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Interesting article, Dawkins shocked! His face cracks me up.

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posted on Aug, 19 2015 @ 06:06 PM
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a reply to: chr0naut

Stop codons - and there are about a half dozen of them - can be modified or deleted. This often leads to genetic diseases. Modified stop codons, or frameshift mutations, are responsible for Tay Sachs disease and cystic fibrosis. The placement of stop codons is not random - they are specific to the organism. In humans, the UGA codon codes for selenocysteine which triggers the release of amino acids which then form the protein.

Dawkins is an evolutionary biologist. He knows his stuff. The debate as to whether there is a "tree of life" is misleading. All organisms on this planet utilize nucleic acids to form the genome. How the code develops for each organisms defines the organism, not the nucleic acids. So in a sense, the "tree" is constructed of nucleic acids. The outcomes of the codes, however, are very different.

Nuclei acids are carbon-based. If carbon was replaced by silica, it would be silica-based life. The rationale for going to Mars is not just to see if similar life exists or has existed. Space exploration seeks to find any form of life - as long as we can recognize it. As Stephen Hawking said: "Nothing," the report concludes, "would be more tragic in the American exploration of space than to encounter alien life and fail to recognize it.”

The article from EvolutionNews is just another purposeful misinterpretation of what the forum was about. If you listen to the entire discussion, that becomes obvious.

But I will thank the OP for posting the link which contained a link to the symposium at UofA. Craig Venter is an innovative scientist who has made some huge leaps in our understanding of "life".




posted on Aug, 19 2015 @ 06:21 PM
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a reply to: Barcs


originally posted by: Barcs
Why do you say that it's not included? It's listed on the main wiki page of modern evolutionary synthesis and scientists have been talking about it for decades.

Because it's not, Barcs. HGT is a mechanism largely utilized by eukaryotes, bacteria and other microbes. The MES says nothing about this type of genetic transfer. Read that page more carefully.

Here is the summary of the central tenants that underly the MES according to that Wiki page:

en.wikipedia.org...

Summary of the modern synthesis

The modern synthesis bridged the gap between the work of experimental geneticists and naturalists, and paleontologists. It states that:

1) All evolutionary phenomena can be explained in a way consistent with known genetic mechanisms and the observational evidence of naturalists.
2) Evolution is gradual: small genetic changes regulated by natural selection accumulate over long periods. Discontinuities amongst species (or other taxa) are explained as originating gradually through geographical separation and extinction. This theory contrasts with the saltation theory of William Bateson (1894).[6]
3) Natural selection is by far the main mechanism of change; even slight advantages are important when continued. The object of selection is the phenotype in its surrounding environment.
4) The role of genetic drift is equivocal. Though strongly supported initially by Dobzhansky, it was downgraded later as results from ecological genetics were obtained.
5) Thinking in terms of populations, rather than individuals, is primary: the genetic diversity existing in natural populations is a key factor in evolution. The strength of natural selection in the wild is greater than previously expected; the effect of ecological factors such as niche occupation and the significance of barriers to gene flow are all important.
6) In palaeontology, the ability to explain historical observations by extrapolation from microevolution to macroevolution is proposed. Historical contingency means explanations at different levels may exist. Gradualism does not mean constant rate of change.


No mention of HGT of course. You are right, it is mentioned at the bottom of that wiki page, however it is listed under the section entitled: "After the Synthesis." I have to wonder why you or anyone else would take this to mean that it's been added as a tenet to the theory? Where does it say so, anywhere?
edit on 19-8-2015 by PhotonEffect because: (no reason given)



posted on Aug, 19 2015 @ 06:31 PM
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originally posted by: chr0naut

originally posted by: peter vlar
a reply to: chr0naut

That's all really well said and all except for it being entirely wrong. See, Dawkins has actually been publishing in respected peer reviewed journals since the late 60's and while he may not publish as often is some of his peers because he does work outside the realm of science as well and isn't chained to a desk that requires him to publish in a regular schedule, he still publishes a considerable amount of research. The only caveat I would give is that his last peer reviewed paper was published in 2004. Despite that, his background in zoology and evolutionary biology combined with his amount of published work is pretty staggering.

en.m.wikipedia.org...


