Is information added to genome by evolution?

[edpell]

Hello is is a continuation of a discussion that got started in the special relativity section but is a split-off and more appropriate here.

The question is does evolution add information to the genome?

 

[edpell]

The question this has brought to my mind is "what is information"? Entropy I have a better idea about. I would say random mutation does not add information it is just a random toss of the dice and the result has no particular meaning. It is only after natural selection that some random changes are "found" to increase reproductive success and other random changes are "found" to decrease reproductive success. So is there in fact any information added by the random changes. It seems in fact that entropy increases. It seems to me that it is the selection process that narrows the combinations down and "raises" the information content?

 

[cesiumfrog]

I'm a bit rusty on Shannon information (the mathematical theory of communication), but wouldn't it say that all mutations (as noise) increase the quantity of information in the gene pool, while (natural) selection decreases entropy (as well as information)?

 

[edpell]

all mutations (as noise) increase the quantity of information in the gene pool, while (natural) selection decreases entropy (as well as information)?

I think we need two ideas gross information versus useful information. I do see that a message with noise injected takes more bits to encode but I do not see that it has more useful information. for example

"hello there, I am fine" versus "helhdlo twhere ,c Ip am fine"

and in the case of DNA long sections of repeats aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa that in fact code for nothing (at least that we know of).

I guess information is just a measure of complexity how many bits does it take to transmit and does not tell us anything about is it interesting.

 

[Frame Dragger]

The question is made more complex by the fact that we're not just one organism really, but a collection of cells. Our DNA allows ancient viral (and who knows what other) DNA/RNA/mRNA to survive. That doesn't benefit US, but from an evolutionary standpoint, WOW, those genes won.

 

[sas3]

Well, gene duplication has been seen, why wouldn’t that be considered an increase in information?
Here is an article on the http://www.nature.com/nature/journal/v428/n6983/full/nature02424.html".

This is an increase of information.

 

[Jon Richfield]

Making allowances for the use of the term “evolution” where “selection” or adaptation would be more precise, yes, it can add information, and commonly does. (There are tricky, though important, classes of cases where a parasite or a creature adapted to a very convenient environment might *lose* part of its genome through adaptation, but ignore them for now.)

But don’t forget that you can get a lot of informational negentropy from a small amount of usable thermodynamic energy. The information is of the order of the log of the thermodynamic energy. The main function of your screen from that point of view is not the energy you receive, but the heating of the room, even if you use a cool screen technology like LCD. So the amount of evolutionary information you can gain from selective effects of thermodynamic processes is *large*!

And thermodynamic negentropy, as you know, comes cheap as long as you remember that you pay more for what you use, than what you get out of it.

But the nature and behaviour of information from various points of view is very, very confusing. Remember that physically speaking noise is also information; information that one does not want. If you are trying to find out what someone is saying, the most glorious music is the purest noise. To an insect or bird on a windswept island, genes for flight can be (genetic) noise of the worst kind, which is why selection produces so many flightless species in islands of various kinds.

Consider a lump of bitumen in a container. If you want it to fit the container, the task of carving it would be demanding and require a high input of information as well as energy. However, if you just leave the lump to settle in its own time, it will fit far better than you could carve it. That is information creation of sorts; it derives the necessary negentropy from the thermodynamic negentropy available from the potential energy of the height of the centre of mass of the bitumen above the floor of the container.

Similarly organisms get the energy needed for the creation of more genetic information from their food, sunlight, and whatever else might be available in the environment. Those that fail contribute their resources to other organisms, luckier or better adapted.

That is just a sliver of the picture, but I hope it helps.

Jon

 

[apeiron]

The question is does evolution add information to the genome?

Selection would reduce information. Reproduction increases the variety and then selection removes it. The two would in general be in an equilibrium balance, keeping a genome continuously adapted to its world.

(BTW, random mutation does count as information. Meaning is something else. Although you could say that the information that is preserved via selection indeed proves itself meaningful of course.)

Creationists incorrectly use the fact that selection reduces variety as an argument to say that novelty cannot evolve.

 

[Jon Richfield]

Selection would reduce information. Reproduction increases the variety and then selection removes it. The two would in general be in an equilibrium balance, keeping a genome continuously adapted to its world.

There is merit to this remark, but it generalises too freely about reducing information. I should like to emphasize that it is quite possible for a new genotype, successful under selection, to contain more information than an older one. In fact it might contain all the old genotype plus something new.

(BTW, random mutation does count as information. Meaning is something else. Although you could say that the information that is preserved via selection indeed proves itself meaningful of course.)

This is perfectly true, but the question of selection and adaptation is very inconsistently correlated to the amount of information gained or lost. Consider our mitochondria for example: they have lost part of their genome outright, and relegated part of what they lost to our host DNA! Part of that seems to have been because they are in the unusual situation of largely needing to minimise their footprint. Most cells, especially eukaryota, happily carry a huge top-hamper of DNA.

Meanwhile other creatures completely dump large chunks of DNA coding for no-longer-wanted functions, although of course more frequently they just leave it lying around until it degrades or loses its meaning. This too can mean physical loss of information content. As you rightly say, there is a distinction between info & meaning. Maybe we could speak of meaning as functional information. Then there has been a loss of functional information.

Creationists incorrectly use the fact that selection reduces variety as an argument to say that novelty cannot evolve.

<siiigh!> Creationists don't seem to be up to either logic or honesty. I suppose that is why they are creationists. They claim to represent the God of Truth, and proceed to do so through error and lies. And they then claim that Darwinism is blasphemy!

In fact of course, selection can entail either loss or gain of info; commonly both at once!

