Watch Evolution in Action

a reply to: cooperton

If the researchers were adhering to due diligence, they would not make such claims until such a protein was found proving that this was evolution through genetic mutation.

Actually they did that. They very carefully sequenced the DNA of the bacteria at each stage and mapped exactly what was happening at each stage of the evolutionary process.

If you had adhered to due diligence you would have read the paper that were posted earlier in this very thread.

originally posted by: rnaa
a reply to: Xenogears

Information is not created nor destroyed.

Conservation laws, when they exist, apply to closed systems. Biological organisms are NOT closed systems. If there is such a thing as 'Conservation of Information' (there is), it cannot be applied to biological organisms.

'Conservation of Information' in actual Information Systems Theory applies to actual CLOSED systems of software and hardware systems. We can understand such CLOSED systems and model them and depend on the results. We have no such confidence in OPEN systems such as biological systems. The entire subject, applied to biological systems is based on a fallacious stretching of an analogy beyond the bounds of credibility.

Even simple numbers such as pi are said to already contain all possible information.

Really? Do you have the beginning of a clue what 'information' is in information systems? There is a very rigorous definition, you know. And Pi isn't it.

Just because Pi is an infinite sequence of non-random and non-repeating digits doesn't mean that it contains any information what-so-ever, let alone 'all possible information'. While the argument can be made that because it is infinite then at some point in the sequence it must contain the encoded works of Shakespeare; that argument does not imply that it contains information.

Also Pi is not simple.

An open system does not create information just as it does not create matter or energy. Energy, matter and information simply change from one state to another. Open systems exchange information, matter, energy which allows for advanced nonequilibrium dynamics.

As for pi if its sequence contains all possible digital patterns it contains all possible information, all possible patterns. IT is simple in the sense that extraordinarily short formulas describe and allow full generation of it.

originally posted by: Astyanax
a reply to: cooperton
Resistance was present in a number of individuals within the population. After the event, it was present in the whole, or nearly the whole population. That is what evolution means.

No new genes evolved, it was a bottleneck effect that favored a particular group of people. As you said, that resistance was already present, no new genes were created. The same is true for the experiment in your OP, the genetics that rendered the bacteria resistant to the antibiotic may have been already present in the population, and it was only a matter of time until these particular microbes made it to the antibiotic layer.

This is not proof of evolution in terms of it being the cause of the diversity of life, it is only proof of bottlenecking which didn't need proof anyway (it is an obvious mechanism). This is what I mean when I say that people mistake provable adaptation mechanisms for the unprovable theory of evolution which was theorized to have given rise to the diversity of life from a single cell long ago. The OP is not observing evolution, it is observing bottlenecking and allelic drift. If you think these are one and the same then I can't argue with such a misunderstanding.

originally posted by: rnaa
a reply to: cooperton

Actually they did that. They very carefully sequenced the DNA of the bacteria at each stage and mapped exactly what was happening at each stage of the evolutionary process.

Did they compare multiple strains and check the initial stage bacteria to see if it was an already present protein that increased its expression in the resilient bacteria? Send me the link to the actual paper please.

originally posted by: cooperton

originally posted by: Astyanax
a reply to: cooperton
Resistance was present in a number of individuals within the population. After the event, it was present in the whole, or nearly the whole population. That is what evolution means.

No new genes evolved, it was a bottleneck effect that favored a particular group of people. As you said, that resistance was already present, no new genes were created. The same is true for the experiment in your OP, the genetics that rendered the bacteria resistant to the antibiotic may have been already present in the population, and it was only a matter of time until these particular microbes made it to the antibiotic layer.

This is not proof of evolution in terms of it being the cause of the diversity of life, it is only proof of bottlenecking which didn't need proof anyway (it is an obvious mechanism). This is what I mean when I say that people mistake provable adaptation mechanisms for the unprovable theory of evolution which was theorized to have given rise to the diversity of life from a single cell long ago. The OP is not observing evolution, it is observing bottlenecking and allelic drift. If you think these are one and the same then I can't argue with such a misunderstanding.

originally posted by: rnaa
a reply to: cooperton

Actually they did that. They very carefully sequenced the DNA of the bacteria at each stage and mapped exactly what was happening at each stage of the evolutionary process.

Did they compare multiple strains and check the initial stage bacteria to see if it was an already present protein that increased its expression in the resilient bacteria? Send me the link to the actual paper please.

