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Author Topic:   Can mutation and selection increase information?
Taq
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Joined: 03-06-2009
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Message 31 of 222 (809478)
05-18-2017 1:07 PM
Reply to: Message 30 by Faith
05-18-2017 1:05 PM


Re: No new information needed
Faith writes:

Quote it if it demonstrates I'm wrong.

You have already refused to read or understand the paper, so what would be the purpose of that?


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bluegenes
Member (Idle past 95 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


(1)
Message 32 of 222 (809480)
05-18-2017 1:09 PM
Reply to: Message 26 by Faith
05-18-2017 12:50 PM


Re: No new information needed
Faith writes:

If that paper is above Percy's pay grade as he put it, it's certainly above mine. I read what I was able to read, and nothing you said gave evidence that new alleles actually exist. As I keep saying the "evidence" of supposed positive selection shown by increased frequency is an illusion if the allele in question is really a neutral mutation, which would be passed on and easily look like increased frequency based on your assumption.

You seem to think that paper actually shows that new alleles give immunity to different parasites, but it doesn't. It assumes it.

I took that hilarious post to the other thread. Message 268


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bluegenes
Member (Idle past 95 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


(1)
Message 33 of 222 (809562)
05-19-2017 4:17 AM


Bump for CRR - copious quantities of genetic information
From the "Debunking the Evolutionary God of Selection" thread. Message 194

CRR writes:

Does the theory of evolution require a gain of copious quantities of genetic information?

Yes it does. Both in Darwin's formulation and in the modern neo-Darwinian version, although Darwin of course knew nothing of genes or DNA.

Both versions believe that the all life on Earth is ascended from primitive ancestors. Darwin lacked the evidence to definitely say only one ancestor but he made it clear that it was his “belief that all animals and plants are descended from some one prototype.” Most proponents of the modern version, on the evidence of DNA, definitely conclude there was a Last Universal Common Ancestor.

In both versions this common ancestor is envisaged as some simple life form of minimal complexity.

In the modern version with a genetic basis this is supposed to be a single celled organism with a minimal functioning genome, perhaps only a few hundred genes. Some believe this ancestor arose naturally on Earth from non-living matter, some propose panspermia, and some believe it was created by God.

However this original life form did not contain or produce more than a fraction of the genes and proteins life today. Nor did it have multi-cellularity, specialised tissues, organs, and appendages. All of these are supposed to have been produced by evolution over billions of years. “[F]rom so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.”

Now I say that to produce all these new attributes would require a vast increase in genetic information. Not only to produce all the new proteins but also to regulate them and to produce the multitude of body plans we see today.

Some object to calling this “genetic information”, saying such a term is meaningless until it can be measured and quantified. Even “Shannon Information” could not be measured and quantified until Claude Shannon published “A Mathematical Theory of Communication” in 1948. This did not mean such information did not exist before then. Just so, even if it can't currently be quantified no reasonable person doubts that this genetic information exists. As I have shown in previous posts progress is being made in measuring and quantifying functional information; but the information already exists or it could not measured.

Conclusion: The Theory of Evolution;
• Has a direction. It is attempting to explain microbes to man, not the reverse
• Requires the development of multicellularity, specialised tissues, organs, and complex body plans
• This development requires the production of new genes and genetic information; in copious quantities

Rather than saying that a theory itself has a direction, it might be better to say that an explanation of natural history would have to explain the direction that that history has taken. That includes the emergence of many complex organisms in the latter part of that history from relatively simple forms, and the presence of an enormous quantity of species from one or several originals.

Put that way, I broadly agree. Although biological "information" is difficult to define and measure, I agree that there appears to have been an enormous increase.

And, from the same thread:

Message 163

CRR writes:

It is the theory of evolution that relies on the gain of copious quantities of genetic information. Creationists are just asking how the theory can be taken seriously when the evidence is that the mutation selection mechanism appears to be insufficient to explain where that information comes from.

Here we have the type of creationist claim that I mentioned in the O.P.

I'd like to ask CRR and any other creationists for their own views on this. Is it that mutation and selection can produce no new information at all, or is it that they just can't produce enough?

Can anyone support either claim?


