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Author Topic:   Introduction to Genetics
AZPaul3
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Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 76 of 236 (719406)
02-13-2014 10:54 PM
Reply to: Message 75 by Faith
02-13-2014 9:47 PM


Re: The Specific Genetics of a Specific Species
30,000 genes in the whole genome? That sounds small somehow. Aren't there thousands on one chromosome?
I erred again, Faith. Please forgive me. I slipped a decimal.
Humans have about 25,000+- genes over 23 pairs of chromosomes. That gives about 500-600 genes for each of the 46 chromosomes.
At this point I think I'll leave this discussion to those more competent than I seem to be at the moment.
Keep asking questions, M'lady. They are good ones.

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dwise1
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Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


Message 77 of 236 (719442)
02-14-2014 1:31 AM


Speciation
In the topic, Bill Nye vs. Ken Ham, we had gotten to the point of needing to determine how long a speciation event would take. I'm talking post-coital barriers, to the point where genetic differences would prevent interbreeding between the new species and the parent species.
How long, in number of generations, would we expect that to take? Is it due to specific mutations, or just a general increase in difference between the genomes?

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 78 of 236 (719455)
02-14-2014 6:06 AM
Reply to: Message 77 by dwise1
02-14-2014 1:31 AM


Re: Speciation
In the topic, Bill Nye vs. Ken Ham, we had gotten to the point of needing to determine how long a speciation event would take. I'm talking post-coital barriers, to the point where genetic differences would prevent interbreeding between the new species and the parent species.
How long, in number of generations, would we expect that to take? Is it due to specific mutations, or just a general increase in difference between the genomes?
It depends on where you start, how much genetic variability is left in the genome of the particular creature at that particular stage in its (micro) evolution along a particular line of variation, and how many individuals each new population starts with -- the fewer the faster you're going to get significant change both phenotypically and genetically.
I think speciation would be due at least in this scenario to a general increase in difference between the genomes, since I don't think mutation contributes anything whatever of benefit.
ABE: I see from Tangle's reply that I'm going to have to state every time that although I use the term "speciation" because it does describe something that actually occurs, I do NOT regard it as macroevolution but merely a subspecies of a species that has become unable to interbreed with others of that species, probably mostly due to changes in the genome. AND I would expect it to have LESS genetic variability than the earlier populations, which certainly doesn't justify the optimism of calling it a new "species" anyway. /ABE
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

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Tangle
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Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


(1)
Message 79 of 236 (719460)
02-14-2014 8:31 AM
Reply to: Message 78 by Faith
02-14-2014 6:06 AM


Re: Speciation
Faith writes:
It depends on where you start, how much genetic variability is left in the genome of the particular creature at that particular stage in its (micro) evolution along a particular line of variation, and how many individuals each new population starts with -- the fewer the faster you're going to get significant change both phenotypically and genetically.
I think speciation would be due at least in this scenario to a general increase in difference between the genomes, since I don't think mutation contributes anything whatever of benefit.
Just on a point of information, as your microevolution here leads, as you say, to speciation, you have accepted macroevolution.

Life, don't talk to me about life - Marvin the Paranoid Android

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 Message 78 by Faith, posted 02-14-2014 6:06 AM Faith has replied

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


Message 80 of 236 (719463)
02-14-2014 9:24 AM
Reply to: Message 75 by Faith
02-13-2014 9:47 PM