Take height, if the taller survive, there will BE VARIATION in the next generation, so there will BE TALLER STILL, greater tallness will occur, it will move in the direction of greater tallness.

Take size, same will happen and from mouse size it can go to whale size. Lifespan, intelligence, speed, strength, all the traits are subject to a new level of variation in each generation PUSHING the EXTREMES of the trait in any particular direction.

Now human compared to bonobo something like 99% identical human to some rodent about 75%, human to banana about 50%. Why does that line up perfectly with the evolutionary expectations? Ponder.

We've an earth billions of years old, we've a known process that can push any trait or combination of traits pretty far to unimaginable extremes. We also know that if two populations separate for too long the accumulation of mutations will make interbreeding impossible even if they look exactly the same.

We can take the some magic happened, and ignore all the evidence, say say last thursdayism is reality. Or we can take the evidence at face value, objectively and accept the conclusions whatever they may be.

The problem here is that truth of the world, reality, is incompatible with their world view, with their religion. But the truth is the truth, and all religions die before the sword of truth, edifices of lies that crumble before the one true light. Reality is not subject to opinion, your words, your thoughts contradict reality, and you're simply wrong, reality determines who's right from who's wrong. And reality is never wrong.

You can claim to know the truth, that you have truth all you want, all you want, if what you have is a lie, it doesn't matter how many times you call it the truth or how many lines in your book call it the truth. A lie is a lie, and the truth is the truth.

originally posted by: cooperton
I can't argue with someone who doesn't know the core tenet of evolution - which is descent with modification. Adaptation occurs within an organisms lifespan and therefore is not a part of evolution. Allelic drift is also not descent with modification because there is no modification, it is simply changing the frequency of genetic combination in a population that is most favorable in the environment.

Are epigenetic changes passed down to the offspring? If so, you have your answer and that is descent with modification. If not, then they will not affect evolution. Evolution is about populations not individuals. Genetic mutations are passed down EVERY generation, even if they are neutral. The gene pool can be modified without having big noticeable morphological changes. Again, you are doing nothing here but redefining scientific terminology to suit your bogus argument.

That is an assumption. Research epigenetics you will potentially realize why it is impossible to evolve in a piecewise manner as proposed by theoretical evolutionary mechanisms.

Again, where did the gene in question come from, if not evolution. Unless you have an alternative theory backed by evidence, the gene evolved like the rest of them did, just like the ability to turn genes on or off. Just because you can't grasp the science itself about the mechanics of how it works doesn't justify your conclusion.

Resilience to the black plague was already present in the population.

Hence, it evolved! Unless you are suggesting that it magically appeared. How did that gene emerge? Please enlighten us.

It makes no difference whether a trait was there prior to a natural selection event. In fact, this is true in most cases. Mammals were around during the dinosaur era, as were the ancestors of birds. After the extinction level event, the bigger non mammals all died out, they didn't suddenly evolve to another type of creature. Mutations always happen first, they don't magically emerge when # is hitting the fan. You accuse me of not understanding the main tenant of evolution, yet you can't fathom how genetic mutations can happen thousands or millions of years before an event happens that actually favors this particular mutation.

originally posted by: cooperton

originally posted by: Astyanax
a reply to: cooperton
Resistance was present in a number of individuals within the population. After the event, it was present in the whole, or nearly the whole population. That is what evolution means.

No new genes evolved, it was a bottleneck effect that favored a particular group of people. As you said, that resistance was already present, no new genes were created. The same is true for the experiment in your OP, the genetics that rendered the bacteria resistant to the antibiotic may have been already present in the population, and it was only a matter of time until these particular microbes made it to the antibiotic layer.

This is not proof of evolution in terms of it being the cause of the diversity of life, it is only proof of bottlenecking which didn't need proof anyway (it is an obvious mechanism). This is what I mean when I say that people mistake provable adaptation mechanisms for the unprovable theory of evolution which was theorized to have given rise to the diversity of life from a single cell long ago. The OP is not observing evolution, it is observing bottlenecking and allelic drift. If you think these are one and the same then I can't argue with such a misunderstanding.

originally posted by: rnaa
a reply to: cooperton

Actually they did that. They very carefully sequenced the DNA of the bacteria at each stage and mapped exactly what was happening at each stage of the evolutionary process.

