Are discussions on faith and science two different catagories?

[Justatruthseeker]

Phylogenetic algorithms don't care whether the DNA sequences used are the same species are not.

https://en.wikipedia.org/wiki/Computational_phylogenetics

"The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa."

So the program is already written to support a hypothesis.....

"The problem of character coding is very different in molecular analyses, as the characters in biological sequence data are immediate and discretely defined - distinct nucleotides in DNA or RNA sequences and distinct amino acids in protein sequences. However, defining homology can be challenging due to the inherent difficulties of multiple sequence alignment. For a given gapped MSA, several rooted phylogenetic trees can be constructed that vary in their interpretations of which changes are "mutations" versus ancestral characters, and which events are insertion mutations or deletion mutations. For example, given only a pairwise alignment with a gap region, it is impossible to determine whether one sequence bears an insertion mutation or the other carries a deletion. The problem is magnified in MSAs with unaligned and nonoverlapping gaps. In practice, sizable regions of a calculated alignment may be discounted in phylogenetic tree construction to avoid integrating noisy data into the tree calculation."

So we agree, when you snip out all the code that doesn't fit, and align only the code that does, while ignoring the gaps you snipped out to make them align, you get weighted results. But only the interpretation the researcher wants to publish is heard.... the rest are discarded.

 

[pitabread]

Hmm, and yet you cant even do that, just make ad-hominem attacks. See post #119.

I'm not attacking you, I'm attacking the content of your posts. And your posts on phylogenetics read like gibberish.

 

[pitabread]

https://en.wikipedia.org/wiki/Computational_phylogenetics

"The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa."

So the program is already written to support a hypothesis.....

Phylogenetics by definition is the study of evolutionary relationships of organisms. Which means that a program which creates phylogenetics will create a tree meant to represent those relationships.

But the point of the post you were responding to is that the program doesn't know or care if the DNA sequences given for construction are the same species or not.

Heck, awhile back I posted phylogenetic reconstructions based on characteristics of vehicles. (Mainly to see if one could get statistically convergent trees based on artificial objects. It turns out one cannot.)

 

[Justatruthseeker]

I'm not attacking you, I'm attacking the content of your posts. And your posts on phylogenetics read like gibberish.

You havent attacked a single content of my posts, just made ad-hominem remarks at all times, with not one single scientific remark on your end...

 

[pitabread]

You havent attacked a single content of my posts, just made ad-hominem remarks at all times, with not one single scientific remark on your end...

Again, it's not an ad-hominem to point out gibberish. What you wrote was gibberish. Whining about others pointing out your gibberish doesn't change that.

And I've already explained why: Phylogenetic algorithms aren't programmed to treat sequences of the same species differently compared to sequences of different species. The algorithm itself has no idea; it's just fed DNA sequences and will construct a tree based on relative similarities and differences in the sequences it is provided.

If you don't believe me, try downloading phylogenetics software yourself and try out tree construction. There are lots of free programs available.

 

[Justatruthseeker]

Phylogenetics by definition is the study of evolutionary relationships of organisms. Which means that a program which creates phylogenetics will create a tree meant to represent those relationships.

But the point of the post you were responding to is that the program doesn't know or care if the DNA sequences given for construction are the same species or not.

Heck, awhile back I posted phylogenetic reconstructions based on characteristics of vehicles. (Mainly to see if one could get statistically convergent trees based on artificial objects. It turns out one cannot.)

You didn't try very hard then. One could easily show the evolution from the model Ford T to the corvette. With basic DNA shared by all species (makes) wheels, with variation, stereos, hood shape, with HGT, light bulb changes. You didn't want to make it work is all.

And as pointed out many interpretations are available. It is only the interpretation that the researcher agrees with that is then printed for publication. If many interpretations are available, then concealing them and favoring only what the researcher wants to publish is concealment. Sniping out half the code, then aligning only what matches, after having snipped out large chunks, has already biased the data towards similarity. If you can't see this you willingly blind yourself to the truth and just that one interpretation.

 

[pitabread]

You didn't try very hard then. One could easily show the evolution from the model Ford T to the corvette. With basic DNA shared by all species (makes) wheels, with variation, stereos, hood shape, with HGT, light bulb changes. You didn't want to make it work is all.

That's a completely unfounded accusation.