Basics of mutations
Which of course implies evolution again. Fewer differences between what and what? I think the evo baggage of that abstract has thrown me. And what "function" is there in "non-coding" regions which I guess refers to pseudogenes or junk DNA that apparently retains some function or what?
I think part of the trouble is that Taq jumped to the punchline without filling in all the details. The problem is the subject is very complex and is difficult to sum-up in a single post. He is trying to get across how we recognize differences in genomes between two separate species. But, I think we should back up and discuss the details in more ... uuhhh ... detail.
A typical Eukaryotic gene consists of a promoter region, a non-coding spacer (~ 30bp), a start codon, introns, exons, a stop codon another non-coding section and a transcription terminator. There is also an initiator sequence upstream of the promotor somewhere between a couple hundred bp to a couple thousand bp. You will see this in the video below swing in and touch the promoter complex to initiate transcription.
The promoter region first must be activated before transcription can occur. Once activated, the double stranded DNA (dsDNA) can be unzipped and the polymerase can bind to the START CODON. Transcription is then initiated and the DNA strand is transcribed into messenger (mRNA). The mRNA is then processed post-transcriptionally, where the INTRONS are snipped out by enzymes and the EXONS spliced back together to from the mature mRNA. Mature mRNA is then translated into a protein that goes from the START CODON to the STOP CODON.
Transcription Video
Translation Video
The protein is made up of various DOMAINS that serve various functions from anchoring to the membrane, engaging target molecules and allowing specific folding patterns.
The next step is to fold the protein into its function 3D shape. This can occur spontaneously or can be assisted by the endoplasmic reticulum (ER) or other enzymes. This folding is critical to the function of the protein. What it does is expose the functional amino acid residues so they can do their job.
Protein folding assumes the form of secondary, tertiary and quatenary structures.
You may be aware of most or all of this, but understanding this is foundational to understanding the significance of mutations and what mutations do to the organism.
I will post more about mutations in a little while.
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 75 by Faith, posted 02-13-2014 9:47 PM Faith has replied

Replies to this message:
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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 81 of 236 (719466)
02-14-2014 10:19 AM
Reply to: Message 73 by Faith
02-13-2014 8:13 PM


Re: The Specific Genetics of a Specific Species
Of course I'd really like to know WHICH stretches have different letters and which the identical sequences because I'm very much interested in which traits are involved.
This paper details some of the problems that exist in answering this question. While we can see by comparison the differences in the two genomes we have a hard time telling which differences are significant and which are not.
For instance, we know that there are code differences in some of the genes dealing with brain chemistry, limb developement, digestion and hearing. What we do not know (yet) is which differences have specific phenotypic effects and how these effects are achieved.
And again I'm still interested in where the genes fit into this. I mean they ARE clearly demarcated segments of the DNA with their start/stop codes, right?
Yes they are.
And they DO determine very specific traits in the organism, right?
In combination with other genes, yes.
... he seemed to think mutation could actually change what a gene DOES, whereas I was arguing that the gene always does whatever it does but that alleles change the specifics of how it does it.
And he is right. Genes are the templates for making proteins. Each different allele makes a different protein. The protein is the actual work unit that makes things and does things. Any mutation may cause a totally different protein to be produced that may make/do something unexpected.
This new protein may have a minor simple effect like displaying a somewhat different shade of the yellow splotches you see in the iris, it may cause no display of yellow at all, it may become a red splotch maker or any number of other things. It may be totally dysfunctional and interrupt signal cascades that lead to blindness.
Like if a gene makes eye color its various alleles are only going to determine WHAT eye color and not change that gene into one that makes eyelashes or bellybuttons. Right?
For the most part that is correct but only because eyelashes and navels require a full complex of multiple other genes to create and, further, the cells in the eye are chemically bound to transcribe the eye color genes while the cells in the eyelid are not. The proteins from the eye color genes do not get made in the skin cells or in the hair follicle cells.
But use caution here. We know that quite a few genes (like the vast majority of them) are used to create multiple different sets of proteins from the same single allele and that genes are often used in different parts of the body with their protein products being used for totally unrelated functions.
Edited by AZPaul3, : added
Edited by AZPaul3, : oops

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dwise1
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Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


Message 82 of 236 (719477)
02-14-2014 10:52 AM


In the topic, Bill Nye vs. Ken Ham, Faith presented a standard creationist claim which we have discussed at length. That claim is that the Ark was loaded with a small number of breeding pairs, each representing one of the basic created kinds and that each pair was front-loaded with an immense amount of genetic variability which then enabled the amazingly rapid evolution into the vast numbers of descendant species that now exist.
Here is how the Wikipedia article, Genetic variability:
quote:
Genetic variability is a measure of the tendency of individual genotypes in a population to vary from one another.
Can it be said that a single pair of organisms possess a vast amount of genetic variability? Or any individual? Or isn't it that you need to have a population in order to compare the individual genomes of its members to determine how much those individual genomes vary with each other?
IOW, in order for there to be a kind on the Ark with a large amount of variability, then you would have had to have loaded an entire population of hundreds or thousands of individuals and not just one single breeding pair?

