An evolutionary dilemma!!!!

a reply to: Phantom423

Yes, they can be related. The obvious reason that they are related is simply the observation that the different organisms contain the same codon i.e. the same SEQUENCE OF NUCLEOTIDES WHICH MAKE UP THE CODON.

God if this isn't the epitome of someone who doesn't understand what I am talking about. Okay I'll do this for you one more time in detail. If you can't get it after that we will just have to agree to disagree.

When the ribosome, the part of a cell that constructs proteins, encounters the codon, UGA, in the messenger RNA of a human cell, it ceases the translation process.

This is not so in Mycoplasma, where UGA codes for the amino acid tryptophan. Once reaching UGA in an mRNA strand, the Mycoplasma ribosome would insert a tryptophan (into the current protein being built) and keep going right along with translation, through the following codons, until it met a stop codon in this environment. Human and Mycoplasma cells do not read their DNA in the same way. Vertebrate and invertebrate mitochondrial ribosomes do not read their mitochondrial DNA the same way.

This is why Craig Venter says the in the video posted on the first page that Mycoplasma code "would not work in your cells." This can be tested by expressing exogenous genes with the Standard Code in Mycoplasma to see if functional products would emerge from ribosomes. They don't. If their ribosomes do not interpret code the same the organisms could not be related, hence the reason Craig Venter also says that the tree of life is an artifact of some early scientific studies that aren't holding up in the lab.

Your sources pulled a conclusion out of a hat and just like magic, it looked good, therefore, it worked - who would ever challenge such an innovative conclusion?!! No objective analysis, no lab work, no corroborating references - just a few pages of unreliable gibberish with no evidence. The usual scenario which suits their agenda.

This is the second time you've posted something I've already mentioned in the OP. You obviously still haven't even understood what the dilemma actually is. You posted a source describing a possible explanation for bacterial genes in eukaryotes that have unexpected branching patterns:

INHERITED CHIMERISM: CUTTING TREES A BIT OF SLACK
As an alternative to supernumerary symbionts, perhaps the too many bacterial genes in eukaryotes are acquisitions, by an archaeal host, via gene transfer from the mitochondrion itself (39), whereby the excess of bacterial genes that do not tend to branch with any bacterial group in particular, including alphaproteobacteria, is best explained as gene acquisitions from the mitochondrion followed by LGT among prokaryotes, in addition to the many technical shortcomings of deep phylogeny (40).

This has absolutely nothing to do with "my codon problem". What this does do is explain how mitochondria and other organelles are thought to have appeared in eukaryotic cells. I explained this simply in the OP:

Current evolutionary theory says that prokaryotic cells evolved first, and at a later date one of these cells engulfed another cell, this cell eventually became the mitochondria for the cell that engulfed it.

This is a simplification of endosymbiotic theory, which is what your paper is some what on though it is attempting to explain why certain bacteria genes are in the DNA of eukaryotic cells it doesn't even mention differences in the translation process with the same codon. Now in the OP I also said lets assume endosymbiotic theory is correct, so I don't know why you think this solves my problem as it was supposed to be assumed to occur before you can even understand my problem. Its obvious you haven't even taken the time to try and understand my position.

a reply to: Noinden

Is this the best you can do? No where in his post did I attack his character and say because of that flaw in his character that his argument was wrong. You don't even know what an ad homenin is, or you just can't read. Calling him a neo-darwinist wasn't an insult. You took it that way because you don't like that I disagree with you. If these snide comments are all you've got go on somewhere and stop derailing the thread.

a reply to: ServantOfTheLamb

You use the terms Darwinist, evolutionist, etc as insults. I've seen you do it often enough. You have a long history of resorting to these phrases, rather than argue the facts.

I don't actually give a monkey's cuss what you believe.

Oh and you still have yet to prove your OP is an evolutionary dilemma What you have illustrated is you do not understand genetics, and mitochondria.

a reply to: Noinden

Cool.

a reply to: Noinden

Because it has a semiotic dimension.

has anyone here heard of the extended theory of evolutionary synthesis? or extended synthesis for short. it is one example of how it is openly admitted that we do not have all the answers, but that isn't to say we have no answers, far from it.

en.m.wikipedia.org...

originally posted by: ServantOfTheLamb
a reply to: Phantom423
Now in the OP I also said lets assume endosymbiotic theory is correct, so I don't know why you think this solves my problem as it was supposed to be assumed to occur before you can even understand my problem.

