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Author Topic:   A test for claimed knowledge of how macroevolution occurs
herebedragons
Member (Idle past 317 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


(3)
Message 514 of 785 (856080)
06-26-2019 10:42 AM
Reply to: Message 510 by Faith
06-26-2019 3:18 AM


Re: Right, the same old same old
Not only did I find out in discussion with RAZD that there are species that don't form nesting hierarchies

Really? Could you elaborate on this?

It is true that there are a substantial number of species that we don't know how they fit into the tree of life (referred to as incertae sedis), but that is different than "don't form nested hierarchies." There are a lot of factors that make classification complicated; such as horizontal gene transfer, the organism is unculturable, the organism has a cryptic lifecycle, and there is just not the financial resources available to study it in depth.

Nested hierarchies are one of the primary biological patterns that Biologists want to explain. It is virtually universal across all life (I only say "virtually" because of the issues mentioned above and that classifying life can be very challenging). So, what are some examples of organisms that "don't form nested hierarchies?"

but there is absolutely nothing at all meaningful about those that do.

It's about patterns, Faith. It takes some kind of organizing principal to create a pattern. When we observe a pattern, or when something is different than what is expected from random chance, that is an indication that some force or factor caused that pattern. Statements that only superficially address a phenomenon without actually offering an explanation for the observed pattern are not useful to science.

For example: Fossils are arranged in a distinctive pattern within the geological record. That pattern is an observation that was made before the ToE was proposed and that the pattern exists is undeniable. "Just a bunch of dead things buried in a massive flood" might be a suitable explanation for you, but for the rest of us, it does not even begin to explain the pattern we observe. Sure, it looks like a bunch of dead things buried in rock, but why the distinctive pattern?

Nested hierarchies are not an artifact of the ToE, but were recognized even before the ToE was proposed (ie. Linnaeus). This pattern is objective and has real biological significance. Many theories have been proposed to explain this pattern but they were all insufficient until the ToE. I don't claim that the ToE is absolutely true (and no one should be making that claim) but it is currently the best explanation for the pattern we observe in biological life.

So you propose a new theory that you claim explains why life falls into this nested hierarchy pattern we observe. I say your explanation for nested hierarchies is as useless as your explanation of the fossil record. Here are a couple reasons why:

1. Your theory only considers sexually reproducing diploids. Roughly 75% of the organisms on earth are not sexually reproducing diploids, but asexual haploids. That means they do not undergo sexual recombination. A theory that only attempts to explain less than 25% of the diversity on earth is useless.

2. The pattern of neutral markers (those that do not affect phenotype) follow the same general pattern as markers that affect phenotype - meaning they also fall into nested hierarchies that fit the same basic patterns as morphological markers. There is just no good reason why a creator would have started off with a pattern of neutral markers that would mimic the patterns we observe. Could it have been done that way... sure. But unless there is an explanation of why that pattern exists, it is meaningless. Consider cytochrome c that Taq mention earlier. Why would the creator use different sequences of cyt c in every organism he created so that when those sequences change over time, the pattern is of a nested hierarchy that includes separately created organisms?

3. Shuffling of alleles alone doesn't account for the diversity we actually observe. If all we had to deal with is 4 alleles at any locus and diversity was due to the reorganization of those 4 alleles, genetic studies would be super easy. But that's not how it is; that just doesn't match our observations. Diversity is much more complicated than 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... 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 510 by Faith, posted 06-26-2019 3:18 AM Faith has not yet responded

  
herebedragons
Member (Idle past 317 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


(3)
Message 544 of 785 (856179)
06-28-2019 9:53 AM
Reply to: Message 539 by Faith
06-28-2019 2:42 AM


Re: The genetic loss idée fixe vs reality
I am actually in the central coastal area of California right now, working with a collaborator on a sequencing project. Last night I visited Point Lobos State Park where you are supposed to be able to see sea lions. I could hear them barking, but they were too far away to see them

I learned this week that California has over 2,000 endemic plant species and one of the most diverse plant communities in the US. There are some very interesting plant types that I have never seen before being from the Midwest. But there were many plants that looked familiar, but not quite... They were just different enough that I knew they weren't a species I was familiar with.

