Science shows that evolution can't create new genes

jamest · **#41** by **jamest** » Dec 31, 2014 2:49 pm

Shrunk wrote:
jamest wrote:Makes you wonder why Lenski didn't extend his experiment accordingly.

Umm, 'cause then it'd be a different experiment. Not this one.

If you were going to observe bacteria for several decades, it seems like common sense to do so within various environmental contexts. Scientists are more than capable of conducting one experiment at a time.

Rumraket · **#42** by **Rumraket** » Dec 31, 2014 2:52 pm

MarioNovak wrote:
Shrunk wrote:
The evolutionary origin of orphan genes

Nature Reviews Genetics 12, 692-702 (October 2011) | doi:10.1038/nrg3053

Diethard Tautz & Tomislav Domazet-Lošo

Abstract

Gene evolution has long been thought to be primarily driven by duplication and rearrangement mechanisms. However, every evolutionary lineage harbours orphan genes that lack homologues in other lineages and whose evolutionary origin is only poorly understood. Orphan genes might arise from duplication and rearrangement processes followed by fast divergence; however, de novo evolution out of non-coding genomic regions is emerging as an important additional mechanism. This process appears to provide raw material continuously for the evolution of new gene functions, which can become relevant for lineage-specific adaptations.

http://www.nature.com/nrg/journal/v12/n ... g3053.html

Just reading this now. So far, no mention of orphan genes being magically created by Jesus as a viable hypothesis, and from the title and the abstract I don't expect that to be included. But I'll let everyone know if it comes up...
As I said above, people must learn to differentiate between scientific knowledge - cognizance of a fact or phenomenon acquired through experiments and observations - and mental constructs of a human mind - ideas, explanations, theories, hipoteses, ad hoc hypothesis, conjectures, etc. I have no doubt that proponents of evolution will find an "explanation" of how orphan genes come into existance. But this is not science, but storytelling.

History of evolutionary thought in biology explaining emergence of observable biological organization is full of mental constructs and magic words like: "might arise". Evolutionary explanations of orphan genes emergence is not different.
"Might appeared", "emerged", "gave rise to", "burst onto the scene", "evolved itself," "derived", "was on the way to becoming", "radiated into", "modified itself", "manufactured itself", "evolution's way of dealing with", "derived emergent properties", "was lucky"...

How do words like "might arise" explain emergence of new genes? Just like magic, the use of this word invokes mysterious powers within unseen universes

What the fuck are you talking about? You know that pervasive transcription is an empirically observed phenomenon right? There are no mysterious powers operating in unseen universes at work here.

The authors are merely hypothesizes that an observed process: mutations - In an observed entity: non-coding DNA - Is producing an observed phenomenon: accidental transcription and translation. And that these three empirically observed factors together explains the origin of Orphan genes.

All of these individual factors are concrete empirical realities. They are being tied together in a theoretical candidate process for the origin of new genes de novo from junk-regions.

Shrunk · **#43** by **Shrunk** » Dec 31, 2014 2:54 pm

jamest wrote:
Shrunk wrote:
jamest wrote:Makes you wonder why Lenski didn't extend his experiment accordingly.

Umm, 'cause then it'd be a different experiment. Not this one.

If you were going to observe bacteria for several decades, it seems like common sense to do so within various environmental contexts.

Why? This experiment was to study how bacteria evolve in a single environment. Changing the environment would not allow them to do that.

jamest · **#44** by **jamest** » Dec 31, 2014 2:55 pm

Shrunk wrote:
jamest wrote:
Shrunk wrote:
jamest wrote:Makes you wonder why Lenski didn't extend his experiment accordingly.

Umm, 'cause then it'd be a different experiment. Not this one.

If you were going to observe bacteria for several decades, it seems like common sense to do so within various environmental contexts.

Why? This experiment was to study how bacteria evolve in a single environment. Changing the environment would not allow them to do that.

As I said, scientists can run more than one experiment at a time.

Blackadder · **#45** by **Blackadder** » Dec 31, 2014 2:57 pm

jamest wrote:
Shrunk wrote:
jamest wrote:
Shrunk wrote:

Umm, 'cause then it'd be a different experiment. Not this one.