Did they compare multiple strains and check the initial stage bacteria to see if it was an already present protein that increased its expression in the resilient bacteria? Send me the link to the actual paper please.

Coop, isn't it about time you put up or shut up? You never support your positions with citations. You continue to pull dead rabbits out of your hat with absolutely no validation. And you are one of those individuals I mentioned in a previous post: you rarely respond to data which refutes or throws your hypothesis out the window.

So, in the interest of REAL science, and in the hopes that YOU finally take the time to read the research articles, here they are again. And this time, I would respectfully request a response, particularly to the methods utilized (except for the article in SA which is a generalized article):

1. Gene Genesis: Scientists Observe New Genes Evolving from Mutated Copies
Researchers have observed in an experiment the exact steps bacterial genes take to evolve a new ability, unexpectedly adding a new twist on an old model

The model explains how novelty is generated in evolution, which is "tremendously exciting," says Gavin Conant, an evolutionary biologist at the University of Missouri—Columbia who was not involved in the study. Whether the model will apply to organisms other than bacteria remains to be seen, but Conant says he would be very surprised if researchers do not eventually find the process in other systems. "They have a step-by-step documentation of the model, essentially proof that this can happen," he says.

www.scientificamerican.com...

2. Link to a previous post about NEW INFORMATION: www.abovetopsecret.com...

Summary:

1. Original virus exhibited no drug resistant mutation
2. Virus mutated TO ADD INFORMATION TO THE VIRAL POLYMERASE GENE
3. The mutated virus WITH THE ADDED INFORMATION was now drug resistant and the patient died.


3. Link to previous post: www.abovetopsecret.com...





Link to post regarding this illustration: www.abovetopsecret.com...

4. This is an important paper - so please pay attention:


Evolution of New Functions De Novo and from Preexisting Genes
Dan I. Andersson, Jon Jerlström-Hultqvist and Joakim Näsvall

cshperspectives.cshlp.org...

Evidence for De Novo Emergence of Genes De novo genes have mostly been attested in eukaryotes in which the availability of high-quality genome sequences with well-supported gene models from closely related species have allowed the delineation of the evolutionary emergence of all genes in a given genome. The gold standard for calling a de novo evolved gene is showing that a gene is a noncoding region in multiple out-group species and that the in-group species transcribes an RNA in the equivalent genomic region, which is translated into an protein species that is validated by proteomic techniques. In practice, evidence fulfilling the stringent criteria outlined above might be difficult to obtain. Typically, de novo gene candidates are identified by bioinformatic filtering of predicted gene catalogs, transcript expression libraries and shotgun proteomic data. Evolutionary divergence characteristics are commonly used as a filter to distinguish de novo gene candidates from neutrally evolving genomic regions. De novo gene emergence have been reported from many organisms such as insects (Begun et al. 2007; Reinhardt et al. 2013), yeast (Cai et al. 2008; Li et al. 2010b), Hydra (Khalturin et al. 2008), primates (Johnson et al. 2001; Knowles and McLysaght 2009; Toll-Riera et al. 2009; Li et al. 2010a; Wu et al. 2011; Xie et al. 2012), mouse (Murphy and McLysaght 2012; Neme and Tautz 2013), Plasmodium (Yang and Huang 2011), and plants (Donoghue et al. 2011). De novo genes are often characterized by being short, often overlapping other genes or being present within intronic sequences. Many de novo genes show weak expression. However, in animals, the highest expression is often found in the testes. This finding might be correlated to the hyperactive transcription in this sexual organ, a feature that leads to overall higher transcription. The increased transcription might lead to an increased selective potential as outlined in the “out of the testes” hypothesis (Kaessmann 2010). De novo genes in plants are often tissue-specifically expressed with stress-induced responsiveness (Donoghue et al. 2011). Even with transcriptional evidence and evolutionary conservation, some de novo genes might be examples of unrecognized noncoding RNAs that experience weaker structural constraints than most coding sequences. Because of the obvious risk of misidentification, it is imperative that proteomic evidence is gathered to support the claim of identified de novo genes. Proteomic evidence has indeed been integral in many de novo gene prediction pipelines, although the amount of proteomic evidence available is often limited.

Now I know you would like to take cover on some remote island rather than address the evidence, but in the interest of your own sanity (and mine), would you please read these papers and report your rebuttal WITH CREDIBLE CITATIONS.

