An evolutionary dilemma!!!!

a reply to: Barcs

Which is why I called this a dilemma Barcs. Either route you take evidence from either genetics or fossils will slap you in the face.

originally posted by: wdkirk
Seems like you posted to the wrong thread. This is a discussion on evolution not propaganda. Part of the discussion is how each views the evidence shown in order to come to a conclusion. Both sides are stating good material and a wealth of knowledge. Somewhere in between is common ground that they both share.

As for bible verses, I'd say you have found your own personal contribution of propaganda.

Nope, he does this all the time. Basically, he ignores the topic and just posts rants in threads about how science minded folk explain things because he can't fathom anything beyond Jehovah's witness propaganda.

a reply to: ServantOfTheLamb

Please.. You folks are well practiced in the art of deception and routinely ignore the evidence in order to force confirmation bias on the rest of us. Lenski's research alone utterly destroys every fallacious lie you Ham minions are trying to sell.

You want to see real intelligence at work? Start here and observe the foundations of stupidity getting soundly served by intelligence.

In June 2008 the popular science magazine New Scientist printed a story about Professor Richard Lenski's twenty-year project examining the evolution of E. coli.[2] They reported that, as a result of several beneficial mutations, his organisms had acquired the ability to metabolize citrate — or more correctly an ability to transport it through the cell wall prior to metabolizing it. This was an entirely new ability for this species — an increase in complexity provided by a beneficial mutation. This beneficial trait was then fixed in the population by natural selection.

It is also important to notice that before acquiring this ability the bacteria acquired a previous potentiating mutation which, although it was not clearly beneficial at the time, subsequently allowed the descendants of that potentiated group the ability to process citrate after a further mutation. Furthermore frozen ancestors of that group, and only the frozen ancestors of that group, retained the ability to re-evolve that favorable trait.

His group did not use genetic engineering to modify the organism (to design it), it was produced entirely by the evolutionary process.

a reply to: flyingfish.


If you want to read the whole paper you are going to have to pay 10 bucks. I own it already so.

Abstract:
Adaptive evolution can cause a species to gain, lose, or modify a function; therefore, it is of basic interest to determine whether any of these modes dominates the evolutionary process under particular circumstances. Because mutation occurs at the molecular level, it is necessary to examine the molecular changes produced by the underlying mutation in order to assess whether a given adaptation is best considered as a gain, loss, or modification of function. Although that was once impossible, the advance of molecular biology in the past half century has made it feasible. In this paper, I review molecular changes underlying some adaptations, with a particular emphasis on evolutionary experiments with microbes conducted over the past four decades. I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre-existing molecular function, and I discuss the possible reasons for the prominence of such mutations.

2010 Quarterly Review of Biology - Experimental evolution, loss-of-function mutations, and “the first rule of adaptive evolution” by Michael Behe

As the abstract points out, adaptive evolution can cause a species to either gain, modify, or lose function. Your rational wiki source claims:

They reported that, as a result of several beneficial mutations, his organisms had acquired the ability to metabolize citrate — or more correctly an ability to transport it through the cell wall prior to metabolizing it. This was an entirely new ability for this species — an increase in complexity provided by a beneficial mutation. This beneficial trait was then fixed in the population by natural selection.

The source you have posted claims the cause of this "new ability" was a gain in function mutation. The peer reviewed source I am looking at from the University of Chicago says:

