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Author Topic:   Evolution Requires Reduction in Genetic Diversity
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(3)
Message 11 of 1034 (691680)
02-23-2013 11:48 PM
Reply to: Message 1 by Faith
02-22-2013 6:14 PM


Hi Faith
Faith writes:
Hip hip hooray. I may have to copy that out, change the font to something formal like Olde English and put it in 72 point and hang it on my wall. Yikes, a tiny little concession. Means SO much.
Lol. I am more than happy to agree with you whenever you are right. Seriously though, I try to be honest and objective. I am not going to disagree just to disagree.
Faith writes:
The problem here is that I've been working on this for something like eight or ten years now and you aren't going to just casually get me to think about some other alternative until you've shown you understand what I'm arguing, which is far from the case at the moment.
Personally, I come to forums like this to help develop my own skills in rhetoric and logic ... I have no illusions that I will change anyone's mind. It also helps me learn as I make sure that anything I post is as well thought out and researched as I can (in any reasonable amount of time )
I am not totally sure where to start with this topic. It is true that genetic events like bottlenecks (a severe reduction in population size), the founder effect (the founders of a new population have only a small proportion of the genes from the original population) or inbreeding (this is essentially the effect artificial selection will have on gene frequency) will reduce genetic diversity. But that is not the whole story.
from Message 459
Faith writes:
I believe there was an enormous lot of variability built into the original genome of each creature so that this is what is playing out over time. Novelty is a pretty standard occurrence in this scenario as there is so much variability new features and functions can come to expression through normal sexual recombination in newly reproductively isolated populations.
This may be a good place to start. This is what I was wanting you to consider when I said
herebedragons writes:
The thing I wanted Faith to think about was that there is more going on that just allele frequency or eliminating Great Dane alleles to breed Chihuahuas.
I know you believe that there was a great flood roughly 4500 years ago. Do you realize the implications of that on your belief that enormous genetic variation was built into the original genome? It would be possible that God created whole populations of critters that contained this enormous amount of diversity, but at the flood there would be a severe (is there a word that means severe times 1000?) bottleneck. All animal populations would be reduced to one breeding pair (ceremonially clean animals would have 7 breeding pairs). At this point there is a maximum of 4 alleles at any locus. Now granted, some alleles control more than one characteristic, but some characteristics are controlled by more than one allele. But the point is there would be virtually no genetic diversity after the flood. Now start removing alleles to produce the various breeds and you quickly run out of alleles.
So you run into a conundrum ... either new alleles must arise in populations (through mutations) or you must abandon the flood bottleneck. I really see no other option. An original population of 1 breeding pair cannot have the kind of genetic diversity that you are thinking of here.
How do you think you could have the amount of genetic diversity it would take to produce all the dog breeds we have today without adding alleles at some point?
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

This message is a reply to:
 Message 1 by Faith, posted 02-22-2013 6:14 PM Faith has replied

Replies to this message:
 Message 14 by Faith, posted 02-24-2013 4:10 AM herebedragons has replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(1)
Message 26 of 1034 (691731)
02-24-2013 11:26 PM
Reply to: Message 24 by Faith
02-24-2013 8:15 PM


Re: Request
Don't feel as if you have to respond to everyone. Limit yourself to only those that will help move your topic forward. Just ignore posts that aren't going the direction you want. For example, I don't think you are looking to have basic evolutionary theory explained to you, you are looking for reasons that your idea does or does not offer a valid explanation. Since you are proposing an alternate theory to the standard model, responses that explain the standard model really don't help you. No one should be offended if you don't respond to everyone. It can be overwhelming.
I hope to keep up this discussion with you, but don't have a lot of spare time right now. You'll have to be patient with me.
Feel better
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

This message is a reply to:
 Message 24 by Faith, posted 02-24-2013 8:15 PM Faith has not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(3)
Message 27 of 1034 (691734)
02-24-2013 11:58 PM
Reply to: Message 25 by Theodoric
02-24-2013 8:39 PM