Replies to this message:
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RAZD
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From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.2


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Message 34 of 222 (809582)
05-19-2017 10:05 AM
Reply to: Message 33 by bluegenes
05-19-2017 4:17 AM


Wings and Walkingsticks: flip flop genetic information?
I'd like to ask CRR and any other creationists for their own views on this. Is it that mutation and selection can produce no new information at all, or is it that they just can't produce enough?

I've posted this elsewhere and thought it would make an interesting example to discuss.

See Figure 1 from Nature 421, 264 - 267 (16 January 2003); doi:10.1038/nature01313 (reproduced below)

Walkingstick insects originally started out as winged insects (blue at start and top row). That diversified.

And some lost wings (red). And diversified.

And some regained wings (blue again). And diversified.

And one lost wings again (Lapaphus parakensis, below, red again).

And this doesn't even address the ones where one sex (usually male) has wings and the other sex doesn't (the red includes these, so it is hard to determine from this graphic how many times the female sex gained and lost wings independent of the winged males).

So which species have more information, which have gained information and which have lost information?

I would think that those that lose wings would lose information, but that those that regain wings must then gain that information back or replace it with new information.

It also appears that this regaining wings information gain must be "copious" enough for several species to evolve.

Enjoy


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bluegenes
Member (Idle past 95 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


(1)
Message 35 of 222 (810200)
05-25-2017 9:08 AM


From "junk" to genes: De Novo information.
The best known way for new coding genes to be formed is via duplication followed by neo/sub functionalization. However, researchers are increasingly finding evidence of new "orphan" genes forming from stretches of non-coding and apparently non-functional DNA.

If that's not new information, what is?

Here they find new lineage specific genes that have rapidly become important, sometimes essential, in fruit flies.

quote:

Abstract

How non-coding DNA gives rise to new protein-coding genes (de novo genes) is not well understood. Recent work has revealed the origins and functions of a few de novo genes, but common principles governing the evolution or biological roles of these genes are unknown. To better define these principles, we performed a parallel analysis of the evolution and function of six putatively protein-coding de novo genes described in Drosophila melanogaster. Reconstruction of the transcriptional history of de novo genes shows that two de novo genes emerged from novel long non-coding RNAs that arose at least 5 MY prior to evolution of an open reading frame. In contrast, four other de novo genes evolved a translated open reading frame and transcription within the same evolutionary interval suggesting that nascent open reading frames (proto-ORFs), while not required, can contribute to the emergence of a new de novo gene. However, none of the genes arose from proto-ORFs that existed long before expression evolved. Sequence and structural evolution of de novo genes was rapid compared to nearby genes and the structural complexity of de novo genes steadily increases over evolutionary time. Despite the fact that these genes are transcribed at a higher level in males than females, and are most strongly expressed in testes, RNAi experiments show that most of these genes are essential in both sexes during metamorphosis. This lethality suggests that protein coding de novo genes in Drosophila quickly become functionally important.

De Novo ORFs in Drosophila Are Important to Organismal Fitness and Evolved Rapidly from Previously Non-coding Sequences.


This may partially explain why eukaryotes have found it useful to carry enormous surpluses of DNA. Those that do have more chance of innovating in an ever changing world.


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Vlad
Junior Member (Idle past 45 days)
Posts: 27
Joined: 06-03-2017


Message 36 of 222 (811018)
06-04-2017 8:10 AM
Reply to: Message 35 by bluegenes
05-25-2017 9:08 AM


Re: From "junk" to genes: De Novo information.
The most significant post From "junk" to genes: De Novo information (bluegenes) has forced me to join the discussion.
Being a dedicated amateur evolutionist, I some time ago have come to the utterly surprising conclusion that biological evolution is a self-learning process: evolution all the time has been learning (by doing) how to better evolve. That is, the evolutionary process has incepted as a “blind watchmaker”, yet it eventually ascended to the “intelligent design” heights. At that, there is nothing supernatural here – just the prose of cybernetics.
Two significant circumstances prompted the conclusion: first, the presence of enormous "junk" DNA amounts in eukaryotic genomes. And, second, the absence of any chances for multi-cellular eukaryotes to accidentally evolve as fast as they actually did. The truth is in measure: even if we were of opinion that accidental changes could have effectively promoted the evolution of prokaryotes, this wouldn’t account for the evolution of comparatively very thin eukaryotic species.
This message is a reply to:
 Message 35 by bluegenes, posted 05-25-2017 9:08 AM bluegenes has responded