Recently, Lenski's group reported the isolation of a mutant E. coli that had evolved a Cit+ phenotype. That is, the strain could grow under aerobic conditions in a culture of citrate (Blount et al. 2008). Wild E. coli cannot grow under such conditions, as it lacks a citrate permease to import the metabolite under oxic conditions. (It should be noted that, once inside the cell, however, E. coli has the enzymatic capacity to metabolize citrate.) The phenotype, whose underlying molecular changes have not yet been reported, conferred an enormous growth advantage because the culture media contained excess citrate but only limited glucose, which the ancestral bacteria metabolized. Blount et al. (2008) marshaled evidence to show that multiple mutations were needed in the population before the final mutation conferred the ability to import citrate; the activating mutation did not appear until after the 30,000th generation. As Blount et al. (2008) discussed, several other laboratories had, in the past, also identified mutant E. coli strains with such a phenotype. In one such case, the underlying mutation was not identified (Hall 1982); however, in another case, high-level constitutive expression on a multicopy plasmid of a citrate transporter gene, citT, which normally transports citrate in the absence of oxygen, was responsible for eliciting the phenotype (Pos et al. 1998). If the phenotype of the Lenski Cit+ strain is caused by the loss of the activity of a normal genetic regulatory element, such as a repressor binding site or other FCT, it will, of course, be a loss-of-FCT mutation, despite its highly adaptive effects in the presence of citrate. If the phenotype is due to one or more mutations that result in, for example, the addition of a novel genetic regulatory element, gene-duplication with sequence divergence, or the gain of a new binding site, then it will be a noteworthy gain-of-FCT mutation. The results of future work aside, so far, during the course of the longest, most open-ended, and most extensive laboratory investigation of bacterial evolution, a number of adaptive mutations have been identified that endow the bacterial strain with greater fitness compared to that of the ancestral strain in the particular growth medium. The goal of Lenski's research was not to analyze adaptive mutations in terms of gain or loss of function, as is the focus here, but rather to address other longstanding evolutionary questions. Nonetheless, all of the mutations identified to date can readily be classified as either modification-of-function or loss-of-FCT.

So the truth is we don't know if that proves gain in function mutations are actually possible. If we are taking inference to the best explanation they are most like loss of function mutations or modification of function mutations. Especially since the ability to metabolize citrate already existed the only thing the bacterium needed to do to use citrate was to find a way to get it into the cell. The rest of the machinery for its metabolism was already there. Another point I would like to make is that your entire post is a Red Herring. Lenski's experiments have nothing to do with different coding languages inside of DNA. They have yet to do anything to show that new morphological features can arise via natural selection and random mutation.

Why don't you just accept that I actually study this stuff and read peer reviewed sources, and that the dilemma I've pointed out isn't from lack of knowledge.

a reply to: flyingfish

It looks like later work by Lenski's team gives us the answer:

www.ncbi.nlm.nih.gov...

This showed that the ability was due to the duplication and rearrangement of a gene for a protein that normally imports citrate into the cell, but only when no oxygen is present. The mutation allowed the protein to work when oxygen was present, as it was throughout the LTEE. Modification of function. Not gain in function as inference to the best explanation would have predicted.

Evolutionary science will never be conclusive .

.... that's why it's just a theory .

Smart money believes in a Creator God , who you WILL meet ,
at your passing .
AT that time , complete submission and respect are necessary
for your eternal peace .

God loves you , but , silly rebellious children are seated in a
dark corner for a while.

Science has brought us great things , .... apostasy , the greatest !

Gimme the history of a platypus or woodpecker , ... evolution MY ARSE !

originally posted by: radarloveguy
Evolutionary science will never be conclusive .

.... that's why it's just a theory .

I too have no scientific literacy.

a reply to: ServantOfTheLamb

It's not your place to comment on science. You're not a scientist. You're a fraud.
Your opinion is meaningless and ill-conceived. In short, you don't count.

End of message.

a reply to: Phantom423

Genetic fallacy again.

i am more inclined to think that the dilemma is concerned with your education in mes. it is difficult to educate yourself when you are more focused on proving that you are smarter than the experts. resist all you want, but posting poorly formulated attacks on a conspiracy forum is probably not the most effective approach.

a reply to: TzarChasm

resist all you want, but posting poorly formulated attacks on a conspiracy forum is probably not the most effective approach.

