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Same Genome, Different Proteome

expressions of phenotype

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#1 gilbo12345

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Posted 27 June 2012 - 09:59 PM

Consider a caterpillar and a butterfly they contain the same genetic material yet have a different phenotype. This phenotype difference is due to the differences in the proteome of the organisms, despite the fact that they have exactly the same DNA.


Considering this, then by what relevance does the degree of similarity of DNA between organisms tell us?...... Practically nothing... (Unless you add in the evolutionary assumptions required)

A more scientific approach would be to study the release / amount / types of mRNA between organisms since THIS is where the differences in expression applies. (DNA only tells us of the potential expression of a gene product, whereas mRNA can tell us of the actual amount of expression of a gene at any given time).

Has there been any form of analysis between organism mRNA?

If so, where?
If not, why?


EDIT: Additionally since we already know this information why is DNA similarity still being proposed as evidence for evolution?

#2 aelyn

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Posted 27 June 2012 - 11:47 PM

DNA determines how the organism as a whole develops over time. The DNA itself doesn't change during the organism's lifetime (aside from somatic mutations) but which genes are expressed varies from cell to cell and from moment to moment. The caterpillar and the butterfly are two different stages of development, like embryos, fetuses, children and adults are in humans; they have a much sharper dividing line than you find in vertebrates but in both cases DNA is expressed differently in different organs and at different times in development.

Biologists do study the genetics of development and compare them between different organisms. Here's an example of a database looking at that :
http://www.rna-seqbl...ssion-database/

#3 gilbo12345

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Posted 28 June 2012 - 03:01 AM

DNA determines how the organism as a whole develops over time. The DNA itself doesn't change during the organism's lifetime (aside from somatic mutations) but which genes are expressed varies from cell to cell and from moment to moment. The caterpillar and the butterfly are two different stages of development, like embryos, fetuses, children and adults are in humans; they have a much sharper dividing line than you find in vertebrates but in both cases DNA is expressed differently in different organs and at different times in development.

Biologists do study the genetics of development and compare them between different organisms. Here's an example of a database looking at that :
http://www.rna-seqbl...ssion-database/


You're first paragraph summarizes my point Posted Image and yes you are correct different expression also occurs between different organs.

Had a quick scan over the database, (as I should be studying for my final exam lol), it looks interesting.

#4 AFJ

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Posted 30 June 2012 - 07:57 AM

Consider a caterpillar and a butterfly they contain the same genetic material yet have a different phenotype. This phenotype difference is due to the differences in the proteome of the organisms, despite the fact that they have exactly the same DNA.


Considering this, then by what relevance does the degree of similarity of DNA between organisms tell us?...... Practically nothing... (Unless you add in the evolutionary assumptions required)

A more scientific approach would be to study the release / amount / types of mRNA between organisms since THIS is where the differences in expression applies. (DNA only tells us of the potential expression of a gene product, whereas mRNA can tell us of the actual amount of expression of a gene at any given time).

Has there been any form of analysis between organism mRNA?

If so, where?
If not, why?


EDIT: Additionally since we already know this information why is DNA similarity still being proposed as evidence for evolution?


I agree with your premise, and a wonderful observation. I have often asked myself, where are the timekeepers of the cell?Of course we know that signal proteins are instrumental in changing the shape of inhibitors http://en.wikipedia....cription_factor , stopping RNA polymerase, which is instrumental in the initiation of of the mRNA template, transcribing it from the actual gene (e.g. gene expression). But past that, what is the "timer" of the cell in meiosis, meitosis, and apoptosis. Of course there must be a cascade of enzymatic activity on each process. Man ruled out vitalism, yet not preprogramming, and has not yet found the cause for these enzymatic cascades which cause the cell to work intelligently with no brain.


Another thing we might want to consider is more public information onspeed of production versus requirement for metabolism. This will also make the preprogrammed guidance issue more apparent. THESE ISSUES MUST BE TITLED AND PROPOGATED TO THE STUDENT, JUST AS EVOLUTIONARY SCIENCE DOES.When I was studying molecular biology, I also found that there are something called "housekeeping genes." These are genes that make up the proteins for say subunits of the ribosomes, enzymes, and cellular machinery constantly in use. Each one of these genes has many many copies. And most all genes have copies. Most pople don't know that. I think it goes without saying that the reason for the many copies is production. It's a factory in there, and you need more housekeeping genes to keep up the metabolism.

I think it's a shame that evos have taken even this as a means of change over time. It's like all data goes through their preconceived evo filter. What's sad is they pick and choose what facts go to students and to the public. Gene copies are presented as one other possible path for the Darwinian dream. When a much more rational explanation of required mechanical upkeep for cellular processes is obvious.

#5 herebedragons

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Posted 10 July 2012 - 07:11 AM

Consider a caterpillar and a butterfly they contain the same genetic material yet have a different phenotype. This phenotype difference is due to the differences in the proteome of the organisms, despite the fact that they have exactly the same DNA.


Considering this, then by what relevance does the degree of similarity of DNA between organisms tell us?...... Practically nothing... (Unless you add in the evolutionary assumptions required)

A more scientific approach would be to study the release / amount / types of mRNA between organisms since THIS is where the differences in expression applies. (DNA only tells us of the potential expression of a gene product, whereas mRNA can tell us of the actual amount of expression of a gene at any given time).


Being a biotech major, I am sure that you realize that mRNA doesn't even tell the whole story. Proteins coded from the same mRNA can be modified in different ways by the golgi apparatus; Enzymes can act as inhibitors or promoters and are expressed differently in different cell types; mRNA can be modified post-translationally, with alternate splicing, phosphorylation etc... Every tissue, every cell type, would have its own unique mRNA expression levels and proteome - a monumental feat to document! Even if you did document every protein and mRNA molecule in every cell type in an organism, what would that tell you about the organism's history?

Comparing DNA can give some insight as to the history of an organism. Take for an example a plant that has undergone a polyploidy event. You may find different levels of expression of some gene products when comparing the two species, but until you compare the genomes of the two you cannot be sure of the mode of speciation or what the connection between the two organisms is.

If your point is: Why do we say things like "Human DNA and chimp DNA are 95%+ similar or Human DNA and worm DNA are 75% (or whatever) similar"? I would agree that that is rather pointless. It only shows how much we have in common in our biological systems. But there is not necessarily indication of common ancestry just because of 95% similarity.

Additionally since we already know this information why is DNA similarity still being proposed as evidence for evolution?



I would agree that DNA similarity expressed as a percent is not very good evidence of common ancestry. (However, It is not the only, nor the best, evidence of common ancestry). Even YECs recognize that species have evolved (ie. changed) since the initial creation, and they would therefore have a common ancestor. Common ancestor in this context doesn't have to mean bacteria-to-man evolution ... for example, dogs all have a common ancestor - the wolf. So, I don't see how indexing huge amounts of mRNA, proteins and expression levels could help us better understand the history of dog breeding. But in comparing DNA sequences we can identify deletions, insertions, inversions, transposons, substitutions etc ... that have occurred during the history of the dog. And in comparing those sequence changes, we have one piece of evidence as to the history of the species' evolution (ie. changes over time).

HBD

#6 joman

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Posted 10 July 2012 - 10:52 AM

It seems to me that on the face of it, if something is 95% identical to some other thing that is vastly different in obvious ways then, the evidence being presented is that there exists a vast amount of ignorance about how the obvious differences are produced.
Because of the mentioning of metamorphisis, and other dna events, occurring inexplicably by mechanistic theories, I thought I'd mention my own view of biology.
I believe in the existence of the soul.
In my view of life I submit to you the notion that there can be no substantial explanation of all cellular expressions, whole body expressions, or social expressions by mechanistic theories..

Curiously, in the book of Job there are some arguments developed on the supposition that mankind can't tell when certain events will occur in populations.

Job 39:1 Knowest thou the time when the wild goats of the rocks bring forth? or canst thou mark when the hinds do calve?

These two things, prediction, and marking of time concerning biological events, show us that God is saying that not all biological events are mechanistic.

Another example is given when Jacob placed sheep in breeding pens and confined them with straked poles. The statistical result of the diversity of kinds of offspring was impacted by the vision of the sheep when mating.

So, what used to be a central dogma of biology was already predicted scripturally as an incorrect understanding of life, biologically.

It seems to me that the scriptures are implying that the soul that inhabits a body effects many of the expressions of the body and its cells.


I also noticed the assumption that dogs came from wolves.
This would be an odd assumption for any bible believer to make would it not?
For, wildness was not created by God but, came to pass in the process of time as the evil of mankind spread over the earth.
Doesn't the fear of man, as predicted in Genesis, an implication that man is justly to be feared by beasts of the earth for historical reasons?

I think the evidence shows that the wolf was produced from tame dogs, not the other way around, since, it is well known that wildness is not removable by man from any dog, but, wildness can easily be instilled by man in any dog.

I don't believe there ever was, for example, a world of dinosaurs as depicted in evolution cartoonland propoganda. Instead, I think man spread violence among creatures on earth, began to eat them, and starved them to make them violent by means of survival instincts, and moreover, began to tamper with genetics so as to create the strange giants we term dinosaurs in such a manner as to create great examples of terror and violence for entertainment and for purposes of trying to prove the nature way of Cain was the stronger more formidable philosophy.
Thus, it was man that starved dogs, and made them fight one another.
It was man that made saber toothed cats that wielded ungainly teeth more suitable for violent sports of terror than for hunting in the wild.
It was man that made the tyrannasaurus rex that is not naturally fit for survival on its own out in the wild where it can fall easily and has no limbs suitable for feeding itself, erecting itself, and whose head appears designed only for terrorizing in an arena. I digress.

But, is it not obvious that wildness is a one way street and lacks elementals of diversity? Notice how boring the wolf is? Yet, how diverse the tame dog is? Wildness is antievolutionary seems to me, since the only parameter of the whole body of the beast is merely the simplistic notion of survival, instead of the far more broadminded paths toward diversity of noble use by mankind. All that man breeds diversifies in many glorious ways far more numerous than the wildness of untamed nature does. As if, in peaceful realms diversity is more expected. Look at the millions and millions of identical bison wandering uselessly across the great plains of North America back when they had no great purposes. And, they ended up not much good for anything. But, consider the diversities of cattle and how wonderful many of them are, and all the good they provide for mankind.

The whole paradigm of the believe that all was primative, and stupid, and banal, and base is a satanic notion seems to me.
Satan is a liar. It was the opposite, and that is what makes sense doesn't it?

There never were stupid idiots evolutionism calls Neanderthals that wandered around without tools, or manners, or nobility for 1oo,ooo years of meaningless existence. It is a sill notion on the face of it. And to think that noble examples of mankind mated with such gross creatures as evolutionists present neanderthals to be is patently ridiculous since, no noble person, possessing language, history, tools and good looks is attracted to brutes.