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bluegenes
Member (Idle past 95 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 37 of 222 (811164)
06-05-2017 1:07 PM
Reply to: Message 36 by Vlad
06-04-2017 8:10 AM


Re: From "junk" to genes: De Novo information.
Vlad writes:

The most significant post From "junk" to genes: De Novo information (bluegenes) has forced me to join the discussion.
Being a dedicated amateur evolutionist, I some time ago have come to the utterly surprising conclusion that biological evolution is a self-learning process: evolution all the time has been learning (by doing) how to better evolve. That is, the evolutionary process has incepted as a “blind watchmaker”, yet it eventually ascended to the “intelligent design” heights. At that, there is nothing supernatural here – just the prose of cybernetics.
Two significant circumstances prompted the conclusion: first, the presence of enormous "junk" DNA amounts in eukaryotic genomes. And, second, the absence of any chances for multi-cellular eukaryotes to accidentally evolve as fast as they actually did. The truth is in measure: even if we were of opinion that accidental changes could have effectively promoted the evolution of prokaryotes, this wouldn’t account for the evolution of comparatively very thin eukaryotic species.

Welcome! I think I know what you mean, and I think you're right. I call it "evolved evolvability". Evolvability itself has been selected for in the past. It does explain junk and other things.


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Vlad
Junior Member (Idle past 45 days)
Posts: 27
Joined: 06-03-2017


Message 38 of 222 (811244)
06-06-2017 8:22 AM
Reply to: Message 37 by bluegenes
06-05-2017 1:07 PM


Re: From "junk" to genes: De Novo information.
Thanks for the kind greeting, bluegenes. Of course, I am aware of the “evolution of evolvability” idea (Richard Dawkins, 1988; Robert L.Carroll, 2002; etc.) Yet, I would like to make a somewhat different and, perhaps, more strong statement.
For the sake of simplicity and clarity, let’s consider a clone of asexually reproducing organisms – say, bacteria. Bacterial genomes already contain some (modest) amounts of seemingly non-functional DNA – this "junk". Suppose, among the "junk" DNA, a genetic instruction accidentally emerges that compels a gene duplication procedure. Then, in case the procedure effectively facilitates the “gemmation” of new viable bacterial forms, the specific genetic instruction would widely proliferate within genomes of the newly originated clones.
More generally, any genetic instruction, which accidentally emerges among the "junk" DNA and effectively facilitates the “gemmation” of new viable lifeforms (of new species, in the world of sexual reproduction), would widely proliferate – quite automatically. This simple hypothesis entails a few rather strong inferences concerning the essence of biological evolution.
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bluegenes
Member (Idle past 95 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


(1)
Message 39 of 222 (811558)
06-09-2017 8:32 AM
Reply to: Message 35 by bluegenes
05-25-2017 9:08 AM


Gene number and Information increase via duplication
Continuing the theme of how mutation and selection can increase information and add new genes, and sticking with Drosophila for now, here's research on the best known way of adding new coding genes, duplication and neofunctionalization.

Neofunctionalization of young duplicate genes in Drosophila.

quote:

Gene duplication is thought to play an important role in the evolution of complex phenotypes. Although studies have revealed that duplicate genes are abundant, there is considerable controversy about how they are maintained throughout evolution. In this study, we develop an approach for comparing genome-wide expression profiles of closely related species to disentangle the evolutionary forces operating on duplicate genes. Application of our approach to pairs of young duplicate genes in Drosophila reveals that nearly all duplicates are retained by the evolution of a novel function in one copy. Further analysis reveals that, although young genes are primarily expressed in testes, their expression broadens as they age, illustrating how new genes become integrated into diverse functional networks over time.


As some lineages, like our own, have clearly added many genes since a relatively simple LUCA, it's interesting to understand the various processes that achieve this.

An added gene with a new function should be significant new "functional information" by any standards.