....oh the irony...

originally posted by: ServantOfTheLamb
a reply to: TzarChasm

resist all you want, but posting poorly formulated attacks on a conspiracy forum is probably not the most effective approach.

....oh the irony...

Im not attempting to cast suspicion on a theory based in facts, observations, and repeatable data to make my own unconfirmed and highly speculative hypothesis look less absurd. the irony is lost on me, it would seem.

a reply to: ServantOfTheLamb

Literally all you said is that cells are self-regulating, thermodynamically open systems which exchange matter and energy with its environment. Yes all of that is true, but again doesn't even attempt to solve the issue I've presented here.

No, that's not all I've said. The point I'm trying to help you understand is that the organism represents an emergent property of the ecological relations it has with it's environment. Do you get what the implication of that is? It means that when the environment changes significantly, the organism's thermodynamic structure either a) adapts by countering the effect of the environment, or b) dies off.

Sometimes, the organism becomes simpler in its organization, whereas other times the organism becomes more complex.Thus, evolution from prokaryotes to eukaryotes to sponge onward is a process of dynamic equilibrium with the environment, and, as the process continues, fusions and symbioses occur between cells, leading to a complexification of the total system i.e more elements, and indeed, symbioses like this entail a sort of "emegent property", where large-scale features of the environment (mechanics in movement, for instance) 'act down' upon the organization of the smallest elements.

I mentioned Terrence Deacon because you would do well to understand the concept of orthograde and contragrade, which helps explain how evolution could progress through non-stop oscillation between stability and organized chaos. An orthograde state corresponds to an attractor (a stable condition or a "structural coupling" with the environment) whereas a perturbation triggers a contragrade state, which, at this point, experiments with different adaptations to the pertubation to maintain its systems continuity. It's in contragrade states that growth and increased coherency can occur - what the ecologist Robert Ulanowicz calls "ascendance".

Also, and for someone who calls himself "seresnt of the lamb", it would be nice if you could be more mindful in your choice of words about what I mean i.e. "Are you just trying to use words you think most people won't take that time to look up?". This isn't an appropriate way of speaking - at least in real intellectual conversations, this would be regarded as an 'ad hominem' attack. Its also cynical and assumes that I am not making sense.

No, what makes sense - and what you should understand, is the diachronic nature of existence. You are obviously committed to a biblical timetable formulated in a period of human history where narrative and story-telling took the place of empirical study. Whatever 'mystical' value ancient thought had has more of a synchronic significance - not historical. I therefore am skeptical of the biblical "7 days of creation", and can accept that ancient Humans relied upon primitive means of knowing the world that didn't afford them a more complex understanding of the objects - living beings - they related with, at least not in a diachronic i.e. time-sense.

I don't think you even know what the problem I've posed is.

Do you pay attention to your emotions when you write? This is another mean-spirited thing to say. I understand you - I'm not an idiot. You don't need to call the other person stupid if it you - in fact, who is having the problem understanding the nature of the criticism I'm making.

Vertebrates supposedly came from invertebrates, do you want to explain how that is possible when their mitochondria use different coding languages?

Buddy - I've already answered this. When you scale back billions of years ago into the precambrian you have nothing but different versions of life. You are assuming that life only happened once. I am assuming that the life we see today is the life that survived.

Now, you seem to think that invertebrates HAD to be the ancestor for modern vertebrates. THAT IS NOT NECESSARY. You are completely overlooking how unnecessary that assumption is - but clearly this is where your focus lies. As I've already written - and to which you felt the need to ignore and then mock - invertebrates may be the evolutionary heir to a DIFFERENT EUKARYOTIC ANCESTOR. This is your issue - I've explained it, have told you that this is not that big a problem, but you apparently see it as the death of the evolutionary theory.

Ok? Yes? What you call 'mitochondria' is really just a cyanobacteria that eats oxygen and produces ATP. An Archea - a different sort of prokaryote, then "engulfs" the mitochondria, and in this process of time the mitochonrdia and the hosts cells nucleus "integrate" their functionality for the sake of the whole system.