OK, I accede that I was being unacceptably harsh on Dawkins.

By Wilson's definition, there would be very few scientists.



you admit that you willfully made a false statement. the same statement, multiple times. that is called lying where i come from. and the only reason you are even acceding anything is because you got caught red handed.

you therefore admit that we can no longer trust your opinion.

good day sir.
edit on 19-8-2015 by TzarChasm because: (no reason given)



posted on Aug, 19 2015 @ 10:56 PM
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originally posted by: Prezbo369

originally posted by: chr0naut

Intelligent Design, not Creationist.



Same/Same

I.D. is just creationism in a cheap lab coat.


... and we all know how lab coat quality is so important to scientific debate!




posted on Aug, 19 2015 @ 11:57 PM
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originally posted by: TzarChasm

originally posted by: chr0naut

originally posted by: peter vlar
a reply to: chr0naut

That's all really well said and all except for it being entirely wrong. See, Dawkins has actually been publishing in respected peer reviewed journals since the late 60's and while he may not publish as often is some of his peers because he does work outside the realm of science as well and isn't chained to a desk that requires him to publish in a regular schedule, he still publishes a considerable amount of research. The only caveat I would give is that his last peer reviewed paper was published in 2004. Despite that, his background in zoology and evolutionary biology combined with his amount of published work is pretty staggering.

en.m.wikipedia.org...


OK, I accede that I was being unacceptably harsh on Dawkins.

By Wilson's definition, there would be very few scientists.



you admit that you willfully made a false statement. the same statement, multiple times. that is called lying where i come from. and the only reason you are even acceding anything is because you got caught red handed.

you therefore admit that we can no longer trust your opinion.

good day sir.


I was quoting E. O. Wilson's opinion. Many of Dawkins' academic accolades are honorary. Several of his "peer reviewed scientific papers" are not anything of the kind but are merely correspondence to scientific publications (being published in a scientific journal does not necessarily mean that the comments are peer reviewed). My comments were unkind but not untrue (as far as I can tell).

I never had any expectation that you should trust my opinion. You should form your own.


edit on 19/8/2015 by chr0naut because: (no reason given)



posted on Aug, 20 2015 @ 01:01 AM
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originally posted by: Phantom423
a reply to: chr0naut

Stop codons - and there are about a half dozen of them - can be modified or deleted. This often leads to genetic diseases. Modified stop codons, or frameshift mutations, are responsible for Tay Sachs disease and cystic fibrosis. The placement of stop codons is not random - they are specific to the organism. In humans, the UGA codon codes for selenocysteine which triggers the release of amino acids which then form the protein.

Dawkins is an evolutionary biologist. He knows his stuff. The debate as to whether there is a "tree of life" is misleading. All organisms on this planet utilize nucleic acids to form the genome. How the code develops for each organisms defines the organism, not the nucleic acids. So in a sense, the "tree" is constructed of nucleic acids. The outcomes of the codes, however, are very different.

Nuclei acids are carbon-based. If carbon was replaced by silica, it would be silica-based life. The rationale for going to Mars is not just to see if similar life exists or has existed. Space exploration seeks to find any form of life - as long as we can recognize it. As Stephen Hawking said: "Nothing," the report concludes, "would be more tragic in the American exploration of space than to encounter alien life and fail to recognize it.”

The article from EvolutionNews is just another purposeful misinterpretation of what the forum was about. If you listen to the entire discussion, that becomes obvious.

But I will thank the OP for posting the link which contained a link to the symposium at UofA. Craig Venter is an innovative scientist who has made some huge leaps in our understanding of "life".



Thanks Phantom423.

I have the classic RNA to amino acid tables but obviously these are not universally applicable to all life. Do you have, or know, of more complete tables that include these other stop codons (other than the two on the human table) and what rules govern their application?

Also, is there any particular system that may explain alternate transcription in biochemical terms? To me, it seems that there would be vast differences in biochemistry that would be required to achieve a different transcription. Do you know if this is the case? Is there, perhaps, a simple and explicable path to achieving this change?


edit on 20/8/2015 by chr0naut because: (no reason given)



posted on Aug, 20 2015 @ 07:39 AM
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a reply to: chr0naut

Answers to your questions get very complex very fast! First of all, DNA codons are used more frequently than the RNA codons to discover genes. That's because we now have computational biology and methods which are more accurate. You can actually predict the genetic code using this tool:

Genetic code prediction tool FACIL: Fast and Accurate genetic Code Inference and Logo

facil-host.cmbi.umcn.nl...