Diversity is probably the number 1 issue that biologists study. It is usually the first question you ask when addressing an issue; "How much diversity is there?", "How is the diversity distributed or structured?", "How does the diversity of this organism compare to the diversity of other organisms?" Diversity is a huge question in biology. It is one of the major features we study. We leverage diversity to make discoveries about processes and gene function. For example, if you want to know what gene controls a particular trait, you first make a diversity panel with lots of individuals that vary for that trait.

The short point here is that biologists have been studying diversity for a long time... and it is still a huge area of study. New genomic tools are allowing us to look at diversity on a whole genome level, not just at individual loci. If your model were correct, we would be finding that out. Instead, we are finding MORE and more diversity. We are discovering diversity we did not previously know existed (unculturable organisms for example) and how diversity looks at a genetic level - not just alleles, but whole genomes.

Here is an example from a 2018 paper looking at the diversity in a plant pathogenic bacterium, Clavibacter michiganensis . Clavibacter michiganensis has been separated into several subspecies based primarily on host range. Remember that bacteria are haploid, non-sexually reproducing organisms - which is also true for roughly 75% of the species on earth. Any model of diversity needs to account for haploid diversity or it is pretty meaningless.

image

**Unfortunately, I can't get the image to display in the thread, but the link should open it in a new window.**

Each genome is a single circular chromosome. The colored blocks represent locally collinear regions - not necessarily specific genes. Subsp. insidiosus (Cmi) is the primary organism being studied, so it is at the top and is the reference genome. Blocks that are above the horizontal line are oriented in the same direction as the reference; those below the line are oriented in the reverse direction. Lines between genomes indicate synteny between blocks on different genomes.

On the Cmc (subsp. capsici) chromosome, there is a section that is below the line that includes a small red block, a large yellow block and a small green block. It is located at the opposite end of the chromosome for Cmi. At some time in the past, it was cut out and reinserted at a different locus in the reverse orientation. In addition, the blocks are different from one another - relative homology is shown in the figure but it is really hard to see.

As you can see, Cms (subsp. sepidonicus) is the most diverse - ie. has the most rearrangements. Interestingly, all the other subspecies have an epiphytic phase, where they can survive on leaves until conditions are right for infection. But Cms does not have an epiphytic phase, but can only survive within potato tubers.

I know one of your objections will be (besides not being able to read it) that this is for bacteria so it doesn't apply to your argument. Well... 1) 75% of the diversity of life on earth works like this, so any model that explains diversity, needs to include haploid, non-sexually reproducing species. and 2) we do see these same patterns in sexually reproducing eukaryotes, it is just much more difficult to work with and display in a readable format.

It just doesn't make any sense that this variation is all built into the genome and just shuffled around by recombination.

I think what I need to do is try to put together a lengthy article trying to cover the whole shebang since I now think I'm leaving too much out of these discussions.

No, what you need to do is come up with evidence that it matches what we observe. Show us a study that supports your position.

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 539 by Faith, posted 06-28-2019 2:42 AM Faith has responded

Replies to this message:
 Message 555 by Faith, posted 06-29-2019 2:03 AM herebedragons has responded

  
herebedragons
Member (Idle past 317 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 558 of 785 (856292)
06-29-2019 11:56 AM
Reply to: Message 555 by Faith
06-29-2019 2:03 AM


Re: The genetic loss idée fixe vs reality
Good grief, HBD

You could try actually reading posts before responding to them since I wasn't say in phenotypic diversity disproves your argument. I was only illustrating how important diversity is to biologists. The main point of my argument was genetic based.

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 555 by Faith, posted 06-29-2019 2:03 AM Faith has responded

Replies to this message:
 Message 559 by Faith, posted 06-29-2019 12:50 PM herebedragons has not yet responded
 Message 560 by Faith, posted 06-29-2019 1:00 PM herebedragons has not yet responded
 Message 561 by Faith, posted 06-29-2019 1:08 PM herebedragons has responded

  
herebedragons
Member (Idle past 317 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 583 of 785 (856382)
06-30-2019 12:45 PM
Reply to: Message 561 by Faith
06-29-2019 1:08 PM


Re: The genetic loss idée fixe vs reality
** Replying to both Message 560 and Message 561 here

...have been studying DIVERSITY.. So? ...genomic tools are allowing us to look at DIVERSITY... So? YOU ARE STILL TALKING ABOUT PHENOTYPES.