Cheers,

Jon

 

[Frame Dragger]

Given the emerging understanding of the role of mRNA, I'm not sure we can still safely assume what genomes are "useless" and which are used. Rather, it's a matter of relative persistance, and as we interact with the environment, possible expression.

I get the idea that some believe you can look at genomes and it reads like a book. Jon you make excellent points, akin to telling someone that they're trying to apply Euler equations to viscid flow.
<s></s>

DAMN this topic is just so frusterating, especially given what Texas is doing to the textbooks so many will use. I would be doomed without the education I recieved, and now I have a "phew, lucky timing!" feel because I missed the DEGRADATION of science by religion! I could scream, or cry.

 

[Jon Richfield]

Hi FD,

Given the emerging understanding of the role of mRNA, I'm not sure we can still safely assume what genomes are "useless" and which are used.

You and a lot of other folks, and not just with RNA! Trying to work out what parts of the cell store and apply information, and in what forms, is like trying to make sense of a population of multiprocessor, multifunction, multi-connection computers with no handbook and little understanding of the operative functions.

Plus, it is pretty obvious that some of the "junk nucleic acid" really is junk, and that some of the rest has non-obvious functions that are not closely related to any particular structure, much as we might absorb leaked oil in a mechanism either with a wad of cotton waste or wood shavings, whichever is to hand. It does not mean that the absorption is unimportant, nor does it mean that the user's manual mentions it!

... telling someone that they're trying to apply Euler equations to viscid flow.

... and now I have a "phew, lucky timing!" feel because I missed the DEGRADATION of science by religion! I could scream, or cry.

I know the feeling. The best you can do is to make sure that you are informed, that you avoid getting people's backs up, and that you are ready with answers for those willing to listen. Don't worry about those who don't want to listen; you are not doing them any favours by wasting your breath on them. Do lots of reading to make sure you are ready to deal with the curve balls that they develop. Remember that scientists don't carry curve balls (much!) simply because they don't want or need them. If they do need them it is no longer science. The anti-scientists (not only anti-Darwinists) must specialise in curve balls because they have no better weapons, no honesty, no wisdom, no humility, none of the stuff that the bible (or Q'ran, or practically any religious writings) praise.
Unfortunately, that means that they become curve ball specialists, and hard to deal with.
Ironically, the non-curve-ballers, the ones that simply put on anti-smiley self-righteous masks are just as hard to handle. "Can't, won't, shan't, don't" deaf-adderism is a powerful weapon.

Think cheerful thoughts!

Jon

 

[Frame Dragger]

Hi FD,



You and a lot of other folks, and not just with RNA! Trying to work out what parts of the cell store and apply information, and in what forms, is like trying to make sense of a population of multiprocessor, multifunction, multi-connection computers with no handbook and little understanding of the operative functions.

Plus, it is pretty obvious that some of the "junk nucleic acid" really is junk, and that some of the rest has non-obvious functions that are not closely related to any particular structure, much as we might absorb leaked oil in a mechanism either with a wad of cotton waste or wood shavings, whichever is to hand. It does not mean that the absorption is unimportant, nor does it mean that the user's manual mentions it!









I know the feeling. The best you can do is to make sure that you are informed, that you avoid getting people's backs up, and that you are ready with answers for those willing to listen. Don't worry about those who don't want to listen; you are not doing them any favours by wasting your breath on them. Do lots of reading to make sure you are ready to deal with the curve balls that they develop. Remember that scientists don't carry curve balls (much!) simply because they don't want or need them. If they do need them it is no longer science. The anti-scientists (not only anti-Darwinists) must specialise in curve balls because they have no better weapons, no honesty, no wisdom, no humility, none of the stuff that the bible (or Q'ran, or practically any religious writings) praise.
Unfortunately, that means that they become curve ball specialists, and hard to deal with.
Ironically, the non-curve-ballers, the ones that simply put on anti-smiley self-righteous masks are just as hard to handle. "Can't, won't, shan't, don't" deaf-adderism is a powerful weapon.

Think cheerful thoughts!

Jon

Well said, and thank you Jon, you've cheered me up. For the record, if I read any more my eyes would bleed. As it stands, when I'm not reading, I listen to unabridged audiobooks. I had trouble getting to sleep around age 8 ("wait, I'm going to die someday? I CANT SLEEP!" was part of the issue) my grandfather gave me an unabridged audiobook cassette of 'Gorky Park' (I know, I know... lol) and 'Farewell My Lovely'. From there I ended up with a very VERY large number of "Old Time Radio (OTR)" such as The Green Hornet, The Shadow, Sherlock Holmes (the second book I read was a compilation of the comolete SH works... so this was BIG DEAL to a young me), and of course,

"The Fat Man! "There he goes across the street into the drugstore, steps on the scale, height: 6 feet, weight: 290 pounds, fortune: Danger..." :rofl:
<s></s>

I then had the fortune to live in Ma, USA and have access to some fantastic libraries and schools. And read... and read...
and read...
...
And then the internet, or more importantly, Mpeg Layer Three...
did I mention that myself, and a few others set up the "techmasters" (i.e. proto IT student labour) at our high school?

Did I mention that we installed modems and such for faculty when they lit up their T1 lines...
...

Did I mention that I snagged a drill from the Theatre workshop (where I avoided sports other than swimming and fencing), and we got some cheap network cards and setup a LAN in our dormitory. Hehhehe... Over a year before my HS would be 'wired', my friends and I were having lan parties via the holes drilled under doors and coax.