I posted the results of my tree reconstructions here: https://www.christianforums.com/thr...-watch-argument.8005539/page-78#post-72402735
Data set I used was here: https://www.christianforums.com/thr...-watch-argument.8005539/page-81#post-72409833

Software used was Mesquite available freely here: https://www.mesquiteproject.org/

You're more than welcome to make your own attempt and post the results of your findings.

And as pointed out many interpretations are available. It is only the interpretation that the researcher agrees with that is then printed for publication. If many interpretations are available, then concealing them and favoring only what the researcher wants to publish is concealment. Sniping out half the code, then aligning only what matches, after having snipped out large chunks, has already biased the data towards similarity. If you can't see this you willingly blind yourself to the truth and just that one interpretation.

I'm not even sure what you are complaining about. Are you complaining about sequence alignments? Because the only way to effectively compare and use DNA sequences for tree reconstruction is to properly align them first which means taking insertions and deletions into account. Otherwise that really will be a case of GIGO.

And I'm not sure what you mean by biasing the data towards similarity? Again, if you're complaining about sequence alignments then you might as well be arguing for the use of improper data sets. Which would be silly.

 

[Justatruthseeker]

That's a completely unfounded accusation.

I posted the results of my tree reconstructions here: https://www.christianforums.com/thr...-watch-argument.8005539/page-78#post-72402735
Data set I used was here: https://www.christianforums.com/thr...-watch-argument.8005539/page-81#post-72409833

Software used was Mesquite available freely here: https://www.mesquiteproject.org/

You're more than welcome to make your own attempt and post the results of your findings.



I'm not even sure what you are complaining about. Are you complaining about sequence alignments? Because the only way to effectively compare and use DNA sequences for tree reconstruction is to properly align them first which means taking insertions and deletions into account. Otherwise that really will be a case of GIGO.

And I'm not sure what you mean by biasing the data towards similarity? Again, if you're complaining about sequence alignments then you might as well be arguing for the use of improper data sets. Which would be silly.

What does manufacturere have to do with it?

According to you there is no manufacturer, and according to creation there is only One.

Number of wheels: 2 (man) 8 spider. Hundreds centipede.
Number of engine cylinders: stomachs? lungs would be carburetor. us 1, cows 4, some organisms none (electric).
Motor location:Human, centipede or bird?
Fuel type: Vegies, meat, both, bacteria.
Number of toes:

we could do the same thing to life as you are doing to cars and make it impossible for any program to collate any sense.....

As I said, i don't think you tried very hard.

 

[Justatruthseeker]

I'm not even sure what you are complaining about. Are you complaining about sequence alignments? Because the only way to effectively compare and use DNA sequences for tree reconstruction is to properly align them first which means taking insertions and deletions into account. Otherwise that really will be a case of GIGO.

And I'm not sure what you mean by biasing the data towards similarity? Again, if you're complaining about sequence alignments then you might as well be arguing for the use of improper data sets. Which would be silly.

Of course they are similar, when you remove everything that isn't. Half the aligned segments do not even have the same function, being in different locations in the genome. And most we don't even know what they do yet, so how can you align portions with different functions (because we know that the location in the genome is as important as its letter string) with those in different locations and claim similarity? let alone aligning those you haven't got a clue yet what they do, you just see similarity, but they could do completely different functions based upon their location in the genome and not really be similar at all.

Of course you don't understand. That would be detrimental to your world view.

 

[Justatruthseeker]

All existing sequencing methods work by breaking DNA strands into tiny pieces, sequencing them and reassembling the resulting "jigsaw". The trouble is that some parts of the human genome - mainly the middle and ends of chromosomes - are so repetitive that it's impossible to put it all back together.

https://www.nature.com/articles/nmeth.1451

"The extent of human genomic structural variation suggests that there must be portions of the genome yet to be discovered, annotated and characterized at the sequence level. We present a resource and analysis of 2,363 new insertion sequences corresponding to 720 genomic loci.......Complete sequencing of 156 of these insertions identified new exons and conserved noncoding sequences not yet represented in the reference genome.

So supposedly the complete genome was sequenced in 2003, but in 2010 they were still finding new sequences and exons.

Stop preaching the standard PR evolutionary junk...... As if we actually understand anything about the genome. If we understood half of what is being preached, we wouldn't keep finding new exons and sequences every-time we look.....