If you were going to observe bacteria for several decades, it seems like common sense to do so within various environmental contexts.

Why? This experiment was to study how bacteria evolve in a single environment. Changing the environment would not allow them to do that.

As I said, scientists can run more than one experiment at a time.

I'm sure you can eat pizza and pick your nose at the same time. So why don't you?

Shrunk · **#46** by **Shrunk** » Dec 31, 2014 2:58 pm

If I may, Rumraket:

Rumraket wrote:This handy little guide will help you how to become a superb ID proponent by educating you on how to interpret what you read about evolution from non-ID/creationist sources.

It will also help you understand how creationists think when they read evolution-related material.

Normal word - Cdesign proponentsist interpretation:

Rare = never ever.
Ulikely/improbable = impossible.
Likely = rare/baseless guess.
Theory = guess/baseless faith.
Guess = biased wish/atheo-materialistic faith.
We don't know = and you never will, therefore god!
Not fully understood = not at all understood, impossible to understand, magic/miracles required.
Unexpected result = all naturalistic explanations ever have been falsified.
Neutral mutation = not beneficial, therefore impossiblee/doesn't exist, cannot be fixed.
Natural selection = Orthodox neo-Darwinistic "party line".
It has a chance of one in 10^16 = It has a chance of one in 10^77
Maybe = biased guess (see: Guess).
Could have = couldn't and didn't (see: Guess).
Beneficial mutation = loss of function/tradeoff and/or loss of information.
New function = loss of information/information was already there.
New information = no new function.
New information and function = still belongs to the same class of enzymes (ex. hydrolases), so not really new.
Improved function = no new information, ability was already there.
Mutation = destroys information, always degrades. Guided by god, not random.
Millions of years = ad hoc excuse invented to explain why we don't see 20 million year macroevolutionary change in a few months of experimental evolution.
Took billions of years = same excuse as above, just worse.
Ancestral Sequence Reconstruction = *crickets*
Molecular phylogeny = phyloschmylo, it's more Darwinist math-tricks.
Observation/experiment = hoax and/or only creationists properly understand the result.
Demonstration = hoax.
Statistics = Wat?
Statistically significant = Nyah nyah! Darwinist math-tricks.
Complex = impossible to evolve, must be designed.
Complicated = Impossible to understand.
Complexity = praise the lord!
Information = immaterial soul-stuff that refutes materialism and all naturalistic expanations ever.
Quantum = immaterial soul-stuff that refutes materialism and all naturalistic expanations ever. Cannot possibly evolve.
Experiment shows how mutations can... = It's still just a bacterium/fruitfly/dog-kind.
Ape = monkey
monkey = ape
evolutionist = ape-monkey
homosexuality = bestiality and rape by ape-monkeys.
evolution = materialism/naturalism/scientism/darwinism/chance/fair coin/abortion/euthanasia/racism and genocide.
darwinism = materialist religious faith.

How many boxes has MarioNovak ticked off already? Play along, it's fun!

Shrunk · **#47** by **Shrunk** » Dec 31, 2014 2:59 pm

jamest wrote:
Shrunk wrote:
jamest wrote:
Shrunk wrote:

Umm, 'cause then it'd be a different experiment. Not this one.

If you were going to observe bacteria for several decades, it seems like common sense to do so within various environmental contexts.

Why? This experiment was to study how bacteria evolve in a single environment. Changing the environment would not allow them to do that.

As I said, scientists can run more than one experiment at a time.

'Cuz scientists are wizards who can conjure time, money, lab techs and grad students out of thin air.

Rumraket · **#48** by **Rumraket** » Dec 31, 2014 3:05 pm

jamest wrote:
Rumraket wrote:
jamest wrote:
MarioNovak wrote:
Well, the biggest scientific observations of evolution in action is E. coli evolution experiment. On February 24, 1988. Richard Lenski and his team at Michigan State University embarked on an ongoing long-term evolution experiment. He started 12 genetically identical lines from a single strain of E. coli. The bacteria reproduced every few hours. The populations reached the milestone of 50,000 generations in February 2010 and 60,000 in in April 2014.
So, what did Lenski experiment show? How many new genes evolutionary processes created after 60,000 generations?
Well, the answer is 0, - ZERO. Most of the changes in this experiment involved streamlining the genome, deleting genes no longer needed, or reducing protein expression.