Re: mutations
So your whole argument basically comes down to this.
Don't confuse me with he facts my mind is made up*
* Not an actual Faith quote
Actually Theodoric, I think she has a reasonably thought out argument here. I am not saying I agree with it, but it deserves more than ridicule. Few creationist do anything but repeat the B.S. they read on creationist websites, so its nice to see someone who has thought something through for themselves. Personally, I have never heard this argument before and it is kind of intriguing.
Maybe her mind is already made up ... but so what. Don't we all suffer from that???
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

This message is a reply to:
 Message 25 by Theodoric, posted 02-24-2013 8:39 PM Theodoric has not replied

Replies to this message:
 Message 32 by Faith, posted 02-25-2013 4:47 AM herebedragons has not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(1)
Message 50 of 1034 (691803)
02-25-2013 1:23 PM
Reply to: Message 14 by Faith
02-24-2013 4:10 AM


Re: The effect of the flood bottleneck
The initial diversity before the Flood was so great that enormous diversity remained in the creatures on the ark. This is all speculative of course but I think you need to think of every gene of every individual as being heterozygous, the maximum genetic diversity you could have, two alleles per gene, and different in each individual as well so that you do have four alleles for each pair of animals,
It seems as if you are thinking of this as if you have this giant pool of diversity from which you could select phenotypes from. In other words, if you have 20,000 genes and 50% heterozygous you could have up to 40,000 different phenotypes. (I am sure that is an exaggerated estimate and you aren't necessarily suggesting that, but I am trying to illustrate the concept of diversity that it seems like you have) But in reality, you have to look at the diversity at a single loci. There are traits that are controlled by a single gene and for this idea to work, the diversity of these traits need to be explained adequately.
I am going to give you some examples of monogenic traits that have multiple alleles. When you start out with only 4 alleles and reduce genetic diversity, you won't come up with 4 or more alleles at any given loci.
Drosophila eye color - 7 different alleles
+ = red
w = white
wch = cherry
we = eosin
wapr = apricot
wiv = ivory
wch = cream
Austrialian Sheperd - 3 and 4 alleles
As = no copper
ay = sable
at = copper
(white trim)
S = little or no white
sp = pie bald
si - irish trim
s = extreme white
C series in dogs - 5 alleles
C = coat color expressed
cch = chinchilla
cd = white with dark eyes
cb = pale gray
c = albino
coat color in siamese cats - 4 alleles
c+ = standard
cb = Birman
cs = siamese
ca - albino
Most people are familiar with the 3 alleles that are associated with the human ABO blood system. But what is less familiar is that there are more than 30 blood group systems that are complicate blood transfusions. Blood group systems
This website Complex Expression says that
quote:
Collectively, over 990 alleles at approximately 39 genes control for the different surface proteins which determine the compatibility of one person’s blood with another’s.
That is an average of 25 alleles per gene! Most of these are rare and are usually not designated when referring to blood type.
BTW, you should read through that site I linked above, complex expression, it has some good information on gene expression.
These are just some examples of relatively easy to find examples of multiple alleles even in domesticated animals. There are certainly many more examples but they probably have not been studied adequately. It is rather complex to unravel genes with multiple alleles. I showed you all of this to explain why I don't think it makes sense that the genome started out with 4 alleles and has undergone subsequent reduction in diversity. Mutant alleles must come into play, even in your scenario.
There is more I want to say here but I just don't the have time right now.
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

This message is a reply to:
 Message 14 by Faith, posted 02-24-2013 4:10 AM Faith has replied

Replies to this message:
 Message 59 by Faith, posted 02-25-2013 2:26 PM herebedragons has not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 232 of 1034 (692359)
03-02-2013 12:38 AM
Reply to: Message 231 by AZPaul3
03-01-2013 11:47 PM


Re: Mutations Don't Add Anything That Could Rescue the ToE
"Selection" is still at the individual, whole genome level.
Actually, if you are being technical, selection only operates on the phenotype not the genome. This is an important distinction to make because there can be a lot of things going on at the genomic level that are not expressed in the phenotype, and therefore, not subject to selection.
But other than that, yea ... traits contribute to individual fitness and selection operates on the whole individual.
Am I being too strict?
Its good to be precise.
I'm not sure its particularly wrong to refer to a trait being selected for or against though. If you assume a fairly stable population that a new, beneficial trait arises in, it would not be wrong to say that the trait was selected for. For example, you could say that bacteria was selected for an antibiotic resistance trait. But sure, the whole individual needs to be selected for.
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