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Taq
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Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 83 of 236 (719478)
02-14-2014 11:00 AM
Reply to: Message 75 by Faith
02-13-2014 9:47 PM


Re: The Specific Genetics of a Specific Species
So are you saying that the indels are the same in the same species but produce gaps in the genomes between the two species?
Indels can vary between individuals within the same species. In fact, forensic scientists use indels to do DNA fingerprinting.
And yes, indels are mutations. Any change in the DNA sequence is a mutation, and that includes the addition or removal of bases.
When you say "moved" or "duplicated" you are implying evolution, but I have to translate that into purely descriptive terms, which comes down to saying that the DNA in question occurs in different positions in the genome of the different species? Or is duplicate in the one but not the other? And I assume you mean as a regular feature of the genome of each?
When I say moved or duplicated I am implying the observed mechanisms of DNA recombination. This wiki page has a decent overview of some of the mechanisms:
Gene duplication - Wikipedia
This results in multiple copies of the same DNA in the same genome.
So, trying to be sure I get this clear in my head, these different situations of the genes are considered to be identifiers of the species, that is they are predictable regular occurrences in the species genome for all individuals?
They are only identifiers if they are specific to that species and common enough that a majority of the individuals have that identifier.
When you say "the same gene" I assume you mean it's a gene that makes the same trait in the organism in both species, say fingernails or eyelashes or whatever.
When I say "the same gene" I mean a homologous gene as determined by sequence comparison. Homology is not determined by function with respect to DNA.
Also, there is no gene for eyelashes or fingernails. Physical features are the result of interaction between many genes.
And again, homologs being genes that determine the same trait in the organism and occur in the same location on the DNA strand,
Again, homology is not determined by function. It is determined by sequence. If two genes performed the same function but lacked similarity at the DNA sequence level then they would be called analogs. Genes that share DNA sequence similarity are homologs, but they don't have to be at the same position in each genome. Genes that share DNA sequence and the same position in the genome are orthologs. Genes that share sequence similarity due to a gene duplication are paralogs.
Of course an article that assumes evolution as this one does is alienating to a creationist.
It is no different than a geologist assuming that the Earth is round. The evidence for shared ancestry is overwhelming, so that is the conclusion that scientists go with. The evidence in the chimp genome paper adds mountains of more evidence, such as the hundreds of thousands of orthologous ERV's shared by chimps and humans.
I wasn't sure how to describe the differences between the indels, except that if there was never any evolution between chimps and humans we can't speak of "events" so the comparison has to be merely between different locations in the genome.
Your first step would be to explain why there are fewer indel differences between humans and chimps than there are between chimps and gorillas. IOW, you would have to explain why a comparison of whole genomes produces a nested hierarchy.
To me this is all pure fiction. I can't even really glean a descriptive fact from it though there must be some such facts buried in there somewhere. Is it saying that humans and chimps have the SAME fixed neutral and slightly deleterious alleles for the same genes or what? Can YOU translate this paragraph into simple descriptive terms for me?
They are using population genetics to find areas of the genome that are more highly conserved than others. When they compared the chimp genome to the human genome they found that some areas were more similar than others. This indicates negative selection of mutations in the areas with less similarity. They also use variation within the human population to do the same.
Which of course implies evolution again. Fewer differences between what and what? I think the evo baggage of that abstract has thrown me. And what "function" is there in "non-coding" regions which I guess refers to pseudogenes or junk DNA that apparently retains some function or what?
If you think they are wrong, then show they are wrong. Throwing out random insults is no way to approach science.
Please don't use terms like "diverging" which implies evolution and requires me to try to figure out what actual simple fact of comparison is being referred to.
If you want to understand genetics then you have to understand evolution. There is no way around it.

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Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 84 of 236 (719479)
02-14-2014 11:06 AM
Reply to: Message 82 by dwise1
02-14-2014 10:52 AM


Can it be said that a single pair of organisms possess a vast amount of genetic variability? Or any individual? Or isn't it that you need to have a population in order to compare the individual genomes of its members to determine how much those individual genomes vary with each other?
Depends on the species and the paif of organisms. A pair of human, identical twins will have nearly identical genomes and near zero variability. A pair of random humans with no recent common ancestor will have much more variability between them. A random set of chimps will have even more variability between them. A random pair of cheetahs will have very little variability because they went through a recent genetic bottleneck.
For the Ark scenario, it can not be said that just 2 individuals can have the same genetic variability as a population. For example, some of the MHC genes have thousands of alleles in the human population. Each person only carries 2 alleles. A pair would only have 4 alleles between them.
The only way around that is if those ark pairs were extreme polyploids, carrying thousands of copies of the genome each.
As to the recent topic of neutral v. deleterious v. beneficial mutations, a gene locus with much higher variability compared to other gene loci is said to be under less selective pressure than those that are more conserved.

