An evolutionary dilemma!!!!

a reply to: Noinden

Thanks for the info!

Chrona seems to think science is about proving things right. Science is more about elimination of bad information and what is left is your probability and more likely to be correct.

a reply to: flyingfish

I think the "proving things right" is a common misconception by those who do not do Science (either in education or for a living). They always seem to forget that science will change its stance, based on the new evidence. Some of the creationists on ATS think that is dishonest of Science. As if being intellectually honest is a terrible thing I could go on and on with the number of times my science has had to change it's stance based on the new evidence.

a reply to: Noinden

Indeed.. It would be impossible to learn new things or know if your information is incorrect if you believe you already have all the answers. That would be a religion.. not science.

a reply to: flyingfish

Mind you some of the creationist crowd accuse Science of being a religion too I think they confuse pseudosciences like say Homeopathy with actual sciences like say Chemistry .

originally posted by: flyingfish
a reply to: chr0naut

If there are multiple phylogenetic trees, then the single common ancestor is a fiction.

No.. But your idea is fiction.
You can add additional information to existing models and update them, but this does not change the fact that all life has a common origin.

If you have information from which you could start a whole new phylogenetic tree originating from a different common ancestor that has no relation, then you have an argument. If you can't then your just making stuff up.

Here is the data base.

The data from which the current (most accurate) phylogenetic tree is built, and the one to which you linked, is using a metagenomic (whole genomic shotgun sequencing) assay based upon only 16 proteins.

The total number of proteins in a human organism's cells (as an example) is estimated to be between 250,000 and 1,000,000.

Of course many types of life will exhibit proteins that are explicitly non-human, so the total number of all possible proteins should be greater (Your bioinformatics should tell you that, assuming an address space based upon 22 proteinogenic amino acids there could be a theoretical maximum of 1,124,000,727,777,607,680,000 proteins and more if you consider amino acid chirality).

So, assuming a very conservative average of about 500,000 proteins as a fair statistical basis representative of all life and giving a degree of confidence in its representation of the proteome of life, the dataset upon which this (and almost every phylogenetic tree) image is currently constructed from, represents barely 0.0032 % of actual.

I'd regard that as not very representational of reality but it makes some really pretty tree structures.

originally posted by: flyingfish
a reply to: Noinden

Thanks for the info!

Chrona seems to think science is about proving things right. Science is more about elimination of bad information and what is left is your probability and more likely to be correct.

In 2009, New Scientist published an article titled "Uprooting Darwin's Tree" (pp. 34-39.) which stated; "The tree of life, one of the iconic concepts of evolution, has turned out to be a figment of our imagination".

In 2011, in the previously linked panel discussion, Craig Venter said; "The tree of life is an artifact of some early scientific studies that aren't really holding up". Richard Dawkins replied that he was "intrigued at Craig saying that the tree of life is a fiction".

Ford Doolittle has argued that "a bifurcating tree is not an adequate metaphor for the evolution of life on earth" and "A single common ancestor and tree relating all of life on earth is not a necessary component of the theory of descent with modification, the essence of evolution".

Carl Woese, recipient of the Leeuwenhoek Medal (microbiology's highest honor), the Selman A. Waksman Award in Microbiology, the National Medal of Science, the Crafoord Prize and membership to the Royal Society, specifically for his work on the phylogenetic tree of life (he added the archaea kingdom). Please note this link from the NCBI site on his more recent views on the phylogenetic tree.

None of this is particularly new and has been discussed publicly, in scientific circles and even in the popular press. I'm not sure how one could work in the field and have missed it?

You'll excuse me if I'd rather take the word of highly renowned scientists, whose studies are specifically on the topic of the phylogenetic tree, who disagree with an outdated, reductionist and simplistic view.

originally posted by: chr0naut

originally posted by: flyingfish
a reply to: Noinden

Thanks for the info!

Chrona seems to think science is about proving things right. Science is more about elimination of bad information and what is left is your probability and more likely to be correct.

In 2009, New Scientist published an article titled "Uprooting Darwin's Tree" (pp. 34-39.) which stated; "The tree of life, one of the iconic concepts of evolution, has turned out to be a figment of our imagination".

In 2011, in the previously linked panel discussion, Craig Venter said; "The tree of life is an artifact of some early scientific studies that aren't really holding up". Richard Dawkins replied that he was "intrigued at Craig saying that the tree of life is a fiction".

Ford Doolittle has argued that "a bifurcating tree is not an adequate metaphor for the evolution of life on earth" and "A single common ancestor and tree relating all of life on earth is not a necessary component of the theory of descent with modification, the essence of evolution".

Carl Woese, recipient of the Leeuwenhoek Medal (microbiology's highest honor), the Selman A. Waksman Award in Microbiology, the National Medal of Science, the Crafoord Prize and membership to the Royal Society, specifically for his work on the phylogenetic tree of life (he added the archaea kingdom). Please note this link from the NCBI site on his more recent views on the phylogenetic tree.