This message is a reply to:
 Message 231 by AZPaul3, posted 03-01-2013 11:47 PM AZPaul3 has seen this message but not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(2)
Message 459 of 1034 (757953)
05-16-2015 11:24 PM
Reply to: Message 438 by Faith
05-15-2015 6:11 PM


Re: genetic diversity
But that's a great error. THE most fundamental error of confusing phenotypic with genetic diversity which is the problem here over and over again.
Part of the problem is that you seem to be using definitions or have an understanding of certain concepts that are foreign to most of us. It makes it hard when we are talking past each other trying to argue from our own understanding of a term or concept. Like the quote above, my understanding of phenotypic diversity and genetic diversity would suggest that genetic diversity is much, much greater than phenotypic diversity. Even when there is little or no phenotypic diversity there can be a significant amount of genetic diversity. We are able to separate phenotypically indistinguishable populations by their genetic diversity. However, this seems to go against the point you are trying to make, so I am unsure what you mean by genetic diversity.
It would therefore be helpful for you to describe what exactly do you mean by "genetic diversity." Here are some questions that should consider for your answer:
1. Do only alleles that have a detectable variation in phenotype count as separate alleles? In other words, what if two alleles differ by 1% of their coding sequence but do not produce any visible effect on phenotype... would they be two separate alleles or the same?
2. Would changes in non-coding regions count as genetic diversity? For example, one of the most commonly sequenced regions in fungi is the ITS (internal transcribed spacer) region. This region lies between the ribosomal RNA (rRNA) subunits and is transcribed into mRNA with the subunits but is not translated into protein along with the rRNA. rRNA sequences are highly conserved and so serve as excellent "flanking" regions where your PCR markers are located - that way they express in many types of fungi. However, the ITS region is highly variable and this variability can be used to identify individual species. So, does the ITS region count as genetic diversity?
3. Does multiple copies of the same gene count as genetic diversity? Gene copies are quite common, particularly for "house-keeping" genes and copy numbers are variable even between closely related species. So one species may have two copies of a particular gene, a sister taxa may have 5 copies of a gene. Even though they may be the same exact sequence, does it count as genetic diversity? What if each copy has small, but distinguishable differences?
4. Does changes in regulatory regions count as genetic diversity? So, an example would be that you have two copies of a gene that are both expressed in all tissue types in species A. Then there is then a sub-population that breaks off and afterwards experiences a change in the regulatory region of one of those copies which is now expressed in only one tissue type (so there is one gene expressed in all tissues and one that is only expressed in a single tissue type). Would that be an increase in genetic diversity?
5. Is it only overall genetic diversity that matters or is it individual loci that must have reduced genetic diversity? So, if the original creature had 3,000 genes and 2 alleles per gene for a total of 6,000 alleles should a sub-population have fewer alleles regardless of what happens at an individual loci, say 5,900 total alleles? Could an individual loci increase in the number of alleles as long as the total number goes down? Would that still be reduced genetic diversity?
There's more, but I think I better stop there. If you can answer the questions above, I think it will give everyone a much clearer picture of what you mean by genetic diversity and what it means for a speciation event to require a loss in genetic diversity. And also how your concept of genetic diversity relates to our own understanding of the concept.
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 438 by Faith, posted 05-15-2015 6:11 PM Faith has not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 469 of 1034 (757974)
05-17-2015 6:35 PM
Reply to: Message 465 by Admin
05-17-2015 2:25 PM


