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Theories - Origin of Life

Discussion of everything related to the Theory of Evolution.

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Postby LeoPol » Fri Apr 15, 2011 7:47 am

How have emerged and have become sensible ones membrane-ids, which for many billions of years ago, have built a peptide-nucleic super-technology - is an open question. But how do these membranoidy appeared on Earth - we can explore ...
http://translate.google.com/translate?h ... .agro.name
And the dream! http://spacenoology.agro.name/?page_id=4904
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Postby BDDVM » Fri Apr 15, 2011 7:55 pm

Leopol, I don't know if your post was nonsense before it was translated but it's certainly nonsense now.
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Re: Theories - Origin of Life

Postby scottie » Sat Apr 16, 2011 7:05 pm

BDDVM

Denominations
Let me try and explain.
(1) There is the modern Standard Theory of Evolution which essentially states .. well
here is a good description from:-
http://www.fossilmuseum.net/Evolution.htm

Evolution and the Tree of Life
The modern theory of evolution is based on two primary tenets:
All living things are related to one another to varying degrees through common decent (share common ancestors), have developed from other species, and all life forms have a single common ancestor.
The origin of a new species results from random heritable genetic mutations (changes), some of which are more likely to spread and persist in a gene pool than others. Mutations that result in an advantage to survive and reproduce are more likely to be retained and propagated than mutations that do not result in a survival to reproduce advantage.
The great Tree of Life is real. It is a phylogenetic tree representing the unique ancestral history of each and every creature. Darwin believed that all creatures on Earth might have originated from a single common ancestor so that each species through geological history fit somewhere in an overarching metaphorical tree;

(2) From Wikipedia ( I am always cautious about using wiki but in this case they have it about right.)
Punctuated equilibrium is a theory in evolutionary biology which proposes that most sexually reproducing species will experience little net evolutionary change for most of their geological history, remaining in an extended state called stasis. Punctuated equilibrium also proposes that stasis is broken up by rare and rapid events of branching speciation called cladogenesis. Cladogenesis is the process by which species split into two distinct species, rather than one species gradually transforming into another.
Punctuated equilibrium is commonly contrasted against the theory of phyletic gradualism, which states that evolution generally occurs uniformly and by the steady and gradual transformation of whole lineages (anagenesis). In this view, evolution is seen as generally smooth and continuous.
In 1972, paleontologists Niles Eldredge and Stephen Jay Gould published a landmark paper developing this theory and called it punctuated equilibria.[2] Their paper built upon Ernst Mayr's theory of geographic speciation,[3] I. Michael Lerner's theories of developmental and genetic homeostasis,[4] as well as their own empirical research.[5][6] Eldredge and Gould proposed that the degree of gradualism commonly attributed to Charles Darwin is virtually nonexistent in the fossil record, and that stasis dominates the history of most fossil species.
http://en.wikipedia.org/wiki/Punctuated_equilibrium

Two opposing views on one of the fundamental pillars of of Darwinian theory.

Another fundamental pillar of Darwinian theory is the notion of Common decent. (Tree of life) as explained above.
(3) Carl Woese and others like Craig Venter disagree fundamentally with this concept.
He describes this as “the doctrine of common decent” and is wrong. There is no tree of life, if any such analogy is to be used then a bush or forest would be more appropriate.

Again on one of the fundamental pillars of the standard theory there is disagreement.

So here briefly are three different theories but there are more.

I could relate Jim Shipiro's Natural Genetic Engineering view which he states is the third way between Creationism and Darwinism.
Or Simon Conway Morris who argues against Gould and Darwin in that evolution far from being quirky and unpredictable is essentially front loaded in that the evolutionary routes are many but the destinations are few.

Or Lynn Margolis... ….I think I had better leave it there in case everyone starts dozing off. :)

The reason I use the term denominations is because each theory has it's own doctrinal fundamentals and the fact that the adherents of one disagree with another, often with a vitriol that smacks of a sort of religious fervour, paints a picture for me.

Does evolution happen? It most certainly does and we have the evidence all around us.
What does that evidence show, well quite simply that all this evolution occurs within species.

Does it produce new species. Well I am waiting for anyone to demonstrate that with evidence and not speculation.

If anyone believes that speciation occurs through evolution by whatever formal theory, I have no problem with that.

It becomes a problem when that belief system is presented a fact.

I hope this clears up some of my points.

btw my comment about birds having a keen sense of taste is actually a quote from the Orlando's sea world website, I gave the link in my response to canolan, here it is again
http://www.seaworld.org/animal-info/inf ... senses.htm
Scroll down to Taste.