Ahhh memories. Sorry, I've gone off on a serious tangent, but this is the first time I've been enjoined to read since I started skipping classes in 3rd grade to sneak books and read in the bathroom for hours!

 

[mgb_phys]

You also have to be careful that advanced, evolved, complex doesn't necessarily mean more information.

Mammals have relatively few genes compared to 'more primitive' (whatever that means) organisms. One reason is that they have a very constant body temperature so generally only need one chemical pathway to manufacture each protein.
Cold blooded animals and especially amphibians often need a dozen different ways of synthesizing the same molecule depending on body and ambient temperature, environment etc. All these pathways need many more genes to code for the proteins and enzymes required.

And of course animals that have a larval stage need 2 or 3 complete genomes for different phases of their lives.

 

[Jon Richfield]

Well said, and thank you Jon, you've cheered me up. For the record, if I read any more my eyes would bleed. As it stands, when I'm not reading, I listen to unabridged audiobooks.

Whoops! I really didn't mean to come out patronising, FD! All I meant was that that was where to acquire your intellectual weapons and prepare to hone them! Sorry about that. You make me feel as though I were tempting an addict with an uncut sample! The fact that I was telling a local where to find the pusher is a mite embarrassing. As a member of a bookish family I can well understand the obsession. And the frustration with folks who think anything of the kind is unnecessary and uncool.

But thanks for the heads-up!

Jon



Ahhh memories. Sorry, I've gone off on a serious tangent, but this is the first time I've been enjoined to read since I started skipping classes in 3rd grade to sneak books and read in the bathroom for hours! [/QUOTE]

 

[Frame Dragger]

You also have to be careful that advanced, evolved, complex doesn't necessarily mean more information.

Mammals have relatively few genes compared to 'more primitive' (whatever that means) organisms. One reason is that they have a very constant body temperature so generally only need one chemical pathway to manufacture each protein.
Cold blooded animals and especially amphibians often need a dozen different ways of synthesizing the same molecule depending on body and ambient temperature, environment etc. All these pathways need many more genes to code for the proteins and enzymes required.

And of course animals that have a larval stage need 2 or 3 complete genomes for different phases of their lives.

Not to mention that twins could have different genes expressed due to environmental causes, so detrmining the utlity of a given region is not at all clear, although as Jon said, some is clearly "Junk"

Of course, there is the question: why does that junk hang around? Did it have a use? COULD it have a use again, should environmental conditions change?

Then, to emphasize mgb's point, think of the maladaptive/adaptive nature of SCA (Sickle-Cell Anemia). In one context you have an affliction, but don't get the "whole shebang" and you just find yourself resistant to Malaria. Clearly SCA is a mutation, of SSA actually, but it survives because of another unrelated organism. If we eliminate Malaria tommorrow, it wouldn't be junk, it would be archaic.

Then the question of perspective arises, and the basic notion that whether or not you get expessed or not, if you're a gene hitching a ride on a whole species, you're doing pretty well.

@Jon Richfield: I didn't take you to be patronizing at all! This is the internet, and we have to communicate to know who we're talking to after all. Telling someone to read is ALWAYS a good idea... then again... I'm biased? :rofl: I was just sharing an anecdote with someone who I thought ( and it seems I was right) would appreciate it.

Don't worry, I'm no longer stuffing books down my pants and slinking away out of boredom. ;)

 

[Jon Richfield]

You also have to be careful that advanced, evolved, complex doesn't necessarily mean more information.

Mammals have relatively few genes compared to 'more primitive' (whatever that means) organisms. One reason is that they have a very constant body temperature so generally only need one chemical pathway to manufacture each protein.
Cold blooded animals and especially amphibians often need a dozen different ways of synthesizing the same molecule depending on body and ambient temperature, environment etc. All these pathways need many more genes to code for the proteins and enzymes required.

And of course animals that have a larval stage need 2 or 3 complete genomes for different phases of their lives.

Hmmm... Interesting point. Thanks.

Small quibble: as you point out, having multiple active copies of pathways does typically entail extra control and accordingly more info, plus:
Having duplicate information does entail having extra information. One measure of that extra information is the difference between the data-compressed versions of the "redundant" and "non-redundant" genomes.

Note that I am not saying that there are compressed versions in nature, only that if one were to compress them, that would show how much information inescapably existed in the genomes in question.

Also, another quibble: "complete genomes" is something of an overstatement surely? It would be an unusual creature that has no autosomal genes used in both the larval and adult stages. Are you aware of any work to assess the respective volumes of genes required by the different stages? It would be interesting to compare say, the genomes of Thysanura with little metamorphosis, with those of beetles of the family Meloidae with a metamorphosis of : egg, triungulin, grub (a few instars), (sometimes a diapause phase), and imago.

I realize that there are definite requirements for the control of such complexity. I also realize, but without accepting the opinion, that some workers urge the view that successive stages of metamorphosis represent ancestor species that hybridised to form metamorphosing species. This hypothesis would be consistent with "2 or 3 complete genomes", though I accept that it is not entailed by it.

Please feel welcome to elaborate,

Jon

 

[mgb_phys]

Having duplicate information does entail having extra information. One measure of that extra information is the difference between the data-compressed versions of the "redundant" and "non-redundant" genomes.

Different pathways to create the same protein don't necessarily share any gene sequence. Just as a C++ and Java program to serve this site wouldn't necessarily have any bytes in common.

Also, another quibble: "complete genomes" is something of an overstatement surely?

Yes a bit - but if you have to be an egg, a caterpillar, a pupae and a butterfly you are going to use a lot more genes than a person.