Re: Moderator Introduced Definitions
Genetic Diversity: I'm open to discussion about this, but unless there are some objections and/or better ideas I'd like to propose the following definition for general usage. For a population, genetic diversity is the number of loci (a locus is a particular gene at a particular location on a particular chromosome) and the number of alleles for each loci across all individuals of that population.
I would say this is ultimately what genetic diversity is, however, for all practical purposes it is impossible (at this time) to quantify this extent of genetic diversity.
For example, if across all individuals there are 38,500 different genes (even if not all individuals have all genes), then that's the number of genes in the population. If that number should rise to 38,501 then that would represent an increase in genetic diversity. Or if across all individuals there are a total of 1,500,000 different alleles across all genes (though of course no individual would have all the alleles), then that's the number of alleles in the population. If that number should rise by one to 1,500,001 then that would represent an increase in genetic diversity.
I raised concern about this in my Message 459 item #5. There is no paper that will describe all 1.5M unique alleles within a population. Showing a "new" allele in a population does not necessarily show that the overall number of alleles has increased.
More important to diversity is what proportion of the loci are polymorphic and what fraction of the individuals are heterozygotic at a given loci. Not only are these the measures that are important to conservation, they are more readily measured. If Faith's hypothesis is correct, I don't think there should be any loci that increase in diversity (she would need to confirm that) so studies that describe even a few loci should be sufficient to show diversity can increase.
Another point about diversity is that it exists in regions that are not considered alleles. Considering, for example, that less than 2% of the human genome is coding sequences and would not be alleles in the classic sense, it would seem unreasonable to exclude 98% of the genetic diversity in discussions of genetic diversity.
To move discussion forward I'd like to introduce simple definitions for species and genetic diversity... But I think these definitions should serve very well most of the time.
Species can be defined reasonably well (despite the problems with defining species), but I don't think that genetic diversity can be as easily defined in the same way. In fact, IMO that is the basic principal at issue in this discussion.
HBD
Edited by herebedragons, : grammar

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 465 by Admin, posted 05-17-2015 2:25 PM Admin has replied

Replies to this message:
 Message 472 by Faith, posted 05-17-2015 7:53 PM herebedragons has not replied
 Message 477 by Admin, posted 05-18-2015 7:36 AM herebedragons has not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 481 of 1034 (758021)
05-18-2015 3:31 PM
Reply to: Message 479 by Denisova
05-18-2015 2:45 PM


Re: Moderator Introduced Definitions
So you think that the original genetic diversity in the genomes of the species, created by God for the first time, is now lost due to deterioration as demonstrated by junk DNA?
"Junk DNA" was a very unfortunate term coined in the early days of genetic sequencing when it was thought that DNA --> Protein was the major player. It is now known that it is not anywhere near that simplistic. We now suspect that the majority of "non-coding" sequences actually have a function. Even spacer DNA that is 1000's of bases long serves an important function even though they don't "do" anything other than keep two segments seperated. The term "junk DNA" really needs to completely fall out of usage.
it should have been a lot of genes that turned into junk DNA, even when we know that not all non-functional DNA is pseudogenes. Because whatever definition you accept for "junk DNA", the proportion of pseudogenes in it must represent thousands of genes that were lost (according to your scenario).
Why do you think the proportion must represent thousands of genes? Are you thinking that each speciation event must mean a loss of one or more genes and there was thousands of speciation events (according to Faith's idea)? I think you would be hard pressed to get ANY creationist to speculate as to how many speciation events there has been since the flood, so that argument won't be much of a deterrent.
you claim the genetic bottleneck occurring during the Flood was the main cause for the loss of genetic diversity. I completely escapes me how a genetic bottleneck could cause a loss of genes. Of alleles that would make sense, but genes?
Good question! Apparently when all the alleles are lost, the gene dies. I don't know...
In this study Thewissen unravels how genetic mechanisms that cause the hind buds in cetacean embryos to start to develop, arrest and degenerate in 5th week of gestation. It turns out that cetaceans still have the genetic outline for developing hind limbs but one crucial Hox gene Sonic Hedgehog (Shh) has been disabled by mutations. It plays an essential role in the molecular cascade that controls limb development in vertebrae.
I suspect that most evolutionary change is due to regulatory changes rather than changes in protein coding sequences. Changes in proteins probably come after the gene regulation has been altered.
ALL of my core points have no[t] been addressed until now.
Just a little tip on your English usage here... "until now" implies that the points have now been addressed. It says they weren't addressed previously, but now they are. What you mean is "they have not been addressed yet."
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 479 by Denisova, posted 05-18-2015 2:45 PM Denisova has replied