My resolution: there were different sorts of bacteria with different genetic organizations of their nucleic acids. To say this is impossible is apparently gainsaid by the reality that vertebrates and invertebrates process oxygen in different ways. This merely means that the mitochondria - or ancient bacteria - had different ways of adapting to the presence of oxygen.

Finally, you put too much weight to this issue. As someone very well read in biochemistry and the origin of life, I am too overwhelmed by countless evidence of hierarchical "expansion" and progression" upon existing structures - particlarly in vertebrates - to be at all bothered by this blip - this rather insignificant find.

As another poster mentioned: evolution is a BUSH, not a tree. The tree is a metaphor that more and more scientists are abandoning for the more accurate "bush" picture.

a reply to: Astrocyte

wouldn't it be more accurate to compare the tree of evolution to a fungus of evolution? like a mushroom kingdom of phyluses and so on. the fungus may spread far and wide and become fractured in places or die off in others, take on different characteristics according to its environment, but it is all one family that has filtered and diluted through the ecosystem over many many years. just a thought.

a reply to: TzarChasm

No, its an interesting take. The point is, life is matter in motion. Everything we see around us is basically energy assuming the shortest-pathways towards equilibrium. Some elements coming together create chaos - others, rigidity, and still others, complex far from equilibrium activity i.e. life.

I'm a very spiritual, somewhat mystically inclined guy - but I follow my reason in all things, and my reason tells me that a) the universe had a beginning b) the way we make that claim i.e. the measurement of background radiation, is sound and legitimate c) life is a diachronic - were born, we die, new people are born, they die etc, down through the generations.

This site is so filled with people with mythological imaginations - and I simply can't "give in" to this, as if the human beings in interaction aren't mutually influencing one another's affectivity i.e. together they are built to 'craft a narrative' to make their experiences coherent.

Doesn't matter where I look, I find "explanations" everywhere. And mystic-explanations are some of the worse. I do not deny spirituality - I'm very spiritual - but I think people are deluding themselves when they interface with the properties of their own imagination.

Evolution is one of those things which sticks to the real-world: I am embedded in a physical context i.e. on a physical planet, hanging in empty space. I study my inner-experience, my phenomenology, with reference to the core theme of evolution: to survive - and so I find that quality in my self, in my thinking and needing to "constrain" and make coherent the experiences I have. Furthermore - given the PLASTICITY of our biological structure - this just adds greater authority to the evolutionary picture, where positive affectivity - which I define as any interpersonal experience where one parties intentional/affective state is positively received and known by another party; at such a moment, the speaker/actor experiences an "enlivenment" via the expressivity of the other parties voice or face. In other words, to evolve a brain, emotions like joy, care, and awe, flow between subjects who desire the Other to know what they experience. In other words, the brain evolves through symmetry i.e. a self-other equivalence that generates real physical effects in the brain.

Evolution - or a diachronic evolution of the universe, is not an issue for me at all. In fact, it seems highly illusory given that consciousness needs to be present to experience time i.e. a memory to hold together the unfolding of the process, and so, we might as well speak of the emergence of 'consciousness' i.e. egotistical awareness, as related to an ecological emergence in time - that is, as something that entails the human modifcation of the physical environment - cities, roads - to facilitate an emergent desire: possessiveness, privatization of property, egotism i.e. this generates a sort of 'stress' that then turns the human being into a time-keeper.

This is a theory I flirt with, but of course its not without its problems. On the other hand, its important to recognize how we process information with the environment - this being the "nexus" of tranformation i.e. the interaction.

a reply to: ServantOfTheLamb

Yes it does I've explained it numerous times if you can't understand it I can't help you.

You didn’t even explain it once.

Maybe if your first response didn't imply that millions of years explains away different coding languages in the mitochondria of vertebrates and invertebrates.

