[_ Old Earth _] How well do you actually know The Theory of Evolution?

[Milk-Drops]

As opposed to Divine creation?

Divine Creation doesn't have a model that can demonstrate how it works. Its a concept taken on faith that God created everything in a specific way. If that is something you believe then, ok.

Since the universe is perfectly designed

Perfection implies that there are ways inwhich the universe could be differnt. In what ways is the universe perfect as opposed to imperfect? How is this perfection gauged?

and nothing happens by "chance" in the universe -- the Law of Cause and Effect --

I don't think you are aware of a mathematical concept called game theory. In Game theory there is always a small percentage of chaos due to a massive amount of factors. You bring up cause and effect, but with cause and effect its understood that for every action there is an equal reaction. That doesn't mean there isn't any chance involved. For instance, I can drop a ball and I know that the kinetic force from the ball will cause it to bounce due to the acceleration of the ball towards a surface caused by gravity. However, there are a ton of mathematical variables. For instance the ball could bounce left or right, or could bounce up then come back down until the kinetic energy reaches rest.

why would evolution make the most sense?

Well, the theory of evolution has nothing to do with the Universe for starters, that would be cosmology, while evolution is biology. Evolution makes the most sense in regards to track ancestry based on the most current understanding of genetics, morphology, eccology, and micro biology.

Even ardent evolutionists have given up on evolution. And here's the reason why:

1. Evolution is not accepted on the basis of scientific merit but as a religious preference by it's proponents.

False. Evolution is the tracking of Gene frequencies in populations. This is fully testable because of the Hardy Weinberg equation. For instance, when I was in college I had to oversee and take down data for lineages in specific plant species and track the geneotypes. I would first identify the Feneotype and then record through generations when mutations would crop up and isolate those mutations. In the wild, we can observe this when a species starts to split off due to isolation from a variety of different factors. Evolution occurs when Allele frequencies shift when the populations are issolated long enough from each other. Ghould noted though that this can happen rapidly if a large event seperates or causes a a flood of new specification.

2. Science has no more proven the doctrines of evolution than it has proven the existence of Peter Pan.

Evolution doesn't have any doctrines. It has mechanics that explain how it functions. Such as natural selection, genetics, population mechanics etc. I think this example is playing off of pop science/ popular acceptance and ignoring the core foundation of science, which is mathematics and mechanics.

3. Evolution is entirely a faith based religion; the evidences that have been fabricated to support it under the banner of science are entirely without mreit and falter under the most benign scrutiny.

Its not a religion because there is no diety, doctrine, dogma, place of worship, etc when it comes to the theory. Natural selection is a vastly studied and accepted mechanic because its easily observable. Genetics is vastly accepted and was founded by a Christian Monk, and the Human Genome was finally sequenced by an Evangelical Christian. Lineages have been mapped due to our understanding of genetics, and breeders use the concepts of Evolution to breed specific lines. The agricultural industry uses evolutionary mechanics to strengthen crop yield. Medicine uses the concepts for gene therapy, watching for family cases for specific disorders and disease, and for developing cures based on how viruses and other foreign organisms react to human genetics. Basically almost all of biology is unified by the theory of evolution because it helps to explain why its all related and how it functions.

4. It is a weak satanic deception standing in mortal opposition to the scriptures to undermine your chances for eternal salvation

The theory of Evolution has nothing to do with salvation or about undermining Christianity. Its simply an observation on natural mechanics and backed up through reams of research. Its not trying to destroy concepts.

For example, the Bible makes statements that things happened in a certain way, but it doesn't explain how these things happened. Science focuses on mechanics. The only discrepancy I really seen between science and religion is that sometimes the numbers don't always add up the same as the Biblical claims. Then again, this has nothing to do with salvation because salvation is based on the acceptance of Jesus Christ as the bridge from original sin to redemption with the Father. Evolution explains why cats are cute, small and fluffy.

I don't see the conflict. To be honest, Christianity has more problems coming from Philosophical arguments than it does from the natural sciences.