 

[Bobber]

In Hebrews 11:6 we are told it is impossible to please God without faith. That we first must believe that He exists and then second believe He rewards those who diligently seek Him. So then are we just supposed to have blind faith that God exists or did He tell us how we can know He exists? In Romans 1:20 we are told that since creation God's invisible attributes are clearly seen (distinguishable) being understood by the things that were made. So much so that all are without excuse.

Good thread Brad. I've been thinking about the Romans 1:20 verses for some time. For man's capacity to KNOW of God when it comes to another subject but when it comes to science and man...here's the thing. We've heard it all our lives the world keeps saying that one just can't prove God exists. Men who resist God and want to reject him obviously will insist on saying such until their dying day.

The question is what does God say about it and not men. Just as in the verse you quoted God said those who suppress the truth based on what they see in creation will be without excuse. Quite interesting. At times I've envisioned the judgment day and people who have rejected God might be exclaiming you didn't show yourself as real but God will say I revealed sufficient enough evidence for you TO KNOW with absolute certainty that I existed and it's not going to be your opinion that counts for anything now...BUT MINE. We can only hope people will choose to see the bigger picture and stop resisting the Creator.

 

[Bobber]

Who's trying to discredit science? I love science. It points me to the Creator of it all.

And that's the thing isn't it. The secularist want to claim they own the ball and bat of science and tell those who are religious they must go home. The game isn't for them.

 

[Jimmy D]

The common descent tests are based upon false premises. Garbage in, garbage out.

"However, somewhat paradoxically, the very process of building phylogenies with molecules revealed the extent of horizontal gene transfer (HGT), and thereby threatened the TOL concept in regard to its core ideas of a unique ever-bifurcating branching pattern. "

I'd explain that to you, but it wouldn't do any good.

or "“The genomic revolution [has]… effectively overturned the central metaphor of evolutionary biology, the Tree of Life, by showing that evolutionary trajectories of individual genes are irreconcilably different."

Know I know you prefer the PR hype That they all point towards a common ancestor instead of the truth, but that's no excuse.

Why do you say this...

"The common descent tests are based upon false premises. Garbage in, garbage out."

...and then quote Koonin talking about how molecular biology allows for credible reconstruction of the gene sets of ancestral life forms?

Very strange.

 

[Jimmy D]

Not if the data is entered correctly, that's why they don't point to an ever-bifurcating branching tree of life but instead point to cross-contamination by HGT and individual gene trajectories that are irreconcilably different.

Yes, we are all aware of, and acknowledge, the existence of HGT. Why you think that it threatens the fact of common descent is the headscratcher.

But before the data was entered correctly, it showed a ever-bifurcating branching pattern because half the data about HGT was ignored during the first decades of genomic research.....

What "data was entered correctly"? Entered into what?

What makes you think that HGT data was ignored? (Specifically, not your usual vague inferences)

Do you realize that what Koonin is suggesting the traditional TOL is replaced with still shows descent from a LUCA and offers no credibility to your unfounded creationist nonsense?


"The question remains open whether evolution of life in its entirety is best depicted as:

1. a consensus tree of highly conserved genes that represents a ‘central trend’ in evolution, with HGT events, including massive ones associated with endosymbiosis, comprising horizontal connections between the tree branches [Figure 1A; (150)], or

2. a complex network where phases of tree-like evolution (with horizontal connections) are interspersed with ‘Big Bang’ phases of rampant horizontal exchange of genetic information that cannot be represented as trees in principle [Figure 1B; (151)].

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651812/

 

[Justatruthseeker]

Again, it's not an ad-hominem to point out gibberish. What you wrote was gibberish. Whining about others pointing out your gibberish doesn't change that.

And I've already explained why: Phylogenetic algorithms aren't programmed to treat sequences of the same species differently compared to sequences of different species. The algorithm itself has no idea; it's just fed DNA sequences and will construct a tree based on relative similarities and differences in the sequences it is provided.

If you don't believe me, try downloading phylogenetics software yourself and try out tree construction. There are lots of free programs available.

Well then since the tactic is sufficient for you.

Gibberish.

No you said, they weren't, yet I showed you their own quote which said many interpretations were available based upon the data. That they were made to create a tree that fit a hypothesis.

The difference is I backed up my assertions, you fail to on every issue. Claiming something is just that, claims.....