 

[Frame Dragger]

Am I the only person who finds the notion of an insect, driven by insticnt to entomb itself and then liquify and reform, really really disturbing? It's nature, and it's beautiful in a way, but the process between "caterpillar" and "butterfly/moth" is :yuck:

 

[Mkorr]

Creationist Myth Exposed: "Evolution does not add information"

1. It is hard to understand how anyone could make this claim, since anything mutations can do, mutations can undo. Some mutations add information to a genome; some subtract it. Creationists get by with this claim only by leaving the term "information" undefined, impossibly vague, or constantly shifting. By any reasonable definition, increases in information have been observed to evolve. We have observed the evolution of

* increased genetic variety in a population (Lenski 1995; Lenski et al. 1991)
* increased genetic material (Alves et al. 2001; Brown et al. 1998; Hughes and Friedman 2003; Lynch and Conery 2000; Ohta 2003)
* novel genetic material (Knox et al. 1996; Park et al. 1996)
* novel genetically-regulated abilities (Prijambada et al. 1995)

If these do not qualify as information, then nothing about information is relevant to evolution in the first place.

2. A mechanism that is likely to be particularly common for adding information is gene duplication, in which a long stretch of DNA is copied, followed by point mutations that change one or both of the copies. Genetic sequencing has revealed several instances in which this is likely the origin of some proteins. For example:

- Two enzymes in the histidine biosynthesis pathway that are barrel-shaped, structural and sequence evidence suggests, were formed via gene duplication and fusion of two half-barrel ancestors (Lang et al. 2000).
- RNASE1, a gene for a pancreatic enzyme, was duplicated, and in langur monkeys one of the copies mutated into RNASE1B, which works better in the more acidic small intestine of the langur. (Zhang et al. 2002)
-Yeast was put in a medium with very little sugar. After 450 generations, hexose transport genes had duplicated several times, and some of the duplicated versions had mutated further. (Brown et al. 1998)

The biological literature is full of additional examples. A PubMed search (at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi) on "gene duplication" gives more than 3000 references.

3. According to Shannon-Weaver information theory, random noise maximizes information. This is not just playing word games. The random variation that mutations add to populations is the variation on which selection acts. Mutation alone will not cause adaptive evolution, but by eliminating nonadaptive variation, natural selection communicates information about the environment to the organism so that the organism becomes better adapted to it. Natural selection is the process by which information about the environment is transferred to an organism's genome and thus to the organism (Adami et al. 2000).

4. The process of mutation and selection is observed to increase information and complexity in simulations (Adami et al. 2000; Schneider 2000).

 

[apeiron]

This is perfectly true, but the question of selection and adaptation is very inconsistently correlated to the amount of information gained or lost. Consider our mitochondria for example: they have lost part of their genome outright, and relegated part of what they lost to our host DNA! Part of that seems to have been because they are in the unusual situation of largely needing to minimise their footprint. Most cells, especially eukaryota, happily carry a huge top-hamper of DNA.

Meanwhile other creatures completely dump large chunks of DNA coding for no-longer-wanted functions, although of course more frequently they just leave it lying around until it degrades or loses its meaning. This too can mean physical loss of information content. As you rightly say, there is a distinction between info & meaning. Maybe we could speak of meaning as functional information. Then there has been a loss of functional information.

Selection of course cannot reduce information it cannot see. If a top hamper stuffed with junk does not reduce fitness, there is no mechanism operating to remove it.

 

[Frame Dragger]

Creationist Myth Exposed: "Evolution does not add information"

Works for me!

Welcome to PF, great first post btw!

 

[Jon Richfield]

Different pathways to create the same protein don't necessarily share any gene sequence. Just as a C++ and Java program to serve this site wouldn't necessarily have any bytes in common.

Uh... Do I detect two correspondents at cross purposes?

I had written in part: "Having duplicate information does entail having extra information." Though the wording was poor (I should have said something more like "...does represent an increased demand for information capacity.") I was referring to a simple reality of information theory. Your wording here suggests to me that you are speaking of not merely duplicate DNA sequences, but possibly totally different mechanisms to produce the same result. I grant that this is possible in principle, though it is a big ask in practice, but in either case, it would require a drastic increase in demand for information capacity, effectively twice as much.

Did I misunderstand you in some respect?

... if you have to be an egg, a caterpillar, a pupae and a butterfly you are going to use a lot more genes than a person.

Generally yes. No problem with that. That was roughly my point, except that I think that I was thinking in terms of fewer extra genes than you were. Mind you, when I think of some of the specialist functions and morphology of some larvae and their adults (even their pupae!) then it is hard to see how any but the basic mechanisms, such as the production of chitin, sclerotin and the like, could work in each stage.

Mind you, people generally underestimate how metamorphic humans themselves are. As babies and embryos we effectively are larvae. Look up the biochemistry of thalassaemia for an example where there is a different gene for fetal and mature haemoglobin. And not all differences between the stages are genetic. Some are physical and others biochemical without invoking specifically genetic mechanisms.

Go well,

Jon

 

[Frame Dragger]

Uh... Do I detect two correspondents at cross purposes?

I had written in part: "Having duplicate information does entail having extra information." Though the wording was poor (I should have said something more like "...does represent an increased demand for information capacity.") I was referring to a simple reality of information theory. Your wording here suggests to me that you are speaking of not merely duplicate DNA sequences, but possibly totally different mechanisms to produce the same result. I grant that this is possible in principle, though it is a big ask in practice, but in either case, it would require a drastic increase in demand for information capacity, effectively twice as much.

Did I misunderstand you in some respect?