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Re:

Postby LeoPol » Sat Apr 16, 2011 8:38 pm

BDDVM wrote:Leopol, I don't know if your post was nonsense before it was translated but it's certainly nonsense now.


But other forum participants such translation is acceptable. "Polypeptide-nucleic nano-technology that underpins life on Earth - is ancient and efficient engineering. Multicellularity as an engineering design, just not as ancient."

I am a molecular geneticist, in addition, cytology in oncology. These conclusions are based on extensive experience in the Biological Institute.
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Re: Theories - Origin of Life

Postby scottie » Sun Apr 17, 2011 12:06 am

canolan

Well I may be wrong, but you have chosen a rather curious way to try to demonstrate your point.
I assume that of the “countless ways” to make two systems communicate and do it more safely one way would be to take a lesson from the snake ie locate the olfactory system in the mouth and make the tongue more sensitive.

You are aware are you not that the snake requires two senses of smell. One which involves the olfactory system located in the nose (not in the mouth as you have stated) and the other, the vomeronasal system that is associated with the constantly flicking tongue, which incidentally has no taste buds.This system is used in conjunction with the standard sense of smell possibly because the their rate of breathing does not allow the air to enter the nostrils fast enough to collect and translate scent particles in the normal way.

I would suggest that just a cursory examination of the needs of the two (humans and snakes) explains the two different systems and in my subjective opinion as opposed to your subjective opinion there is nothing “clunky” about either system.

However a far more fundamental point is at issue here.
You contend that the human sense of taste and smell evolved from preexisting structures that constrained them so much that a better design was not possible.

This raises two questions which I would appreciate you clarify
(1)From what lineages were these preexisting structures inherited?
(2)Can you provide the evidence for this please.

Finally you are clearly using a designed piece of software to demonstrate how something can't be designed because of design flaws. Am I right in assuming that this is the logic you are using to support you point, or am I missing a trick somewhere?

I have read Stephen Gould quite extensively, I would be happy to discuss his book(s) later if you wish.

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Re: Theories - Origin of Life

Postby scottie » Sun Apr 17, 2011 12:17 am

sorry canalon for spelling error

Not sure if posts can be edited for such mistakes
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Postby BDDVM » Sun Apr 17, 2011 1:25 am

Scotty,
Where you see differences in doctrinal fundamentals I see differences in detail. The arguements you site are akin to whether ionic or doric collumns are better. They are both collumns.
As for the vitreol and furvor you see in science are simply explained by the fact that humans are involved. Science is not devoid of bias but we make an effort to understand and mitigate those biases.
If you espouse faith as a tool toward fact I would suggest it's a tool with a very poor record.
After all, If you have enough faith you can believe anything.
As for my current understanding ( I avoid having beliefs, they are too hard to abandon when better evidence is presented) I see the tree of life as being very likely. One or a small handful of projenitors.
Punctuated equalibrium vs gradualism? It depends on the situation(niche).
Some situations cause fast change, some, don't change and some change gradually.
If you want to get a feel for real time evolutionary change I would suggest you read "The Beak of The Finch" by Jonathan Weiner
about the Grants study of Finches in The Galopagos.
It's not overly technical so the main theme comes through well.
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Re: Theories - Origin of Life

Postby scottie » Tue Apr 19, 2011 11:04 pm

BDDVM
Sorry for the delay but I am a bit tied up on other matters and have not been able to get back to my computer.

I will get back and respond tomorrow just as soon as I am free.
I appreciate this discussion very much because a respectful exchange of ideas and thoughts is always refreshing.

I will try to explain my point of view in order not to be misunderstood.

To me science and faith are two different concepts.
Science is limited to natural laws and any explanation must be confined within the limits of known natural laws.

Now Darwin proposed a theory or model that explained the Origin of Species. Now because it could be tested within the confines of Natural laws it is a valid scientific theory simply because it can be falsified.
He introduced the concept of Natural selection acting on random variation on given species that over time gradually change into another and different species. So this process can be tested and indeed has and continues to be.

If I state that species arrived by an act(s) of a God i.e. by supernatural means then that statement cannot be tested in a scientific way and therefore cannot be regarded as a scientific theory,
That is a belief system that I would be adhering to.

Belief can and often is simply blind and doesn't require evidence.

Faith on the other hand is something more than belief.
Faith should be based on evidence which maybe directly observed or by strong circumstantial evidence.
In a court for example a person may be convicted of murder although no one actually witnessed the crime but other evidence allows the jury to conclude that the crime was committed by that person.

