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Author Topic:   Introduction to Genetics
Faith
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Posts: 32935
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 61 of 236 (719293)
02-12-2014 8:33 PM
Reply to: Message 59 by Taq
02-12-2014 5:45 PM


Re: The Specific Genetics of a Specific Species
Thank you for the answer. I want to spend some time on it, checking the links and so on, but I have a question right off:

The question that brought me back to this thread is really a wish to know what differentiates the genome of one species from another.

The answer is the order of nucleotides on the DNA strands.

Irrespective of genes or what? How long a strand are you talking about?

Like they say there is only about 5% difference between the human genome and the chimp genome.

That means that when you compare 2 homologous strands of DNA there will be the same base 19 out of 20 times when comparing the two genomes.

Again, my question is what is a "strand" of DNA, how long a strand, in relation to a gene for instance, or a chromosome, etc.


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 Message 59 by Taq, posted 02-12-2014 5:45 PM Taq has responded

Replies to this message:
 Message 62 by Taq, posted 02-12-2014 11:51 PM Faith has responded
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Taq
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Posts: 8012
Joined: 03-06-2009
Member Rating: 4.6


Message 62 of 236 (719299)
02-12-2014 11:51 PM
Reply to: Message 61 by Faith
02-12-2014 8:33 PM


Re: The Specific Genetics of a Specific Species
Irrespective of genes or what? How long a strand are you talking about?

Yep, irrespective of genes. DNA is DNA.

As to the length of strands, the human genome is broken up into 46 strands, otherwise known as chromosomes, that are open at the ends. For bacteria, they have a single circular chromosome plus a few smaller plasmids which are also circular. Think of it as bacteria having a genome like a rubber band and eukaryotes having multiple strings.

Again, my question is what is a "strand" of DNA, how long a strand, in relation to a gene for instance, or a chromosome, etc.

A strand is an unbroken DNA polymer which is a continuous sugar-phosphate backbone. Below is a single strand of DNA where the pentagram structures are the sugars and the phosphates act as connectors to form the polymer. The phosphates link the 5' carbon from one sugar to the 3' carbon of the next sugar, and DNA is replicated and transcribed in the 5' to 3' direction.

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.


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Replies to this message:
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AZPaul3
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Posts: 4512
From: Phoenix
Joined: 11-06-2006
Member Rating: 4.2


Message 63 of 236 (719317)
02-13-2014 7:37 AM
Reply to: Message 61 by Faith
02-12-2014 8:33 PM


Re: The Specific Genetics of a Specific Species
Faith, just to add some context to Taq's message 62 above:

In the diagram the upper left grouping of atoms is the Thymine molecule. That is the "T" you see in a DNA sequence list. The next one down is the Adenine, the "A", molecule. The next is the Cytosine, "C", and the lower right is the Guanine, "G". The sequence represented in the diagram is TACG and it goes on from there.

[abe]

To complete the picture there is another molecule attached to each of these that is not shown. An A attaches to the upper right of that top T, a C attaches to the upper right of the G, always T-A and C-G. Each of those companion molecules is attached to another phosphate group (the thicker dark line grouping) which is the backbone for the other side of the complete strand.

[/abe]

Again, my question is what is a "strand" of DNA, how long a strand, in relation to a gene for instance, or a chromosome, etc.

This string of molecules, by the millions, would be the DNA strand or chromosome. Genes are parts of this strand, identified by certain start/stop sequences. Each chromosome contains thousands of genes.

Edited by AZPaul3, : No reason given.


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New Cat's Eye
Inactive Member


Message 64 of 236 (719337)
02-13-2014 11:38 AM
Reply to: Message 56 by Faith
02-12-2014 12:34 AM


Re: The Specific Genetics of a Specific Species
The question that brought me back to this thread is really a wish to know what differentiates the genome of one species from another. Like they say there is only about 5% difference between the human genome and the chimp genome. That 5% of the human genome then must contain the coding for what is specifically human and not ape, and same with the ape genome.

Think about it like

a blueprint, or
a set of instructions for creating the organism.

Both the chimp and human DNA instruct the creation process to be making (not necessarily in order) bilateral symmetry, then an anus*, and then form a mouth, a spinal cord, head, two arms, two legs, fingers and toes, etc.

Those instructions for forming those things are the same DNA in both chimps and humans.

*as Deuterostomes, which means the anus forms before the mouth, all of us at one point in our lives, were just assholes

Edited by Catholic Scientist, : hid blueprint


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NosyNed
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Posts: 8860
From: Canada
Joined: 04-04-2003
Member Rating: 4.8


Message 65 of 236 (719339)
02-13-2014 11:55 AM
Reply to: Message 64 by New Cat's Eye
02-13-2014 11:38 AM


NOT like a blueprint
Think about it like a blueprint, or a set of instructions for creating the organism.