Were the bacteria all maintained within the same unchanging environment?

Yes. In other words, everything they carried of genes to survive in their natural environment (the mammalian gut) was eventually discarded through the accumulation of mutational deletions, because the environment to which they were introduced and subsequently adapted never changed and only contained a select few nutrients. So they naturally lost all the additional capacities they had that were not related to doing well in this particular environment.

What happened was as expected, they became much, much better at working well in this new environment. For evolutionary novelty to happen there needs to be the opportunity for novelty. The environment must be changing and fluctuating, new types of nutrients must occasionally enter it and so on. None of these conditions were part of the experiment. So the Long term evolution experiment with E coli has so far basically been an experiment in the ability of natural selection to streamline a single organism to function extremely well under one single living condition.

Makes you wonder why Lenski didn't extend his experiment accordingly.

That depends on what he wants to test.

You have to start somewhere. The experiment has been a tour de force in the operation of natural selection and the frequency of mutational patterns. For example, what has been learned is that one of the most frequent types of mutations is gene duplication. Genes are constantly duplicated.

The experiment has also served as an empirical test of the ability of contemporaneously used phylogenetic methods ability, to reconstruct evolutionary history. Since ancestral stages in the experiments have been saved and frozen down, these can (and have been) thawed and sequenced to see what mutations have happened in them, and subsequently the data(how evolution happened) has been compared to how the predictions of phylogenetic algorithms build evolutionary trees.

This is another reason we can trust the results we get from phylogenetics with high confidence, because the algorithms are highly accurate, and become even more accurate the more data we have. Which is a further argument against the need to see things happen in real time, because we can instead simply reconstruct the evolutionary history that happened millions of years ago by using these same phylogenetic methods on the datasets we have from extant life.

That's how we know that you share genetic ancestry with all known life and why we can be relatively confident that this is true, and that the mechanism responsible for this diversification of life was indeed the process of evolution. Because, in point of fact, the phylogenetic algorithm successfully reproduces the branching patterns we get from running real-life experiments in evolution.

Human beings don't live for 25 million years, we are never going to re-create or directly observe the origin of terrestral tetrapods from lobe-finned fish (or anything else that patently requires 25 million years of mutation and natural selection). So we do the next-best thing we can, we build models of the process and test their predictions against real world data. If the models faithfully reproduce real-life results, we can have confidence in the models.

Tough shit, we can't travel in time, get over it. That doesn't mean we cannot have good reason to think certain events happened the way scientists postulate. But to understand the reasons for their postulates requires bothering to educate oneself about the work they do and the previous works of other scientists it rests on. What will emphatically NOT give you any answers is to INSIST on ignorance, misdirection and deceitful reinterpretation as our dear OP does.

EDIT: Spelling and grammar.

Rumraket · **#49** by **Rumraket** » Dec 31, 2014 3:10 pm

Shrunk wrote:If I may, Rumraket:

Rumraket wrote:This handy little guide will help you how to become a superb ID proponent by educating you on how to interpret what you read about evolution from non-ID/creationist sources.

It will also help you understand how creationists think when they read evolution-related material.

Normal word - Cdesign proponentsist interpretation:

Rare = never ever.
Ulikely/improbable = impossible.
Likely = rare/baseless guess.
Theory = guess/baseless faith.
Guess = biased wish/atheo-materialistic faith.
We don't know = and you never will, therefore god!
Not fully understood = not at all understood, impossible to understand, magic/miracles required.
Unexpected result = all naturalistic explanations ever have been falsified.
Neutral mutation = not beneficial, therefore impossiblee/doesn't exist, cannot be fixed.
Natural selection = Orthodox neo-Darwinistic "party line".
It has a chance of one in 10^16 = It has a chance of one in 10^77
Maybe = biased guess (see: Guess).
Could have = couldn't and didn't (see: Guess).
Beneficial mutation = loss of function/tradeoff and/or loss of information.
New function = loss of information/information was already there.
New information = no new function.
New information and function = still belongs to the same class of enzymes (ex. hydrolases), so not really new.
Improved function = no new information, ability was already there.
Mutation = destroys information, always degrades. Guided by god, not random.
Millions of years = ad hoc excuse invented to explain why we don't see 20 million year macroevolutionary change in a few months of experimental evolution.
Took billions of years = same excuse as above, just worse.
Ancestral Sequence Reconstruction = *crickets*
Molecular phylogeny = phyloschmylo, it's more Darwinist math-tricks.
Observation/experiment = hoax and/or only creationists properly understand the result.
Demonstration = hoax.
Statistics = Wat?
Statistically significant = Nyah nyah! Darwinist math-tricks.
Complex = impossible to evolve, must be designed.
Complicated = Impossible to understand.
Complexity = praise the lord!
Information = immaterial soul-stuff that refutes materialism and all naturalistic expanations ever.
Quantum = immaterial soul-stuff that refutes materialism and all naturalistic expanations ever. Cannot possibly evolve.
Experiment shows how mutations can... = It's still just a bacterium/fruitfly/dog-kind.
Ape = monkey
monkey = ape
evolutionist = ape-monkey
homosexuality = bestiality and rape by ape-monkeys.
evolution = materialism/naturalism/scientism/darwinism/chance/fair coin/abortion/euthanasia/racism and genocide.
darwinism = materialist religious faith.

How many boxes has MarioNovak ticked off already? Play along, it's fun!

I think the red ones are so far the ones he's come closest to implying. Let's see how many we can cross off when the thread dies out. :lol:

Rumraket · **#50** by **Rumraket** » Dec 31, 2014 3:38 pm

MarioNovak wrote:Ear is different than eye, heart is different than kidneys, DNA polymerase is different ATP synthase, mechanical gears in jumping insects are diferent then bacterial flagellum, knee is different than jaw, liver is differnt then stomach...

So, you cant just randomly duplicate existing genetic code for a particular organ or part of the organ, add few hundred random mutations and voilà, new organ or molecular machine will emerge.

Wait - why not? The latter statement does not seem to follow from the former. Which makes me wonder why you start the second sentence by writing "So, ..." when what you write before it does not establish the truth of the later. There is no "So, you can't just..."

If I copy a word and then start replacing the letters one by one, I will eventually have created a new word with nothing left of the original word.

I can even do that with an entire sentence. If I copy the sentence and start mutating letters, commas and spaces one by one, eventually I can create a new one with nothing left of the original. Why can't the same process of duplication and subsequent accumulation of hundreds of point mutations produce new organs or molecular machines? It seems to be that it actually makes perfect sense that this is how it happened.

By the way, genes aren't actually words(the constraints on the functionality of proteins are physical and chemical, the contraint on the meaning of words is simply due to human convention), so just because there are some words that have to pass through nonsensical stages unlike any known word, doesn't mean actual proteins cannot be mutated while retaining functionality despite them passing through stages that look nothing like any extant protein.

MarioNovak · **#51** by **MarioNovak** » Dec 31, 2014 3:51 pm

Rumraket wrote:
MarioNovak wrote:
Shrunk wrote:
The evolutionary origin of orphan genes

Nature Reviews Genetics 12, 692-702 (October 2011) | doi:10.1038/nrg3053

Diethard Tautz & Tomislav Domazet-Lošo

Abstract

Gene evolution has long been thought to be primarily driven by duplication and rearrangement mechanisms. However, every evolutionary lineage harbours orphan genes that lack homologues in other lineages and whose evolutionary origin is only poorly understood. Orphan genes might arise from duplication and rearrangement processes followed by fast divergence; however, de novo evolution out of non-coding genomic regions is emerging as an important additional mechanism. This process appears to provide raw material continuously for the evolution of new gene functions, which can become relevant for lineage-specific adaptations.

http://www.nature.com/nrg/journal/v12/n ... g3053.html

Just reading this now. So far, no mention of orphan genes being magically created by Jesus as a viable hypothesis, and from the title and the abstract I don't expect that to be included. But I'll let everyone know if it comes up...
As I said above, people must learn to differentiate between scientific knowledge - cognizance of a fact or phenomenon acquired through experiments and observations - and mental constructs of a human mind - ideas, explanations, theories, hipoteses, ad hoc hypothesis, conjectures, etc. I have no doubt that proponents of evolution will find an "explanation" of how orphan genes come into existance. But this is not science, but storytelling.