Your responses to everyone's posts is like a broken record. This is not good for your health. Please take the time to read and understand how genetics works. Thank you in advance.

originally posted by: Phantom423
you rarely respond to data which refutes or throws your hypothesis out the window.

Post the link to this data so I can review their methods.

Now human compared to bonobo something like 99% identical human

From what I recall, they compared the same genes to come to that percentage. saying they are 99% similar when bonobos have 48 chromosomes and humans have 46 makes this an obviously false estimate. Even if it was 99% similar that in no way proves evolution. Phenotypically similar organisms would intuitively have similar genetic coding.

Further evidence

a reply to: Xenogears

An open system does not create information just as it does not create matter or energy. Energy, matter and information simply change from one state to another. Open systems exchange information, matter, energy which allows for advanced nonequilibrium dynamics. As for pi if its sequence contains all possible digital patterns it contains all possible information, all possible patterns. IT is simple in the sense that extraordinarily short formulas describe and allow full generation of it.

I think you're confusing the 1st Law of Thermodynamics with open/closed systems in nature. Open systems in nature assume that there is an infinite amount of energy available to the system. The borders of biological systems are "open", or permeable, and can take in or give out matter and/or energy.

Scientists have stumbled upon some very non-intuitive observations in quantum theory which may turn our concept of the laws which we consider absolute on their head. An interesting article about that:

Does Quantum Mechanics Flout the Laws of Thermodynamics?

blogs.scientificamerican.com...

As for Pi, you're wrong. Pi is just a number on a line. It has the "flavor" of infinite decimal places and has no finite value. It is also non-repeating. The notion that all information in the universe is contained in Pi is simply wrong - and you can deduce that just by thinking about how the value extends into infinity. It's simply an irrational number i.e. it can't be converted into a fraction. Hope that makes sense.

a reply to: VP740

SO do you do much science? OR at least read scientific journals? Out of curiousity

Now as to what I said, you are misrepresenting that.

When one talks about evolution in the modern sense, one talks about genetic mutations.

Darwin did not know what drove the hereditary changes that cause evolution.


Thus to say "the core tenant of evoultion is decent with modification", is not understanding the modern framework by which we understand evolution.

Viz

(1) The change in genetic composition of a population over successive generations, which may be caused by natural selection, inbreeding, hybridization, or mutation.

(2) The sequence of events depicting the evolutionary development of a species or of a group of related organisms; phylogeny.

Both of those are much more accurate as to what is central to evolution.

Thus, "Decent by modification" is a loose term, which is better explained through .... adaption via mutation.

originally posted by: Phantom423
a reply to: Xenogears

An open system does not create information just as it does not create matter or energy. Energy, matter and information simply change from one state to another. Open systems exchange information, matter, energy which allows for advanced nonequilibrium dynamics. As for pi if its sequence contains all possible digital patterns it contains all possible information, all possible patterns. IT is simple in the sense that extraordinarily short formulas describe and allow full generation of it.

I think you're confusing the 1st Law of Thermodynamics with open/closed systems in nature. Open systems in nature assume that there is an infinite amount of energy available to the system. The borders of biological systems are "open", or permeable, and can take in or give out matter and/or energy.

Scientists have stumbled upon some very non-intuitive observations in quantum theory which may turn our concept of the laws which we consider absolute on their head. An interesting article about that:

Does Quantum Mechanics Flout the Laws of Thermodynamics?

blogs.scientificamerican.com...

As for Pi, you're wrong. Pi is just a number on a line. It has the "flavor" of infinite decimal places and has no finite value. It is also non-repeating. The notion that all information in the universe is contained in Pi is simply wrong - and you can deduce that just by thinking about how the value extends into infinity. It's simply an irrational number i.e. it can't be converted into a fraction. Hope that makes sense.

Well it can't be converted into a fraction but that does not mean that the digital pattern representing all particular fractions aren't found within it. Extraordinarily simple programs are said to be able to generate all computable universes, all possible universes. Even if pi didn't have all possible finite patterns within it, it need only have the pattern for this program and it would effectively have a formula for generating all possible information.

Even a program that carries out simple increment addition will generate all possible finite digital patterns if given enough memory. All possible information.