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


Message 85 of 236 (719481)
02-14-2014 11:19 AM
Reply to: Message 75 by Faith
02-13-2014 9:47 PM


Point Mutations
Ok, so we will deal with one specific type of mutation in this post; what we call point mutations.
Point mutations are changes in a single nucleotide. They fall into tree categories: substitutions are changes from one base pair to another base pair. Insertions and deletions should be self explanatory and are what Taq referred to as indels.
So what are the effects of point mutations?
Let's review the structure of a gene again:
a promoter region, a non-coding spacer, a start codon, introns, exons, a stop codon another non-coding section and a transcription terminator.
Introns are clipped out of the pre-mRNA and are typically disassembled and recycled (there are occasions where they contain regulatory sequences, but they are usually non-coding). Introns can represent a significant portion of the pre-mRNA - 60% of the pre-mRNA can be introns. There are also non-coding sections between the promoter and the start codon and also at the terminal end of the mRNA. Any point mutation within these regions will be effectively neutral, since they are not translated into proteins. As you might imagine, this is where the vast majority of mutations will be preserved.
So what happens if a point mutations occurs in a coding region?
As you may know, a protein is encoded by a sequence of 3 bases (*) that are called codons.
Note: this chart is the coding for the mRNA - DNA bases would be complimentary.
The START CODON is Methionine (Met) which has the aa sequence of AUG. A mutation in this codon will inactivate the gene and prevent transcription.
An insertion or deletion within a coding region is typically fatal to the gene since it will cause a frameshift which would drastically alter the protein sequence.
A substitution, however, can have various effects on a gene.
Let's say you have a codon with the sequence CUU which codes for Leucine (Leu) and there is a substitution in the third position that substitutes an A for the U. Now look on the chart and you will see that CUA also codes for Leu. So the effect of the substitution is neutral - absolutely no effect on the gene. This is referred to as a silent mutation or synonymous substitution.
Now what if you had a mutation in that CUU codon in the first position that substituted a G for the C. Now the codon is GUU and it codes for Valine (Val). So now you have a protein with a different aa sequence. This is referred to as a missense mutation. There are basically three types of missense mutations, conservative, semi-conservative and radical. A conservative substitution replaces an amino acid with an amino acid with very similar properties. The effect can be very small to virtually neutral. A semi-conservative substitution replaces an amino acid with one that has different properties such as from a basic amino acid to an acidic amino acid. The result can be mild to severe depending on the domain in which the substitution occurs. A radical substitution replaces an amino acid with one that is radically different. This often results in problems, however, it can provide the protein with a novel function.
As you can see by the codon chart above, there are lots of substitutions that could occur that would have neutral effects on the protein as they would be synonymous substitutions.
A third type of substitution is a non-sense mutation. In this case the change in aa sequence results in a stop codon. For example, UAU codes for Tyrosine (Tyr). If there is a mutation in the third codon where an A is substituted for the U, the result is a stop codon. This substitution will result in a truncated protein, which would normally result in a non-functional protein. However, if there is another copy of the gene somewhere in the genome, the newly truncated protein may actually serve a functional purpose (but that is another story).
A note as to the source of these mutations. Most mutations in DNA occur during replication. While replication is very accurate, it is not perfect. Occasionally, the wrong base is inserted and repair mechanisms just don't catch it and the change is simply conserved in the organism. Another source is DNA damage. DNA can be damaged by various sources, such as UV radiation, and when a break occurs, repair mechanisms try and put it back together. However, the damage can be bad enough that the repair mechanisms can't figure out what the original strand was like, so it does the best it can. This can lead to cancerous growth.
Another point; since we are talking about heritable mutations, these mutations must occur in sex-cells. Mutations in somatic cells are not transmitted to the offspring. If you understand the process of meiosis, you would know that that process is ripe for these types of mutations. If you would like more information on meiosis and mitosis, I can do something on that as well.
As a final point, these processes described above are not speculation but are well studied in the laboratory using model organisms such as the fruit fly, C. elegans and Arabidopsis. How we can go from this information to evidence for evolution will take a lot more work.
Has this helped at all?
HBD
ABE: Taq pointed out that indels are not really considered point mutations. For the sake of this post and the types of mutations I am meaning to discuss, I am referring to indels of a single nucleotide only, which could be considered a point mutation, but more technically are not.
Edited by herebedragons, : (*) I meant 3 bases not amino acids
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.