Generally yes. No problem with that. That was roughly my point, except that I think that I was thinking in terms of fewer extra genes than you were. Mind you, when I think of some of the specialist functions and morphology of some larvae and their adults (even their pupae!) then it is hard to see how any but the basic mechanisms, such as the production of chitin, sclerotin and the like, could work in each stage.

Mind you, people generally underestimate how metamorphic humans themselves are. As babies and embryos we effectively are larvae. Look up the biochemistry of thalassaemia for an example where there is a different gene for fetal and mature haemoglobin. And not all differences between the stages are genetic. Some are physical and others biochemical without invoking specifically genetic mechanisms.

Go well,

Jon

As I said, environmental changes (including stressors such as age) help to determine which genes are expressed, in what combination, and when. Looking at DNA is akin to looking at uncompiled code. Tay-Sachs, now that... is illustrative, and sad... along with all of the degenerative diseases with a genetic link. LOTS then becomes the natural next step, and moving on to the various "-sons".

Given that, I'm not sure that mechanisms even such as those you describe DO work. They COULD, but they could also be inadequate or unable to "work" with the the new metabolic pathways, etc.

 

[Jon Richfield]

As I said, environmental changes (including stressors such as age) help to determine which genes are expressed, in what combination, and when. Looking at DNA is akin to looking at uncompiled code. Tay-Sachs, now that... is illustrative, and sad... along with all of the degenerative diseases with a genetic link. LOTS then becomes the natural next step, and moving on to the various "-sons".

Given that, I'm not sure that mechanisms even such as those you describe DO work. They COULD, but they could also be inadequate or unable to "work" with the the new metabolic pathways, etc.

FD, I am not sure how much of what you say here, I follow. Is your main point that new genetic material might not at first be compatible with an existing genome, but could become compatible through selection? If so, then yes, that is true.

BTW, forget to mention... a fencer are you? Some of the best folks are. I should know! Do you have a favourite weapon?

Cheers,

Jon

 

[Jon Richfield]

Selection of course cannot reduce information it cannot see. If a top hamper stuffed with junk does not reduce fitness, there is no mechanism operating to remove it.

There is a great deal of merit to this, but it underplays a vitally important principle, what I call selective burden. Genetic material, whether junk or not, if it is functionally irrelevant, tends to undergo what you might call entropic decay. In short, like a picture repeatedly copied, it loses its information and noise gathers. Our genome is full of such material; it is a large part of our "junk" DNA, and like much of our other junk, it varies in its relevance.

Now, of course, there is some slight incentive, even if only "aesthetic", for getting rid of the "junk".

But consider: Suppose you have a large population subject to selection, and varying as randomly as you like, though not so intensively as to endanger the health of the population as a unit. OK?

This would imply a roughly constant (probably exponential) rate of mutation.

Suppose that the population were subject to some moderate intensity of selection for some particular adaptation.

Now, since the location of mutation is effectively random, there could be mutation in the junk area as easily as anywhere else (in fact, other things being equal, most mutation would be in the junk, because there is more of it.) Now, as long as the change is from junk to junk, such a mutation would have no special effect. Right?

But suppose it were in something that nominally is not junk, but a gene. Let us say it changes the skin colour. What effect would that have? It that were the only effect and the creature were a troglobyte, always in deepest darkness, there would be no effect to speak of, and the rest of the adaptive selection could carry on normally.
But outside in the open a change in skin colour could be advantageous, or harmful, or lethal; it could reduce the sexual attractiveness, or ruin the camouflage. Suppose the effect were lethal, then it would reduce the size of the pool available for selection for the main line of adaptation.

This has major effects. Consider our troglobyte: It has perhaps a few hundred genes responsible for its colour. They don't matter in the dark, so mutation in that region of the genome does not affect selection for the main adaptation, which can proceed full steam ahead.

Every attribute that must remain unchanged is at least as active a location of Darwinistic selection as any attribute that is actively changing for adaptation.

Every such location is a selective burden on the rate of selection for every other attribute because it reduces the pool available for selection.

Therefore there is no special process of adaptive shedding or maintenance of adaptively irrelevant or inactive genetic material, so the more irrelevant the code may be, the weaker its maintenance is likely to be. Typical examples are the loss of colour or eyesight in troglobytes and the loss of wings on islands. The procedures are slower than active adaptation, but they proceed fairly inevitably as a rule, so much so that many people see this as an active process, rather than a passive one.

There are also active cases. Wing loss on windy islands may be an adaptation that protects organisms from being blown out to sea. Eye loss in burrowing animals can protect from traumatic eye damage and infection. Such adaptation does act as a selective burden to other adaptations. It does reduce the pool of selection free from eye damage or wind casualties.

My ha'porth!

Jon

 

[Frame Dragger]

FD, I am not sure how much of what you say here, I follow. Is your main point that new genetic material might not at first be compatible with an existing genome, but could become compatible through selection? If so, then yes, that is true.

BTW, forget to mention... a fencer are you? Some of the best folks are. I should know! Do you have a favourite weapon?

Cheers,

Jon

I am saying that, and I am a fencer! I started with foils, flirted with sabre, but Epee (sorry accent marks!) is what I love. I'm a big tall guy, so I'm not what you'd call someone with a "fencer's build", even in the proper stance. Epee tends to level that field, by requiring that defense be more universal, and one good lunge isn't a guarantee.

Do you fence Jon? If so, what's your fav?

 

[Jon Richfield]

I am saying that, and I am a fencer! I started with foils, flirted with sabre, but Epee (sorry accent marks!) is what I love. I'm a big tall guy, so I'm not what you'd call someone with a "fencer's build", even in the proper stance. Epee tends to level that field, by requiring that defense be more universal, and one good lunge isn't a guarantee.