And none of this denies that information can neither be created nor destroyed. That was one of the issues with black holes, the doubt about whether they could somehow eliminate information.

a reply to: Xenogears

That isn't my understanding of Pi, but perhaps you can post a citation that supports your position. The decimal series may be infinite but it's really an expansion series - we don't know how to characterize "infinite" - we're just assuming it's infinite based on our current perception and calculation capability. I don't think it's possible to know that ALL possible patterns are contained somewhere in Pi. That would make it deterministic and non-random. We assume that it's random, but I don't think we know that either. How exactly would you go about proving that it contains all that information? Can you demonstrate that mathematically?

The probability that Pi contains all truths is equal to the probability that Pi contains all falsehoods. I don't think you can prove otherwise. I'd be interested to know if anyone can provide more insight - that's the of limit of my knowledge on Pi, I'm afraid.

a reply to: cooperton

I have to find the paper again- it got deleted from my library folder for some unknown reason. I'll find it and post it later.

a reply to: Astyanax

I am South Asian and live surrounded by Buddhists, Hindus and Asian religious and philosophical movements. I am sympathetic to the pantheism of people like Spinoza but see no effective difference between it and atheism.

I love the Dalai Lama! Most righteous indeed..

“If scientific analysis were conclusively to demonstrate certain claims in Buddhism to be false, then we must accept the findings of science and abandon those claims.”
- Dalai Lama-

a reply to: Noinden

Honestly I don't do much science, and I rarely look past laymen's material.

Decent with modification still applies though. It's just a more general term. Since you poked fun at Cooper for characterizing evolution by it, I figured it was fair to poke fun at you for rejecting it.

a reply to: Xenogears

An open system does not create information just as it does not create matter or energy.

An open system can be influenced by outside agencies. Energy, matter, and, yes, information (in the case of biological systems at least energy = information) can be added from outside the system.

All that is beside the point because biological systems are not information systems. Biological systems are biological systems. The ideas in information theory can only be applied to biological systems as analogies, and the application of analogies can go only so far, they can help visualize a complex process with a simple easy to understand model, but when taken too far, they can hide more than they reveal.

a reply to: Phantom423

Apparently Pi hasn't been proven to be a Disjunctive sequence yet: mathoverflow.net

Pi is definitely deterministic and nonrandom: Finding the N-th Digit of Pi. Do you mean normal?

As for the information contained... you could write a program to translate sequences of Pi into whatever you want. But you could do that with any number sequence.

Eta: Pi has been proven to be transcendental: Wikipedia

a reply to: VP740

Did I say I rejected it? Is English your first language?

Lets make it simple:

Adaption is a modification, it is cause by mutation. Thus the simplest bit in all that is ... mutation, a genetic thing.

I "made fun" of Cooper for not actually understanding how the science works. After all he seems to think that the only time one should publish these things, is when the protien the mutation codes for has been isolated. He is wrong.

a reply to: VP740

I will accept your post as valid since I cannot challenge your statement based on knowledge - I'm a biochemist and a specialist in spectroscopy. Perhaps you would like to explain how Pi can be deterministic as well as random. I'm familiar with pseudorandom number generators - but how they work and what they mean isn't in my skill set. But I certainly would be interested to learn more about it. Randomness is an area of interest to me, not just in science, but in finance. I've programmed a number of HFT algorithms which seek to defy randomness in the nanosecond range. Not an easy task. In any case, if you have knowledge in the field, please share your knowledge.

a reply to: Phantom423

Perhaps you would like to explain how Pi can be deterministic as well as random.

You misread that part. He said it was non-random. But maybe that was a correction made after you read it.

a reply to: Phantom423

I have no special knowledge in the field, just some grasp of the basics. I'm still not clear what you mean by 'random'. When I hear random, I think of Kolmogorov complexity (the length of the shortest program generating the given string). By that definition, Pi is far from random (Code Golf - Calculate 500 Digits of Pi).

As far as determinism goes, of course Pi is deterministic. It's a mathematically defined constant: discovering-pi. As I understand determinism vs non-determinism, it goes like this:

deterministic(x, y, z) //send the same numbers, you receive the same result
[
return f(x,y,z); //we perform specific operations on the variables we receive. No variables are added.
]

nondeterministic(x,y,z) //even with the same numbers, your result may vary
[
cin>>w; //w doesn't have to be the same each time this is called, even if x,y and z happen to reuse their previous values
return f(x,y,z,w); //the output isn't just determined by x,y and z anymore
]

This looks like a nice entry point for those wanting to learn about randomness: Cristian S. Calude Randomness & Complexity, from Leibniz to Chaitin