History of evolutionary thought in biology explaining emergence of observable biological organization is full of mental constructs and magic words like: "might arise". Evolutionary explanations of orphan genes emergence is not different.
"Might appeared", "emerged", "gave rise to", "burst onto the scene", "evolved itself," "derived", "was on the way to becoming", "radiated into", "modified itself", "manufactured itself", "evolution's way of dealing with", "derived emergent properties", "was lucky"...

How do words like "might arise" explain emergence of new genes? Just like magic, the use of this word invokes mysterious powers within unseen universes

What the fuck are you talking about? You know that pervasive transcription is an empirically observed phenomenon right? There are no mysterious powers operating in unseen universes at work here.

The authors are merely hypothesizes that an observed process: mutations - In an observed entity: non-coding DNA - Is producing an observed phenomenon: accidental transcription and translation. And that these three empirically observed factors together explains the origin of Orphan genes.

All of these individual factors are concrete empirical realities. They are being tied together in a theoretical candidate process for the origin of new genes de novo from junk-regions.

And that is why we have experiments - orderly procedure carried out with the goal of verifying, refuting, or establishing the validity of a hypothesis. Since research identified a total of 60 protein-coding genes that originated de novo on the human lineage since divergence from chimp, which indicates that the rate of origin of de novo genes is 1 gen per 4,000 generations, and since experimental evolution in 60,000 generations produced 0 orphan genes, hypothesis has been refuted.

By the way, the second longest evolutionary experiment, this time in sexual populations, also produced some interesting results.

Genome-wide analysis of a long-term evolution experiment with Drosophila.
http://www.ncbi.nlm.nih.gov/pubmed/20844486

In this laboratory experiment fly populations were selected for accelerated development. But new alleles did not arise and take control in these populations as evolutionary theory predicts. The results suggest problems for evolution. In a subtext autors conclude:

Our work provides a new perspective on the genetic basis of adaptation. Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments. This suggests that selection does not readily expunge genetic variation in sexual populations, a finding which in turn should motivate efforts to discover why this is seemingly the case.

Thus, the two longest evolutionary experiments demonstrate a complete inability of evolutionary mechanisms to create something new and we are supposed to believe that they are able to construct every observable level of biological organisation, all three-dimensional cellular structures and arrangements, organs, signaling and regulatory networks, checkpoints are control mechanisms, molecular machines, metabolic pathways.

MarioNovak · **#52** by **MarioNovak** » Dec 31, 2014 3:56 pm

Alan B wrote:
MarioNovak wrote:
Alan B wrote:
MarioNovak wrote:Science shows that evolution can't create new genes

I see.

So, er, "Therefore, God?" Is that what you are suggesting?

I am suggesting what is logically necessary. If genes exist and observable processes cannot create them, then it logically follows: - new genes are the result of the "processes" science cannot observe.

No, it does not logically follow that the "processes" science cannot observe (at present) will never be able to be observed in the future.

Of course, in the future we may discover currently unknown laws of nature that cause distortion of our perception in a way that we perceive the round Earth. That is why the idea that the Earth is flat is walid scientific theory? Am I right?
Have you ever heard of the term pseudoscience?

Pseudoscience is a claim, belief or practice which is falsely presented as scientific, but does not adhere to a valid scientific method, lacks supporting scientific evidence or plausibility, cannot be reliably tested, or otherwise lacks scientific status. Pseudoscience is often characterized by the use of vague, contradictory, exaggerated or unprovable claims, an over-reliance on confirmation rather than rigorous attempts at refutation, a lack of openness to evaluation by other experts, and a general absence of systematic processes to rationally develop theories.