DNA is not at all like a blueprint, not a bit. If you look at a blueprint you see no instructions for making anything at all. What you see is a picture (representation) of the result desired.

If we have to have a simple analogy DNA is a little bit like a recipe. There is generally no picture of the finished result (or at least it is not necessary to get the result). Instead there are actual instructions (add this, add that, mix, heat) and the result comes out from that.

The analogy breaks down because in the DNA there are in fact no instructions at all. There is simple a chemical pattern and a chemical environment that, when ingredients are available, the result follows from chemical reactions. In a recipe there is no need for an instruction to make CO2 to rise the bread. When the right ingredients are there it happens.


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New Cat's Eye
Inactive Member


Message 66 of 236 (719340)
02-13-2014 12:21 PM
Reply to: Message 65 by NosyNed
02-13-2014 11:55 AM


Re: NOT like a blueprint
Yeah, you're right. I always think of a "blueprint" as a set of instruction. I was using that 'or' as an i.e. But blueprints are not instructions, they're pictures, and DNA is no picture.

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Taq
Member
Posts: 8012
Joined: 03-06-2009
Member Rating: 4.6


Message 67 of 236 (719342)
02-13-2014 12:32 PM
Reply to: Message 66 by New Cat's Eye
02-13-2014 12:21 PM


Re: NOT like a blueprint
Yeah, you're right. I always think of a "blueprint" as a set of instruction. I was using that 'or' as an i.e. But blueprints are not instructions, they're pictures, and DNA is no picture.

If I were to use an analogy I would compare DNA to the gears in a clock, or the punchcards used in a Jacquard loom.

"The Jacquard loom is a mechanical loom, invented by Joseph Marie Jacquard, first demonstrated in 1801, that simplifies the process of manufacturing textiles with complex patterns such as brocade, damask and matelasse.[4][5] The loom was controlled by a "chain of cards", a number of punched cards, laced together into a continuous sequence.[6] Multiple rows of holes were punched on each card, with one complete card corresponding to one row of the design."
http://en.wikipedia.org/wiki/Jacquard_loom

Edited by Taq, : No reason given.


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Faith
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Posts: 32935
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 68 of 236 (719343)
02-13-2014 1:18 PM
Reply to: Message 62 by Taq
02-12-2014 11:51 PM


Re: The Specific Genetics of a Specific Species
So a strand is basically a chromosome?

So it's just the sequence of nucleotides irrespective of genes, and 19 out of 20 in the sequence are identical between the two species in question? Chimps and humans.

So that means for the two species being compared the same genes are in that sequence in the same order with the same stop codes and all that? The only difference is the one out of twenty nucleotides that is different along the whole strand and those occur in the genes of course but for some reason the genes themselves aren't relevant?

But there must be different genes in the different species, no? ABE: Of course the difference in nucleotides would make for different genes, but I'm thinking of different genes as entirely different segments of DNA, entirely different locations on the strand. From what you are saying it's all the same as far as the location and order of the genes go, only the one in twenty nucleotides along the entire strand is the defining thing. /ABE

Is there a clearcut pattern to the location of the species-identifying nucleotides in that chain of 20? I mean does it occur at predictable intervals or just show up willy-nilly so you have to sort out the entire strand to recognize them? I'm not sure this question makes sense. I guess I'm trying to get an idea of how regular or predictable or how much of a recognizable pattern is involved.

If these questions don't make sense that's OK.

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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 Message 62 by Taq, posted 02-12-2014 11:51 PM Taq has responded

Replies to this message:
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AZPaul3
Member
Posts: 4512
From: Phoenix
Joined: 11-06-2006
Member Rating: 4.2


Message 69 of 236 (719359)
02-13-2014 4:08 PM
Reply to: Message 68 by Faith
02-13-2014 1:18 PM


Re: The Specific Genetics of a Specific Species
Is there a clearcut pattern to the location of the species-identifying nucleotides in that chain of 20? I mean does it occur at predictable intervals or just show up willy-nilly so you have to sort out the entire strand to recognize them?

No. No predictable pattern. There are long stretched of the genome where every letter is different between chimp and human and there are even longer stretches of code where the sequences are identical. Over the entirety of the 2 genomes there is the 5% difference.

And to muddy the waters even more for you consider this:

Depending on our separate heritages there may be more difference in the genomes between you and me than between you and any specific bonobo. The important thing is where these differences occur.

I'm not sure this question makes sense.

Yes, they make sense. The only questions that don't make sense are those that go unasked. You are doing very well indeed.