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Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 86 of 236 (719483)
02-14-2014 11:54 AM
Reply to: Message 85 by herebedragons
02-14-2014 11:19 AM


Re: Point Mutations
Just a few friendly corrections.
Ok, so we will deal with one specific type of mutation in this post; what we call point mutations.
Point mutations are changes in a single nucleotide. They fall into tree categories: substitutions are changes from one base pair to another base pair. Insertions and deletions should be self explanatory and are what Taq referred to as indels.
Point mutation and substitution mutation are synonyms. Indels are not point mutations.
As you may know, a protein is encoded by a sequence of 3 amino acids (aa) that are called codons.
Codons are a sequence of 3 DNA bases, not amino acids.

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NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 87 of 236 (719484)
02-14-2014 12:13 PM
Reply to: Message 83 by Taq
02-14-2014 11:00 AM


Understanding Genetics
If you want to understand genetics then you have to understand evolution. There is no way around it.
I disagree. At least to start with. As Faith has tried to do it is possible (for a time) to avoid "events", "changes" etc. and simply discuss the differences between genomes. The observations of homologs, paralogs etc. can be made without (at first) discussing how those patterns came to be.
BTW- I am learning from these discussions - thank you. I think it is moving just a bit quickly though. Are there perhaps some nice cartoon diagrams representing homologs, paralogs etc?
Of course, when one looks at the grand patterns in the genomes of a variety of critters they become awfully hard to explain (in fact are unexplainable) without concluding evolution but that can come later.

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


Message 88 of 236 (719485)
02-14-2014 12:19 PM
Reply to: Message 86 by Taq
02-14-2014 11:54 AM


Re: Point Mutations
Indels are not point mutations.
Yeah, OK. I was thinking about a deletion / insertion of a single base which I would refer to as a point mutation, but you're right, it really isn't.
Codons are a sequence of 3 DNA bases, not amino acids.
Ooppps. That was a "typo"
Thanks
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 86 by Taq, posted 02-14-2014 11:54 AM Taq has not replied

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


Message 89 of 236 (719487)
02-14-2014 12:51 PM
Reply to: Message 87 by NosyNed
02-14-2014 12:13 PM


Re: Understanding Genetics
At least to start with. As Faith has tried to do it is possible (for a time) to avoid "events", "changes" etc. and simply discuss the differences between genomes. The observations of homologs, paralogs etc. can be made without (at first) discussing how those patterns came to be.
I agree with you. The impression that comes with these discussions is often that we start with the assumption of an old earth and evolution. As soon as old ages are mentioned or chimp / human relationship a barrier is immediately put up which makes further discussion very difficult. The point is we should be able to start with the facts and evidence and understand it on its own merit without making evolutionary / old earth assumptions. It is not until AFTER you examine the evidence that the conclusion of evolution and an old earth becomes inevitable.
So, yes, to begin with we need to explain what it is that leads us to come to the conclusions that we do. Not to start with a conclusion and try to prove it.
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 87 by NosyNed, posted 02-14-2014 12:13 PM NosyNed has not replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 90 of 236 (719488)
02-14-2014 1:09 PM
Reply to: Message 79 by Tangle
02-14-2014 8:31 AM


Re: Speciation
No, I guess I need to say it every time it comes up, I do not regard speciation as macroevolution, it is an event that does occur though so I keep the name for it, but it is merely a population, a race, of a particular species that has lost its ability to interbreed with others of that species, probably most often due to changes in the genome. And the kicker is that it should have less, little or no ability to vary further, making it an odd misnomer within the ToE anyway.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

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