So faith and belief are in themselves two different concepts although they are very very often used as synonyms.

Now I don't argue from a point of belief, nor indeed in matters of science do I argue from a point of faith.

What I will try and explain tomorrow is why I argue the way I do, not from a standpoint of belief or faith but from the standpoint of corroborating evidence, because this is a science forum.
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Re: Theories - Origin of Life

Postby canalon » Tue Apr 19, 2011 11:08 pm

scottie wrote:Now I don't argue from a point of belief, nor indeed in matters of science do I argue from a point of faith.

What I will try and explain tomorrow is why I argue the way I do, not from a standpoint of belief or faith but from the standpoint of corroborating evidence, because this is a science forum.


Now I prepare my self the popcorn and will settle in the seat and I am waiting impatiently to see the evidence for the existence for god and its implication in creation being presented. The trailer is good, I hope that the main feature will be up to the task. 8)
Patrick

Science has proof without any certainty. Creationists have certainty without
any proof. (Ashley Montague)
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Postby BDDVM » Tue Apr 19, 2011 11:39 pm

Scotty,
I think your definitions of faith and belief might be peculiar to you. In common usage faith refers to beliefs instilled by authority without evidence beyond the word of the authority. As a recovering catholic I can recount first hand the "because God said so" argument. Belief simply refers to ones understanding of reality regardless of how it came about.
To argue another point, I feel that theology is a fine topic for science.
The scientific process is the best tool we have to get to the truth. It isn't perfect but it's the best we have come up with yet.
Besides, it was the creationists who claimed that they were scientists.
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Re: Theories - Origin of Life

Postby scottie » Fri Apr 22, 2011 12:25 pm

Sorry for the delay but life is a bit hectic at the moment.

Ok
The theories of evolution attempt to describe the process by which species arrive.

Now because we are discussing process it is important to understand which process you are subscribing to, as there are various differing theories.

Hence my question as to which theory (process)you subscribe to.
Since you have refrained to address the question I will assume you subscribe to the
first of my descriptions I presented you with, i.e. the Darwinian concept of decent from a single common ancestor. This process of decent being by random mutations within the genetic mechanism and sifted by Natural selection. The whole process operates by the gradual accumulation of changes to produce new species.
(If I am wrong please correct me.)

Let me try and explain my understanding.
The cell is a highly regulated biological information processing system that produces function. By it’s very nature this system is governed by the laws of information theory. Three essential ingredients are required.
A coding system using symbols --- the cell has that
A decoding system recognising those symbols ---- the cell has that
And a channel for communication--- the cell has that.

This system uses the physical laws (physics, chemistry etc) to provide this function.

Now you appear to have indicated that I concentrate on “doctrine” and you on detail.
I am at a loss to understand how you could draw that conclusion, however lets look at some detail of the cell.

In order for a eukaryotic organism to develop and form, cell division takes place.
There are various stages to this cell cycle.

The cell contains several control mechanisms that are referred to as checkpoints and these come into action at various stages of the cycle.

These control mechanisms by their very nature check and verify whether the processes that led up to the particular stage are accurately completed before allowing progression to the next stage.

An important function of many checkpoints is to assess DNA damage.
When damage is found, the checkpoint uses a signal mechanism either to stall the cell cycle until repairs are made or, if repairs cannot be made, to target the cell for destruction via another mechanism.

Now this is but a very small part of the control the cell exercises before it divides, but it is enough to reveal some fundamental points.

(1) DNA damage (which is at the heart of Darwinian theory for speciation) is identified at virtually every stage in cell division and it is either repaired or it is passed on for destruction, except in some special situations. This demonstrates that decisions are being made by the cell, by way of biological algorithms, to eliminate the damage. Damage in the cell is regarded as noise in an information processing system which of course the cell is. Now engineers devote great time and effort to eliminate or at least reduce noise in any system, simply because noise corrupts information. Is it not strange that the very thing that corrupts information is being regarded as one of the fundamental driving forces of evolutional theory, of whatever shade?

(2) Decision points or nodes like this, and there are several in the cell, where the process is directed one way or another cannot come about by chance because natural laws do not work this way. Laws are discovered because endless amounts of dynamic data can be reduced down into mathematical formula, and the reason this can be done is because the behaviour pattern being examined is highly ordered, fixed, and low in information. However degrees of freedom is exactly what is required by the cell systems in living organisms. So not even some yet undiscovered law can address this issue.

(3) This is simply why I recognise design in biology. It has nothing to do with doctrine or belief or faith. It is about science.