#7 herebedragons

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Posted 10 July 2012 - 09:02 PM

Because of the mentioning of metamorphisis, and other dna events, occurring inexplicably by mechanistic theories,


These things are not inexplicable. We may not understand all cellular processes, but that doesn't mean they can't be figured out.

I believe in the existence of the soul.


So ... this is your first point about biology? I believe in the existence of the soul also, but it has nothing to do with biology.


In my view of life I submit to you the notion that there can be no substantial explanation of all cellular expressions, whole body expressions, or social expressions by mechanistic theories..

Curiously, in the book of Job there are some arguments developed on the supposition that mankind can't tell when certain events will occur in populations.

Job 39:1 Knowest thou the time when the wild goats of the rocks bring forth? or canst thou mark when the hinds do calve?

These two things, prediction, and marking of time concerning biological events, show us that God is saying that not all biological events are mechanistic.


You need to read the whole of Job chapters 38 - 41. They culminate in God saying "Do you have an arm like God's, and can your voice thunder like his?" God is not making declarations about biological mechanisms. He is comparing man's puny existence to his immense greatness. Is this one question all that difficult? All you need to do is Google it and you can know when mountain goats give birth and when deer have fawns. Are you (or is God) really suggesting that reproduction in these animals does not have a mechanism? I think you are taking this scripture completely out of context to fit your "notion".

I think the evidence shows that the wolf was produced from tame dogs, not the other way around, since, it is well known that wildness is not removable by man from any dog, but, wildness can easily be instilled by man in any dog.



This is an interesting thought. However, the evidence that you use to support your notion is that God did not create wildness. Yet Gen 1:25 says that "God made the wild animals according to their kinds, the livestock according to their kinds, and all creatures that move according to their kinds." Any other evidence?

I don't believe there ever was, for example, a world of dinosaurs as depicted in evolution cartoonland propoganda. Instead, I think man spread violence among creatures on earth, began to eat them, and starved them to make them violent by means of survival instincts, and moreover, began to tamper with genetics so as to create the strange giants we term dinosaurs in such a manner as to create great examples of terror and violence for entertainment and for purposes of trying to prove the nature way of Cain was the stronger more formidable philosophy.
Thus, it was man that starved dogs, and made them fight one another.
It was man that made saber toothed cats that wielded ungainly teeth more suitable for violent sports of terror than for hunting in the wild.
It was man that made the tyrannasaurus rex that is not naturally fit for survival on its own out in the wild where it can fall easily and has no limbs suitable for feeding itself, erecting itself, and whose head appears designed only for terrorizing in an arena. I digress.



​Nonsense. You believe they had genetic engineering more than 6000 years ago? And do you have any idea as to the diversity of known dinosaur types? Humans in an agrarian society were able to accomplish all that? We don't have that capability today, genetic engineering is still crude and clumsy (yet developing rapidly). What evidence is there of the types of engineering and breeding facilities that would have been needed? Where is evidence of the terror arenas? And why do you think T-Rex was not fit for survival? No limbs suitable for feeding itself? He could swallow many of the other creatures of his time in one gulp - which is how many lizards today still feed. They don't use limbs to feed. ???? Posted Image

The whole paradigm of the believe that all was primative, and stupid, and banal, and base is a satanic notion seems to me.
Satan is a liar. It was the opposite, and that is what makes sense doesn't it?



No, makes no sense. Satan may be a liar indeed, but the Creation certainly is not. If the Creation was a lie, that would make God a liar, since it is his revelation. The "opposite" is not what we observe in the fossil record. And besides, who said anything about early life being primitive, stupid and banal. Would you consider bacteria to be stupid? They are amazingly complex and perfectly adapted to do what they do. Simple (as in a simple body plan or few differentiated tissues) is not the same as stupid and basal. Its a meaningless argument.

And to think that noble examples of mankind mated with such gross creatures as evolutionists present neanderthals to be is patently ridiculous since, no noble person, possessing language, history, tools and good looks is attracted to brutes.



My wife mated with me so ... idk :lol:

HBD

#8 gilbo12345

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Posted 10 July 2012 - 09:39 PM

Being a biotech major, I am sure that you realize that mRNA doesn't even tell the whole story. Proteins coded from the same mRNA can be modified in different ways by the golgi apparatus; Enzymes can act as inhibitors or promoters and are expressed differently in different cell types; mRNA can be modified post-translationally, with alternate splicing, phosphorylation etc... Every tissue, every cell type, would have its own unique mRNA expression levels and proteome - a monumental feat to document! Even if you did document every protein and mRNA molecule in every cell type in an organism, what would that tell you about the organism's history?

Comparing DNA can give some insight as to the history of an organism. Take for an example a plant that has undergone a polyploidy event. You may find different levels of expression of some gene products when comparing the two species, but until you compare the genomes of the two you cannot be sure of the mode of speciation or what the connection between the two organisms is.

If your point is: Why do we say things like "Human DNA and chimp DNA are 95%+ similar or Human DNA and worm DNA are 75% (or whatever) similar"? I would agree that that is rather pointless. It only shows how much we have in common in our biological systems. But there is not necessarily indication of common ancestry just because of 95% similarity.

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I would agree that DNA similarity expressed as a percent is not very good evidence of common ancestry. (However, It is not the only, nor the best, evidence of common ancestry). Even YECs recognize that species have evolved (ie. changed) since the initial creation, and they would therefore have a common ancestor. Common ancestor in this context doesn't have to mean bacteria-to-man evolution ... for example, dogs all have a common ancestor - the wolf. So, I don't see how indexing huge amounts of mRNA, proteins and expression levels could help us better understand the history of dog breeding. But in comparing DNA sequences we can identify deletions, insertions, inversions, transposons, substitutions etc ... that have occurred during the history of the dog. And in comparing those sequence changes, we have one piece of evidence as to the history of the species' evolution (ie. changes over time).

HBD


I believe I was referring to differences in expression, post transcriptional variations can occur via regulatory RNA (siRNA / RNAi, etc). Yes in eukaryotes splicing occurs and there are multiple splicing options available (I think one gene's mRNA in a fruit fly, can have over 10,000 variants of splicing)... Yet this adds in more drama for the evolutionist since by what mechanism can this be explained? Say we have a gene and it has 30 different splicing options, how does the cell "know" which option to utilise? Once we know that mechanism, then we can ask... how did such a system "evolve" via a "bit-by-bit" progression as per Darwin.



DNA similarities do nothing to determine an organisms history anyway, (unless you add the evolutionary assumptions required), it merely points out the potential expression of the DNA rather than what is expressed.

As I have mentioned in previous threads the method by which DNA similarity is deduced invalidates it as evidence anyway.
1- Evolution is assumed to have occured which allows the use of gaps in the alignment... Use of this as evidence of evolution is therefore circular reasoning since you had to assume evolution occured to account for the method used.
2- Alignment is based solely on the DNA samples being aligned, DNA sequences aligned multiple times with different sequences each time will create totally different results with different position and amounts of gaps. Therefore the entire alignment process is arbitrary, since there is no way to verify which alignment of the same DNA is correct.



I agree with your third paragraph, personally I think evolutionists are drawing too big a bow for the "evidence" they have.

#9 herebedragons

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Posted 11 July 2012 - 09:05 PM

I believe I was referring to differences in expression, post transcriptional variations can occur via regulatory RNA (siRNA / RNAi, etc). Yes in eukaryotes splicing occurs and there are multiple splicing options available (I think one gene's mRNA in a fruit fly, can have over 10,000 variants of splicing)... Yet this adds in more drama for the evolutionist since by what mechanism can this be explained?




Yes, all these processes and more are what determines expression levels, which is what would make using mRNA practically impossible to use as a tool to compare organisms.

DNA similarities do nothing to determine an organisms history anyway, (unless you add the evolutionary assumptions required), it merely points out the potential expression of the DNA rather than what is expressed.



Right. It is the differences that determine historical relationships. Remember, evolution is about change over time, so how the genome changes is a clue as to the history. In addition, whole DNA is not normally used to determine relationships. Often you will hear of mitochondrial DNA (or mtDNA) being used in studies. The reason for this is that mtDNA is inherited almost exclusively from the mother - (sperm have very few mitochondria). This means they do not undergo recombination and are much more highly conserved than nuclear DNA.

Another method that is used to establish heredity is protein sequences. Not the entire proteome or different levels of expression (as we already discussed that would be extremely cumbersome) but rather scientists have found proteins that appear to be well conserved through time. Some examples of these are cytochrome c, myoglobin, and the large subunit of RNA polymerase II.

Also I think you have a misconception about how scientists study similarity / differences in DNA. They don't compare entire DNA sequences. They cut the DNA in to manageable pieces and compare those pieces. They look at individual genes. Not entire pieces of DNA (humans have over 3 billion base pairs, 23 chromosomes and roughly 23,000 genes) How could all of that be aligned and compared?

1- Evolution is assumed to have occured which allows the use of gaps in the alignment... Use of this as evidence of evolution is therefore circular reasoning since you had to assume evolution occured to account for the method used.



It is not necessarily an invalid assumption. Let's look at a simple example - The Red-shafted flicker and the Yellow-shafted flicker. The Yellow-shafted flicker, Colaptes auratus lives in eastern N. America. The Red-shafted flicker, lives in western N. America. They were once thought to be separate species, but now are considered to be subspecies of the Northern Flicker. They can freely interbreed where their ranges overlap. Why would you not assume these two populations were at one time a single population. They were kept apart by some barrier and have continued to undergo mutation and selection until they are now significantly different from one another. Wikipedia http://en.wikipedia....orthern_Flicker

Now, when you study the genome of these two subspecies, what would you expect to find? Very similar DNA with some small differences. You wouldn't expect them to be vastly different or identical, These differences would indicate what has changed since the original founding population was split into two sub-populations. I can't imagine why that logic would cause an issue.

So ... what is to stop you from applying that logic to the entire Colaptes family? They have ranges all over the Americas. Is there some point (let's just stay within the genus for the sake of this discussion) that you would assume that the species did not have an ancestor? No. You would expect all the species in that genus to be very similar with some differences. So, you could apply this concept of change in DNA sequence to the entire genus and create a map - a history of that change for the genus Colaptes.

2- Alignment is based solely on the DNA samples being aligned, DNA sequences aligned multiple times with different sequences each time will create totally different results with different position and amounts of gaps. Therefore the entire alignment process is arbitrary, since there is no way to verify which alignment of the same DNA is correct



Remember, no one should be basing an evolutionary history on only one criteria. There should be multiple lines of evidence that agree with each other. There is often disagreement about phylogenies because of contradictory evidence or inconclusive evidence. So yeah, in some ways it is arbitrary. Which gene they choose, how they choose to splice it, how they choose to hybridize it (align it). But all these choices are outlined in scientific papers. Other scientists read them and critique them. They write rebuttals based on their own lines of evidence. Next time you see a claim of evolutionary relationship, pick up the actual paper (not a journalists summary) and use your biotech training to analyze the methods used to reach the conclusion they did. I guarantee it will be more than "We just arbitrarily thought this based on our own assumptions."