None of this is particularly new and has been discussed publicly, in scientific circles and even in the popular press. I'm not sure how one could work in the field and have missed it?

You'll excuse me if I'd rather take the word of highly renowned scientists, whose studies are specifically on the topic of the phylogenetic tree, who disagree with an outdated, reductionist and simplistic view.

he is not arguing with evolution, he is arguing with the tree representation of it. what is your point here? because it clearly isnt that evolution is false or that it is based in assumption as that is not what ford or Craig said. your dilemma appears to be with the botanical metaphor of the theory rather than the theory itself.

a reply to: chr0naut

You again are very good at posting other peoples ideas, with no context, as if it is proof.

I return to the questionH

Have you done the experiments?

originally posted by: chr0naut

originally posted by: flyingfish
a reply to: Noinden

Thanks for the info!

Chrona seems to think science is about proving things right. Science is more about elimination of bad information and what is left is your probability and more likely to be correct.

In 2009, New Scientist published an article titled "Uprooting Darwin's Tree" (pp. 34-39.) which stated; "The tree of life, one of the iconic concepts of evolution, has turned out to be a figment of our imagination".

In 2011, in the previously linked panel discussion, Craig Venter said; "The tree of life is an artifact of some early scientific studies that aren't really holding up". Richard Dawkins replied that he was "intrigued at Craig saying that the tree of life is a fiction".

Ford Doolittle has argued that "a bifurcating tree is not an adequate metaphor for the evolution of life on earth" and "A single common ancestor and tree relating all of life on earth is not a necessary component of the theory of descent with modification, the essence of evolution".

Carl Woese, recipient of the Leeuwenhoek Medal (microbiology's highest honor), the Selman A. Waksman Award in Microbiology, the National Medal of Science, the Crafoord Prize and membership to the Royal Society, specifically for his work on the phylogenetic tree of life (he added the archaea kingdom). Please note this link from the NCBI site on his more recent views on the phylogenetic tree.

None of this is particularly new and has been discussed publicly, in scientific circles and even in the popular press. I'm not sure how one could work in the field and have missed it?

You'll excuse me if I'd rather take the word of highly renowned scientists, whose studies are specifically on the topic of the phylogenetic tree, who disagree with an outdated, reductionist and simplistic view.

No one "missed it". These scientists themselves would tell you that there's no proof of concept. There are possibilities and speculation, some of which is very rational. However, as posted ad infinitum on this topic, there's no way to prove definitively what happened millions of years ago unless it can be reproduced in the lab. Which it can't - at least up until now.

I don't know why you don't read the responses that some of us have given up to this point. All this has been covered. You seem to want to create a bible out of anything that supports your position. We don't do that in science. Everything is open to re-evaluation with new evidence and new ideas including the tree of life.

a reply to: chr0naut

Why don't you select any one of those articles which you posted (I personally like Venter) and discuss the pros and cons of context. That's how you learn something - not just by posting other people's opinions and adopting them as your own.

originally posted by: TzarChasm

originally posted by: chr0naut

originally posted by: flyingfish
a reply to: Noinden

Thanks for the info!

Chrona seems to think science is about proving things right. Science is more about elimination of bad information and what is left is your probability and more likely to be correct.

In 2009, New Scientist published an article titled "Uprooting Darwin's Tree" (pp. 34-39.) which stated; "The tree of life, one of the iconic concepts of evolution, has turned out to be a figment of our imagination".

In 2011, in the previously linked panel discussion, Craig Venter said; "The tree of life is an artifact of some early scientific studies that aren't really holding up". Richard Dawkins replied that he was "intrigued at Craig saying that the tree of life is a fiction".

Ford Doolittle has argued that "a bifurcating tree is not an adequate metaphor for the evolution of life on earth" and "A single common ancestor and tree relating all of life on earth is not a necessary component of the theory of descent with modification, the essence of evolution".

Carl Woese, recipient of the Leeuwenhoek Medal (microbiology's highest honor), the Selman A. Waksman Award in Microbiology, the National Medal of Science, the Crafoord Prize and membership to the Royal Society, specifically for his work on the phylogenetic tree of life (he added the archaea kingdom). Please note this link from the NCBI site on his more recent views on the phylogenetic tree.

None of this is particularly new and has been discussed publicly, in scientific circles and even in the popular press. I'm not sure how one could work in the field and have missed it?

You'll excuse me if I'd rather take the word of highly renowned scientists, whose studies are specifically on the topic of the phylogenetic tree, who disagree with an outdated, reductionist and simplistic view.

he is not arguing with evolution, he is arguing with the tree representation of it. what is your point here? because it clearly isnt that evolution is false or that it is based in assumption as that is not what ford or Craig said. your dilemma appears to be with the botanical metaphor of the theory rather than the theory itself.

My point is that if you hold on to disproven paradigms, that isn't science.

The science indicates that life did not progress sequentially from a single start. It does not negate evolution as a principle or negate that the path of evolution is likely to have bifurcated into tree like structures. It does, however, falsify the assumption that life diversified, in sequence, from a single common ancestor species.