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 Message 68 by Faith, posted 02-13-2014 1:18 PM Faith has responded

Replies to this message:
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NosyNed
Member
Posts: 8860
From: Canada
Joined: 04-04-2003
Member Rating: 4.8


(1)
Message 70 of 236 (719360)
02-13-2014 4:14 PM
Reply to: Message 69 by AZPaul3
02-13-2014 4:08 PM


Differences
Depending on our separate heritages there may be more difference in the genomes between you and me than between you and any specific bonobo. The important thing is where these differences occur.

You're going to have to do a lot more than assert this to convince me it's true. It seems unlikely in the extreme.


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AZPaul3
Member
Posts: 4512
From: Phoenix
Joined: 11-06-2006
Member Rating: 4.2


(1)
Message 71 of 236 (719367)
02-13-2014 5:06 PM
Reply to: Message 70 by NosyNed
02-13-2014 4:14 PM


Re: Differences
That is a wee bit aggressive, yes.

Withdrawn.


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Taq
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Posts: 8012
Joined: 03-06-2009
Member Rating: 4.6


Message 72 of 236 (719370)
02-13-2014 5:43 PM
Reply to: Message 68 by Faith
02-13-2014 1:18 PM


Re: The Specific Genetics of a Specific Species
So a strand is basically a chromosome?

Keeping in mind that DNA is double stranded . . . A chromosome is one continuous DNA molecule (with two complementary strands).

Think of it like a strand of hair. If you take one strand of hair and cut it in the middle you now have two strands. Cut each again, and you have 4 strands. In fact, we use enzymes and even physical shearing to break long strands of DNA into shorter strands.

"Strand" just refers to the continuous nature of the molecule.

So it's just the sequence of nucleotides irrespective of genes, and 19 out of 20 in the sequence are identical between the two species in question? Chimps and humans.

As a gross oversimplification, that is the jist of it.

There are also insertions and deletions, which we call indels (a mash up of the two words). This produces gaps when we try to align the two DNA sequences. You can see the indels in this alignment:

The indels are marked by the dots between the letters.

The next type of difference is recombination where DNA is moved from one position in the genome to another, or even duplicated. When we compare genomes we determine if two genes are orthologs, homologs, or paralogs. An ortholog is a homologous gene found at the same spot in both genomes. A homolog is the same gene, but not necessarily in the same spot in each genome. A paralog is a duplicate gene.

But there must be different genes in the different species, no? ABE: Of course the difference in nucleotides would make for different genes, but I'm thinking of different genes as entirely different segments of DNA, entirely different locations on the strand. From what you are saying it's all the same as far as the location and order of the genes go, only the one in twenty nucleotides along the entire strand is the defining thing. /ABE

I can't find the info very readily, but if memory serves, there are only a handful of genes in chimps and humans that do not have homologs in the other species. If I were to ball park it, I think there are around 20 genes in chimps that do not have homologs in humans compared to about 30,000 genes overall. If I run across the info again I will give you an update.

Is there a clearcut pattern to the location of the species-identifying nucleotides in that chain of 20?

There are many patterns, enough to fill this entire paper:

http://www.nature.com/...al/v437/n7055/full/nature04072.html

. . . and then some.

Overall, there are fewer differences in gene and functional non-coding regions. However, that's a bit circular since function in non-coding regions is determined by divergence rates. Perhaps it is better to say that some regions are diverging at a slower rate than others. The conserved parts of the genome are spread out all over. Suffice it to say that there are a lot of papers covering signals of selection in the human and chimp genome, so I can't really summarize it all here.


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 Message 68 by Faith, posted 02-13-2014 1:18 PM Faith has responded

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Faith
Member
Posts: 32935
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 73 of 236 (719383)
02-13-2014 8:13 PM
Reply to: Message 69 by AZPaul3
02-13-2014 4:08 PM


Re: The Specific Genetics of a Specific Species
No. No predictable pattern. There are long stretched of the genome where every letter is different between chimp and human and there are even longer stretches of code where the sequences are identical. Over the entirety of the 2 genomes there is the 5% difference.

I'll ignore your remark about the bonobo and I'm glad Nosy called you on it. But thanks for this answer, it's informative.

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.

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? And they DO determine very specific traits in the organism, right? (Referring to discussion with Devils Advocate where 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. 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?

Edited by Faith, : change stop to start/stop


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NosyNed
Member
Posts: 8860
From: Canada
Joined: 04-04-2003
Member Rating: 4.8


Message 74 of 236 (719390)
02-13-2014 8:31 PM
Reply to: Message 72 by Taq
02-13-2014 5:43 PM


Us vs Them Differences
I seem to recall that many of the coding region difference between us and then are in genes known to be involved with brain development. However, I couldn't find anything on this with a quick search.