There's another tool where you can calculate the codon frequency for different organisms. So if you wanted to know the frequency of a particular STOP codon, you could run this program to identify how many times that STOP codon occurs. If you wanted to know how many times the TAA STOP codon occurs in eColi, the program run would show 7356 per thousand.
www.genscript.com...



NCBI is the best source for tools, databases and references. As I said, this stuff gets complicated very fast, but at least the tools can give you a general idea as to how it all comes together.

For instance, there's a database and online software to analyze sequences and determine similarities of sequences in eukaryotes and prokaryotes.
www.ncbi.nlm.nih.gov...

National Center for Biotechnology Information
www.ncbi.nlm.nih.gov...

As far as alternate transcription is concerned (and I assume you mean how and why individual organisms develop), this goes to evolutionary biology which explains mutations, code variation, and distribution of sequences like STOP codons. Now that we can sequence entire genomes, it's just a matter of time before all organisms are completely sequenced and compared. Human and Neanderthal genomes have been totally sequenced and compared. I'm sure there's research papers out there that describe the differences, similarities and what they might mean.

I posted the DNA and RNA codon charts below. GenScript has a wealth of information at their website including online software tools.

www.genscript.com...


My field is spectroscopy, not molecular biology, but you posed good questions so I did the research.










edit on 20-8-2015 by Phantom423 because: (no reason given)



posted on Aug, 20 2015 @ 07:46 AM
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a reply to: chr0naut

I know the question of an "intelligent designer" has come up frequently on this forum. No one can say definitively one way or the other. However, self assembly of nucleic acids is a well known phenomenon. I think Craig Venter's work has focused quite a bit on self assembly.



posted on Aug, 20 2015 @ 08:05 AM
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a reply to: Phantom423




I know the question of an "intelligent designer" has come up frequently on this forum. No one can say definitively one way or the other. However, self assembly of nucleic acids is a well known phenomenon. I think Craig Venter's work has focused quite a bit on self assembly.


I don't think guys in a laboratory making the conditions just right for the things to form is considered true "self-assembly"



posted on Aug, 20 2015 @ 08:47 AM
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a reply to: ServantOfTheLamb

That's not how self assembly is observed. Look it up and stop making assumptions you know nothing about.



posted on Aug, 20 2015 @ 01:00 PM
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a reply to: PhotonEffect

I don't think you are reading the list carefully.


1) All evolutionary phenomena can be explained in a way consistent with known genetic mechanisms and the observational evidence of naturalists.


Please explain how HGT is inconsistent with known genetic mechanisms. The truth is, it IS a known genetic mechanism. I understand that you look at that list and take as it as some kind of absolutist dogma, but that's not how it is at all.


Natural selection is by far the main mechanism of change; even slight advantages are important when continued. The object of selection is the phenotype in its surrounding environment.


MAIN mechanism. Not ONLY mechanism.


Gradualism does not mean constant rate of change.


Enter punctuated equilibrium. Remember, gradualism does not mean every single species follows the same rate of change. It is different for most of them. Gradualism is what we observe looking at the big picture over millions to billions of generations. It doesn't mean that certain species haven't developed quickly, it's looking at the process as a whole.

We were discussing this in our last encounter and I made what I thought was a compelling argument that suggested epigenetics is NOT evolution, and DOES NOT belong in Modern Synthesis. Epigenetics is something entirely different. I never got a response to that last argument. I was interested in your thoughts on that.


edit on 20-8-2015 by Barcs because: (no reason given)



posted on Aug, 20 2015 @ 01:45 PM
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a reply to: Barcs



I understand that you look at that list and take as it as some kind of absolutist dogma, but that's not how it is at all.

When anyone refers to the MES, it's that list of absolutist dogma he or she is supporting. You keep saying that these other mechanisms are included. They are not. Until you can provide real sources that show the MES has been updated to include things like HGT or epigenetic mechanisms, I'll just stay where I've been on this.