This is not irrelevant to evolution.

If an assumed link between domains cannot have occurred, then phylogenies built upon such links MUST be discarded and new developmental relationships be sought. An evolutionary path based upon disproven concepts is probably, and reasonably, false.

Because of the current diversity of life and the differences in transcription between different domains, it is rational to assume that there must have been multiple, unconnected, abiogenetic events.

Evolution has nothing to tell us about abiogenesis. Abiogenesis is more about what happened before evolution (although multiple abiogenetic events may have been synchronous with the evolutionary development of existing organisms, even to providing selection pressures). An understanding of abiogenesis, be it multiple or singular, does have importance in the determination of what came afterwards.

a reply to: chr0naut

Because of the current diversity of life and the differences in transcription between different domains, it is rational to assume that there must have been multiple, unconnected, abiogenetic events.

If that is true, why do all organisms share a common core of DNA elements? Transcription, different domains comes much later in the process. It's the common elements that tell us that we have a common ancestry - regardless how many times it started.

Personally, I don't think it's thermodynamically efficient to do the same thing over and over. If nature did that, we would have a multitude of organisms with fundamentally different genetics, unrelated to ours. To our knowledge, we don't see that in nature.

a reply to: chr0naut

So you commit science for a living? What claims to subject matter expert are you claiming? Because you are saying science holds on to disproven paradigms. With out proof

a reply to: Phantom423

I'm awaiting vague comments about Codons to be fired back as an answer. I'm not sure he knows what he is talking about. Because he's using other peoples arguments with out citing the source.

originally posted by: Noinden
a reply to: chr0naut

So you commit science for a living? What claims to subject matter expert are you claiming? Because you are saying science holds on to disproven paradigms. With out proof

I'd like to know the answer to that as well - where's the data?????

a reply to: Phantom423

IF anyone else is wondering why I am asking this. I'm a professional scientist. A chemist, and bioinformatics jokey. If the Christians here do not like being told what their religion does/says (and they do not, rightfully so perhaps), guess what neither do I. I have bleed for my science (lab glass cuts), I've been destitute to get the silly little letters after my name, just so I know "what science is"

a reply to: chr0naut

Evolution has nothing to tell us about abiogenesis. Abiogenesis is more about what happened before evolution (although multiple abiogenetic events may have been synchronous with the evolutionary development of existing organisms, even to providing selection pressures). An understanding of abiogenesis, be it multiple or singular, does have importance in the determination of what came afterwards.

Abiogenesis is not difficult to understand. If every organism shares the same nucleotides as building blocks, then those organisms have a relationship. If organisms do not share fundamental building blocks, then they are not related. No matter how many times life started, the current outcome is that all organisms on this planet share the same fundamental building blocks. What happens later during the evolutionary process is entirely different dynamics which relates to evolution and speciation.

You've got your flow chart all screwed up.

a reply to: chr0naut

Because of the current diversity of life and the differences in transcription between different domains, it is rational to assume that there must have been multiple, unconnected, abiogenetic events.

How do you draw that conclusions when diversity is a result of evolution? You made a point of saying that abiogenesis and evolution are unrelated. But diversity didn't arise from abiogenesis. If it did, we would see different fundamental building blocks for some organisms and we don't. Diversity is a direct result of evolution and speciation.

originally posted by: Noinden
a reply to: chr0naut

You again are very good at posting other peoples ideas, with no context, as if it is proof.

I return to the questionH

Have you done the experiments?

Are you suggesting that there is some sort of contextual confusion going on?

Is it a requirement that everyone who makes a comment upon science must personally have "done the experiments"? If so, what qualifies Dick Dawkins for his podium?

I'm actually fairly confident that peer reviewed reports and replicated experimentation are sufficiently credentialled to not require my personal verification.

Perhaps you could determine contextual issues with the following publications?:

The tree of one percent

Is It Time to Uproot the Tree of Life?

Woese on the received view of evolution

Evolutionary change and phylogenetic relationships in light of horizontal gene transfer

Genome trees and the tree of life.

The net of life: reconstructing the microbial phylogenetic network.

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes.

originally posted by: Noinden
a reply to: Phantom423

IF anyone else is wondering why I am asking this. I'm a professional scientist. A chemist, and bioinformatics jokey. If the Christians here do not like being told what their religion does/says (and they do not, rightfully so perhaps), guess what neither do I. I have bleed for my science (lab glass cuts), I've been destitute to get the silly little letters after my name, just so I know "what science is"

I know the drill well!! He insists that life emerged more than once without having an iota of evidence. It's mere speculation as all the scientists that he quoted have said. There are a number of ways the tree of life could evolve. But as I said several times, unless you can show that some organisms on this planet DO NOT SHARE fundamental building blocks, then they all have commonality on a very fundamental level. I don't know why this is so difficult to understand.

How many times do we have to say it? And how many times does he have to contradict what is already known? If he has evidence, then he should present it. He's totally misread the articles and drew conclusions that fit his model - paid absolutely no attention to what is known vs what isn't known.