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Author Topic:   Can mutation and selection increase information?
bluegenes
Member (Idle past 737 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


(1)
Message 1 of 222 (809221)
05-16-2017 8:27 AM


It seems to be a common creationist claim that evolutionary processes either cannot produce new "functional information," or that if they can, they cannot produce enough to account for the life forms we see in the world today. Yet I've never known any creationist show that either is actually the case.

So, I propose a thread on which creationists can support either or both of those claims, and on which evolutionists can support the opposing view that novel functions (presumably requiring "new functional information") can be added to the life system, and that the known evolutionary processes should be adequate to account for the evolution of any "information" present in modern life from one or several relatively simple ancestral forms.

Some may also want to argue that "biological information" is ill defined, undefined, or that there's no such thing etc., all of which is fine on this thread.

(Biological evolution forum, please)


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bluegenes
Member (Idle past 737 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 2 of 222 (809222)
05-17-2017 8:06 AM
Reply to: Message 1 by bluegenes
05-16-2017 8:27 AM


Bumpety Bump: Long overdue information thread!
Hi, Percy.

I think you agreed on the debunking selection thread that we need this: Message 219


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bluegenes
Member (Idle past 737 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


(2)
Message 13 of 222 (809392)
05-18-2017 10:11 AM
Reply to: Message 4 by RAZD
05-17-2017 9:40 AM


Re: functional information ... DNA function
RAZD writes:

So maybe a useful parameter would be DNA function. We can measure genes and we can find cross links between genes in doing certain functions. It's not just the number of genes then, but also how they interact.

And genes duplicate.

I'm arguing on another thread that YECs should need to add mutation and positive selection of new "information" to their model, because there are many functioning alleles in modern populations that couldn't have been present in Adam and Eve (and in bottleneck Ark pairings of animals).

I'm trying to start a new breed of informationalist-creationist. It's fun!


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bluegenes
Member (Idle past 737 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 14 of 222 (809398)
05-18-2017 10:22 AM
Reply to: Message 5 by Taq
05-17-2017 10:50 AM


Looking at the past
Taq writes:

bluegenes writes:

It seems to be a common creationist claim that evolutionary processes either cannot produce new "functional information," or that if they can, they cannot produce enough to account for the life forms we see in the world today. Yet I've never known any creationist show that either is actually the case.

Additionally, I have yet to see a creationist demonstrate that evolution needs to produce "new genetic information" in order to produce all the species we see today from a universal common ancestor. In my experience, they define "new genetic information" so that the mechanisms of evolution can not produce it, but in the process their definition no longer has any bearing on actual biology.

I find that the goalposts generally get moved to avoid anything that can be directly observed, which always becomes a rearrangement of old information, rather than "true" novelty. This has a heavy reliance on pretending that we cannot observe past events from the present. But we can.

As you know, we can identify historic gene duplications, and detect duplicates which have new functions, and if that's not "new information", then evolution certainly doesn't need it!

Edited by bluegenes, : typo


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bluegenes
Member (Idle past 737 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 19 of 222 (809423)
05-18-2017 11:39 AM
Reply to: Message 15 by Faith
05-18-2017 11:02 AM


Mutation! Errors create more!
Faith writes:

Would you please explain to me how genes duplicate? Since they occupy a position along the DNA strand, and they are thousands of codons long, and the replication process follows the strand codon by codon how does a copy of a gene get separately inserted into the strand?

You won't like it. Errors while reproducing. There are several different types. Chunks of DNA duplicate quite often, and when there's a gene in the segment, that's a duplicate.

It's common. You've got loads of duplicates in your genome.

This will tell you the different ways.

Gene duplication

Didn't you know it happened?

ABE: a bit redundant, because Taq got there first and linked to the same article.