A cool exercise I did for one of my courses was to create a phylogenetic tree using protein sequences. I did mine on the genus Utricularia (the bladderworts). What you do is choose a protein such as cytochrome c and obtain the amino acid sequence for that protein for each of your choice of organisms. Protein database can be found here: http://www.ncbi.nlm....fcgi?db=Protein. The sequence is then formatted in FASTA which is you begin with the character ">" followed by the name of the organism then the amino acid sequence with no spaces. Example :


>horsecytc
gdvekgkkifvqkcaqchtvekggkhktgpnlhglfgrktgqapgftytdanknkgitwkeetlmeylenpkkyipgtkmifagikkkteredliaylkkatne

Collect your sequences and paste them into the alignment box at the following site: http://www.genome.jp/tools/clustalw

Be sure to have one outgroup - a totally unrelated organism (like if you are doing mammals then the outgroup could be a reptile or a bird)

The program will align the sequences and generate the dendrogram. You can look at the alignment and see where changes have occurred and maybe get an idea of why the program nested the group the way it did. Give it a try, it may be insightful.

HBD

#10 gilbo12345

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Posted 12 July 2012 - 12:05 AM

[/color]


Yes, all these processes and more are what determines expression levels, which is what would make using mRNA practically impossible to use as a tool to compare organisms.

[/color]

Right. It is the differences that determine historical relationships. Remember, evolution is about change over time, so how the genome changes is a clue as to the history. In addition, whole DNA is not normally used to determine relationships. Often you will hear of mitochondrial DNA (or mtDNA) being used in studies. The reason for this is that mtDNA is inherited almost exclusively from the mother - (sperm have very few mitochondria). This means they do not undergo recombination and are much more highly conserved than nuclear DNA.

Another method that is used to establish heredity is protein sequences. Not the entire proteome or different levels of expression (as we already discussed that would be extremely cumbersome) but rather scientists have found proteins that appear to be well conserved through time. Some examples of these are cytochrome c, myoglobin, and the large subunit of RNA polymerase II.

Also I think you have a misconception about how scientists study similarity / differences in DNA. They don't compare entire DNA sequences. They cut the DNA in to manageable pieces and compare those pieces. They look at individual genes. Not entire pieces of DNA (humans have over 3 billion base pairs, 23 chromosomes and roughly 23,000 genes) How could all of that be aligned and compared?

[/color]

It is not necessarily an invalid assumption. Let's look at a simple example - The Red-shafted flicker and the Yellow-shafted flicker. The Yellow-shafted flicker, Colaptes auratus lives in eastern N. America. The Red-shafted flicker, lives in western N. America. They were once thought to be separate species, but now are considered to be subspecies of the Northern Flicker. They can freely interbreed where their ranges overlap. Why would you not assume these two populations were at one time a single population. They were kept apart by some barrier and have continued to undergo mutation and selection until they are now significantly different from one another. Wikipedia http://en.wikipedia....orthern_Flicker

Now, when you study the genome of these two subspecies, what would you expect to find? Very similar DNA with some small differences. You wouldn't expect them to be vastly different or identical, These differences would indicate what has changed since the original founding population was split into two sub-populations. I can't imagine why that logic would cause an issue.

So ... what is to stop you from applying that logic to the entire Colaptes family? They have ranges all over the Americas. Is there some point (let's just stay within the genus for the sake of this discussion) that you would assume that the species did not have an ancestor? No. You would expect all the species in that genus to be very similar with some differences. So, you could apply this concept of change in DNA sequence to the entire genus and create a map - a history of that change for the genus Colaptes.

[/color]

Remember, no one should be basing an evolutionary history on only one criteria. There should be multiple lines of evidence that agree with each other. There is often disagreement about phylogenies because of contradictory evidence or inconclusive evidence. So yeah, in some ways it is arbitrary. Which gene they choose, how they choose to splice it, how they choose to hybridize it (align it). But all these choices are outlined in scientific papers. Other scientists read them and critique them. They write rebuttals based on their own lines of evidence. Next time you see a claim of evolutionary relationship, pick up the actual paper (not a journalists summary) and use your biotech training to analyze the methods used to reach the conclusion they did. I guarantee it will be more than "We just arbitrarily thought this based on our own assumptions."

A cool exercise I did for one of my courses was to create a phylogenetic tree using protein sequences. I did mine on the genus Utricularia (the bladderworts). What you do is choose a protein such as cytochrome c and obtain the amino acid sequence for that protein for each of your choice of organisms. Protein database can be found here: http://www.ncbi.nlm....fcgi?db=Protein. The sequence is then formatted in FASTA which is you begin with the character ">" followed by the name of the organism then the amino acid sequence with no spaces. Example :


>horsecytc
gdvekgkkifvqkcaqchtvekggkhktgpnlhglfgrktgqapgftytdanknkgitwkeetlmeylenpkkyipgtkmifagikkkteredliaylkkatne

Collect your sequences and paste them into the alignment box at the following site: http://www.genome.jp/tools/clustalw

Be sure to have one outgroup - a totally unrelated organism (like if you are doing mammals then the outgroup could be a reptile or a bird)

The program will align the sequences and generate the dendrogram. You can look at the alignment and see where changes have occurred and maybe get an idea of why the program nested the group the way it did. Give it a try, it may be insightful.

HBD


No it wouldn't be impossible, just monumental. However by using this at least it means that evolutionists can be basing their claims on actual data rather than the superficial "data" they have. As I have claimed potential expression is not actual expression and is not a good basis to determine similarities in expression. Yet I predict that when such data is available there would be a large decrease in similarity between organisms and this is not something to be wanted for an evolutionist.



Yet you still need to add the initial evolutionary assumptions, therefore anything claimed from such is not a scientific statement since it is based on a mere unverified assumption, (unless assumptions are now claimed as valid science......). This overthrows any and all arguments. Even in your reply you have exposed the uncertainty of the "history" that can be deduced... SInce not ALL the mitochondrial DNA comes from the mother then there is a level of doubt about it ancestry, hence nothing can be claimed for certain. It is merely taken on faith. I am sorry, I don't deem assumption-based faith "science" as anything resembling the scientific method or the empirical sciences.





Point one shows that it is reasoning within a circle.... Would you claim that such thinking is logical?

Point two shows how the method is arbitrary and therefore includes a level of doubt as to which is real. You have compounded this by claiming that it is up to the researcher, hence with such a high degree of control over the outcome who is to say that the results reflect reality at all? Furthermore I showed how that you can get multiple different alignments for the exact same sequence hence how do we know that the one we use this time is correct? It demonstrates that the program used is aligning for similarity despite if it is there or not, therefore it can be deduced that the program is increasing the amount of similarity between sequences via its arbitrary method.

You've done nothing to address this, merely stating that scientists allow it does nothing. What I have stated here demonstrates that the method used to determine the similarity in DNA is not reliable and is biased to finding similarities even when they may not be there. I leave you with this old saying

"what is popular is not always right, and what is right is not always popular"

Consider this when you claim that scientists allow it, since it is an attempt at argumentum ad populum which is a logical fallacy.



I have made many phylogenetic trees, (we have had many many topics based on evolution in my degree.... hence why I believe its akin to indoctrination). Actually it was playing around with the data and trees that I realised point two above.

#11 herebedragons

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Posted 12 July 2012 - 07:53 AM

Believe me, Gilbo. I am not trying to convince you that evolution - in the bacteria-to-man sense is true. I am not convinced that the observable processes that we have (microevolution) are sufficient to explain the large scale changes that the fossil records show (macroevolution). Which is why I used the example of the Northern Flicker; there is no crossing over of any boundaries between "kinds". It is an example of evolution that I would think even a YEC could accept. Even within the genus, It appears that the entire genus is extant except for one subspecies of C. auratus. So we should be able to use this example to talk about phylogenetics.

Do you accept that this genus originated from a single ancestral population or do you believe that God created them as is? Either way do you not start with an assumption?

[qs]Yet you still need to add the initial evolutionary assumptions, therefore anything claimed from such is not a scientific statement since it is based on a mere unverified assumption, (unless assumptions are now claimed as valid science......). This overthrows any and all arguments. [/qs]

Of course you need to start with some assumptions. But then you test those assumptions. I don't mean to sound like I am taking shots at your education, but it doesn't seem to me like you understand. I am not saying that you need to "get with the program" and accept evolution in order to succeed at your career. But I am saying that you need to understand how science really works - and I am sorry, but it seems to me that you have this attitude that you have a "new", better way of doing science and those that are doing science now are merely dupes who have strayed down the path of "assumption science". This is why I am interested in engaging you in this discussion, not to convert you to an evolutionist - so please don't take me the wrong way. And if I have misunderstood you, I am sure we will clear it up quickly.

[qs]Even in your reply you have exposed the uncertainty of the "history" that can be deduced... SInce not ALL the mitochondrial DNA comes from the mother then there is a level of doubt about it ancestry, hence nothing can be claimed for certain. It is merely taken on faith. I am sorry, I don't deem assumption-based faith "science" as anything resembling the scientific method or the empirical sciences.{/qs]

This is the kind of comment that leads me to believe what I said above. ALL science is uncertain. ALL scientific theories are subject to modification or can potentially shown to be false. Falsification is essential to any scientific theory. A good scientific theory always has a level of "uncertainty". You do know that the atomic theory is "just a theory" and there is "uncertainty" about it. Some evidence could come along and completely disprove the atomic theory - although extremely unlikely. So just because there is some "doubt" or some "uncertainty" does not in the least invalidate the conclusion. What does invalidate a conclusion is contrary evidence. Not speculation - evidence.

How is your view as a YEC different from the "assumption-based faith science" that you are opposed to?

[qs]Point one shows that it is reasoning within a circle.... Would you claim that such thinking is logical?[/qs

I showed you it was logical in the case of the Northern Flicker. Why would it not be logical to conclude that that the Yellow-shafted version and the Red-shafted version came form an original single population? Why would it not be logical to assume that any particular bird had parents that had passed on their genetic material? If they each had parents, then you could trace that parentage back through time. Actually you would say that your hypothesis is that those two populations diverged from a single ancestral population and then you test that hypothesis.

[qs]Point two shows how the method is arbitrary and therefore includes a level of doubt as to which is real. You have compounded this by claiming that it is up to the researcher, hence with such a high degree of control over the outcome who is to say that the results reflect reality at all?[/qs]

So ... who should determine the methodology? Do you think that a researcher just arbitrarily pulls a method out of the air? Let's say your assignment is to develop a new crop variety that has better disease resistance. How will you approach it? Will you will arbitrarily pull some method out of the air? Of course not! You will use a methodology that another scientist has developed and shown to work. Then you test to see that that method worked. Then you report your results. In your report you explain your methodology and the justification for it. Let's say the variety you developed was to be resistance to a rust fungus, but the organism you arbitrarily chose to test it on was a bacteria. When you reported that the resistance was positive, it would immediately be obvious to others that your methodology was flawed since you tested for resistance to a fungus using a bacteria. I made this example ridiculous just for illustrative purposes, not to imply you would actually do that. Scientists scrutinize each other's methods and make judgments about the validity of the results. How else should it be?