Let's not. Let's wait for the first piece of proper evidence that this event is even possible, let alone deciding whether or not it happened in the way it is described.

I understand for what purpose you allowed that assumption, and this is not an expression of disagreement with doing that. Just offering an alternate subject to think about involving fancy storytelling and research that is based on fancy storytelling followed by debates about fancy beguiling myths. It's like debating with someone who believes in the existence of fairies but refuses to even present a single logical reason for doing so, let alone proper convincing evidence while they call you gullible and delusional for dealing with the facts and reality and drawing conclusions from them by induction. Which reminds me of the terminology used regarding "the hypothesis of abiogenesis" (by natural processes alone, or caused by the laws or forces of nature alone) a.k.a. "the chemical evolution theory of life" a.k.a. "chemical evolution" a.k.a. "abiogenesis", and so on. The first 2 quotations are from Huxley and Haldane+Oparin respectively.

Or let's think (not necessarily talk) about the deceptive nature of introducing a myth (false story) as a hypothesis and then having others give the impression that it's already a (scientific) "theory", or 'scientific', or 'science' (by publishing about it as such in so-called "peer reviewed" papers or books+other media pretending to be about science).

“To take a line of fossils and claim that they represent a lineage is not a scientific hypothesis that can be tested, but an assertion that carries the same validity as a bedtime story—amusing, perhaps even instructive, but not scientific.”—In Search of Deep Time—Beyond the Fossil Record to a New History of Life, by zoologist Henry Gee*, pp. 116-117

The same counts for the bedtime story about the prokaryotic bacteria that experienced endosymbiosis in the manner described and all stories derived from it such as endosymbiotic gene transfer from prokaryotic pangenomes.

*: Henry Gee does not suggest that the theory of evolution is wrong. His comments are made to show the limits of what can be learned from the fossil record. Specimens placed in the series are often separated by what researchers estimate to be millions of years. Regarding the time spans that separate many of these fossils, Henry Gee says: “The intervals of time that separate the fossils are so huge that we cannot say anything definite about their possible connection through ancestry and descent." (on page 23)

Speculations built upon speculations built upon speculations, that's your house of cards for ye. Pretty much every fallacy (perhaps every) or behaviour the man in the video below complains about I have observed from the type of people he is discussing, and their fans or victims (allthough I don't agree with the way he phrases everything, especially when he's quoting about "science" in the bible in a rather confusing manner; I also disagree with the use of the words "maniac", "clown" and "pathetic" among other little things):

originally posted by: Astyanax
a reply to: chr0naut

Genetecist Craig Venter (of the Human Genome Project among other things) in a science forum at Arizona State University, in April 2011, with other scientists discussing evolution, made the comment that there was not likely to be a single tree of life, but rather - many bushes.

Other panelists - like the journalist and writer Richard Dawkins, suggested that Venter, the preeminent genetecist in the world, was wrong, primarily because they hold to the paradigm of a single "tree of life".

You are repeating a Creationist lie.

The truth is at the link. As usual, you receive the benefit of the doubt as to your motives, although it is remarkable how many Creationist lies you have posted, implying them to be true, in your career at ATS.

As for the premise of this thread, it is mudwallowing gibberish.

Of course, it's all a Creationist lie.

Venter, Dolittle, Woese, everyone who has questioned the phylogenetic tree from a universal common ancestor, they all must be Creationists, and sneaky ones, too.

Since science actually has all the answers to everything (especially in regard to the development of life on Earth), we can all stop thinking now.



Honestly, the advancement of science sometimes requires someone challenging the assumed default paradigm. If it didn't, we'd all still believe in Platonic and Aristotlean ideas of science.

Like those old 'Evolution of the modern Horse' Eohippus to Equus charts, the phylogenetic tree of life may be more of an artefact of us trying to intuit an order on a vast volume of data, ignoring the contradictory data because it doesnt fit our nice neat little model.

originally posted by: Noinden
a reply to: ServantOfTheLamb

Why do people keep assuming DNA is like a language, or programming language? That is an analogy, and all analogies eventually fail.