Replies to this message:
 Message 482 by Faith, posted 05-18-2015 3:49 PM herebedragons has not replied
 Message 483 by Dr Jack, posted 05-18-2015 6:20 PM herebedragons has not replied
 Message 484 by Denisova, posted 05-18-2015 7:16 PM herebedragons has replied
 Message 486 by Faith, posted 05-18-2015 7:53 PM herebedragons has replied
 Message 492 by Taq, posted 05-18-2015 9:22 PM herebedragons has replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 515 of 1034 (758084)
05-19-2015 11:30 AM
Reply to: Message 484 by Denisova
05-18-2015 7:16 PM


Re: Moderator Introduced Definitions
Ask Faith, it's her vehicle and also read the thread first.
I have been following the thread and besides, I have heard it all before. I just don't have the time to be heavily involved in a debate with Faith, as you can see, it can be time consuming with not much productive feedback. Beside, I think you are handling it pretty well, so there is no need to overwhelm her.
One thing I try to do is figure out what the core misunderstanding is and try to address that. In this case, what I see is Faith has latched on to this idea of there being so much "junk DNA" in the genome that it must be because there was more diversity in the past. I was trying to address this and point out that most "junk DNA" does not fit this idea at all. Perhaps it is overstating it to say that the majority has a function. Function implies a useful purpose or a necessary use to the organism and that is not really what I meant. What Faith is looking for specifically is pseudogenes - introns, SSRs, functional RNAs and centromere associated sequences, ect. don't qualify (perhaps she could make a case for LINEs, but they don't seem like good candidates to me).
For example from Message 487
Faith writes:
So in your view what are all those dead genes in the genomes of so many species? 95% or more.
She thinks "dead genes" constitute 95% of the genome.
So I take her argument and bring it to its logical consequences and see what happens.
Very, very hard to do - trust me (cue accusations of misrepresenting her argument) but its all you can do with such limited hypotheses.
My opinion on speciation and its relationship to genetic diversity is spelled out numerous times in my previous posts, if you don't mind, i am not going to repeat that here again.
Yea, no problem. I understand how speciation works. I was referring to how you were extrapolating her argument, and it wasn't meant to be critical. I don't think she would expect that humans have ever speciated, so, just wondering where the expectation of thousands of pseudogenes came from.
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 484 by Denisova, posted 05-18-2015 7:16 PM Denisova has replied

Replies to this message:
 Message 518 by Denisova, posted 05-19-2015 7:31 PM herebedragons has not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 516 of 1034 (758095)
05-19-2015 12:13 PM
Reply to: Message 492 by Taq
05-18-2015 9:22 PM


Re: Moderator Introduced Definitions
Junk DNA is a perfect term. It is disposable DNA. It is DNA we can throw out.
We now suspect that less than 10% of the human genome has selectable function.
I disagree that "junk DNA" is a perfect term. It is not specific enough. I will withdraw the statement that the majority has a "function," function has implications that I don't really mean, and which depends on what is meant by "function." For example, does spacer DNA have a function? Is it a "selectable function?" Maybe not, but could it just be clipped out? Probably not, separation of genes does affect expression and having two genes back to back may cause problems with transcription. Is that a function?
I think it is more appropriate to refer to it as "non-coding DNA" and then to refer to specific types of non-coding DNA. You would never say "I sequenced a region of junk DNA..."
In fact, some species have chucked a majority of their junk DNA. In the case of the bladderwort, it is probably due to the lack of phosphates in the environment.
Sure, but why haven't all species done that? If there wasn't some evolutionary constraint acting to preserve these non-coding sequences all genomes should be minimized. The tremendous amount of resources that must go into maintaining >50% of our genome that is simply disposable should experience significant negative selection.
In the end, I think junk DNA is a perfect term.
I just think it is too generalized and unspecific and gives a false impression of what it represents. Non-coding DNA is better. Reference to more specific types of non-coding sequences is even better.
In the context of this discussion, there is not 95% of the human genome that is "dead genes." That is one example of how the term "junk DNA" is misleading.
HBD
Edited by herebedragons, : No reason given.