 

[rthom7]

I think it has more to do with there just being so much to understand and only so much time to actually teach it. Its the main reason why specialization and concentrations are so large once you expand outside of the 101 classes. For instance I mentioned that my specialty is on Anatomy and Phylogeny/Taxonomic classification. A microbiologist would be better suited for explaining the flagellum because a microbiologist is more versed in the minutia of cellular development and interaction. Especially among bacteria.

As I mentioned, this has a lot to do with specialization and concentration. The first example being about Code vs hardware. The professor doesn't really need to know much about overall computer functions on the mechanical level to create architecture for, say chipset function with the main processing power. He would just need to be able to do the math to figure out that specified needs for the chip set. Me and my cousin both have our degrees in the computer sciences but we difference in our fields of knowledge, where is I specialized in troubleshooting and repair work, he focused on coding. I don't know how to code In Java, HTML, or C/C+. He is next to useless when it comes to networking and configuration a workstation. I started picking up Networking as well and that is expanding outside his level even more. He is more on the design side, while I'm on the trades side.

Basic is awesome. I need to spend more time on the coding side of Compute science to fully grasp it. I know some kids that can run circles around me when it comes to setting up servers, so Its going to be an interesting world.

Sounds good, I'm relaxing for a minute since I just woke up from a nap. Helped family out when I got off work and will be helping them a little later today. I think I'm going to focus the videos on explaining the basics of evolution first so that anyone who has any fundamental problems will be able to see where I'm coming from, then I'll move on after questions are gathered. Talk to you later.

Perhaps you might like to help me out with this link....

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0069924

So our conclusions are perhaps three-fold. Firstly we have provided a strong quantitative test rejecting a non-evolutionary model that amino acid sequences do not become more similar as we go back in time. Secondly, we have raised the problems of the number of parameters required of some alternatives, and finally we shift the requirement onto doubters to provide testable alternatives. On this third aspect, there does appear to also be a similar reaction from climate change advocates on placing responsibilities onto doubters [32]. Other aspects of evolution have been tested [33]–[35] and further aspects of evolution could be tested, perhaps especially the ‘random’ nature of mutations that occur without regard for any ‘need’ of the organism, but this is outside the scope of the present work. Indeed, there has always been excellent support for evolution from fossils and comparative morphology, and molecular data enables this to be quantitative. We can say that, as yet, no features of genomes have yet been found that are not understandable by ‘causes now in operation’ [4].

It can be a bit hard reading such high levels of English

From the scientific point of view, there is no doubt that evolution has occurred, and there really were a continuous set of intermediates connecting individuals, populations, varieties, species, genera, families, etc. Nevertheless, as scientists we need to ensure that we have good quantitative tests available of all our favoured models. Given our results, we suggest that researchers need to be more assertive that evolution has both occurred, and continues to occur. It is essential that any person who does not accept the continuity of evolution puts forward alternative testable models. As we tell our first year undergraduates, ‘belief is the curse of the thinking class’.

So I hope I am not quote mining here, but they are saying using a computer simulation program such as PAML
that the evolution process can explain the random purpose changes of DNA 'GTAC' strands within the genome of any organism species.

http://web.mit.edu/6.891/www/lab/paml.html PAML may be useful if you are interested in the process of sequence evolution. The two main programs, baseml and codeml, implement a number of sophisticated models, which you can use to construt likelihood ratio tests of evolutionary hypotheses

So I had a look at how this program functions and works.

View attachment 5817
Here are there results in table 2

Can you explain what p(X2) means ? They gleefully explain probabilities of 10 to the -19 and 10 to the -23.
My understanding of chi square numbers this probability is zero, and in fact anything less than 0.5 is random showing no relationship between samples...

Am I right here ? Or is my understanding wrong ?

Thanks....Shalom

 

[Malachi]

Divine Creation doesn't have a model that can demonstrate how it works. Its a concept taken on faith that God created everything in a specific way. If that is something you believe then, ok.