 

[BradB]

Gene and chromosome duplication shows exactly how mutations to existing genes make new genes. That icefish blood antifreeze that used a digestive enzyme as a template is one such. The Hox genes , humans have 4 sets . Some Hox genes are identical, some are mutated, a few are missing from one or more of the sets

All should please note that I specifically asked for an observed biological mutation in which information was added to the chromosomal DNA of an organism that improved the species survivability. I wasn't referring to a mutation in which already existing information was duplicated or where existing information is deleted or damaged. In order to get from bacteria to a baseball players, there has to be some kind of mechanism to add genetic information like the genes that make legs, arms, eyes, brains etc... A cyclically lost, gained or replaced gene does not fit the bill for the addition of new information to the DNA message.


Regarding duplications, these are not examples of new genes being added with new functions. For example the mutations studied in yeast had both HXT6 and HXT7 genes, and a “hybrid” duplicate copy of the two. Promoter portion of HXT7 is attached to the coding portion of HXT6. Except, the combined genes aren't much of a “hybrid” because there's only a five nucleotide difference between the two. The authors of the paper even state that these two genes may themselves be the result of a previous gene duplication in the parent strain. Under certain circumstances, a duplication is advantageous to the species, but it is not an example of what we need to see to get from molecules to man.

 

[pitabread]

All should please note that I specifically asked for an observed biological mutation in which information was added to the chromosomal DNA of an organism that improved the species survivability.

What does "information being added" actually mean to you? What is your definition and measurement of information with respect to DNA? How do you quantify whether information is being added or subtracted?

 

[Brightmoon]

All should please note that I specifically asked for an observed biological mutation in which information was added to the chromosomal DNA of an organism that improved the species survivability. I wasn't referring to a mutation in which already existing information was duplicated or where existing information is deleted or damaged. In order to get from bacteria to a baseball players, there has to be some kind of mechanism to add genetic information like the genes that make legs, arms, eyes, brains etc... A cyclically lost, gained or replaced gene does not fit the bill for the addition of new information to the DNA message.


Regarding duplications, these are not examples of new genes being added with new functions. For example the mutations studied in yeast had both HXT6 and HXT7 genes, and a “hybrid” duplicate copy of the two. Promoter portion of HXT7 is attached to the coding portion of HXT6. Except, the combined genes aren't much of a “hybrid” because there's only a five nucleotide difference between the two. The authors of the paper even state that these two genes may themselves be the result of a previous gene duplication in the parent strain. Under certain circumstances, a duplication is advantageous to the species, but it is not an example of what we need to see to get from molecules to man.

. This is a good example of creationist newspeak. It sounds nice and science-y but it’s nonsense . These ARE evolutionary processes . Creationists indulge in denial and they pretend to deny evolution by giving it another name .

 

[Justatruthseeker]

All should please note that I specifically asked for an observed biological mutation in which information was added to the chromosomal DNA of an organism that improved the species survivability. I wasn't referring to a mutation in which already existing information was duplicated or where existing information is deleted or damaged. In order to get from bacteria to a baseball players, there has to be some kind of mechanism to add genetic information like the genes that make legs, arms, eyes, brains etc... A cyclically lost, gained or replaced gene does not fit the bill for the addition of new information to the DNA message.


Regarding duplications, these are not examples of new genes being added with new functions. For example the mutations studied in yeast had both HXT6 and HXT7 genes, and a “hybrid” duplicate copy of the two. Promoter portion of HXT7 is attached to the coding portion of HXT6. Except, the combined genes aren't much of a “hybrid” because there's only a five nucleotide difference between the two. The authors of the paper even state that these two genes may themselves be the result of a previous gene duplication in the parent strain. Under certain circumstances, a duplication is advantageous to the species, but it is not an example of what we need to see to get from molecules to man.

There exists no known new genetic information added to the genome by mutations. As you stated they are copy errors (errors in copying what already exists) or deletions, or switching on or off traits.

The only known way to add new information is by mating. Genes which didn't exist in one are combined together to create a new life. And the two shall be one flesh. IMO it wasn't a rib taken from Adam to build Eve, but half of that perfect genome that has degraded over time because of mutations. We should at this point note, to forestall absurd claims from certain segments, that bacteria are also capable of obtaining genes from their environment, dead bacteria or other living bacteria.

 

[Justatruthseeker]

. This is a good example of creationist newspeak. It sounds nice and science-y but it’s nonsense . These ARE evolutionary processes . Creationists indulge in denial and they pretend to deny evolution by giving it another name .

Hmmm, that sounded suspiciously like a good example of evolutionist newspeak, but it didn't even sound science-y. It just sounded like unsupported rhetoric and PR.