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 492 by Taq, posted 05-18-2015 9:22 PM Taq has replied

Replies to this message:
 Message 517 by caffeine, posted 05-19-2015 1:22 PM herebedragons has not replied
 Message 630 by Taq, posted 05-26-2015 4:34 PM herebedragons has not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(2)
Message 524 of 1034 (758171)
05-20-2015 11:48 PM
Reply to: Message 486 by Faith
05-18-2015 7:53 PM


Re: Moderator Introduced Definitions
I suspect that most evolutionary change is due to regulatory changes rather than changes in protein coding sequences. Changes in proteins probably come after the gene regulation has been altered.
I didn't know what you meant by this at first; now I gather it's another way of talking about junk DNA. Right? All those "regions" that affect diversity but don't code for proteins are what is usually called Junk DNA, right? Leaving that 2% you said do code for proteins.
No not at all. Gene regulation is a complex and multi-leveled process. It involves proteins, histone modifications, cis-regulatory elements (on the same strand of DNA), ssRNA, miRNA, cAMP, etc. These all work together to determine where and when genes get expressed. Changing the amino acid sequence of a protein can be detrimental to the organism if a non-functional protein is produced. However, changes in regulation can modify where and when the gene is expressed and produce significant phenotypic changes - without modification of the protein itself.
A good example of this is found in three-spine sticklebacks
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 486 by Faith, posted 05-18-2015 7:53 PM Faith has not replied

Replies to this message:
 Message 529 by Denisova, posted 05-21-2015 11:41 AM herebedragons has not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(1)
Message 527 of 1034 (758181)
05-21-2015 8:28 AM
Reply to: Message 519 by Faith
05-19-2015 7:33 PM


Re: Pseudogenes caused by bottleneck
I don't mean to be saying that the genes became junk DNA IN the bottleneck but as a result of it due to the loss of so many alleles for so many traits.
Unclear. Alleles don't contribute something to a gene so that it is functional; the alleles ARE the gene. I assume you realize this, but the way you word these statements at times makes it seems like you think alleles and genes are different things. Alleles are different FORMS of a gene. If a gene is functional then there must be at lest one allele; if there is at least one allele, the gene is functional. Losing alleles in and of itself does not affect gene function.
The bottlenecked population's genes aren't changed, it's only as they inbreed for a few generations that the loss of alleles becomes apparent and we find many fixed loci developing for lack of alternative alleles.
Just a clarification. Inbreeding itself does NOT change the proportion of alleles (ie. it does not eliminate alleles), it only shuffles them into homozygotes. An extreme inbreeding event (such as selfing which humans are not very good at) would result in 1/2 the population homozygous for allele A and 1/2 homozygous for allele B. Unless there is now some barrier generated, these populations will eventually begin to outcross and will restore the heterozygous proportion rather quickly. A change in allele frequency requires drift or selection, both of which can result from inbreeding, but are not necessarily a consequence. So, diversity is reduced by the bottleneck but would then remain stable unless acted on by drift or selection.
In the case of cheetahs and elephant seals it is mostly selection that is causing a lack of recovery. In the case of humans after the flood, it doesn't seem to me that the population had any difficulty recovering. Do you have an argument as to why selection was acting on the post-flood population and it was unable to recover rapidly?
Then in the formation ... small subpopulations in the wild which we've been discussing, the reduced genetic diversity should also trend to an increase in fixed loci due to its loss of alleles that remain in the larger general population.
This is a statement that you should be able to back up with evidence. Show us some subpopulations where it has been demonstrated that the subpopulation has increased in the number of fixed alleles.
In the case of domestic breeding the more fixed loci the more "pure" the breed.
A more accurate way of saying this is that to ensure that a trait always breeds true then the trait needs to be homozygous in both breeding individuals. You want the traits you are selecting for to be homozygous, but traits not being selected for you want to have variability.
Many genes would eventually be reduced to fixed loci and come to characterize the subpopulations that migrated to different parts of the planet.
Another statement you should be able to provide some evidence for. What "fixed loci" characterizes human populations today? There has been quite a bit of work done looking at the diversity of human populations and "races."
I did have in mind that simply the existence of many fixed loci could result eventually in the loss of function of many of those genes, but right now I'm thinking there is no real reason why that would be so: destructive mutations would have to occur for that to happen, and destructive mutations should have been on the rise after the Flood too.
Also, if you have a population of say 1000 individuals, all homozygous at a particular loci, how many destructive mutations (mutations that deactivate a gene) would there need to be for that deactivated gene to propagate throughout the population - that is, until the entire population lost function of that gene? Or another way to phase the question, what would have to happen for that deactivated gene to become fixed in the population?
It is enormous, for sure, but it does seem to be what happened. To my mind it speaks to the far more enormous original genetic diversity all species had. The loss is incalculable, but here we are.
Yes, here we are... Faith's assertion of what happened without evidence. You have described your observations but have not provided empirical support that your conclusions about those observations are valid.
If some junk DNA isn't just disabled genes it would be much less of an effect but the vast majority do seem to be formerly functioning genes.
Case in point! What percentage of the human genome is "disabled genes?" How would you detect a "disabled gene," what would it look like. What are some examples of "disabled genes" from the literature. What is your estimate of the number of "disabled genes" and how do you arrive at that estimate?
Unless you provide answers to questions like these, all you have is an observation from which you have drawn an unsupported conclusion.
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 519 by Faith, posted 05-19-2015 7:33 PM Faith has replied