Its a concept taken on faith because there is Divine Revelation. This is not blind faith but trust in the veracity of God who cannot lie.

Perfection implies that there are ways inwhich the universe could be differnt. In what ways is the universe perfect as opposed to imperfect? How is this perfection gauged?

As just one example of this perfection, study fractals:

A fractal is a natural phenomenon or a mathematical set that exhibits a repeating pattern that displays at every scale. If the replication is exactly the same at every scale, it is called a self-similar pattern. An example of this is the Menger Sponge. Fractals can also be nearly the same at different levels.

Who created this natural and mathematical phenomenon? Certainly not time and chance. So what's the alternative? Mathematics requires a mathematician, and for fractals a Divine Mathematician.

 

[Barbarian]

The usual creationist response to these findings (which have been known from various lineages studied individually) is that a "common designer" looks just like evolution. But it doesn't. Homologies, for example, like the bacterial flagellum and the Type IV secretory apparatus have no reason to be similarly constructed, but there they are. Legs on horses and wings of birds have no design reason to be homologous, but there they are.

My understanding of chi square numbers this probability is zero, and in fact anything less than 0.5 is random showing no relationship between samples...

The result of 0.5 means a 5% likelihood of the hypothesis being correct. Typically, the test will be for the 95th percentile, so if the text is 0.5 or below, the hypothesis is rejected. It doesn't mean a likelihood of 0.0.

 

[Milk-Drops]

Perhaps you might like to help me out with this link....

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0069924

So our conclusions are perhaps three-fold. Firstly we have provided a strong quantitative test rejecting a non-evolutionary model that amino acid sequences do not become more similar as we go back in time. Secondly, we have raised the problems of the number of parameters required of some alternatives, and finally we shift the requirement onto doubters to provide testable alternatives. On this third aspect, there does appear to also be a similar reaction from climate change advocates on placing responsibilities onto doubters [32]. Other aspects of evolution have been tested [33]–[35] and further aspects of evolution could be tested, perhaps especially the ‘random’ nature of mutations that occur without regard for any ‘need’ of the organism, but this is outside the scope of the present work. Indeed, there has always been excellent support for evolution from fossils and comparative morphology, and molecular data enables this to be quantitative. We can say that, as yet, no features of genomes have yet been found that are not understandable by ‘causes now in operation’ [4].

It can be a bit hard reading such high levels of English

From the scientific point of view, there is no doubt that evolution has occurred, and there really were a continuous set of intermediates connecting individuals, populations, varieties, species, genera, families, etc. Nevertheless, as scientists we need to ensure that we have good quantitative tests available of all our favoured models. Given our results, we suggest that researchers need to be more assertive that evolution has both occurred, and continues to occur. It is essential that any person who does not accept the continuity of evolution puts forward alternative testable models. As we tell our first year undergraduates, ‘belief is the curse of the thinking class’.

So I hope I am not quote mining here, but they are saying using a computer simulation program such as PAML
that the evolution process can explain the random purpose changes of DNA 'GTAC' strands within the genome of any organism species.

http://web.mit.edu/6.891/www/lab/paml.html PAML may be useful if you are interested in the process of sequence evolution. The two main programs, baseml and codeml, implement a number of sophisticated models, which you can use to construt likelihood ratio tests of evolutionary hypotheses

So I had a look at how this program functions and works.

View attachment 5817
Here are there results in table 2

Can you explain what p(X2) means ? They gleefully explain probabilities of 10 to the -19 and 10 to the -23.
My understanding of chi square numbers this probability is zero, and in fact anything less than 0.5 is random showing no relationship between samples...

Am I right here ? Or is my understanding wrong ?

Thanks....Shalom

I'll have to double check, but I think in the context of this paper, p is supposed to represent ( proportion of pairwise alignment). I'll go over it again, Its been awhile since I had to comb through such a paper that even I went cross eyed as half the math. The results look solid, but I'll get back to you on what p is supposed to stand in for.