[qs]Consider this when you claim that scientists allow it, since it is an attempt at argumentum ad populum which is a logical fallacy.[/qs]

I wish you would break my quote up so I knew what I said that you were referring to. I don't know where I claimed that scientists "allow" anything. I never even used the word allow, so I don't know what you are referring to.

I will break down my rebuttal to the OP into 4 main points:

1. Agreed that DNA similarity receives a lot of undeserved hype (for example human / chimp 95% similar) which really doesn't tell us a whole lot or confirm ancestry. But it is the differences, the changes, that are useful in determining history. This is not based upon circular reasoning, rather it is a hypothesis that can be tested and either verified or discarded. Every scientific investigation begins with a question, a hypothesis. The null hypothesis is typically the assumption that that hypothesis is true. The alternate hypothesis is typically that the hypothesis is not true or not supported by the evidence. This is basic, foundational scientific investigation.


2. No single method is suitable for developing a phylogeny. Multiple lines of evidence are considered from differing disciplines. Molecular studies, morphological studies, paleontology data, geographical data, homology and the concept of parsimony are all considered when developing a phylogenetic tree. Yes, there are uncertainties. Yes, there are disputes and difficulties. But that makes it no less valid of a science. In order to invalidate an accepted phylogenetic hypothesis, present evidence that the hypothesis is incorrect.

3. Determining the proteome of every cell type at each stage of development would be too cumbersome to use as a comparative tool. Methods have been developed and tested that, at the present time, are considered effective. These methods are NOT arbitrarily chosen, but are tested, examined, and reported by the researcher for scrutiny by other scientists.

4. mRNA is not particularly stable and subject to degradation. It would not be especially useful to use it as a tool for comparing organisms. In addition there are many factors that would alter the products of mRNA that would be difficult to detect and utilize for this application.


HBD

#12 gilbo12345

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Posted 12 July 2012 - 11:18 AM

1. Believe me, Gilbo. I am not trying to convince you that evolution - in the bacteria-to-man sense is true. I am not convinced that the observable processes that we have (microevolution) are sufficient to explain the large scale changes that the fossil records show (macroevolution). Which is why I used the example of the Northern Flicker; there is no crossing over of any boundaries between "kinds". It is an example of evolution that I would think even a YEC could accept. Even within the genus, It appears that the entire genus is extant except for one subspecies of C. auratus. So we should be able to use this example to talk about phylogenetics.

2. Do you accept that this genus originated from a single ancestral population or do you believe that God created them as is? Either way do you not start with an assumption?

[qs]Yet you still need to add the initial evolutionary assumptions, therefore anything claimed from such is not a scientific statement since it is based on a mere unverified assumption, (unless assumptions are now claimed as valid science......). This overthrows any and all arguments. [/qs]

3. Of course you need to start with some assumptions. But then you test those assumptions. I don't mean to sound like I am taking shots at your education, but it doesn't seem to me like you understand. I am not saying that you need to "get with the program" and accept evolution in order to succeed at your career. But I am saying that you need to understand how science really works - and I am sorry, but it seems to me that you have this attitude that you have a "new", better way of doing science and those that are doing science now are merely dupes who have strayed down the path of "assumption science". This is why I am interested in engaging you in this discussion, not to convert you to an evolutionist - so please don't take me the wrong way. And if I have misunderstood you, I am sure we will clear it up quickly.


4. This is the kind of comment that leads me to believe what I said above. ALL science is uncertain. ALL scientific theories are subject to modification or can potentially shown to be false. Falsification is essential to any scientific theory. A good scientific theory always has a level of "uncertainty". You do know that the atomic theory is "just a theory" and there is "uncertainty" about it. Some evidence could come along and completely disprove the atomic theory - although extremely unlikely. So just because there is some "doubt" or some "uncertainty" does not in the least invalidate the conclusion. What does invalidate a conclusion is contrary evidence. Not speculation - evidence.

5. How is your view as a YEC different from the "assumption-based faith science" that you are opposed to?


6. I showed you it was logical in the case of the Northern Flicker. Why would it not be logical to conclude that that the Yellow-shafted version and the Red-shafted version came form an original single population? Why would it not be logical to assume that any particular bird had parents that had passed on their genetic material? If they each had parents, then you could trace that parentage back through time. Actually you would say that your hypothesis is that those two populations diverged from a single ancestral population and then you test that hypothesis.



7. So ... who should determine the methodology? Do you think that a researcher just arbitrarily pulls a method out of the air? Let's say your assignment is to develop a new crop variety that has better disease resistance. How will you approach it? Will you will arbitrarily pull some method out of the air? Of course not! You will use a methodology that another scientist has developed and shown to work. Then you test to see that that method worked. Then you report your results. In your report you explain your methodology and the justification for it. Let's say the variety you developed was to be resistance to a rust fungus, but the organism you arbitrarily chose to test it on was a bacteria. When you reported that the resistance was positive, it would immediately be obvious to others that your methodology was flawed since you tested for resistance to a fungus using a bacteria. I made this example ridiculous just for illustrative purposes, not to imply you would actually do that. Scientists scrutinize each other's methods and make judgments about the validity of the results. How else should it be?



8. I wish you would break my quote up so I knew what I said that you were referring to. I don't know where I claimed that scientists "allow" anything. I never even used the word allow, so I don't know what you are referring to.

I will break down my rebuttal to the OP into 4 main points:

1. Agreed that DNA similarity receives a lot of undeserved hype (for example human / chimp 95% similar) which really doesn't tell us a whole lot or confirm ancestry. But it is the differences, the changes, that are useful in determining history. This is not based upon circular reasoning, rather it is a hypothesis that can be tested and either verified or discarded. Every scientific investigation begins with a question, a hypothesis. The null hypothesis is typically the assumption that that hypothesis is true. The alternate hypothesis is typically that the hypothesis is not true or not supported by the evidence. This is basic, foundational scientific investigation.


2. No single method is suitable for developing a phylogeny. Multiple lines of evidence are considered from differing disciplines. Molecular studies, morphological studies, paleontology data, geographical data, homology and the concept of parsimony are all considered when developing a phylogenetic tree. Yes, there are uncertainties. Yes, there are disputes and difficulties. But that makes it no less valid of a science. In order to invalidate an accepted phylogenetic hypothesis, present evidence that the hypothesis is incorrect.

3. Determining the proteome of every cell type at each stage of development would be too cumbersome to use as a comparative tool. Methods have been developed and tested that, at the present time, are considered effective. These methods are NOT arbitrarily chosen, but are tested, examined, and reported by the researcher for scrutiny by other scientists.

4. mRNA is not particularly stable and subject to degradation. It would not be especially useful to use it as a tool for comparing organisms. In addition there are many factors that would alter the products of mRNA that would be difficult to detect and utilize for this application.


HBD


Believe me, Gilbo. I am not trying to convince you that evolution - in the bacteria-to-man sense is true. I am not convinced that the observable processes that we have (microevolution) are sufficient to explain the large scale changes that the fossil records show (macroevolution). Which is why I used the example of the Northern Flicker; there is no crossing over of any boundaries between "kinds". It is an example of evolution that I would think even a YEC could accept. Even within the genus, It appears that the entire genus is extant except for one subspecies of C. auratus. So we should be able to use this example to talk about phylogenetics.

Do you accept that this genus originated from a single ancestral population or do you believe that God created them as is? Either way do you not start with an assumption?

[qs]Yet you still need to add the initial evolutionary assumptions, therefore anything claimed from such is not a scientific statement since it is based on a mere unverified assumption, (unless assumptions are now claimed as valid science......). This overthrows any and all arguments. [/qs]

Of course you need to start with some assumptions. But then you test those assumptions. I don't mean to sound like I am taking shots at your education, but it doesn't seem to me like you understand. I am not saying that you need to "get with the program" and accept evolution in order to succeed at your career. But I am saying that you need to understand how science really works - and I am sorry, but it seems to me that you have this attitude that you have a "new", better way of doing science and those that are doing science now are merely dupes who have strayed down the path of "assumption science". This is why I am interested in engaging you in this discussion, not to convert you to an evolutionist - so please don't take me the wrong way. And if I have misunderstood you, I am sure we will clear it up quickly.

[qs]Even in your reply you have exposed the uncertainty of the "history" that can be deduced... SInce not ALL the mitochondrial DNA comes from the mother then there is a level of doubt about it ancestry, hence nothing can be claimed for certain. It is merely taken on faith. I am sorry, I don't deem assumption-based faith "science" as anything resembling the scientific method or the empirical sciences.{/qs]

This is the kind of comment that leads me to believe what I said above. ALL science is uncertain. ALL scientific theories are subject to modification or can potentially shown to be false. Falsification is essential to any scientific theory. A good scientific theory always has a level of "uncertainty". You do know that the atomic theory is "just a theory" and there is "uncertainty" about it. Some evidence could come along and completely disprove the atomic theory - although extremely unlikely. So just because there is some "doubt" or some "uncertainty" does not in the least invalidate the conclusion. What does invalidate a conclusion is contrary evidence. Not speculation - evidence.

How is your view as a YEC different from the "assumption-based faith science" that you are opposed to?

[qs]Point one shows that it is reasoning within a circle.... Would you claim that such thinking is logical?[/qs

I showed you it was logical in the case of the Northern Flicker. Why would it not be logical to conclude that that the Yellow-shafted version and the Red-shafted version came form an original single population? Why would it not be logical to assume that any particular bird had parents that had passed on their genetic material? If they each had parents, then you could trace that parentage back through time. Actually you would say that your hypothesis is that those two populations diverged from a single ancestral population and then you test that hypothesis.

[qs]Point two shows how the method is arbitrary and therefore includes a level of doubt as to which is real. You have compounded this by claiming that it is up to the researcher, hence with such a high degree of control over the outcome who is to say that the results reflect reality at all?[/qs]

So ... who should determine the methodology? Do you think that a researcher just arbitrarily pulls a method out of the air? Let's say your assignment is to develop a new crop variety that has better disease resistance. How will you approach it? Will you will arbitrarily pull some method out of the air? Of course not! You will use a methodology that another scientist has developed and shown to work. Then you test to see that that method worked. Then you report your results. In your report you explain your methodology and the justification for it. Let's say the variety you developed was to be resistance to a rust fungus, but the organism you arbitrarily chose to test it on was a bacteria. When you reported that the resistance was positive, it would immediately be obvious to others that your methodology was flawed since you tested for resistance to a fungus using a bacteria. I made this example ridiculous just for illustrative purposes, not to imply you would actually do that. Scientists scrutinize each other's methods and make judgments about the validity of the results. How else should it be?

[qs]Consider this when you claim that scientists allow it, since it is an attempt at argumentum ad populum which is a logical fallacy.[/qs]

I wish you would break my quote up so I knew what I said that you were referring to. I don't know where I claimed that scientists "allow" anything. I never even used the word allow, so I don't know what you are referring to.