Replies to this message:
 Message 528 by Faith, posted 05-21-2015 10:15 AM herebedragons has replied
 Message 549 by Faith, posted 05-22-2015 6:16 PM herebedragons has replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 531 of 1034 (758192)
05-21-2015 12:36 PM
Reply to: Message 528 by Faith
05-21-2015 10:15 AM


Re: Pseudogenes caused by bottleneck
Yes, for sure. Take care of your eyes! Sounds like it is happening more frequently recently (or maybe it is just that you are now mentioning it?)
But do want to say I've thought through the idea that junk DNA was a result of the Flood and now agree that it couldn't be. I hate to give up on it, I really liked the idea.
Good. Very reasonable.
But then you go on to say this:
At least the Flood accounted for such a huge loss, now it's a bigger loss than I thought.
So, I am unsure of what you mean... do you mean that you thought the flood explained it?
But of course to me it IS a loss, no way these are just genes we didn't need or some such nonsense.
What genes are these? There have been no genes identified which we can make an informed decision as to whether they were needed or not. I think you mean pseudogenes... so what are the homologs of these pseudogenes that they appear they might have at one time been that you feel we did or didn't need?
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 528 by Faith, posted 05-21-2015 10:15 AM Faith has replied

Replies to this message:
 Message 532 by Faith, posted 05-21-2015 12:58 PM herebedragons has not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(1)
Message 539 of 1034 (758218)
05-22-2015 9:20 AM
Reply to: Message 536 by PaulK
05-22-2015 2:08 AM


Re: Pseudogenes caused by bottleneck
If the "junk" is even mostly pseudogenes, we'd have had to have lost a huge number of them - many times what we have now.
Interestingly, there are estimated to be ~20,000 pseudogenes in the human genome which matches up nicely with the roughly 20,000 - 25,000 protein producing genes. The protein coding genes make up less than 2% of the human genome so it would mean the amount of pseudogenes take up roughly the same amount of space in the genome <2%.
In addition, many (maybe most?) of the pseudogenes that have been identified have homologs that are functioning genes within the human genome. You may be aware of this but others may not, one hypothesis is that vertebrates have undergone two whole genome duplications during the course of their evolutionary history. 2R hypothesis This idea seems to fit well with the pseudogene pattern and also fits with what we know about duplications and subsequent adaptation of gene copies.
A diagram illustrating this hypothesis using theoretical gene patterns:
quote:
Pattern predicted for the relative locations of paralogous genes from two genome duplications
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 536 by PaulK, posted 05-22-2015 2:08 AM PaulK has not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 558 of 1034 (758276)
05-23-2015 10:07 AM
Reply to: Message 549 by Faith
05-22-2015 6:16 PM