Perhaps because, generally, particular sequences of DNA get transcribed to particular sequences of RNA which code for particular amino acids.

The thing is that, depending upon the particular type of life, the DNA codes can code for different amino acids to what other types of life code for.

originally posted by: Phantom423
a reply to: chr0naut

I agree with you. Life could have started multiple times. But the complexity of the topic is so deep that discussing it here on ATS without a set of references that cover the entire subject, makes it a useless endeavor. Just my opinion.

The OP has no working knowledge of science. Probably has never been in a lab, doesn't understand how the scientific method works - on and on. In other words, anyone who responds to the OP, is obliged to begin with the basics.

I'm not a molecular biologist. I'm a biochemist and my specialty is spectroscopy. I have a Ph.D. in biochemistry and biophysics. I don't mind diving into a topic as long as others make an equal contribution. So if you want to start a serious thread about the tree of life and questions surrounding it, I'm happy to participate. But every time someone starts a serious thread, it devolves into a food fight defending one's self against the fraud and deception of Creationism.

So up to you. If you want to discuss the topic, happy to do so. It's very interesting and everyone can learn something by doing the research.

If natural processes gave rise to abiogenesis, then why couldn't life have always continually been starting in multiple abiogenic events (at an assumed low probability, because if it was happening all the time we'd probably see it).

It takes a particular faith that it happened only once.

Also, the 'life' created from abiogenesis would likely have been more basic and primitive than that coded and regulated in DNA. It would probably have been pre-genetic. As such, many different approaches to transmission of traits may have occurred, with DNA, probably built from RNA sequences, being the most successful.

a reply to: ServantOfTheLamb

You're acting like this is the whole story, I'm sure it's not finished yet. We are only beginning to understand the mysteries of DNA...

a reply to: chr0naut

I don't know the answer to that question. But abiogenesis as a one-time event is not dogma. It has been challenged and discussed in multiple research publications. Browsing through a few papers, the general consensus is that conditions on early Earth were suitable for a "life plan" as one paper describes it (see below). On the other hand, if life can initiate spontaneously at any time, why is it so difficult to replicate it in the lab? It's a topic loaded with questions with no definitive answers. My opinion is that life is ubiquitous in this universe, that it can begin under many conditions and not just carbon-based life. In fact, the limiting factor might be the elements themselves. At some point, it has to come down to the chemistry - we just don't exactly what that chemistry was and why it can't be replicated today.

Big Bang or Continuous Creation: Does life have multiple origins?
Gregory A. Konesky*
K-Plasma, Ltd., 3 Rolling Hill Rd., Hampton Bays, NY 11946-3716

Abstract
The generally accepted notion of a single origin of life from a primordial soup on the early Earth has been challenged recently by the suggestion of a “second life,” “shadow life,” and even “biological dark matter.” The problem in classifying these microorganisms is in the difficulty or complete failure of the 16s genetic fingerprinting process, suggesting a different underlying biochemistry resulting from at least a second origin of life. We consider an extension of this concept to include continuous origination of life throughout Earth’s history, up to the present. The consequences for interpreting the “tree of life” are also considered.

Keywords: Origin of Life, Multiple Origins of Life, Abiogenesis, Parabiogenesis, Second Life, Biological Dark Matter, Horizontal Gene Transfer, Panspermia.

1. INTRODUCTION
A variety of possible models have been proposed for the origin of life, ranging from a primordial pre-biotic soup in a reducing environment, to hydrothermal deep sea vents, to a radioactive beach hypothesis, and a great many others. While changing environments, over geological time frames, have eliminated many of these proposed environments, some, such as hydrothermal vents, continue to persist to this day. We consider the possibility that they may continue to originate life on an on-going basis through abiogenesis. An even more intriguing question is whether pre-existing life inhibits or promotes the re-origination of more life, a “parabiogenesis.” Possible inhibitors include the generation of oxygen, and evolution-derived survival mechanisms that can simply out-compete newly emerged forms. On the other hand, pre-existing life presents a rich brew of post-biotic soups from which both simple and advanced building materials would be readily available. The premise of a “second life” approach is that evolutionary diversity would produce a clearly discernable life form, such as the somewhat controversial arsenic-based life. However, when one considers the huge range of potential organic compounds that can be made, only a very limited subset is embraced by life. Horizontal gene transfer may further complicate the ability to recognize recently arrived new life. While great evolutionary diversity is seen towards the outer limbs of the tree of life, the roots, so to speak, have very limited evolutionary trajectories, again perhaps making it difficult to discern recent new life from ancient new life. Panspermia hypothesis is another re-origination route.