I didn’t imply that. I plainly stated that mitochondrial DNA in vertebrates and invertebrates would be different after millions of years of evolution. I said nothing about ‘different coding languages’ because that is, as Phantom pointed out, absolute balderdash. Genes are expressed differently depending on their chemical environment. That is hardly news.

If you think you have something that shows I am wrong, then quit beating around the bush and explain it.

You don’t even have a proposition, just a stupid claim. It’s not intelligent enough to be wrong; it’s just empty nonsense.

originally posted by: TzarChasm
i am more inclined to think that the dilemma is concerned with your education in mes. it is difficult to educate yourself when you are more focused on proving that you are smarter than the experts. resist all you want, but posting poorly formulated attacks on a conspiracy forum is probably not the most effective approach.

Surely the MES preceeded modern genetics by at least a decade.

Juliam Huxley wasn't prophetic. He didn't know any future scientific discoveries. The MES was on a best effort basis using the knowledge of the day. Many genetic quirks were not anticipated in the MES (horizontal transfer and epigenetics, etc).

There are things, like the variation in coding used in different 'branches' of the theorised phylogenetic tree, that are beyond the MES to speak to.

There are currently about 26 differences in coding identified to date (not all are successful enough to have living representative organisms). These coding differences do occur and for the life of me I cannot see how a living and successful organism would change its coding methodology. I can't imagine any scenario as to why and organism would turn coding for Uracil to a Stop, I can't see how it would be successful and I can't see any forces that would induce such a change.

If abiogenesis happened once, why not many times?

If there are many origins to life, why not differences in how genetic coding is interpreted and applied.

a reply to: ServantOfTheLamb

Every single one of those items listed is a not just a different sequence of genes, but they interpret the same codon's completely differently. That shows all the different coding languages and explains which codons are read how for each code. So yes it does acknowledge these things, but rather than state it as a number they have listed them out and explained how to read some of their codons, which is unique to that cell type or structure. So you'd have to count them, which it appears there are more than 19 now, surprise surprise. You are either being deliberately dishonest or you simply didnt scroll down on the NBCI link. You'll notice the vertebrate and invertebrate mitochondrial DNA is on that list. Its exactly what I was talking about in th OP.

Idiot, if everyone had the same sequence of nucleotides, everyone would look the same and be the same. The four base pairs make up the codons. And of course they are read differently because they code for different functional parts of an organism. It's like the alphabet - there are 26 letters that can form millions of words. The alphabet is the database that's used to form words. In English it's "yes", Spanish "Si", French "Oui". They all mean the same thing - different combinations which communicate the same idea. Genetic code is less complicated - it only needs the four base pairs for the required number of permutations to construct a unique condon.

Get over it. Your sources are wrong. Not only are they wrong, but if they were right, the genetic code would be chaotic and there would be no genetic relationship among species on this planet. Common ancestry. It's so obvious that even one of your primate ancestors could figure it out.



I suggest you call NCBI and ask them if there are 19 different "languages".

a reply to: chr0naut

Those are good questions. You should look up the answers because they're all in the literature.

Use Google Scholar.

scholar.google.com...

a reply to: ServantOfTheLamb

So the truth is we don't know if that proves gain in function mutations are actually possible. If we are taking inference to the best explanation they are most like loss of function mutations or modification of function mutations.

No.. the truth is we observe gain in function in mutations leading to novel phenotype everywhere we look, from primates to plants. If you actually study this stuff you would know this.

Lenski's experiments have nothing to do with different coding languages inside of DNA. They have yet to do anything to show that new morphological features can arise via natural selection and random mutation. Why don't you just accept that I actually study this stuff and read peer reviewed sources, and that the dilemma I've pointed out isn't from lack of knowledge.

I reject the idea you "actually study this stuff." You may skim through it and reinterpret with Jesus colored classes, but it's obvious you don't know what your talking about or you're deliberately misinterpreting the information.