Now the argument has been put forward that bad design is evidence of randomness.
However bad design can only be an example of bad design.

Randomness cannot produce the prescriptive design we see in the cell. It is not scientifically possible.

The analogy of the Panda’s Thumb sadly is the perpetuation of this myth.

In 1978 Stephen Gould proposed this as an example of bad design to support his view that bad design is evidence of randomness. However he did not fully understand what he was examining, because he did not have the technology available to examine thoroughly.
Some 20 years later however around 1998 and as technology had greatly advanced, his idea was put to the test and was found wanting.
You will find the paper in Nature (peer reviewed of course) here
http://www.nature.com/nature/journal/v3 ... 309a0.html
This is how the abstract reads
“The way in which the giant panda, Ailuropoda melanoleuca, uses the radial sesamoid bone — its 'pseudo-thumb' — for grasping makes it one of the most extraordinary manipulation systems in mammalian evolution1, 2, 3, 4, 5. The bone has been reported to function as an active manipulator, enabling the panda to grasp bamboo stems between the bone and the opposing palm2,6, 7, 8. We have used computed tomography, magnetic resonance imaging (MRI) and related techniques to analyse a panda hand. The three-dimensional images we obtained indicate that the radial sesamoid bone cannot move independently of its articulated bones, as has been suggested1, 2, 3, but rather acts as part of a functional unit of manipulation. The radial sesamoid bone and the accessory carpal bone form a double pincer-like apparatus in the medial and lateral sides of the hand, respectively, enabling the panda to manipulate objects with great dexterity. (my emphasis)”

The panda has specific needs (stripping bark off bamboo for some 12 hours a day is not an activity normally associated with other mammals)
This is good design and therefore hardly an icon of bad design.
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Re: Theories - Origin of Life

Postby scottie » Fri Apr 22, 2011 6:10 pm

Canalon

By the way I am not trying to prove the existence of anything except design.
You should not presume to ascribe motives to me. Don't demonstrate fear of discussing science by trying to turn it towards some form of religion.

Now how much pop corn do you have?
Why not put it to good use and investigate evidences of Good design in Nature that science learns from.

As the Whale turns
http://www.naturalhistorymag.com/biomec ... hale-turns
Read the whole article you will learn something but here is a taster.
“The Humpback Whale….
And underwater, the animals move with such astonishing agility that they’ve caught the attention of naval engineers, who hope that some of the principles learned from the study of the humpback’s flippers can be applied to designing submersible vehicles of unprecedented maneuverability.”


How about Heat exchanger Design
Here is an acknowledgement from by Arthur P Fraas in his book “Heat Exchanger Design”
You will find some extracts here
http://books.google.com/books?id=rdtKXC ... &q&f=false

On page 2 he says
“ It is interesting to note that nature presents us with one of the best examples of a highly efficient counterflow system in the blood vessel system in the legs of wading birds such as herons. The warm blood moving outward into the leg from the heart is passed through a system of tiny parallel blood vessels that are interspersed in checkerboard fashion with similar vessels returning from the extremity of the birds leg, giving one of the worlds most effective regenerative heat exchangers. The heat transfer performance of this blood vessel configuration is so good that the warm blood is cooled almost to the ambient temperature before reaching the region immersed in cold water, and thus the bird loses relatively little heat through the skin of it’s leg.”

These are but a couple of examples of design that scientists and engineers look to, when designing their machines. I could go on about the seagull’s wings, the low drag design of the boxfish that the concept car imitates, the shock-absorbing properties of the abalone shells, or the sonar in dolphins etc etc.

So many good ideas have come from nature that researchers have established a database that already catalogs thousands of different biological systems so that scientists can search this database to find natural solutions to their design problems.

http://www.economist.com/node/4031083?story_id=4031083

The June 9th 2005 edition of the Economist reports .. in part

“This process is entirely the wrong way round, says Dr Vincent. “To be effective, biomimetics should be providing examples of suitable technologies from biology which fulfil the requirements of a particular engineering problem,” he explains. That is why he and his colleagues, with funding from Britain's Engineering and Physical Sciences Research Council, have spent the past three years building a database of biological tricks which engineers will be able to access to find natural solutions to their design problems. A search of the database with the keyword “propulsion”, for example, produces a range of propulsion mechanisms used by jellyfish, frogs and crustaceans.”

Now if Bad design is evidence of randomness as you argue to then do tell
What is Good design evidence of?


I would say Non-randomness, wouldn’t you or would your theology prevent that conclusion?

Got any pop corn left? :)
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