 

[Milk-Drops]

As just one example of this perfection, study fractals:

Who created this natural and mathematical phenomenon? Certainly not time and chance. So what's the alternative? Mathematics requires a mathematician, and for fractals a Divine Mathematician.

How exactly does this relate to evolution? Considering that Evolution has nothing to do with non biological life?

 

[Malachi]

How exactly does this relate to evolution? Considering that Evolution has nothing to do with non biological life?

This is simply to prove the absurdity of evolution, which even Darwin recongnized:

Darwin confessed, "To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree."

 

[Milk-Drops]

This is simply to prove the absurdity of evolution, which even Darwin recongnized:

as I keep pointing out. The theory of evolution has nothing to do with the formation of the universe. That is cosmology, evolution deals with allele frequencies of living organisms.

Also on the Darwin eye thing. Its one of the oldest quote mines from creation websites. Here is both the full quote and an explanation.
http://www.talkorigins.org/indexcc/CA/CA113_1.html

 

[rthom7]

The usual creationist response to these findings (which have been known from various lineages studied individually) is that a "common designer" looks just like evolution. But it doesn't. Homologies, for example, like the bacterial flagellum and the Type IV secretory apparatus have no reason to be similarly constructed, but there they are. Legs on horses and wings of birds have no design reason to be homologous, but there they are.




The result of 0.5 means a 5% likelihood of the hypothesis being correct. Typically, the test will be for the 95th percentile, so if the text is 0.5 or below, the hypothesis is rejected. It doesn't mean a likelihood of 0.0.

Thanks Barbarian , but detail me again, if p chi square ranges from 0 to 1. If the value is 0.7 or higher we say the two groups studied by the chi squared are showing a trend. if the value is 0.5 or less, the chi square is not showing any functional relationship...ie more random relationship.... Is this your understanding ?

So for Angiosperm and Gymnosperm we see the control p value is 0.9 showing they are functionally related.... but when they are tested using PAML for moving DNA sequences from one strange to another, by various mutational changes, we get the p value of 1.23 to the base -29....in other words a value very close to zero....Does this not show no functional relationship here ? And I missing something in the PAML analysis ?

 

[rthom7]

I'll have to double check, but I think in the context of this paper, p is supposed to represent ( proportion of pairwise alignment). I'll go over it again, Its been awhile since I had to comb through such a paper that even I went cross eyed as half the math. The results look solid, but I'll get back to you on what p is supposed to stand in for.

Yes please do....thanks....

 

[Barbarian]

Thanks Barbarian , but detail me again, if p chi square ranges from 0 to 1. If the value is 0.7 or higher we say the two groups studied by the chi squared are showing a trend.

Rather, it's the level of confidence you have that the hypothesis is correct. (or false, depending on the test). Here's a table of values that correspond to the different confidence levels:
https://onlinecourses.science.psu.edu/stat414/node/147

if the value is 0.5 or less, the chi square is not showing any functional relationship...ie more random relationship.... Is this your understanding ?

So for Angiosperm and Gymnosperm we see the control p value is 0.9 showing they are functionally related.... but when they are tested using PAML for moving DNA sequences from one strange to another, by various mutational changes, we get the p value of 1.23 to the base -29....in other words a value very close to zero....Does this not show no functional relationship here ?

Ah, I see what you're saying. They are testing for the null hypothesis, that is, the likelihood that such a thing could have happened by chance. Which is effectively zero, indicating common descent.

 

[rthom7]

Rather, it's the level of confidence you have that the hypothesis is correct. (or false, depending on the test). Here's a table of values that correspond to the different confidence levels:
https://onlinecourses.science.psu.edu/stat414/node/147





Ah, I see what you're saying. They are testing for the null hypothesis, that is, the likelihood that such a thing could have happened by chance. Which is effectively zero, indicating common descent.

I see

View attachment 5829
Than if the null hypothesis is tested, why is the control false, and the other true ?

 

[Malachi]

How exactly does this relate to evolution? Considering that Evolution has nothing to do with non biological life?