Re: Pseudogenes caused by bottleneck
Inbreeding doesn't change the proportion of alleles, but it can mix a new set of gene frequencies in ways that appreciably change a subpopulation.
You mean genotypic frequency rather than gene frequency. Gene frequency is often used interchangeably with allele frequency, however, this is not really correct. Genes don't change frequency; genotypes and alleles are what change frequency.
I think inbreeding of a new set of gene frequencies in a new subpopulation alone can make a change in the genetic substrate over time, though I can't say I know how it works well enough to lay it out.
Yes, a particular allele can become fixed in a subpopulation so that all individuals become homozygous for that allele. And yes, the phenotype could be significantly different in the subpopulation, but "genetic substrate?" What could that mean?
The new gene frequencies alone constitute a "selection" event that over time changes the character of the new population, or both populations that formed from the original population, if both have significantly changed gene frequencies.
You put "selection" in quotations (I am not sure why), but no, it is not a selection event. Selection would change allele frequency; recombination only shuffles alleles around.
So when two highly inbred isolated populations do happen to meet, you'll have well developed traits from the same set of genes that are different enough, based on different enough allelic mixes for those same genes either to make interbreeding impossible or to come up with such an entirely new combination the hybrid will be dramatically different itself. This is what I'm thinking, but again spelling out how all the different combinations could occur is beyond me.
You need more than just shuffling alleles around to create reproductive isolation. Think about it... those combinations would have existed in the original population, even if one subpopulation were completely homozygous for one allele and the other were completely homozygous for the other allele, when they recombine, it would just result in the formation of heterozygotes again.
In the case of cheetahs and elephant seals it is mostly selection that is causing a lack of recovery.
How would that work? Both populations have such a high number of fixed (homozygous) loci brought about by the "selection" event of the bottleneck that brought about their current genetic condition there are no alternate alleles to be selected for those particular traits.
The problem with these genetic bottlenecks is that fitness is greatly reduced and there is not enough genetic diversity to contribute to improving fitness. Therefore, the population cannot respond to increased pressure and they struggle to survive. This is selection and and how inbreeding depression can cause the extinction of a species.
I think Darwin was wrong about natural selection being a significant cause of microevolutionary changes, but evolutionists aren't looking for evidence that Darwin was wrong, or anything that would question the basic tenets of evolution, they mostly take them for granted and add further assumptions according to their support of the theory.
Natural selection has some of the strongest empirical support of any of the tenets of evolution. It has been studied extensively, its hardly an assumption anymore.
He didn't have genetic evidence available anyway, he just figured the changes in the finches' beaks were a response to the environment and that became the engine that drives the ToE
True, he didn't have genetic evidence and most of what he thought about heredity was flat out wrong.
but what if the changes came about randomly through changes in gene frequency due to migration of a subpopulation of finches?
Migration is part of the ToE and would certainly contribute to changing allele frequency. One way conservationists introduce genetic variation into inbred populations is to introduce individuals from a distinct population.
I can propose the idea but I don't have any more evidence than Darwin had and it's not something mainstream science has any motivation to test.
There has been tons of work done on these issues. There is much more evidence now than Darwin had. You should be able to examine the literature and find examples that you can critique and show that the evidence supports your hypothesis better than the hypothesis the authors propose. Some examples have already been presented, I could give you some others.
Despite your accusation that researchers are just trying to toe the party line, it is just not true. Some things are so firmly established they just no longer need to continue being argued. However, there are still some very contentious aspects in evolutionary theory.
So, to bring this back around to the topic... speciation has been extensively studied in evolutionary biology - it is the central topic of evolution after all. You should be able to find examples of speciation that demonstrate that a reduction in genetic diversity is required. I can present you some papers that discuss speciation if you wish...
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 549 by Faith, posted 05-22-2015 6:16 PM Faith has replied

Replies to this message:
 Message 560 by Faith, posted 05-23-2015 4:50 PM herebedragons has replied

  
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