Do you fence Jon? If so, what's your fav?

I used to fence for some 20-30 years, though much of that was just fencing along as coach. Mostly the local university club. I liked all weapons, but did best at epee. Later on I started doing better at foil, but never as well as at epee. I am of medium build, but did fairly well against the big guys as a rule, usually because they rely on long arms without controlling their distance and timing well enough. A good big guy is a problem, but the run of the mill let you inside their distance and then they are dead. Also, it doesn't matter how long your arm is with epee if you don't control point as well as wrist; it just means that you are presenting a target closer to the opponent.
Right?
Generally I not only liked the sport, but the folks who participated. In fact, in my circles I generally found that the combat sport chaps were very relaxed and congenial, off the mat or piste anyway! But generally fencing suited my temperament best. What is more, that is how I met my wife. If fencing never did another thing for me, that would have been a fat profit!
But maybe that all is just a matter of where I was.
Unfortunately where we are, fencing is such a minority sport that we simply couldn't maintain a stable population, and I am no organiser, so I dropped out. I am sorry to say that I don't even know what the current local status is. I no longer have time for sport as such. Life literally is too short. For youngsters sport has other functions as well, but I reckon that anyone who spends his retirement years on the golf course or bowling green just doesn't have the capacity to do anything else with the time remaining. (Not that that isn't better than spending the time at the bar, as some do!) But a golf course, sterile as it is, still is of more interest as an environment than as a place to put balls where no one sensible would want them. Walking round with family in Australia I spotted a pair of frogmouths in a Banksia off an adjacent fairway, and THAT made my day! I cheerfully forgive her for the golf!

Cheers,

Jon

 

[Frame Dragger]

I used to fence for some 20-30 years, though much of that was just fencing along as coach. Mostly the local university club. I liked all weapons, but did best at epee. Later on I started doing better at foil, but never as well as at epee. I am of medium build, but did fairly well against the big guys as a rule, usually because they rely on long arms without controlling their distance and timing well enough. A good big guy is a problem, but the run of the mill let you inside their distance and then they are dead. Also, it doesn't matter how long your arm is with epee if you don't control point as well as wrist; it just means that you are presenting a target closer to the opponent.
Right?
Generally I not only liked the sport, but the folks who participated. In fact, in my circles I generally found that the combat sport chaps were very relaxed and congenial, off the mat or piste anyway! But generally fencing suited my temperament best. What is more, that is how I met my wife. If fencing never did another thing for me, that would have been a fat profit!
But maybe that all is just a matter of where I was.
Unfortunately where we are, fencing is such a minority sport that we simply couldn't maintain a stable population, and I am no organiser, so I dropped out. I am sorry to say that I don't even know what the current local status is. I no longer have time for sport as such. Life literally is too short. For youngsters sport has other functions as well, but I reckon that anyone who spends his retirement years on the golf course or bowling green just doesn't have the capacity to do anything else with the time remaining. (Not that that isn't better than spending the time at the bar, as some do!) But a golf course, sterile as it is, still is of more interest as an environment than as a place to put balls where no one sensible would want them. Walking round with family in Australia I spotted a pair of frogmouths in a Banksia off an adjacent fairway, and THAT made my day! I cheerfully forgive her for the golf!

Cheers,

Jon

Now that is a truly august history in the sport! I can't say I ever thought about WHO fences, but upon reflection... you're right. People in it for "sword fighting" usually drop out immidiately... you have to be in it for the strategy and perfection.

There's more too now that you mention it. I was introduced to fencing by a friend of mine (still a friend 14 years or so later) was a junior olymian fencer, coached by a bloody bronze medalist! A tiny lady, who could probably lunge into orbit if she were so inclined...

Anyway, I was this big guy in the midst of (mostly) small women/girls! My friend, a guy, was the only one who stuck around, so I had to learn the kind of defense you mentioned very quickly. This tiny Korean girl would just take control and BAM... force just doesn't work that well. Add that force to a bit of clever, and a history of playing videogames... The people there were really interesting... and meeting your wife there?! Now that has to be one hell of a marriage!

I suppose you need a bit of perfectionism, intellect, instinct, and a desire to really sink into yourself to fence. I liken it a bit to playing the trumpet (probably because I play trumpet lol), in that it requires very fine tuning and concentration. The instrument in both cases is relatively simple (sword, 3 valve fricative metal tube...), and in both cases it's a combination of physical and mental effort that gets you a sweet note or a win.

I'm sorry that your local community doesn't have a club... that has to be painful. Now, I have to admit Golf is REALLY not my thing (although mini-golf can be fun ;) ), but as you say, at least you're having a walk with friends outside. The bar is never a good move as a hobby unless you're in Alaska at the wrong time of year... (never have been, but I knew a guy...).

I still fence sometimes, but never as much as I'd like for all the reasons you described. I'm lucky enough to have a fencing club about 30+ minutes by drive, but you pointed out how tough it is to keep them cohesive. Alas, fencing is Catch as catch can in a world of 18 holes, carts, and beer on the green. :grumpy:

There's always swimming and martial arts however! They won't be going out of style in my lifetime (I HOPE!)

Thank you for the insight Jon, I hadn't thought about these matters from this view before. Congrats on finding such a clearly compatible wife as well (golf aside)!

Oh, and I had no CLUE what a "frogmouth in a banksia" was, but thanks to the wonders of the internet, I do now! They rest horizontally?! Australia... love the people, but the fauna seems to range from beautiful and odd, to deadly and odd. I'm not even touching the flora... no pun intended.