Edited by bluegenes, : pipped to the post


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bluegenes
Member (Idle past 737 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


(1)
Message 22 of 222 (809431)
05-18-2017 11:51 AM
Reply to: Message 7 by Faith
05-17-2017 8:54 PM


Re: No new information needed
Faith writes:

Well, I'd been assuming that new information WAS needed for all the diversity of life to exist, because that's often claimed, but now I don't think anything new is needed, it was all built in to the original genome of each Kind at Creation, most or all of it provided through genes for traits made up of two and only two forms or alleles. As I showed on the thread about YEC supposedly needing mutations and positive selection, a mere two genes with two alleles each provide sixteen different versions of a trait simply by combining the effects of the four different proteins produced by the four different alleles. Since many traits have quite a few more genes than two the possible variation in only one trait is enormous.

No mutations needed, no extra alleles needed, just the combining of the two-form genes through sexual recombination. (I'm only thinking of sexually reproducing creatures).

So, if a mutation did produce a new functional allele with a new effect on the phenotype, wouldn't you agree that that constitutes new information, whether it's "needed" or not?


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bluegenes
Member (Idle past 737 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 25 of 222 (809458)
05-18-2017 12:43 PM
Reply to: Message 23 by Faith
05-18-2017 12:21 PM


Re: No new information needed
Faith writes:

bluegenes writes:

So, if a mutation did produce a new functional allele with a new effect on the phenotype, wouldn't you agree that that constitutes new information, whether it's "needed" or not?

I would figure it had managed to replicate an existing allele probably at another gene,.....

Why and how would you figure that?

Faith writes:

.....not anything actually new, but so far I'm not convinced that anything new at all, even in that sense, is ever created by a mutation.

Evidence you gave on the other thread was all based on a supposed high frequency which I think is just an illusion based on assuming a new allele instead of a neutral mutation which doesn't change the protein or the function of the original allele.

No, different alleles are known to give immunity to different parasites, and you'd know that if you'd read the extracts from the paper on MHC that I posted there.

My question was conditional. If a new mutation created something new in the phenotype (even if you don't believe this actually happens) would it constitute new information?


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bluegenes
Member (Idle past 737 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 737 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?


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bluegenes
Member (Idle past 737 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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bluegenes
Member (Idle past 737 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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bluegenes
Member (Idle past 737 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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bluegenes
Member (Idle past 737 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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bluegenes
Member (Idle past 737 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 53 of 222 (812336)
06-16-2017 4:07 AM
Reply to: Message 46 by Vlad
06-13-2017 8:33 AM


Re: Mutations and new information
Vlad writes:

Bluegenes comments right on the point. Of course, without constraints, there is no such thing as function.....

.....The thing is that living entities spontaneously evolve,...

One of the synonyms for "spontaneous" is "unconstrained".

As you don't seem to be using it that way, are you trying to express the view that evolution is contingent/unpredictable?

There's a significant difference between "unconstrained" and "unpredictable", so perhaps you could clarify that point.


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bluegenes
Member (Idle past 737 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 54 of 222 (812341)
06-16-2017 4:54 AM
Reply to: Message 49 by Vlad
06-15-2017 9:05 AM


Re: Mutations and new information
Vlad writes:

Spontaneous evolution takes place, in the model, and you may trace various feasible paths of advancement yourself. And also evaluate the probabilities of evolutionary progressions up to some interesting forms. Of course the accidental emergence of a new “viable” form by no means always signifies any quantitative increase in information content. Say, mutant form “bat” is quite “viable” yet the quantity of information it carries remains the same as in the primordial noun “bit”.

If "meaning" = "function" in your analogy, then an increased number of letters doesn't really mean that there's a "quantitative increase in information content". Neither "bite" nor "bat" can necessarily be described as having more meaning than "bit".

By some descriptions of "functional information" for biology, or "meaningful information" in your analogy, the "meaning" measure of the words would depend on the number of synonyms that could convey that meaning. The fewer the ways of conveying the meaning, the higher the information content.

However, we can use your analogy to say with confidence that changing bit to bat or bite creates new information, and that if "bit" is retained alongside a new word, as in "tit bit", then we have a clear increase in information.

But as we could do that with examples from biology, I don't think that your analogy really brings much meaningful function to this thread.


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