I guess you are not familiar with fractals. They are present in biological life like you have no idea! See below, ponder, and scrap evolution altogether.
https://www.google.ca/search?q=fractals in nature&biw=683&bih=423&tbm=isch&tbo=u&source=univ&sa=X&ei=wZW0VM2FJMKyoQSK2YGICA&sqi=2&ved=0CBwQsAQ

 

[Milk-Drops]

I guess you are not familiar with fractals. They are present in biological life like you have no idea! See below, ponder, and scrap evolution altogether.

I know what fractals are and it doesn't scrap evolution at all. They are repeating patterns, that we as humans have put mathematical values on. It does not do anything to disprove genetics, homology, or taxonomy. Its a cool concept, but doesn't break anything.

 

[Milk-Drops]

As just one example of this perfection, study fractals:

What makes a repeating pattern perfect?

Who created this natural and mathematical phenomenon?

Why do you assume its a who? How do you know this was created and not just a natural phenomenon?

Certainly not time and chance. So what's the alternative?

Don't you mean, what do we know about fractals and how they occur?

Mathematics requires a mathematician, and for fractals a Divine Mathematician.

Actually, what it is, is we found some stuff in nature with repeating patterns and we applied mathematic principles that we as humans invented and found out that some stuff in nature repeat a pattern.

 

[Malachi]

What makes a repeating pattern perfect?

Certainly NOT natural selection, as old Mr. Darwin admitted honestly.

Why do you assume its a who?

And what would you assume? Have you seen precise mathematical pattern just form themselves?

How do you know this was created and not just a natural phenomenon?

"Nature" has no mind and no designing ability. Why are you dodging the inevitable conclusion?

Don't you mean, what do we know about fractals and how they occur? Actually, what it is, is we found some stuff in nature with repeating patterns and we applied mathematic principles that we as humans invented and found out that some stuff in nature repeat a pattern.

Mathematical principles exist in the universe, and human beings simply apply their intelligence to DISCOVER them. All natural laws were established by God, but since you refuse to acknowledge that, you simply dance around the inevitable conclusions. To see those fractals in biological life (which you first denied) and then to deny that there is a Divine Designer is to be wilfully blind. And God cannot help those who wilfully deny His existence.

 

[Milk-Drops]

Certainly NOT natural selection,

Natural selection is a biological principle that applies to population Mechanics. I don't know why this is so hard to understand. It has nothing to do with the formation of space, or minerals, or anything that doesn't reproduce by biolgoical means. You are simply confused.

as old Mr. Darwin admitted honestly.

No he did not, did you actually click on the link I provided that shows that the quote mine you put up was completely out of context?

And what would you assume?

You have to support your claim, this isn't a dichotomy.

Have you seen precise mathematical pattern just form themselves?

You are aware that we as humans invented the mathmatical concepts and use them and change them to better understand our surroundings right?

"Nature" has no mind and no designing ability. ['/quote] Exactly, and I don't anthropomorphism it.

Why are you dodging the inevitable conclusion?

I'm not dodging, you are making statements, I'm being skeptical and asking you to explain why. Considering you are relying on quote mines and are resorting on pushing the burden of proof off your claims, I'm not impressed.

Mathematical principles exist in the universe, and human beings simply apply their intelligence to DISCOVER them.

Can you explain what a physical concept of a mathematical principle is?

All natural laws were established by God, but since you refuse to acknowledge that, you simply dance around the inevitable conclusions.

No, you are making the claim God did it and assuming that because of God that everything works in such a way. I'm being skeptical and asking you how you know it. Since I don't have the same foundation, it should be obvious that I wouldn't take your assumptions at face value. Its not dancing, its called skepticism.

To see those fractals in biological life (which you first denied) and then to deny that there is a Divine Designer is to be wilfully blind.

No, here is the difference. You are assuming that because of God that fractals are designed by him. I am of the position that due to chemical compositions, and physics that structures will have identifiable patterns. Its evidence that sometimes matter acts in a certain way.