Be Well,

FD

EDIT: Wow, something about the way you said "I spotted a pair of frogmouths in a Banksia..." that made me think of, "A damsel with a dulcimer in a vision once I saw..." ... and I'm not sure why...

 

[apeiron]

Genetic material, whether junk or not, if it is functionally irrelevant, tends to undergo what you might call entropic decay.

I'm more with the camp that expects junk DNA to actually have epigenetic function, so it would be visible to selection anyway.

But it there is actual junk, then as you say, it would seem to be at least weakly visible. So it may pay for itself by occasionally being a useful pool of mutation - enough to balance its metabolic drag.

However another thought. If junk DNA is actually parasitic, then it may have evolved mechanisms so as not to be visible. It may have evolved mechanisms to ensure it stays switched off and out of the gene pool. It may have evolved to be non-living, or non-evolving, in effect.

 

[Frame Dragger]

I'm more with the camp that expects junk DNA to actually have epigenetic function, so it would be visible to selection anyway.

But it there is actual junk, then as you say, it would seem to be at least weakly visible. So it may pay for itself by occasionally being a useful pool of mutation - enough to balance its metabolic drag.

However another thought. If junk DNA is actually parasitic, then it may have evolved mechanisms so as not to be visible. It may have evolved mechanisms to ensure it stays switched off and out of the gene pool. It may have evolved to be non-living, or non-evolving, in effect.

As Jon said, some testing really has confirmed the "junk" nature of some, but others do seem to be useful in odd ways (mRNA as referenced earlier). That said, you assign too much purpose to our genome, which as always, is concerned with the survival of the genes, not us.

As for mechanisms to remove junk, that would take evolution, and we're not that old as a species, and everything else evolves as well. Remember, that "Drag" has to be significant enough to be a selective trait, or not, and it may be that once it DID have a function. Now, it's junk...

Maybe some of those stretches are useful for the next ice age, or like, or not. Either way, we're efficient in terms of what is transcribed and codes proteins, but not necessarily in terms of what sticks in the DNA as a whole.

 

[apeiron]

As Jon said, some testing really has confirmed the "junk" nature of some, but others do seem to be useful in odd ways (mRNA as referenced earlier). That said, you assign too much purpose to our genome, which as always, is concerned with the survival of the genes, not us.

As for mechanisms to remove junk, that would take evolution, and we're not that old as a species, and everything else evolves as well. Remember, that "Drag" has to be significant enough to be a selective trait, or not, and it may be that once it DID have a function. Now, it's junk...

Maybe some of those stretches are useful for the next ice age, or like, or not. Either way, we're efficient in terms of what is transcribed and codes proteins, but not necessarily in terms of what sticks in the DNA as a whole.

This sounds like a reply, but it really isn't.

 

[Frame Dragger]

This sounds like a reply, but it really isn't.

Ok, if you want a technical reply, there's that as well.

By thinking of the human organism as a whole, with its genome being entirely streamlined for current conditions is a fantasy. Each cell in our body has the same copy of our DNA, and it is the propagation of those genes that is subject to this discussion. We are in direct competition with much of the life in this planet (or all of it from the genetic point of view), and the assumption that we have the capacity to simply remove junk code in a time-frame such as the one you specify is unlikely.

To be "visible" to selection is the issue, but you're being anthrocentric, when the issue really is much more global. You posit that some is not "visible" to selection, and my reply is that is simply silly from the view of molecular biology, although bioinformatics sometimes gets into that. Our DNA is simply not subject to a mechanism for hiding, except by symbiosis, or just parasitism.

Of course, as I mentioned earlier in the thread referencing SCD and Malaria, some adaptations become less useful, then junk. Assuming no medicine, SCD would be highly visible, and selection would do the rest. That's obviously not the case now, but what of regions for more hair, or a bit of tail, etc...?

This is all complicated by the fact that again, reading a genome is extremely UNilluminating on its own. So, if you want to say that this junk is there for mutation, who can say otherwise at this point? I doubt that, as mutation can occur without the junk, and selection for potential future mutations is not really natural. Perhaps those regions provide material for 5`, 3`, or other portions used during transcription, editing, etc... That doesn't work to express proteins, but again, who knows. Some genes regulate other genes expression, and that can be hard to see, but it's not junk. That said, I can see such genes becoming junk over time, and being harder than most to 'remove'.

What IS known now, is that mRNA and miRNA play much larger roles than previously thought, and no, I don't know (nor does anyone) what the full extent of that role is. Remember when people thought that simply mapping our genome would be the end of all mysterious illness and such? Yeah, now we worry about how they code proteins, why some are activated by environment, and the realization that genes act in concert beyond (any) expectations.

That's damned complex, and therefore what is junk and what is not may be up for grabs. There is JUNK however... but maybe the issue is how you define junk. Finally, while we're up for selection always, we're following the model of an apex predator and then some. It's hard to say why, but our DNA is full of junk compared to saaaay, the favourite of biologists everywhere: Drosophila (melanogaster).

What can I say, mammals in general, and humans in particular just have not been subject to natural selection for the duration that saaaaaaay... crocodilians have. That has a profound effect, especially when I question the impact of this "drag". It's not as though much of that material won't be recovered upon apoptosis (traumatic damage... who knows).

You asked a brief and general question. You got a brief and general answer... I don't believe that it requires the response you gave it. If you'd like to offer your view beyond vagaries, I'd be more than happy to engage more deeply.

 

[apeiron]

You asked a brief and general question. You got a brief and general answer... I don't believe that it requires the response you gave it. If you'd like to offer your view beyond vagaries, I'd be more than happy to engage more deeply.