I will break down my rebuttal to the OP into 4 main points:

1. Agreed that DNA similarity receives a lot of undeserved hype (for example human / chimp 95% similar) which really doesn't tell us a whole lot or confirm ancestry. But it is the differences, the changes, that are useful in determining history. This is not based upon circular reasoning, rather it is a hypothesis that can be tested and either verified or discarded. Every scientific investigation begins with a question, a hypothesis. The null hypothesis is typically the assumption that that hypothesis is true. The alternate hypothesis is typically that the hypothesis is not true or not supported by the evidence. This is basic, foundational scientific investigation.


2. No single method is suitable for developing a phylogeny. Multiple lines of evidence are considered from differing disciplines. Molecular studies, morphological studies, paleontology data, geographical data, homology and the concept of parsimony are all considered when developing a phylogenetic tree. Yes, there are uncertainties. Yes, there are disputes and difficulties. But that makes it no less valid of a science. In order to invalidate an accepted phylogenetic hypothesis, present evidence that the hypothesis is incorrect.

3. Determining the proteome of every cell type at each stage of development would be too cumbersome to use as a comparative tool. Methods have been developed and tested that, at the present time, are considered effective. These methods are NOT arbitrarily chosen, but are tested, examined, and reported by the researcher for scrutiny by other scientists.

4. mRNA is not particularly stable and subject to degradation. It would not be especially useful to use it as a tool for comparing organisms. In addition there are many factors that would alter the products of mRNA that would be difficult to detect and utilize for this application.


HBD


1. Yes you are quite right everything begins with an assumption, (of which many people, scientist and layman alike forget). I guess what we can hope for is the realization of the premise "is this assumption the most logical assumption that can be made in this instance with all the current knowledge known". I believe that the assumption of God is the most logical and simplest (Occams razor, for those who prefer that), which would make it much superior to anything the naturalist can imagine up.... Consider the formation of the universe with its fine tuning and the assumptions required, then the complexity of life and the multitudes of assumptions required for its formation, then consider the multitude of assumptions required for evolution... ;) The assumption of God, is a much more simplistic and therefore logical choice.


2. Either way seems fine with me. I very much accept change within a species, therefore we can get the many varieties of dogs via one or two ancestral breeds, (however please keep in mind they are still dogs ;) ). Either life was formed as is, or was formed with the capacity to adapt within its limits... (ie- humans won't normally grow a 3rd arm or wings etc).




3. Assumptions are required in the formation of the hypothesis, and as you said it is tested. However assumptions are not allowed in the formation of the conclusion, doing such defies the scientific method and also defies the entire point of testing your hypothesis. This is the kind of assumptions I oppose, when you assume the conclusion, (which is what evolutionists do), then you are not following the scientific method and therefore not being scientific.

The evidence itself should depict the conclusion empirically, I don't allow imagination to fill in the gaps, and if it is required it must always be with caution and in doubt. Unfortunately this was the biggest change to science evolution brought about.... it was the revival of the assumption-science, where I observe something and then I can assume X caused it... for example we find fossils that look similar we can assume "evolution did it", much like if I observe the sun and stars going round the Earth I can assume that the Earth is the centre of the universe. Of course this has been shown to be wrong which is my point. Assuming the conclusion means our own tiny minds are creating what we deem to be the truth. Who is to say that we know the full picture? How can we make such a judgement on what the conclusion is if we do not have all the information? Therefore doing such makes the "truth" a relative truth which is not actual truth.

This is why I am a big fan of empiricalism and why I don't allow assuming the conclusion, of course in a discussion I can write about the potential causes for X, Y and Z however until empirical verification they will always remain potential causes, not actual ones.



4. Yes there is speculation to some degree, however with empirical verification laws are derived. Empirical verification would lessen the level of doubt because it is an empirical, physical demonstration of the claims being made. What you have written has demonstrated what I was claiming before, with assumption-"science" (assuming the conclusion), nothing can be claimed for certain because there is no empirical verification to back up claims. This basically devolves science to the level of whimsical debate where truth is decided on ideology rather than hard facts.... (which ironically is how Darwin introduced evolution in his book, there was very very little empirical evidence, if at all, and as far as I know from asking many it wasn't verified empirically... Darwin introduced evolution as an ideology and that is how it continues to exist).



5. I for one don't assume the conclusion. For example

Premise 1: The universe is expanding
Premise 2: If the universe is expanding then there must have been a point of origin
Premise 3: Therefore the universe (time and space), has a begining
Premise 4: If the universe, (time and space), has a beginning then matter and energy would have a beginning
Premise 5: Natural law dictates that energy cannot be created
Premise 6: Therefore the beginning of energy defies natural law,
Premise 7: Supernatural things defy natural law
Premise 8: Therefore since the beginning of energy defies natural law this implies a supernatural cause for the beginning of energy in this universe

I am agnostic as to who / what this cause is hence my assumption here is verified by logic and science.




6. You're dodging my point, with a red herring which has nothing to do with what I am saying. I demonstrated how DNA similarity is determined on a method which is based on circular reasoning. What do you say to this? (I do not care about the "Northern Flicker" etc, I want you to address this point or to at least not give a red herring answer and leave it blank).


7. Huh? How does what you're saying have anything to do with my claims? You should at least appreciate that the method being used for claiming ancestry of origins based on similarity of DNA sequences, is fundamentally flawed of which nullifies it as evidence to go by. (I would also put forward that it is mass deception / indoctrination tool).

The method can still be used to locate similar sequences in organisms, since the assumptions being made and the flaws in the method do not prohibit this from occurring. Again it is the assumption in the conclusion I do not allow.... see what I mean, we observe similarities in DNA and then evolution is assumed as the conclusion (see point 3 and 4)... See how this brand of voodoo "science" permeates evolutionary ideas.

If you start with a flawed method, what will you get? Flawed results..... None of what you said makes any sense pertaining to what I said. I am scrutinizing the method right now and I have demonstrated to you that it is fundamentally flawed and that any claims about origins from this "evidence" would not be logical.


8. This is what I was writing to

"Remember, no one should be basing an evolutionary history on only one criteria. There should be multiple lines of evidence that agree with each other. There is often disagreement about phylogenies because of contradictory evidence or inconclusive evidence. So yeah, in some ways it is arbitrary. Which gene they choose, how they choose to splice it, how they choose to hybridize it (align it). But all these choices are outlined in scientific papers. Other scientists read them and critique them. They write rebuttals based on their own lines of evidence. Next time you see a claim of evolutionary relationship, pick up the actual paper (not a journalists summary) and use your biotech training to analyze the methods used to reach the conclusion they did. I guarantee it will be more than "We just arbitrarily thought this based on our own assumptions."

You seem to believe in the infallibility of scientists in that they are the be-all-end-all of knowledge... Claiming "peer review" is not a catch all argument which allows any claim to be made with wanton abandon and yet still allows the full creditability which science has. Peer review is fundamentally flawed in that it is undertaken by people. People are flawed, scientists are flawed. The biggest flaw occurs in that every person is biased considering that most scientists are evolutionists what do you think this means..... Its not a hard question. However it may be hard to admit ;)

There is a paper claiming about the origin of multicellular life, it was peer reviewed yet it is the biggest load of #### I have ever seen.

- they used a centrifuge, (a centrifuge didn't exist before multicellular life, nor does nature have the potential to create that environment)
- over time the inner cells replicated and pushed the outer cells out, showing that they were not a "multicelluar organism", instead they were merely cells arbitrarily stuck together (via the centrifuge). As the outer cells fell off, this was claimed to be "reproduction".... Serious?
- cells that died due to decreased nutrient supply or the force from the centrifuge were claimed to be cell specialization... A dead cell is a specialization of a healthy cell... who knew?
- they worked out the fitness levels and STILL the fitness level for the single cells were higher than that of the "multi-cellular" therefore meaning that selection would favour single celled organisms and that mulit-cellular organisms wouldn't "evolve" anyway... (so their experiment disproved evolution)

Even with multiple criteria if they follow the same assumptions then of course they will all fit together because you've allowed the same assumptions to conform with what you want, (see the biggest problem of assuming the conclusion is that it allows us to insert our own biases into the equation, hence what we want to be true will be more likely to be "true" when we can assume what we want to be "true").



I can guarantee to you that if you remove your Darwinism glasses and see the evidence and claims for what they really are, (without your preconceived assumptions) then you will see that they actually do claim what you said.

#13 joman

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Posted 12 July 2012 - 12:11 PM

These things are not inexplicable. We may not understand all cellular processes, but that doesn't mean they can't be figured out.

I said they are not explicable by mechanistic means. The view that one day all things can be explained mechanistically is a faith based view not a scientific one.


So ... this is your first point about biology? I believe in the existence of the soul also, but it has nothing to do with biology.

I think the existence of the soul is the primary purpose of all biology. And, that all body cells serve the soul. Therefore, I reason that many processes are regulated by the soul and not by physical mechanisms.

You need to read the whole of Job chapters 38 - 41. They culminate in God saying "Do you have an arm like God's, and can your voice thunder like his?" God is not making declarations about biological mechanisms. He is comparing man's puny existence to his immense greatness. Is this one question all that difficult? All you need to do is Google it and you can know when mountain goats give birth and when deer have fawns. Are you (or is God) really suggesting that reproduction in these animals does not have a mechanism? I think you are taking this scripture completely out of context to fit your "notion".

I advise readers to read the scriptures I referred to that apply to this topic as I pointed out.
As for reading the whole of Job, and because of having done that, with comprehension, I am aware that all of Job is not in any way contextual to this particular topic. I selected a few verses that are on topic and have no clue as to what point you suppose you are making in your quote which I have cited above.


This is an interesting thought. However, the evidence that you use to support your notion is that God did not create wildness. Yet Gen 1:25 says that "God made the wild animals according to their kinds, the livestock according to their kinds, and all creatures that move according to their kinds." Any other evidence.

Genesis 1:25 And God made the beast of the earth after his kind, and cattle after their kind, and every creeping thing of upon the earth after his kind; and God said that it was good.

Note that it "was" good, not "is" good.
Note that a beast is not defined as being wild. Wild means unruly, rebellious, untamed.
Thus the quote given using the words "wild animals" is a modern corruption probably invented to make the scriptures appear to be in accord with modern notions of evolution, survival of the fittest etc.
This quote is provably corrupt because it produces contradictions, such as, "wild animals" are good, and the following...

Genesis 6:7 ...It repenteth me that I have made them.

This shows that the "good" that man and beasts once were had become "not good."

Genesis 6;13 ...the end of all flesh is come before me; for the earth is filled with violence through them...

This verse shows that all flesh was participating in filling the earth with violence contrary to the former goodness.

Genesis 6:12 And God looked upon the earth, and , behold, it was corrupt, for all flesh had corrupted his way upon the earth.