Come on Faith... someone who has spent so much time studying and thinking about genetics should know that genotypic diversity and phenotypic diversity are connected. Where there is high genotypic diversity, there is also high phenotypic diversity.

As I said... diversity is the main biological feature that biologists study. It used to be limited to phenotypic diversity but with the development of genomic tools, we are able to study genomic diversity in more and more detail - to the point where we can do comparisons of whole genomes.

The "POINT", the "SO WHAT?" is that this is what we study, day in and day out. If your model were true, we would have published on it. Genomic studies would be EASY. But instead, we are finding the exact opposite to be true; genetic diversity is NOT being reduced in the formation of new species.

Anyway I can't figure out what you are saying and that's the bottom llne.

Well that definitely invalidates my argument and is a typical Faith discussion stopping strategy. Ignoring real world evidence and failing to consider it in your model is a sure way to be right. Have you presented ANY real world genetic evidence in favor of your model? Or have you only presented phenotypic evidence... Blue wildebeests "look"... this or that "looks" homogeneous... What genomic evidence have you presented other than speculation about what MUST happen?

Also, if you've read even a tenth of my argument you should know I'm talking about how populations develop into species by losing genetic diversity, and I don't focus on the genome level at all.

It is real hard for us to understand your argument when you don't even understand it yourself. You DO focus on the genome level because you say one gene is insufficient to test your model, but it is allele altered frequencies across a lot of genes, ie. the whole genome, that causes "speciation".

And I really **** having to address bacteria,

Bacteria have small genomes and can be easily worked with. Displaying and discussing Eukayotic genomes is very difficult and would be even harder for you to understand.

The first part doesn't give me any encouragement to think the rest will be any more illuminating.

You are obviously very convinced that your model is correct and I doubt that any amount of real genetic data will convince you otherwise. And what you can do to avoid real world genetic data is just not understand it and make no attempt to understand it. I don't know why I expected anything else...

When I get a chance I will do a post describing how changing allele frequencies would look from a genomic perspective. Maybe in the meantime you could give a specific example of what allele frequencies would look like in two very closely related species (ones that developed from a common ancestor). If I provide values, you will just say that it looks nothing like your model, so how about you give me an example? Maybe using allele frequencies for 5 - 10 genes, something manageable?

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 561 by Faith, posted 06-29-2019 1:08 PM Faith has responded

Replies to this message:
 Message 585 by Faith, posted 06-30-2019 1:02 PM herebedragons has responded

  
herebedragons
Member (Idle past 317 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


(1)
Message 590 of 785 (856402)
06-30-2019 3:48 PM
Reply to: Message 585 by Faith
06-30-2019 1:02 PM


Re: The genetic loss idée fixe vs reality
- but I'm sure they have very high genetic diversity

And your evidence of this is.... that you want or need it to be true to support your argument?

But then you go on to say...

again all I can do is point out that to get any kind of domestic breed REQUIRES losing the genetic stuff for all other breeds.

So they have low genetic diversity compared to the original population.

We have all agreed that this is generally true.

What is not true is that changing allele frequencies alone is sufficient to explain the origin of new species. And it simply does not match what is observed.

I honestly do not know what you think you are observing, but I am very very sure it is not what you think it is, or what you think *I* think it is or whatever

I actually work with real genetic data from real organisms and do real projects that involve molecular (read genetic) ecology. So yea, we are definitely talking about different things.

You are wrong that I'm ever talking from the genomic perspective

So you're not talking about genotypes and you're not talking about phenotypes? You're only talking about allele frequencies that cause populations to look different but this is neither a genetic or phenotypic issue?

If there is any confusion of terms, it's you that's confused.

And please do NOT give your genomic perspective... and no I don't want to try to cope with your illustration of changing allele frequencies.

In other words... You don't really want a fact based discussion; you just want to continue making baseless assertions and disparage members who don't agree with you.

Well... I can post what I want. If you want to ignore it and avoid actual evidence... thats your choice.

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 585 by Faith, posted 06-30-2019 1:02 PM Faith has responded

Replies to this message:
 Message 593 by Faith, posted 06-30-2019 9:42 PM herebedragons has not yet responded

  
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