If science shows that evolutionary processes can not create a single gene and someone claims evolutionary processes created all genes we observe in living organisms, then this is pseudoscience.

Rumraket · **#53** by **Rumraket** » Dec 31, 2014 4:16 pm

MarioNovak wrote:
Rumraket wrote:
MarioNovak wrote:
Shrunk wrote:

Just reading this now. So far, no mention of orphan genes being magically created by Jesus as a viable hypothesis, and from the title and the abstract I don't expect that to be included. But I'll let everyone know if it comes up...
As I said above, people must learn to differentiate between scientific knowledge - cognizance of a fact or phenomenon acquired through experiments and observations - and mental constructs of a human mind - ideas, explanations, theories, hipoteses, ad hoc hypothesis, conjectures, etc. I have no doubt that proponents of evolution will find an "explanation" of how orphan genes come into existance. But this is not science, but storytelling.

History of evolutionary thought in biology explaining emergence of observable biological organization is full of mental constructs and magic words like: "might arise". Evolutionary explanations of orphan genes emergence is not different.
"Might appeared", "emerged", "gave rise to", "burst onto the scene", "evolved itself," "derived", "was on the way to becoming", "radiated into", "modified itself", "manufactured itself", "evolution's way of dealing with", "derived emergent properties", "was lucky"...

How do words like "might arise" explain emergence of new genes? Just like magic, the use of this word invokes mysterious powers within unseen universes

What the fuck are you talking about? You know that pervasive transcription is an empirically observed phenomenon right? There are no mysterious powers operating in unseen universes at work here.

The authors are merely hypothesizes that an observed process: mutations - In an observed entity: non-coding DNA - Is producing an observed phenomenon: accidental transcription and translation. And that these three empirically observed factors together explains the origin of Orphan genes.

All of these individual factors are concrete empirical realities. They are being tied together in a theoretical candidate process for the origin of new genes de novo from junk-regions.

And that is why we have experiments - orderly procedure carried out with the goal of verifying, refuting, or establishing the validity of a hypothesis.

Some hypotheses cannot be directly empirically tested because the timescales involved are practically not achievable. That's when we use phylogenetics or computer simulations instead. These testify that evolution did in point of fact happen, get over it.

As an analogy, nobody has seen an entire star form from a coalescing disc of interstellar dust and gas. We can only see snapshots of the process by taking pictures of distant stars, but the timescales are still way beyond practical human timescales. It's the same with evolution and geological time. We cannot practically reconstruct this process in the laboratory, stars are bigger than our planet, the masses, distances and timescales involved are beyond all human capacity to control. Some things really just are too big, or take too long a time, for us to be able to directly observe and control them in nice experimental fashion. This is where we build models instead, out of practical necessity. And then we test the predictions of the models against observations in the real world, whether those be pictures of distant stars and galaxies, or sequences of proteins in living organisms.

These models in turn then serve as justification for the claim that evolution (or gravity) produced the diversity of life (stars).

MarioNovak wrote:Since research identified a total of 60 protein-coding genes that originated de novo on the human lineage since divergence from chimp, which indicates that the rate of origin of de novo genes is 1 gen per 4,000 generations, and since experimental evolution in 60,000 generations produced 0 orphan genes, hypothesis has been refuted.

You cannot compare the rate of origin of de novo genes in an experimental bacterial population to the evolution of large multicellular eukaryotes WHEN THE FORMER HAVE NO JUNK-DNA.

MarioNovak wrote:By the way, the second longest evolutionary experiment, this time in sexual populations, also produced some interesting results.

Genome-wide analysis of a long-term evolution experiment with Drosophila.
http://www.ncbi.nlm.nih.gov/pubmed/20844486

In this laboratory experiment fly populations were selected for accelerated development. But new alleles did not arise and take control in these populations as evolutionary theory predicts.

Wait, new alleles did not arise and take control? What qualifies as a "new" allele? What does that even mean "and take control"? Where has this prediction been made?

