. It seems to help take some of the emotion out.
The reason I don't site peer revieved papers in this forum is that I agree with Albert Einstien when he said (aproximately) You can't say you understand a theory until you can explain it to your grandmother.
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Re: Theories - Origin of Life

Postby scottie » Fri May 06, 2011 10:21 pm

BDDVM
Sorry once again for the delay in responding. I have a very busy life and it does take me away from the forum often for days at a time. I have the weekend ahead so can devote more time to this discussion.

First define species, relatively easy for sexually reproducing organisms, very difficult for bacteria. Bacteria would be nice because of the relatively short time per generation but the definition problem makes this a non starter.


You are right about the need to define species.
Now I can only rely on biologists who provide that definition.
As you say with sexually producing organisms it is fairly well defined.
In the case of bacteria it could perhaps be more subjective.

However I can only take on board what biologists themselves say.
When Richard Lenski who is (was) in the forefront of bacteria investigation in connection with the evolutionary process says quite clearly that no new species had emerged in the course of his investigation, he clearly had a definition in mind.

The E.coli he started with was still E.coli when he concluded.

Another place to look is in a very small system like Darwins finches in the Galopago islands. "The Beak of The Finch" chronicles the Grants' herculean multiyear study of these finches separating into 3 species during bad years and hybridizing back into one big genetic blob during high rainfall years. It's quite readable. They actually captured, measured, and followed every single bird on the Island for many years.


Now I am familiar with the Grants work.
As far as I am aware all the finches they were studying are sexually reproducing and able to reproduce with each other.
Am I correct?

So,are you saying that finches with different size beaks are now being regarded as different species. Is that correct?

This is how this forum defines species

Species
Definition
noun, singular or plural: species
(taxonomy)
(1) The lowest taxonomic rank, and the most basic unit or category of biological classification.
(2) An individual belonging to a group of organisms (or the entire group itself) having common characteristics and (usually) are capable of mating with one another.

Supplement
A species is given a two-part name: the generic name and the specific name (or specific epithet). For example, Allium cepa (commonly known as onion)
http://www.biology-online.org/dictionary/Species


Now according to this definition are all the finches, that the Grants or indeed Darwin himself studied, of the same species or not?

What you are mistakenly doing is noting variation within a given species depending on environmental conditions and promoting it as evidence of one species changing into another.

The finches still remained finches.
Lenski’s E.coli bacteria still remained E.coli bacteria.

I'm still curious about your version of a designer. Please describe


Natural Laws can and do produce design. A good example of this is the snowflake.
This site describes nicely how the design in snowflakes is produced.
http://chemistry.about.com/od/molecules ... wflake.htm

So one “version of a designer” is Natural Laws and as the site above shows this design can be explained scientifically.

There is another type of design, for example the cell. The Design clearly seen in it’s operation cannot be explained by natural laws alone. Natural laws are in operation but are controlled by what are referred to as biological algorithms.

Algorithms by their very nature are the product of an outside agency.
So the question is, what is that outside agency?
This is a question that science is simply unable to answer because analytical science can only describe natural phenomena.

So I have two “versions of a designer”. One science can describe and the other science cannot describe.

Now regarding the latter a description of this outside agency must naturally be a matter of belief and not science. That belief can be regarded as a religion or philosophy and therefore cannot be analysed by the scientific method.

Let me remind you that this discussion is about a scientific theory(s).

Now I can understand why you appear to want to move this debate on to belief systems because on a scientific basis the argument for species change (origin) by natural phenomena is being lost.

All the arguments you are putting forward are based on a philosophical approach and not as I am arguing, a scientific one.
Some would regard that as a religious approach.

The reality is, you don’t need to know what I believe, to show that what I state is scientifically incorrect. All you have to do is produce the evidence that rebuts my statements.

The reason I don't site peer revieved papers in this forum is that I agree with Albert Einstien when he said (aproximately) You can't say you understand a theory until you can explain it to your grandmother.


So please tell, what are you doing making statements you claim are based on science and in a scientific forum if you are not prepared to support them with any recognised scientific evidence. (Although once again you contradict yourself because you refer to the Grant studies of finches)

btw The standard theory i.e. "decent from a common ancestor by random mutation and natural selection" is quite a simple theory and one that my grandson understands. Not sure about my grandmother!

If something is factual you will be able to show it with evidence, if you cannot then it is a belief .
Why not just admit that what you have been arguing is based on a belief system.
That would be a consistent way of presenting your point.
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Postby BDDVM » Sat May 07, 2011 12:11 am

New species created in lab. May 3 issue Proceedings of National Acadamy of Sciences.
I do not agree that Religeous/ Phylosophical beliefs are beyond the reach of science. If it comes out of someones mouth it's biased BS until the scientific process has been applied. Even then look at it a couple thousand more times.
I can't disprove or prove your beliefs if you refuse to tell me what they are. Why? are you ashamed? Worried that you might have to rethink your world view?
This is the strongest, most insideous bias there is. Being emotionally invested in your theory.
To test for this bias, simply immagine how you would feel if someone were to prove to you that your beliefs are wrong.
I know , I know, there is no way to disprove the existence of a deity.
But hypothetically, Say a giant intergallactic spaceship arrived and the inhabitants mentioned that they dropped off some bacteria here 3 billion years ago and were just stopping by to see how things were going.
How would you feel?
The most biased statement ever. "I'm not biased, you are."
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