MAIN mechanism. Not ONLY mechanism.

Sure- I never claimed the MES stated it to be the only one. But it's not even the main mechanism either. Adherents to the neutral theory and many other biologists would agree on this point. Gould and Lewontin supported this view as well.



We were discussing this in our last encounter and I made what I thought was a compelling argument that suggested epigenetics is NOT evolution, and DOES NOT belong. Epigenetics is something entirely different. I never got a response to that last argument. I was interested in your thoughts on that.


Right, about that. I had this whole post written up ready to go, then poof, I lost it when my browser refreshed. Very frustrating. I've been meaning to rewrite it but life keeps getting in the way. The short of my sentiment is that your post seemed to misunderstand what epigenetics is or how it works. To think that it would/should not be included in evolutionary theory is totally off base. It involves modifications to genes that are not part of the DNA sequence, but still influence the expression of phenotypes. These have been shown to be transgenerational too. As we all know, phenotypes play a role in evolutionary trajectories. I really don't understand your view on this, but we should continue the convo sometime soon...
edit on 20-8-2015 by PhotonEffect because: (no reason given)



posted on Aug, 20 2015 @ 02:34 PM
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a reply to: Phantom423

Many, many thanks!

It's going to take me a bit to get up to speed on all that great linkage goodness but cheers!



posted on Aug, 20 2015 @ 03:22 PM
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a reply to: ServantOfTheLamb

I want to thank you for posting this. I was unaware of the extent of variation in DNA coding. The site mentioned in the article is up to 25 known variations, not 17, and they do not refer to single organisms but to families, each of which must have had an earliest ancestor.

My opinion is that the process of the origin of life went like this:
stanericksonsblog.blogspot.com...

It would be support for this process that there are multiple variations of DNA coding. The process in the post is that DNA became the common language for coding after there were self-replicating organisms, of a very simple kind. Self-replication first, then coding.

Thanks again for the fascinating read.



posted on Aug, 20 2015 @ 03:26 PM
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a reply to: chr0naut

You are making the assumption that life began with coding. Perhaps it began with self-replicating chemicals which later evolved into coding mechanisms (several to be exact).

More details:
stanericksonsblog.blogspot.com...



posted on Aug, 20 2015 @ 04:15 PM
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originally posted by: StanFL
a reply to: chr0naut

You are making the assumption that life began with coding. Perhaps it began with self-replicating chemicals which later evolved into coding mechanisms (several to be exact).

More details:
stanericksonsblog.blogspot.com...


As I have noted in several posts, the process of chemistry to life is abiogenesis, not evolution. But Dick Dawkins seems to hold to this process (abiogenesis) only having occurred once. Which leads to a single "tree of life" and a single progenitor ancestor. Craig Venter is suggesting multiple instances of abiogenesis, producing several "bushes of life".

There is a really informative thread (& video) on abiogenesis here on ATS

The insistence upon DNA as the source 'definition carrying' molecule for all life is that we have nothing that we would define as life, that does not use the mechanism. Even virii (which are arguably not 'alive') utilize the structure (in RNA) and rely on the DNA replication processes of hosts.

If Venter is right and abiogenesis occurs multiple times, it does speak to the rise of life other than the carbon based one we have observed. For instance, if silicon based life is possible and abiogenesis occurs at random, why don't we see any examples of silicon based life here on Earth? The raw materials are here, the opportunity is here. No doubt the circumstance for abiogenesis are also likely to be here, but we see no outcome.


edit on 20/8/2015 by chr0naut because: (no reason given)



posted on Aug, 20 2015 @ 04:23 PM
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originally posted by: Barcs
a reply to: PhotonEffect

I don't think you are reading the list carefully.


1) All evolutionary phenomena can be explained in a way consistent with known genetic mechanisms and the observational evidence of naturalists.


Please explain how HGT is inconsistent with known genetic mechanisms. The truth is, it IS a known genetic mechanism. I understand that you look at that list and take as it as some kind of absolutist dogma, but that's not how it is at all.


Natural selection is by far the main mechanism of change; even slight advantages are important when continued. The object of selection is the phenotype in its surrounding environment.


MAIN mechanism. Not ONLY mechanism.