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Faith
Member
Posts: 32935
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 75 of 236 (719395)
02-13-2014 9:47 PM
Reply to: Message 72 by Taq
02-13-2014 5:43 PM


Re: The Specific Genetics of a Specific Species
There are also insertions and deletions, which we call indels (a mash up of the two words). This produces gaps when we try to align the two DNA sequences. You can see the indels in this alignment:

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 are mutations, though, aren't they? (Meaning, I guess, that there would be gaps between the DNA of two individuals of the same species too, wouldn't there?)

ABE: OR, are you saying that the indels simply reflect differences in the presence or absence of certain sequences between the two species; that is, that the indel is defined BY its difference from the other species? /ABE

The next type of difference is recombination where DNA is moved from one position in the genome to another, or even duplicated.

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 we compare genomes we determine if two genes are orthologs, homologs, or paralogs. An ortholog is a homologous gene found at the same spot in both genomes. A homolog is the same gene, but not necessarily in the same spot in each genome. A paralog is a duplicate gene.

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? If so, such differences ought then to be important identifiers of a species. 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. What exactly does a duplicate gene do in the organism?

It's really amazing to think that a sequence of protein-making chemicals can build a trait at all of course.

But there must be different genes in the different species, no? ABE: Of course the difference in nucleotides would make for different genes, but I'm thinking of different genes as entirely different segments of DNA, entirely different locations on the strand. From what you are saying it's all the same as far as the location and order of the genes go, only the one in twenty nucleotides along the entire strand is the defining thing. /ABE

I can't find the info very readily, but if memory serves, there are only a handful of genes in chimps and humans that do not have homologs in the other species. If I were to ball park it, I think there are around 20 genes in chimps that do not have homologs in humans compared to about 30,000 genes overall. If I run across the info again I will give you an update.

And again, homologs being genes that determine the same trait in the organism and occur in the same location on the DNA strand,

30,000 genes in the whole genome? That sounds small somehow. Aren't there thousands on one chromosome?

And again of course I'd be particularly interested in those genes that DON'T have homologs in the other species.

Is there a clearcut pattern to the location of the species-identifying nucleotides in that chain of 20?

There are many patterns, enough to fill this entire paper:

http://www.nature.com/...al/v437/n7055/full/nature04072.html

. . . and then some.

Everything to this point was something I could deal with. Now it gets into mystowacko evo territory:

From the abstract:

Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor,.

Of course an article that assumes evolution as this one does is alienating to a creationist. I have to try to translate the references to supposed evolutionary changes between the two species into purely descriptive terms. And if I may say so, that's what such a paper should do to begin with, to be genuinely scientific: stick to a simple description of the phenomena and avoid that tendentious interpretive baggage that assumes evolutionary transformation, or confine it to a part of the article for that interpretive purpose.

It would then read something like this:

"...we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor between humans and chimpanzees."

And I might as well do the same for the rest of it:

constituting approximately thirty-five million single-nucleotide changes [differences], five million [different] insertion/deletion events [locations?], and various chromosomal rearrangements [differences in arrangement].

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. Again, I think it's VERY unscientific to assume evolution and use such tendentious language in a paper like this, not just because I'm a creationist but because it's unscientific. But that's how we find it everywhere, also in presentations for the public. It's not right. Even if evolution were true it's not right. First you have to simply identify the comparisons you are making and then you can interpret it in terms of evolution, but even then you should be aware that it IS an interpretation, there is nothing in the facts themselves that demands that interpretation.

The rest of it may be too hard to translate:

We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.

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?

Well, it's just the usual presumptuous assumption of evolution. And of course since I'm convinced it's all an illusion, all this conjuring of supposed evolutionary differences is someday going to collapse in a great scary muddle leaving you all perplexed to the max. But oh well.

Anyway, at least you yourself have been mostly helpfully descriptive, thanks, but now you are going to stop being helpfully descriptive. You go on:

Overall, there are fewer differences in gene and functional non-coding regions. However, that's a bit circular since function in non-coding regions is determined by divergence rates.

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?

Perhaps it is better to say that some regions are diverging at a slower rate than others.

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.

The conserved parts of the genome are spread out all over. Suffice it to say that there are a lot of papers covering signals of selection in the human and chimp genome, so I can't really summarize it all here.

I can't make sense out of "signals of selection" I need simple descriptive facts, as in "this differs from that" and so on. Thanks.

Well, I was doing OK through the homologs and all that, but now I'm lost.

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, : add the ABE about indels


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