And God cannot help those who wilfully deny His existence.

The thing is God is never defined in a way to actually test for him scientifically. Every creation theory has the same problem, it goes to the limits of understanding and plugs God in there. To me that does not say God, that simply says we don't understand.

You haven't demonstrated evidence for God, but pointed out things you don't understand and use the design argument to then say that God did it. I'm not convinced.

 

[rthom7]

In my earlier link,

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069924

on the PAML study of DNA sequences : the scientists write "

In the case of evolution, a strong prediction of Darwin’s ‘descent with modification’ [4] is that, as we go further and further back in time, the sequences for a given protein should become increasingly similar – we call this either ‘ancestral convergence’ or ‘reverse convergence’. The prediction from evolutionary theory is that DNA or protein sequences carrying out the same basic functions in different organisms are generally inherited from a common ancestor.

From looking at evolution videos on origins, I see much of their evidence is similar to Intelligent Design...When GOD created the animals it seems He used a common genome for all living things, thus we find a common ancestor (DNA for all proteins) is already present in all living things , and what we see is different kinds of organism's with switching information within the other bits of DNA, the non protein sequences of DNA, the other 98% scientists attribute as junk...it's the switching that makes us different...almost the same as evolution, the ancestor DNA is already in all organisms....

It becomes difficult as I watch these video's how does one theory disprove another ? Thus as one person said and I agree, rather than postulate intermediate forms of complexity, the premise for Intelligent Design or Evolution, should be; is the organelle currently evolving, or has the basic structure been programmed from the beginning (allowing for mirco-evolution or small changes) ?

I was hoping somebody would help me with the table 2 showing P chi square analysis, if one column shows close to 0 and the control 0.9 how can either a null hypothesis or true hypothesis make any conclusion, since both test and control groups are radically different ?

This is a good video on evolution and attacks quote mining and complex irreducibility... how similar are type III secretory systems to bacteria flagella?
Can't find any scientist willing to really detail this ?

This video is really good, and I was surprised the scientist comments on the complexity of flagella is designed, and cannot be formed from secretory III system to flagella....too complex....

MlkDrops, and others, are there any real good videos of evolutions, willing to discuss evolution of flagella as good as this video above ?

Shalom

 

[Barbarian]

Than if the null hypothesis is tested, why is the control false, and the other true ?

It appears then null hypothesis has less than a 5% probability, which effectively rules it out.

 

[Barbarian]

is the organelle currently evolving

Yep.
http://www.ncbi.nlm.nih.gov/pubmed/20547844

Even more impressive, the evolution of organelles like mitochondria and chlorplasts (which are essentially endosymbiotic bacteria with their own, bacterial DNA) has been directly observed:
The large, free-living amoebae are inherently phagocytic. They capture, ingest and digest microbes within their phagolysosomes, including those that survive in other cells. One exception is an unidentified strain of Gram-negative, rod-shaped bacteria that spontaneously infected the D strain of Amoeba proteus and came to survive inside them. These bacteria established a stable symbiotic relationship with amoebae that has resulted in phenotypic modulation of the host and mutual dependence for survival.
http://www.sciencedirect.com/science/article/pii/S0962892400889667

The video is a bit out of date. It is now known that there isn't just one sort of prokaryotic flagellum. There are two basic types, and variations in those. Irreducible complexity fell apart as an argument, when it became obvious that the Type III apparatus didn't have all the components of the flagellum, but still had a function.
Cavalier-Smith T (1987). "The origin of eukaryotic and archaebacterial cells". Ann. N. Y. Acad. Sci. 503 (1): 17–54.

So, some simpler versions:

Even more to the point, the evidence shows that the flagellins are evolved from cell dynens.
"Molecular analysis of archael flagellins: similarity to the type IV pilin-transport superfamily widespread in bacteria". Canadian Journal of Microbiology 40 (1): 67–71

Behe has recently agreed that irreducible complexity can evolve naturally. Would you like to see some ways it could?

These are a few reasons why molecular biologists have rejected ID.