MarioNovak wrote:The results suggest problems for evolution. In a subtext autors conclude:

Our work provides a new perspective on the genetic basis of adaptation. Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments. This suggests that selection does not readily expunge genetic variation in sexual populations, a finding which in turn should motivate efforts to discover why this is seemingly the case.

Where's the problem? The experiment shows that even strong natural selection does not successfully weed out large genetic variation.

That's what they conclude, I've highlighted the key sentence for you.

MarioNovak wrote:Thus, the two longest evolutionary experiments demonstrate a complete inability of evolutionary mechanisms to create something new

As just shown, they do nothing of the sort. By the way, you have never detailed a rigorous metric for "newness". And regardless, we already know evolution has created basically the entire biosphere, we know this from phylogenetic evidence.

I notice you have completely ignored the rather large first post I made in this thread where I present some of this evidence. Why is it that ID proponents are invariably always totally silent on phylogenetics? It's almost as if the field does not exist in your minds.

MarioNovak wrote:and we are supposed to believe that they are able to construct every observable level of biological organisation, all three-dimensional cellular structures and arrangements, organs, signaling and regulatory networks, checkpoints are control mechanisms, molecular machines, metabolic pathways.

Yes, because we have actual concrete empirical evidence that it did from phylogenetics.

laklak · **#54** by **laklak** » Dec 31, 2014 4:21 pm

I'd say the OP was as full of shit as a Christmas Turkey, but you can't fit that much shit into a turkey.

kennyc · **#55** by **kennyc** » Dec 31, 2014 4:23 pm

laklak wrote:I'd say the OP was as full of shit as a Christmas Turkey, but you can't fit that much shit into a turkey.

It's a consensus then and that proves the hypothesis!

:clap:

Rumraket · **#56** by **Rumraket** » Dec 31, 2014 4:26 pm

MarioNovak wrote:
Alan B wrote:
MarioNovak wrote:
Alan B wrote:

I see.

So, er, "Therefore, God?" Is that what you are suggesting?

I am suggesting what is logically necessary. If genes exist and observable processes cannot create them, then it logically follows: - new genes are the result of the "processes" science cannot observe.

No, it does not logically follow that the "processes" science cannot observe (at present) will never be able to be observed in the future.
Of course, in the future we may discover currently unknown laws of nature that cause distortion of our perception in a way that we perceive the round Earth. That is why the idea that the Earth is flat is walid scientific theory? Am I right?
Have you ever heard of the term pseudoscience?

The mere claim that the Earth is flat is not in and of itself a pseudoscientific claim. Pseudoscience refers to a process of deliberately pretending to use the methodology of science, while never submitting claims or results to proper review and intentionally working to discredit or stifle dissenting opinions or independent tests or verifications.

In this respect, the claim that the Earth is flat, in so far as it is made, is a valid scientific theory that has simply been shown to be false. That does not mean that it is not, in point of fact, theoretically or logicall possible that some time in the future some hitherto undiscovered physical phenomenon has produced some kind of weird optical distortion.

The possibility of this is of course extremely remote, which is why it's not being taken seriously, that doesn't mean it's pseudoscience.

MarioNovak wrote:If science shows that evolutionary processes can not create a single gene

But it doesn't, you have mistakenly conflated two different circumstances: experimental bacterial evolution vs Orphan genes in large multicellular eukaryotes. You cannot take the results from one experiment and extrapolate it into an area where it isn't valid. The purpose and conditions of the experiment were also not set up to be conducive to observe the production of novel protein coding genes.

and someone claims evolutionary processes created all genes we observe in living organisms, then this is pseudoscience.

Except that this claim is based on phylogenetic evidence, which you have conveniently ignored.

You also really need to bother to define a metric for "newness". At what point does mutations in a duplication turn a gene into a "new" one? How many mutations? Must the function be new? Must the entire sequence of amino acids be replaced, with nothing left of the ancestral sequence? Must the chemical reaction catalyzed by the enzyme be completely unrelated? What does "new" really mean under your definition?