Note the wilfullness of the corruption. The males were responsible among each kind.
The way of the creatures had changed and violence became the result.
Survival of the fittest became the law of the unruly jungle.

Genesis 9:2 ...the fear of you and the dread of you shall be upon every beast of the earth....

Genesis 9:3 Every living thing that moveth shall meat for you; even as the green herb have I given you all things.

Genesis 9:5 ...your blood of your lives shall I require; at the hand of every beast shall I require it...

Thus, we see that formerly man was authorized only to eat herbs.
And, that beasts had been eating man.



Nonsense. You believe they had genetic engineering more than 6000 years ago? And do you have any idea as to the diversity of known dinosaur types? Humans in an agrarian society were able to accomplish all that? We don't have that capability today, genetic engineering is still crude and clumsy (yet developing rapidly). What evidence is there of the types of engineering and breeding facilities that would have been needed? Where is evidence of the terror arenas? And why do you think T-Rex was not fit for survival? No limbs suitable for feeding itself? He could swallow many of the other creatures of his time in one gulp - which is how many lizards today still feed. They don't use limbs to feed.

I will get back to you readers about these comments, since, I have to make time to do so. But, they aren't formidable questions and apparently many folks aren't critiquing the nonsense modern fable makers masquerading as scientists are publishing as cartoons and whatnot about ages of which there is no shred of evidence of ever having occurred as fabled by the evolutionists and mechanistic thinkers of today.



No, makes no sense. Satan may be a liar indeed, but the Creation certainly is not. If the Creation was a lie, that would make God a liar, since it is his revelation. The "opposite" is not what we observe in the fossil record. And besides, who said anything about early life being primitive, stupid and banal. Would you consider bacteria to be stupid? They are amazingly complex and perfectly adapted to do what they do. Simple (as in a simple body plan or few differentiated tissues) is not the same as stupid and basal. Its a meaningless argument.

This hardly needs a response since the primal state of all things is a very basic fable of evolutionism.



My wife mated with me so ... idk Posted Image

I appreciate the humor but, it greatly misses the point.
Beastiality is no natural, never was and never will be.
Surely intelligent readers are aware that it is against nature to mate with other kinds of creatures.

#14 herebedragons

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Posted 12 July 2012 - 08:12 PM

Hi Gilbo,

I understand your need for empirical evidence. I agree that is what science is about. But then you say:

I believe that the assumption of God is the most logical and simplest (Occams razor, for those who prefer that), which would make it much superior to anything the naturalist can imagine up.... Consider the formation of the universe with its fine tuning and the assumptions required, then the complexity of life and the multitudes of assumptions required for its formation, then consider the multitude of assumptions required for evolution... Posted ImageThe assumption of God, is a much more simplistic and therefore logical choice.



I truly affirm the scripture in John 1 "Through him all things were made; without him nothing was made that has been made." This entire universe owes its existence to Almighty God who made everything through Christ Jesus. I do not doubt that at all. But when it comes to understanding the natural world we can do it without invoking "God-did-it". I can look at a flower and declare "My God! What a marvelous and magnificent creation you have given us. Its beauty is beyond compare." Now let's see how it works. And I can learn the parts of the flower, how it reproduces, biological systems etc. If there comes a point where I no longer can understand something in the design or function of the flower, there is no need to invoke "God-did-it". It is just something that in time someone may figure out. I expect and assume if you will, that there is a naturalistic explanation for naturalistic processes. It is the same for historical processes.

You made much in your post about empirical evidence, and rightly so. It is all we as scientists can deal with. But the "assumption of God" is not empirically testable. It is only an answer when we come to a dead end in our knowledge. But our knowledge grows and our understanding is always increasing, what is a dead end today is answered tomorrow. When we invoke God on those dead ends, and then later find that there is an explanation, IMHO, we cheapen God and his craftsmanship.

You're dodging my point, with a red herring which has nothing to do with what I am saying. I demonstrated how DNA similarity is determined on a method which is based on circular reasoning. What do you say to this?



It seems you are dodging my point. I said No! it is not circular reasoning for the following reasons ...

(I do not care about the "Northern Flicker" etc, I want you to address this point or to at least not give a red herring answer and leave it blank).



But this is an example of the reason why I don't think it is circular reasoning. Which by the way is an empirical example.

Observe: two populations of similar but different birds that interbreed when ranges overlap
Induce: Hypothesis: These two populations descended from a common ancestral population.
Deduce: Testable prediction: The DNA should be very similar with only small genomic changes
Test: Compare DNA sequences
Evaluate: If the prediction is true, then the hypothesis is confirmed

So no 'red herring' here, I am totally not dodging your point. I am saying NO it is not circular reasoning because ... I am not just simply hand-waving it away, but giving you the logic behind my reasoning.

In the case of this paper which you refer to, perhaps they overstate their case, but that is not how science in general works.

7. Huh? How does what you're saying have anything to do with my claims?



You stated:

Point two shows how the method is arbitrary and therefore includes a level of doubt as to which is real. You have compounded this by claiming that it is up to the researcher, hence with such a high degree of control over the outcome who is to say that the results reflect reality at all?



My response was ... "Who should determine the appropriate methodology to use besides the researcher?"

You seem to believe in the infallibility of scientists in that they are the be-all-end-all of knowledge...



Certainly not! Which is what the peer-review process is about. Is it perfect? no. Is there a better way? Idk ... The peer review process is supposed to identify flaws in methodology and is done by other experts in the field. So you claim that the peer review process is biased, would you be unbiased when reviewing an evolutionist paper?


I can guarantee to you that if you remove your Darwinism glasses



I have contacts :))

and see the evidence and claims for what they really are, (without your preconceived assumptions) then you will see that they actually do claim what you said.



So I am right?? :)

Seriously. About 5 years ago, I was a YEC. Mostly by default; I had never really given it much thought. It was just what Christians believed. But I began actually looking at the facts, and exploring the evidence and I came to the conclusion that the earth was not young and there was substantial evidence that the theory of evolution was, in fact, true. I must say, that it shook my faith. I was told by the likes of Jonathon Serfati and Ken Ham that if evolution were true, then Genesis was wrong and if Genesis was wrong, then the whole Bible was wrong. This began my quest to reconcile my faith and the empirical evidence that I could no longer deny. I no longer feel torn, but believe I have found a middle ground. I know you see it as selling out, or compromising. But that is not how I see it. I see it as reconciling the revelation of God's Word with the revelation of God's creation.

Anyway, I really appreciate this discussion. I participate on another forum, and while the scientific discussion is much more in-depth, I really can't discuss spiritual things like this over there. So its good. Thanks

HBD

#15 herebedragons

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Posted 12 July 2012 - 09:46 PM

I said they are not explicable by mechanistic means. The view that one day all things can be explained mechanistically is a faith based view not a scientific one.



How is your faith-based approach different from the one you are criticizing?

I think the existence of the soul is the primary purpose of all biology. And, that all body cells serve the soul. Therefore, I reason that many processes are regulated by the soul and not by physical mechanisms.



What evidence do you present to support this? Name some of the processes that are regulated by the soul.

I advise readers to read the scriptures I referred to that apply to this topic as I pointed out.
As for reading the whole of Job, and because of having done that, with comprehension, I am aware that all of Job is not in any way contextual to this particular topic. I selected a few verses that are on topic and have no clue as to what point you suppose you are making in your quote which I have cited above.



I advise readers to not take scriptures out of context and try to make them say what you want them to say.

You quoted one verse, joman; Job 19:1 Knowest thou the time when the wild goats of the rocks bring forth? or canst thou mark when the hinds do calve? which I pointed out was out of context and has nothing to do biological mechanisms but is instead, in context, comparing God's great power and glory to Job's puny, insignificant existence.

Note that it "was" good, not "is" good.
Note that a beast is not defined as being wild. Wild means unruly, rebellious, untamed.
Thus the quote given using the words "wild animals" is a modern corruption probably invented to make the scriptures appear to be in accord with modern notions of evolution, survival of the fittest etc.
This quote is provably corrupt because it produces contradictions, such as, "wild animals" are good, and the following..



Creation "is" not good?

I quoted the NIV that referred to "wild animals". You consider the NIV to be corrupt. To have intentionally mistranslated the ancient texts to accommodate evolution? Come on... do you think maybe its you that is distorting scriptures?

"wild animals" are not good? doesn't God care for the animals. Even a sparrow can't fall to the ground with out the Father knowing. Lions, tigers, sharks etc... are all evil, corrupt creatures because they are "wild"? Because they eat meat? I hardly think so. They are beautiful and glorious creatures.

I will get back to you readers about these comments, since, I have to make time to do so. But, they aren't formidable questions and apparently many folks aren't critiquing the nonsense modern fable makers masquerading as scientists are publishing as cartoons and whatnot about ages of which there is no shred of evidence of ever having occurred as fabled by the evolutionists and mechanistic thinkers of today



They aren't formidable questions, huh? You are going to produce evidence of genetic engineering thousands of years ago and dinosaur death matches? Or just more speculation? Its ok to think about stuff or come up with theories, but you need to back them up with real evidence not just conjecture.

This hardly needs a response since the primal state of all things is a very basic fable of evolutionism.



It does require a response. Your whole point was that evolution teaches that creatures started out "basal and stupid" and evolved into something good. Instead, you think the opposite is true, that God made animals "good" and they have now devolved to a primitive state. My response was that evolution doesn't teach that "primitive" creatures were basal and stupid. But every creature that has lived on this earth is glorious and magnificent in its own way. Evolution may teach that life started out simple, but simple is a relative term. How "simple" is a sponge, or an anemone, or a Trilobite, or a nematode, or a bacteria. Every creature is "good" in its own way. To refer to them as basal and stupid is an insult to the creator. And my other point was that the fossil record does not show "more better" creatures devolving into more "primitive" creatures, it shows "primitive" creatures evolving into more "complex" creatures.

I appreciate the humor but, it greatly misses the point.
Beastiality is no natural, never was and never will be.
Surely intelligent readers are aware that it is against nature to mate with other kinds of creatures



I didn't miss the point, it was just a well ... a dumb point. Here is your point:

There never were stupid idiots evolutionism calls Neanderthals that wandered around without tools, or manners, or nobility for 1oo,ooo years of meaningless existence. It is a sill notion on the face of it. And to think that noble examples of mankind mated with such gross creatures as evolutionists present neanderthals to be is patently ridiculous since, no noble person, possessing language, history, tools and good looks is attracted to brutes.



You say there never were Neanderthals. Well we have fossils that we have called Neanderthals, so, whatever you think they are, man or beast - they are Neanderthals. And there you go again with the name calling of God's creatures - "stupid idiots, gross creatures, brutes." And evolutionists that believe that early humans and Neanderthals mated, well they don't think that humans were "noble examples of mankind" possessing "language, history, tools and good looks." They were just as "stupid, gross and brutish" as their Neanderthal cousins. Oh and if they could mate and have viable offspring, that would have made them the same species or at least very, very closely related. So the point was ... pointless (and off topic).