You are responding to something you imagined.

I said if there is junk DNA, then it is indeed an issue over how it is invisible to the winnowing force of selection.

1) It could be just that the timescales don't allow a clear-out (selection would act very weakly on the junk).

2) It could be that the junk is functional in some fashion (either as a reserve of mutation potential or because it is actually epigenetic machinery - and the existence of epigenetic machinery of course does not rule out also the existence of an element of junk).

3) The actually different possibility I then raised was that junk DNA is properly parasitic and has evolved defences against being noticed, therefore being removed by selection.

Parasites do evolve to fly below the radar of a host's immune system, a genome's selective processes. And the mRNA example is relevant if you take the very attractive symbiotic hypothesis of Lynn Margulis concerning organelles generally.

So 3) was the question, as much as I was raising a question here. You can focus on that if you like.

 

[Frame Dragger]

You are responding to something you imagined.

I said if there is junk DNA, then it is indeed an issue over how it is invisible to the winnowing force of selection.

1) It could be just that the timescales don't allow a clear-out (selection would act very weakly on the junk).

2) It could be that the junk is functional in some fashion (either as a reserve of mutation potential or because it is actually epigenetic machinery - and the existence of epigenetic machinery of course does not rule out also the existence of an element of junk).

3) The actually different possibility I then raised was that junk DNA is properly parasitic and has evolved defences against being noticed, therefore being removed by selection.

Parasites do evolve to fly below the radar of a host's immune system, a genome's selective processes. And the mRNA example is relevant if you take the very attractive symbiotic hypothesis of Lynn Margulis concerning organelles generally.

So 3) was the question, as much as I was raising a question here. You can focus on that if you like.

Again, the notion of parasitic genes is one that I don't feel requires any more answer than #1. Given time, it COULD be winnowed out... remember, no plan means that chance plays a factor as well. The other side of #1, is that while our machinery removes the junk, more junk is inserted. In 100K years, what will be junk? I'm saying your entire premise is essentially flawed; our genome has had viral success, and when our species inevitably perishes, it will be the genetic material that is in the game for selection, or not.

Again, I believe you need to define the magnitude of "drag" that parasitic genetic material exerts. The symbiosis hypothesis works well in my mind, but not for ALL of this material, nor does the epigenetic approach. I also question how a virus for instance, evolves outside of the context of a host? It comes down to genomic war, and I don't know that it matters if the DNA is HIGHLY visible. In the end it will be raw material again, with fairly minimal loss. Unless the material results in saaay... genital warts (or any Herpes)... where I think everyone appreciates that in a different time it would be a HIGHLY selective feature.

If you simply have a few hundred base-pairs however, that is normally used during transcription... well, maybe junk material in small quantities is useful, but not inherently so.

As for a question... fair enough, but this is at least a discussion. Replace "asked a brief and general question" with "Made brief and general statement I disagree with.". I didn't imagine what you said, and I am deeply unimpressed that you are leading with rhetoric first.

Clearly you favour Lynn Margulis... who's hypothesis (or wild swing...) is far from mainstream, or accepted. She's under constant fire for pushing her views, and using her position to do so. I am unimpressed by her theory compared with timescales. Anthrocentrism... again.

If you don't want to talk about this, probably, this isn't the right thread for you? If you do, at least have the courtesy to do more than be terse. I certainly won't retain anything like this semblance of polite discourse in that case, nor do I feel I should. If this were in Physics end, I'd just reply "ATM", and blow you off, and rightly so. Proof, if such were needed that biology is a truly weak and derivative science. At this point molecular genetics, physics and chemistry are far better lenses into these matters... biology is merely the result of that. My view of course, but I figure... one ATM view for another.

 

[apeiron]

Again, the notion of parasitic genes is one that I don't feel requires any more answer than #1.

I wish you could follow the simplest of arguments. If the answer is 1, then there is just junk and no need to invoke the higher level of complexity that a parallel with parasitism implies.

I'm saying your entire premise is essentially flawed

What entire premise? The standard idea that selection reduces variety?

I didn't imagine what you said, and I am deeply unimpressed that you are leading with rhetoric first.

That made me laugh out loud. Someday you will surprise me by referring to recognisable bodies of theory and offer clear references. Windy, unfocused rhetoric is all we get instead from you.

Clearly you favour Lynn Margulis... who's hypothesis (or wild swing...) is far from mainstream, or accepted. She's under constant fire for pushing her views, and using her position to do so. I am unimpressed by her theory compared with timescales. Anthrocentrism... again.

Why the ad hominen attack on Margulis? Can you cite who these people are who feel it is a wild swing, that she is using her position to push her views?

And then what else do you do in academia? If you don't have view that you are pushing, and you haven't earnt a position, then you are in the wrong game.

If you don't want to talk about this, probably, this isn't the right thread for you? If you do, at least have the courtesy to do more than be terse. I certainly won't retain anything like this semblance of polite discourse in that case, nor do I feel I should. If this were in Physics end, I'd just reply "ATM", and blow you off, and rightly so. Proof, if such were needed that biology is a truly weak and derivative science. At this point molecular genetics, physics and chemistry are far better lenses into these matters... biology is merely the result of that. My view of course, but I figure... one ATM view for another.

Oh yeah. We've heard all this before. How you are being very patient with a lightweight like me and at any moment you are going to pull out your super-duper intellectual weaponry (which has been cleverly concealed thus far) and terminate me, dude. Physics uber alles! you will holler as you pull your (sadly imaginary) trigger.