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Vlad
Junior Member (Idle past 45 days)
Posts: 27
Joined: 06-03-2017


Message 40 of 222 (811729)
06-11-2017 8:35 AM


Mutations and new infirmation
Well, it is time to consider the actual parts of (random) mutations, on the one hand, and of natural selection, on the other hand, in creation new genetic information. In order to avoid usual blah-blah, let’s consider the most simple and transparent “lexical” model. Suppose, the appellative noun “bit” is “viable” and therefore is able to produce its “digital” copies – just like bacteria in the course of binary fission. The copies are so accurate that they also able to produce their own copies: the process of self-replication takes place. Besides, archaea and bacteria are natural self-replicators, so this peculiar phenomenon is literally omnipresent.
Suppose, being “viable”, the form “bit” is also more or less “fit” (say, rated by the Google Ngram Viewer statistics) with regard to certain – say, the English literary – environment. Then the clone “bit” would grow in number exponentially, and from time to time, some (point) mutations inevitably would happen. Mutant forms would spontaneously emerge: “ait”, …, “bt”, …, “bite”, …, “rbit”, …, etc.
In general, any appellative noun is considered “viable” – granted, first, it comprises at least three characters of the Roman alphabet. And second, it is present in a dictionary of at least one of the languages which make use of this very alphabet. Obviously, almost all mutations are quite barren, and resulting mutant forms – such as “ait”, “bt”, “rbit”, etc. appear “inviable”. And yet, very rarely, fortunate mutation happens, so that resulting mutant turns out “viable” – as for example the form “bite”.
The process diverges, diverse nouns emerge, and some of them reveal greater complexity (by number of characters) than their progenitors. In other words, spontaneous evolution takes place.
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JonF
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Message 41 of 222 (811737)
06-11-2017 10:28 AM


An analogy is not an argument. It can be used to explain an argument. Make your argument about biological evolution then, if necessary, explain it with an analogy.
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RAZD
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Posts: 19332
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.2


Message 42 of 222 (811743)
06-11-2017 12:04 PM
Reply to: Message 41 by JonF
06-11-2017 10:28 AM


Start with an inadequate analogy, end up with an inadequate argument.

Words don't reproduce and die, there is no selection mechanism there.

Useless to less than useless.


we are limited in our ability to understand
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NosyNed
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Message 43 of 222 (811744)
06-11-2017 1:07 PM
Reply to: Message 42 by RAZD
06-11-2017 12:04 PM


Words
But they do reproduce and die. Words are a good analogy and maybe more than an analogy they are actually undergoing evolution. Evolutionary methods are used to uncover language relationships.

https://en.wikipedia.org/wiki/Evolutionary_linguistics


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RAZD
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Posts: 19332
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.2


Message 44 of 222 (811754)
06-11-2017 3:36 PM
Reply to: Message 43 by NosyNed
06-11-2017 1:07 PM


Re: Words
But they do reproduce and die. Words are a good analogy and maybe more than an analogy they are actually undergoing evolution. Evolutionary methods are used to uncover language relationships.

Yes evolution is a good analogy for studying words changing over time, but it doesn't work the other way. Words can evolve outside nested hierarchies as well as inside. You see horizontal transfer from one language to another for instance.

Enjoy


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
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bluegenes
Member (Idle past 95 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 45 of 222 (811792)
06-12-2017 8:52 AM
Reply to: Message 40 by Vlad
06-11-2017 8:35 AM


Re: Mutations and new infirmation
vlad writes:

Suppose, being “viable”, the form “bit” is also more or less “fit” (say, rated by the Google Ngram Viewer statistics) with regard to certain – say, the English literary – environment. Then the clone “bit” would grow in number exponentially, and from time to time, some (point) mutations inevitably would happen. Mutant forms would spontaneously emerge: “ait”, …, “bt”, …, “bite”, …, “rbit”, …, etc.

In general, any appellative noun is considered “viable” – granted, first, it comprises at least three characters of the Roman alphabet. And second, it is present in a dictionary of at least one of the languages which make use of this very alphabet.

"Bit" needs a language environment to give it meaning. Without context, there is no meaningful information, and the context (in your analogy, the dictionaries of languages that use the Roman alphabet) is the equivalent of a physical environment for chemical self-replicators. "Bit" in a void has no meaning, and self-replicators in a void have no function. In both cases, all mutant variants would have equal meaning/function. Zero.

So, in a life system, environmental input would be an inevitable part of the process of adding new functional information. Functional novelty must at least pass the environmental test on arrival (be close enough to neutral) or be advantageous.

Without constraints, there's no such thing as function. Without light, there would never be the functional information for eyes.


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