HBD

#16 gilbo12345

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Posted 12 July 2012 - 10:31 PM

Hi Gilbo,

I understand your need for empirical evidence. I agree that is what science is about. But then you say:

[/font][/color]

I truly affirm the scripture in John 1 "Through him all things were made; without him nothing was made that has been made." This entire universe owes its existence to Almighty God who made everything through Christ Jesus. I do not doubt that at all. But when it comes to understanding the natural world we can do it without invoking "God-did-it". I can look at a flower and declare "My God! What a marvelous and magnificent creation you have given us. Its beauty is beyond compare." Now let's see how it works. And I can learn the parts of the flower, how it reproduces, biological systems etc. If there comes a point where I no longer can understand something in the design or function of the flower, there is no need to invoke "God-did-it". It is just something that in time someone may figure out. I expect and assume if you will, that there is a naturalistic explanation for naturalistic processes. It is the same for historical processes.

You made much in your post about empirical evidence, and rightly so. It is all we as scientists can deal with. But the "assumption of God" is not empirically testable. It is only an answer when we come to a dead end in our knowledge. But our knowledge grows and our understanding is always increasing, what is a dead end today is answered tomorrow. When we invoke God on those dead ends, and then later find that there is an explanation, IMHO, we cheapen God and his craftsmanship.



It seems you are dodging my point. I said No! it is not circular reasoning for the following reasons ...



But this is an example of the reason why I don't think it is circular reasoning. Which by the way is an empirical example.

Observe: two populations of similar but different birds that interbreed when ranges overlap
Induce: Hypothesis: These two populations descended from a common ancestral population.
Deduce: Testable prediction: The DNA should be very similar with only small genomic changes
Test: Compare DNA sequences
Evaluate: If the prediction is true, then the hypothesis is confirmed

So no 'red herring' here, I am totally not dodging your point. I am saying NO it is not circular reasoning because ... I am not just simply hand-waving it away, but giving you the logic behind my reasoning.

In the case of this paper which you refer to, perhaps they overstate their case, but that is not how science in general works.



You stated:



My response was ... "Who should determine the appropriate methodology to use besides the researcher?"



Certainly not! Which is what the peer-review process is about. Is it perfect? no. Is there a better way? Idk ... The peer review process is supposed to identify flaws in methodology and is done by other experts in the field. So you claim that the peer review process is biased, would you be unbiased when reviewing an evolutionist paper?


[/font][/color]

I have contacts Posted Image)



So I am right?? Posted Image

Seriously. About 5 years ago, I was a YEC. Mostly by default; I had never really given it much thought. It was just what Christians believed. But I began actually looking at the facts, and exploring the evidence and I came to the conclusion that the earth was not young and there was substantial evidence that the theory of evolution was, in fact, true. I must say, that it shook my faith. I was told by the likes of Jonathon Serfati and Ken Ham that if evolution were true, then Genesis was wrong and if Genesis was wrong, then the whole Bible was wrong. This began my quest to reconcile my faith and the empirical evidence that I could no longer deny. I no longer feel torn, but believe I have found a middle ground. I know you see it as selling out, or compromising. But that is not how I see it. I see it as reconciling the revelation of God's Word with the revelation of God's creation.

Anyway, I really appreciate this discussion. I participate on another forum, and while the scientific discussion is much more in-depth, I really can't discuss spiritual things like this over there. So its good. Thanks

HBD


I am glad you are enjoying the discussion.

I am not proposing a "God did it" conclusion as to "fill in the gaps". I am proposing deductive reasoning by which evolution is falsified and a creator is proven. For example if natural laws or prerogatives of reality are defied then that logically implies a supernatural cause, since a natural cause abides by natural law only a supernatural one can defy it.

Point 5 gave you a logical progression of premises by which if they are all true then it logically follows that there was a supernatural agent for the creation of the universe. Here is another for the falsification of evolution, (this is from another thread so if you wish to discuss it in detail I ask you to place your questions in the chirality thread)

Premise 1: The evolution of life origins is claimed to be 100% natural complying to natural laws and prerogatives of reality
Premise 2: DNA / RNA / Protein are made up of chiral molecules (nucleotide bases / amino acids)
Premise 3: In nature chiral molecules exist as enantiomers
Premise 4: It is a natural prerogative that enantiomers are always found with a 50-50 mix, (ie- there can never be an uncaused occurance of a 100% solution, since 100% solutions made in a lab are claimed to revert back to the 50-50 mix over time)
Premise 5: The formation of DNA / RNA / protein requires only one form of enantiomer, and the addition of one "wrong" enantiomer wrecks the molecule
Conclusion: Therefore the formation of DNA / RNA / protein defies the natural prerogatives of enantiomers. Therefore the naturalist claim of the origins of life defies the naturalists expectation of 100% compliance to reality and natural law.
Premise 7: Only the supernatural can defy natural laws or prerogatives of reality
Ultimate Conclusion: The origin of life had a supernatural cause


A very simple one can be

Premise 1: DNA contains information, including the information for the structures to encode and decode and make use of said information
Premise 2: Information like that found in DNA requires intelligence, (ie- it doesn't arise uncaused or from a purely natural cause- like the rain or the waves on the beach etc)
Question: What was the intelligence that created the information within DNA?


Consider your flower analogy. Consider the complexity of cellular mechanisms and the inter-connectedness of parts from which no gradualistic evolution can occur. I mention this in another thread (well actually quite a few and can elaborate if you need me to). Of course a theistic evolutionist can claim "God did evolution" however I am sure others here would support the claim that that conclusion is not justified via Biblical representation of God. Therefore it would be a case of what "God" are you talking about? Furthermore this would be exactly the same reasoning as "God did it".

What we know about how life operates on the cellular level defies what is claimed with evolution. It is this evidence I base my own assumptions on, yes I cannot escape assumptions however at least I have a solid basis for doing so, unlike the evolutionist who continually must seek to defy reality and / or natural law in order to uphold their worldview.



Yes God cannot be empirically tested however the conclusion of God can be logically derived as the null hypothesis. Please regard point 5 in the post you responded to, whereby I demonstrated that our empirical knowledge of reality gives evidence of a supernatural cause. Yes it cannot be confirmed that God is this cause, however what we can confirm is that a supernatural cause does indeed exist. This is the same with the chirality premises and the DNA with information. All the knowledge we have on reality one way or another points to a supernatural creator.
It is by this deductive method that I do not cheapen God since the conclusion is there for all to see. When you find something that defies natural law, (which by definition is supernatural) then the only way to prove that nothing was supernatural about it is to change the law to accommodate the defiance. Considering that natural laws / prerogatives of reality are based on repeated empirical experiments, (that is why they are laws), then I feel quite safe that what I am claiming won't be found wrong any time soon ;)



Yes you are dodging my point since I am talking about the process of alignment in DNA matching programs I am not refering to what you are claiming hence what you are citing IS a red herring. Please go back and re-read my original point and respond to that, (as I said I do not care about the Northern Flicker)

What I do care about is how evolution is assumed to occur which allows the addition of gaps for the alignment process, then aligned DNA is used as evidence for evolution.... Despite the fact that you had to assume evolution occurred to allow the method you used. It is a very simple demonstration and the fact that you're talking about some other totally irrelevant topic says to me that you do realise how absurd it is, you just don't want to deal with it... so you posit a different scenario instead... (which is dodging the question).




The paper only served to demonstrate how peer review is a total sham. Of course there will be some honest people, but then there will be some dishonest ones, and then you also have the honest ones but because they are fixed on their worldview they cannot perceive anything else outside of it, ie- tunnel vision / limited by bias.

The first video of this blog thread gives a very good demonstration of tunnel vision, (with Richard Dawkins no less).

http://subversivethi...Jime's Iron Law


Personally I would rather it be forum reviewed ( not like this forum lol) as in reviewed by more people than just the scientists and their mates, furthermore make the review itself public so people can see what is going on.. This would allow for increased academic integrity since I am sure there will be less dodgy stuff when it is open to the public eye... I am sure if the paper I spoke of was publicly reviewed it wouldn't have been given a minutes notice.



Who should determine the methodology beside the researcher? As I said before, just because researchers allow a flawed method doesn't make that method correct. In fact it means that the researcher isn't being scientific, therefore any conclusions drawn are also not scientific. I have demonstrated that the method is inherently flawed, intellectual integrity would demand that the method be revised or disused.... Yet this doesn't happen... Hmm



I am glad that you are content within your worldview, however I would urge you to perhaps re-examine the "evidence" for evolution without giving in to the media hype and evolutionary assumptions. I am quite sure if you read through a few of the other threads on here, you'll begin to see that there is much to doubt evolution that is not being shared publicly.

#17 joman

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Posted 13 July 2012 - 06:08 AM

All quotes by herebedragons.

How is your faith-based approach different from the one you are criticizing?

The difference is that I don’t pretense my faith about creation, my understanding of purpose, and such things as science. I do expect there to exist no contradictions between the natural sciences and the Holy Bible. I partly do because of my own curiosity about things scientific and technological. However, I also do so to help other Christians see that many of the theorizing and suppositions of modern science are not scientific, and are apparently designed to disagree with scripture, as the Bible predicted would occur at this time. True science as I comprehend it, is solely based on valid and repeatable scientific experimentation. If we discern and maintain separation between assumption and fact then the non-scientific junk is exposed, and can be minimized.

What evidence do you present to support this?

This was one of my main points. I believe that if scientists quit wasting their minds trying to subject experimentation to fit the paradigms of macro-evolution and instead aimed then there are many experiments that can be done to determine the truth about life. I have no problem with science being regulated by systematic, mechanistic experimentation. But, like all real science, the outcome is technology not fantasies. And with all technology we discover that purpose remains the primary thing since what we do with science magnifies who we are at heart. When Craig Venter and his group synthesized the genome of the simplest known organism and inserted it into a cell empty of the genomic information base, he approaches the discerning of the existence of the soul. If a cell has all that it needs to live but, doesn’t live then something is missing.
The reason the subject of the existence of the soul is important, I think, is because, it is analogous to determining the existence of God, in that, it also is unseen, yet, is implicated,the difference being that experiments about the existence of the soul could be done, but experiments about God cannot.