Shrunk · **#57** by **Shrunk** » Dec 31, 2014 4:35 pm

MarioNovak wrote:And that is why we have experiments - orderly procedure carried out with the goal of verifying, refuting, or establishing the validity of a hypothesis. Since research identified a total of 60 protein-coding genes that originated de novo on the human lineage since divergence from chimp, which indicates that the rate of origin of de novo genes is 1 gen per 4,000 generations, and since experimental evolution in 60,000 generations produced 0 orphan genes, hypothesis has been refuted.

No, what is refuted is the claim that new genes are produced out of thin air thru magic by Baby Jesus, since that was never observed in the study. Or whatever alternative "hypothesis" you are suggesting.

You seem to think that Lenski was somehow able to model his experiment in such a way that only evolutionary processes occurred, and if genetic novelty were produced by Baby Jesus or "intelligent design," or whatever alternative to evolution you are suggesting, it could not have occurred in the experiment. How do you figure that? By whatever process genetic novelty is produced, whether evolution or something else, it should have been observed in this experiment. Or is there some reason that "intelligent design" only occurs when no one is looking? :dunno:

By the way, the second longest evolutionary experiment, this time in sexual populations, also produced some interesting results.

Genome-wide analysis of a long-term evolution experiment with Drosophila.
http://www.ncbi.nlm.nih.gov/pubmed/20844486

In this laboratory experiment fly populations were selected for accelerated development. But new alleles did not arise and take control in these populations as evolutionary theory predicts. The results suggest problems for evolution. In a subtext autors conclude:

Our work provides a new perspective on the genetic basis of adaptation. Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments. This suggests that selection does not readily expunge genetic variation in sexual populations, a finding which in turn should motivate efforts to discover why this is seemingly the case.

Obvious quote mine is obvious.

For an explanation of this paper by someone who is not trying to misrepresent it as some sort of religious apologetic, please see the following:

http://blogs.discovermagazine.com/gnxp/ ... KQjDHuFn7s

Shrunk · **#58** by **Shrunk** » Dec 31, 2014 4:37 pm

MarioNovak wrote:If science shows that evolutionary processes can not create a single gene and someone claims evolutionary processes created all genes we observe in living organisms, then this is pseudoscience.

Still waiting for your example of a "new gene" of the sort you are describing ever arising, anywhere.

Alan B · **#59** by **Alan B** » Dec 31, 2014 5:21 pm

My remark:

No, it does not logically follow that the "processes" science cannot observe (at present) will never be able to be observed in the future.

Does not in any way indicate or imply 'pseudoscience'.
How you jumped from my statement above to this...

MarioNovak wrote:Of course, in the future we may discover currently unknown laws of nature that cause distortion of our perception in a way that we perceive the round Earth. That is why the idea that the Earth is flat is valid scientific theory? Am I right?
Have you ever heard of the term pseudoscience?

Pseudoscience is a claim, belief or practice which is falsely presented as scientific, but does not adhere to a valid scientific method, lacks supporting scientific evidence or plausibility, cannot be reliably tested, or otherwise lacks scientific status. Pseudoscience is often characterized by the use of vague, contradictory, exaggerated or unprovable claims, an over-reliance on confirmation rather than rigorous attempts at refutation, a lack of openness to evaluation by other experts, and a general absence of systematic processes to rationally develop theories.

If science shows that evolutionary processes can not create a single gene and someone claims evolutionary processes created all genes we observe in living organisms, then this is pseudoscience.

...is mind-boggling. :doh:

Have you ever heard of pseudorational thinking?

This is used by people of, shall we say, a religious persuasion when employing the knowledge of science to justify their irrational position. The approach that is usually used is to extract science quotes in the manner of quoting verses from holy texts, not realising that what is scientifically valid one week can be overthrown the next week due to revised or new data.

Rumraket · **#60** by **Rumraket** » Dec 31, 2014 5:36 pm

Shrunk wrote:
MarioNovak wrote:If science shows that evolutionary processes can not create a single gene and someone claims evolutionary processes created all genes we observe in living organisms, then this is pseudoscience.

Still waiting for your example of a "new gene" of the sort you are describing ever arising, anywhere.

We don't just need an example, we need well defined metrics for determining what does and does not qualify as "new".

How much must one gene differ from another to be considered "new"?

Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

Re: Science shows that evolution can't create new genes

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