www.researchgate.net...

a reply to: Phantom423
Just to be clear, in 2008, Professor of Biology Alexandre Meinesz stated that over the last 50 years, “no empirical evidence supports the hypotheses of the spontaneous appearance of life on Earth from nothing but a molecular soup, and no significant advance in scientific knowledge leads in this direction.” (How Life Began—Evolution’s Three Geneses, by Alexandre Meinesz, translated by Daniel Simberloff, 2008, pp. 30-33, 45.)

And they are still not hypotheses. The spontaneous appearance of life elsewhere (followed by Panspermia) still has the same logical requirement or implication regarding a molecular soup (just elsewhere then, and the word "spontaneous is referring to what I referred to as the requirement or implication of natural processes alone being the cause, i.e the forces of nature alone). Obviously, that's conveniently left out of the claims and stories about Panspermia, hydrothermal vents, etc. in your article and you can still give it another terminology to argue that it's not a "soup" or something. The key factor is natural processes alone from nonliving molecules, not whether or not "soup" is the appropiate terminology. Besides, the exact same thing counts for all the other myths as the article in question also does not provide any logical reasonable and proper evidence for any of the myths mentioned because that's not part of the game being played.

And again, more mythology presented as science by you, the writers of that article and anyone involved in the websites or journals that publish it.

Practice makes perfect:
Real science, knowledge about realities compared to philosophies and stories

a reply to: chr0naut

I am fully aware of that. Its not a language however. No programming language self assembles.

a reply to: Noinden

Precisely my point. Neither could DNA Self Assemble. Semiotic dimension only arises from intelligent input.

a reply to: ServantOfTheLamb

Show proof. DNA self assembles due to chemical potential. There is no need to have a hand of deity involved. Lower energy states are all you need.

originally posted by: Noinden
a reply to: chr0naut

I am fully aware of that. Its not a language however. No programming language self assembles.

Actually, there are new AI type language routines that self-define.

For example, the Google Translate engine uses an intermediary machine generated 'language' (word concept lookup or relationship table?) to equate different human languages and thereby provide a reasonable equivalence. This table is modified through analysis of online text gathered by web crawling bots (and from user response) which apply known definitions and syntactic rules, among other things, to build the interrim tables.

a reply to: Noinden

Show proof. DNA self assembles due to chemical potential. There is no need to have a hand of deity involved. Lower energy states are all you need.

DNA carries a semiotic dimension. Codons act as sign vehicles for the ribosomes, this would be the syntax of a progamming language and its environment, and depending on what environment you are in determines whether the the ribosome will produce a functional protein. It may very well look from the human perspective as though DNA self assembled. My claim is not that the parts couldn't have fallen together by suitable conditions but rather, that the abstract information stored in DNA could not have been the product of physical causes and self assembly. I think God spoke things into existence, so its not like I would expect some magical hand of deity. In fact I would simply expect to find a physical process that describes how inorganic matter came to organic matter and then from the information in organic matter we would probably find many body plans arising probably in different areas and places over some period of time and these body plans would have variation among them as natural selection and random mutation took hold. What makes me infer that DNA did not self assemble in the way you speak of it self assembling is its semiotic nature!

originally posted by: Noinden
a reply to: ServantOfTheLamb

Show proof. DNA self assembles due to chemical potential. There is no need to have a hand of deity involved. Lower energy states are all you need.

would you mind showing some examples of this? genetic self assembly?

a reply to: ServantOfTheLamb

Do you ever not just cut and paste? Because it looks very much like you've been reading Gods Undertaker