As Jesus said of the spirit, that it is as when a wind blows and moves things about, in that, the wind is unseen, but, no man pretends ignorance of its existence. That is, the Spirit effects things we see, nad the spirit of man effects deeds, and the soul effects functions of the body. So, yes, I suggest that experiments can be presented to rationally determine if all life associated with mechanisms can be expected to be explainable solely by mechanisms.
I have already pointed out that there have been studies to determine where the will of a person resides in the body, as in, where is the organ of the will of man?
Are emotions simply related to mechanistic functions of the body? Are emotions, for example, unrelated to what occurs outside the body?
I don’t see how we would ever suppose that. For, we know that when we emote we trigger biological mechanisms. It is obvious, isn it not, that the particular emotion was was the original trigger, and was triggered by outside experiences such as, a person observing some poignant event of life, or upon hearing a suggestion of another person? And, are those outside influences soulish ones?
Not to sound, paranormal, but, I do think that a person’s sense of being loved, their personal faith in God, and other soul things effect healing of ones body by encouraging the body authoritatively, to not give up, but, to instead maintain proper function. I do not think the soul can itself be viewed experimentally, but, as with many scientific conclusions, the evidence of science often demands a rational verdict about unseen things. Compare that with how macro-evolution adherents suggest they know all about whole environments of some imagined ancient age, solely because they dug up a few rocks, and ended up producing PBS cartoon specials describing creatures, their habits, and thier habitats.... all sight unseen.
So, I think scientific study of the existence of the soul is obviously a far more pertinent and therefore, rational use of the time and thought, of real scientists.

#18 joman

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Posted 13 July 2012 - 06:35 AM

Quotes by jerebedragons

Name some of the processes that are regulated by the soul.

Instincts. Emotions, attitudes, body movement, regulation of food intake, wilfulness, etc etc etc. Either man claims such things are biologic mechanisms functioning only mechanistically, or, they are representative of soulish things triggering biologic mechanisms to correspond with the dictates of one's own soul (will).

I advise readers to not take scriptures out of context and try to make them say what you want them to say.

I presented the scriptures and that is as fair minded as I can be. If a person reads the narrative of Genesis where Jacob statistically effects the outcome of the sheep of his flock,they should be able to tell that the scripture is saying that the straked poles Jacob used, caused the offspring of his flock to tend to be spotted. If you can’t see that then maybe I can point to other examples.

You quoted one verse, joman; Job 19:1 Knowest thou the time when the wild goats of the rocks bring forth? or canst thou mark when the hinds do calve? which I pointed out was out of context and has nothing to do biological mechanisms but is instead, in context, comparing God's great power and glory to Job's puny, insignificant existence.

THis claim of yours is out of context.
I gave my reasons for presenting those scriptures. And you have not proven me wrong, have you?
Is not God saying to man, that we don’t know the time when wild goats of the rocks bring forth? and that we can’t mark when the hinds will calve?

Now you said such knowledge can be gained by googling it, well? Have at it!... and get back with me with your means of predicting such things.

I claim that the birth process of beasts such as hinds, and goats, is biological.
Your claim that such things are not biological is hard to accept since, how are offspring brought forth if not by biological mechnism?

Are you unaware that the biological study of reproduction, growth in the womb, and birthing they are deemed to be notably unpredictable, and unprovable as to how all the many decisions being made throuhout the processes are accomplished and timed?

I think it possible that you have assumed I am ignorant, because of the way I approach these topics.
I approach these things differently than you do, and many others, and I do so purposely, because I think many of your arguments about dna, splicing, aligning, comparing for example and etc, are useless, since, none of it proves anything about the faith based belief in macro-evolutionary events, past, present or future.
Your flicker bird reasoning was nothing new, was it?
When you’re done with these cellular things, and all the data is assembled, we will not then discover that all creatures departed from the ark of Noah? No fact of science forbids that conclusion and many facts support it.
If I were a young biologist today, I would spend my time proving the truth rather than waste time trying to prove the fabulous theories of unscientific philosophers.

#19 joman

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Posted 13 July 2012 - 07:20 AM

Quotes by herebedragons.

Creation "is" not good?

This misrepresents what I clearly stated, The creation... “was” good, and is not now good, but is corrupted by, violence, bloodshed, diseases, short life spans, sinful behavior, rebellion, inefficiency, earthquakes, volcanic eruptions, famines, pestilences...need I go on? None of which things are as God created them to be. But, all as evolutionists wish it always was so they can claim there is no God, or if that fails them, that he was not a good God. Your shoeing the wrong horse and as it turns out its a mule.
The purpose and reasoning of evolutionism is to deny God, insult the intelligence of any person who has had the good sense, and wit, to think for themselves, and to realize how proven true the Holy Bible narrative is. And, to note how idiotic the modern fables are.

I quoted the NIV that referred to "wild animals". You consider the NIV to be corrupt.

Did I ask you to take my word for it? No. I said that if you change the Holy Bible to read “wild animals” as you liked it to read, then the way we know its a corruption of the true scritpure is by the contradictions it creates, some of which contradictions I stated for the readers benefit lest they have not the inclination to go and check it out.
Is the NIV corrupt? Yes.
Is that a unwarranted opinion? No.
But, that is another topic isn’t it?
I dealt with the corruption of it that you presented as you attempted to insert the “wildness” notion of evolutionary thinking into the Genesis narrative.

To have intentionally mistranslated the ancient texts to accommodate evolution? Come on... do you think maybe its you that is distorting scriptures?

N, for I can present all the objective evidences proving what is false and what is true. So, I leave it to the readers to make up their own minds as to who and what they believe. But, when you debate with me you will go away without any excuse for having accepted the lies of lying men that go about corrupting minds of children, and who think no book on earth is holy.
The corruption of the NIV largely originates in it's source texts, which texts were invented around 1880.
So, the truth is this, that the text of the NIV there is not ancient. The resulting corruption is ,enormous and easily proven by straightforward comparison with the true scriptures that consistently exhibit not containing foolish and contradictory statements.

"wild animals" are not good?

God told Noah that if a beast kills a man that beast is to be killed as in held accountable. So, I cannot be proven as inventing a incorrect view of nature. Nature doesn’t work right, and that fact isn't knews
It is well proven that all of natureis set on the road to lights extinction. If any of you want to survive, for real, you must be born again and obtain a new nature, instead of sticking with the old one that has been sentenced to death. God doesn’t throw away good things.

Doesn’t God care for the animals?

God sends rain on the evil and the good. So, the notion that all is good is incorrect. As I said, one has to get a proper view of what exactly the definition of good is. Which, is why God put the tree of the knowledge of good and evil in the garden of Eden so that in the process of time man would learn the difference and choose good and not evil.

Even a sparrow can't fall to the ground with out the Father knowing. Lions, tigers, sharks etc... are all evil, corrupt creatures because they are "wild"? Because they eat meat? I hardly think so. They are beautiful and glorious creatures.

But, they weren’t originally made to eat meat according to scripture.
This argument that, the beauty that remains visible in nature is to be interpreted as meaning all nature is good, is illogical. Evil often appears cute, and harmless, and beautiful.
Notice that the change of creatures toward more violent, ruthless behaviors is not the evolution of higher value and usefulness, but, is rather, the proof of the degradation of nature by corruptive influences.

Your whole point was that evolution teaches that creatures started out "banal and stupid" and evolved into something good.

I said that evolutionism claims man was once banal and stupid etc.
That is the lie set contrary to the narrative of Genesis.

Sure evolution teaches that the things we think are good develop by chance with no God of the Bible involved. That way, nature gets the credit and not the creator.

Instead, you think the opposite is true, that God made animals "good" and they have now devolved to a primitive state.

I have shown that, that is what the Genesis narrative says occurred. And, I point it out to show the evolutionism for the lie that it is, and I suggest the lies of evolutionism are religiously based attacks on the God of the Holy Bible and are unrelated to any scientific facts or any laws of nature.

My response was that evolution doesn't teach that "primitive" creatures were banal and stupid. But every creature that has lived on this earth is glorious and magnificent in its own way.

I leave it to all readers to go educate themselves on the evolutionary myth of Neanderthals.

#20 joman

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Posted 13 July 2012 - 07:36 AM

Quotes by herebedragons.

Evolution may teach that life started out simple...Simple is a relative term. How "simple" is a sponge, or an anemone, or a Trilobite, or a nematode, or a bacteria. Every creature is "good" in its own way.

Why should we confuse the definition of “simple” and “good”? Your declaration of what is good is not equal to God's. And, remember God destroyed the whole former world of Noah because it was vile.

To refer to them as banal and stupid is an insult to the creator.

I referred to “wildness”, not the structure of bodies? I pointed out the insults of evolutionary theory that contradict the declaration of God that his creation was originally “good”. Evolutionary thinking is the culprit that... a) Denies the existence of God.b. Teaches children to deny God and science. c) Claims man was once a beast. d) Teaches that creatures become more advanced without God. e) Blaspheme the genealogy of Jesus of Nazareth by claiming Adam was the son of a beast instead of the son of God. True science doesn’t offend God, blaspheme God, ridicule faith in God, nor impugn man’s nobility by assertion of vile parentages as if unwanted, unexpected bastards by birth.

And my other point was that the fossil record does not show "more better" creatures devolving into more "primitive" creatures, it shows "primitive" creatures evolving into more "complex" creatures.

The fossil record shows that vast numbers and diversities of creatures were buried in a gigantic global flood of waters by huge amounts and diversities of water borne sediments, all sorted out into layers in one event, exactly as the Genesis narrative states. It can’t be coincidence that the ancient, supposedly scientifically ill informed authors, and copyists of the Genesis narrative describing a global flood involving all creatures on earth, just happens to correspond with modern global evidences of that very kind of event.

You say there never were Neanderthals. Well we have fossils that we have called Neanderthals, so, whatever you think they are, man or beast - they are Neanderthals.

First, there are no fossils of Neanderthals. There are bones with dna in them that has proven the artifacts to be man, not monkey, or any other creatre, simply man, same as you and I are now. You have been swallowing a cartoon level story not related to any scientific fact whatsoever. And, sad to say, its designed for children not adults.

And there you go again with the name calling of God's creatures - "stupid idiots, gross creatures, brutes."

How is it you reason I insulted what I told you "never existed?"

And evolutionists that believe that early humans and Neanderthals mated, well they don't think that humans were "noble examples of mankind" possessing "language, history, tools and good looks." They were just as "stupid, gross and brutish" as their Neanderthal cousins.

There you have it folks. This poster accused me of insulting beasts that I stated never existed, and then turns around and admits that its the evolutionists who are the blasphemers of the creativeness of God, and his determination that his creation was originally “good”. Evolutionism, as I understand it, is really the formulation of philosophy produced within the context of a antichrist religion that is necessarily forced to try and disguise itself as a false science, which always results in simplistic, absurd, and unscientific interpretations of nature.

Oh and if they could mate and have viable offspring, that would have made them the same species or at least very, very closely related. So the point was ... pointless (and off topic).

I said it is all nonsense. That is, there is no crossing over of kinds, no macroevolution of any new kind. And, no different kinds of creatures don’t mate. And man has no natural desire to mate with beasts of another kind. But, that is level of thinking the fable of macroevolution has lowered man to. In this quote here, you use the evolutionary undefinable notion of “species”. The absurd notions of evolutionism will always require these smoke and mirror words that must purposely be made empty, and vague, since, it is unscientific to its core. Evolutionism cannot allow certain words to be defined..such as...
a) Species.
b...Kind.
c) Proof.
d) evolution.
e) Design.
f) Intelligence.
g) Fact.
h) Evidence.

And whatever other common sense thing that would publically embarrasses the simplistic philosophies of evolutionism.




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