Gradualism does not mean constant rate of change.


Enter punctuated equilibrium. Remember, gradualism does not mean every single species follows the same rate of change. It is different for most of them. Gradualism is what we observe looking at the big picture over millions to billions of generations. It doesn't mean that certain species haven't developed quickly, it's looking at the process as a whole.

We were discussing this in our last encounter and I made what I thought was a compelling argument that suggested epigenetics is NOT evolution, and DOES NOT belong in Modern Synthesis. Epigenetics is something entirely different. I never got a response to that last argument. I was interested in your thoughts on that.



Epigenetics expresses real traits. Under natural selection, those traits may have an advantage. Those unable to express those advantageous epigenetic traits are likely to be selected against (or the respective opposite cases for disadvantageous traits). What would preclude epigenetics from evolution?


edit on 20/8/2015 by chr0naut because: (no reason given)



posted on Aug, 20 2015 @ 05:20 PM
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a reply to: StanFL

From your blog:

"Self-replication is a tricky business, and is not exactly like catalysis. Self-replication in a stew of precursor molecules means all of the components needed have to be gathered, and put into the right place. Catalysis is often thought of as a change in the form of a target molecule, or the addition of a component to the target molecule, or the merging of two target molecules. For self-replication to work, the precursor molecules have to be held in place while the other ones are being collected. Thus there must be a binding of each of the precursors to the original molecule. When there is a collection made, then the components must be joined, or that may have occurred earlier as each component falls into place. There is also a third step. The original molecule must let go of the newly formed copy of itself."

I think you need to update your definitions. Self replication does require instruction from the initial molecule. Regardless how primitive, it still can be considered a code.

Catalysis is the rate change of a chemical reaction due to a "catalyst". The catalyst can be any molecule, or combination of molecules, which causes the reaction rate to change but doesn't participate in the reaction. In other words, the catalyst remains the same. The Vmax, is the maximum rate of any reaction when the substrate is attached to the enzyme. This is given by the Michaelis-Menton equation which was derived from know reaction energetics. Your description would have the catalyst included in the chemical equation

Chemical equations for catalytic conversions are written like the jpg below.



the "Pt" over the long arrow is platinum, or the catalyst in this catalytic conversion.

Your blog is interesting but you've skipped over the most significant part of developing a theory: the mathematics. The mathematics, like enzyme kinetic math, gives you something to take into the laboratory. Ordinary language simply cannot describe processes which require measurements.






edit on 20-8-2015 by Phantom423 because: (no reason given)

edit on 20-8-2015 by Phantom423 because: (no reason given)

edit on 20-8-2015 by Phantom423 because: (no reason given)



posted on Aug, 20 2015 @ 05:40 PM
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a reply to: chr0naut

I agree with Venter as well - without evidence of course, but just because the statistics make sense. And it doesn't have to be just on this planet - it could be anywhere in our universe. We already know that meteorites and comets have chemical compounds which mimic the ones on Earth. There are many nucleic acids which aren't typically used in the genetic code - perhaps we'll find a life form which does use these exotic nucleic acids. Also, who's to say that the pentose sugar + heterocyclic amine compounds are the only configuration that can form stable molecules. As Hawking said, we have to be ready to recognize life - whatever form it may take.
And even if none of that occurs, the probability is that replicating molecules popped up independently. I don't believe it was one unique event.



posted on Aug, 20 2015 @ 06:46 PM
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When I hear evolution biology I think along the lines of a pet psychic ..

Evolution is a theory period.. It cannot be simulated in a lab, they cannot make a self replicating single cell.. Hell they don't even know why a cell divides in the first place..The time they got close they created tar and other compounds that are toxic to life.. Scream, yell, cry, poop, fart and holler.. No matter how many people claim it.. It's not fact it's theory.. Math maticians can tell you the numbers don't work.. The number becomes so large that it's beyond absurd..

Today a cell splits and forms an exact copy of its self.. The DNA , the information is the same, you can develop traits but not new species.. The only way to do that is direct manipulation of the code.. Speaking of code, where did the information come from in the first place?

With today's advancements in the fields of science, it still boggles my mind the number of people that still cling to this idea that life just popped up out of thin air..



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