question about HGT

[sfs]

Can you cite even one biologist who has said that a singular gene can evolve, as the OP claimed?

Oh, and I'm a biologist, and I just said that a singular gene can evolve.

 

[In situ]

What makes it not clear, is when the poster also claims; God concepts are ludicrous.

Well, I know two things, 1) there is no third, naturalistic, alternative to evolution and 2) Whois has a very unfamiliar way of reasoning and writing to me. I dunno why this is...it just is. People are different I guess.

Unless they believe, aliens did the creating.

I say that is still a belief in creation since it does not explain where aliens comes from and since there is no 3rd alternative I say Whois is a creationist.

 

[In situ]

Oh, and I'm a biologist, and I just said that a singular gene can evolve.

*giggles*

 

[whois]

I have no idea what's going on in this thread. Note: genes evolve. Proteins evolve. Genomes evolve. That's language that biologists use all the time.

the question is:
how do scientist know a HGT gene when they see one, as opposed to an "evolved" gene.
example:
scientist see 2 genes A and B, and determine B is an HGT gene, how do they determine that?

speaking of evolved, do base pairs add one pair at a time or must they add a complete codon?

 

[sfs]

To answer the original question. . . The basic idea is pretty simple. If you find a gene in a species that has close sequence similarity to a gene in a distantly related species, and that is absent in more closely related species, you have a good candidate for horizontal gene transfer. The closer the sequence similarity, the more distantly related the species, and the more relatives it's missing from, the greater the confidence that HGT has taken place. I don't work on HGT so I wouldn't know the nuances of searching for them, but that's the gist of the idea.

 

[sfs]

speaking of evolved, do base pairs add one pair at a time or must they add a complete codon?

Most commonly, a single base pair changes into a different base pair (single base substitution). When DNA is added (an insertion), a single base pair can be added, or two, or three, or twenty, or one million. One base is the most common. If the insertion occurs in coding sequence, any number of bases added that is not a multiple of three will be a frame-shift mutation, which has a high probability of disrupting the function of the gene and which will usually be deleterious and weeded out by purifying selection.

 

[whois]

Most commonly, a single base pair changes into a different base pair (single base substitution).

like transposons maybe?

When DNA is added (an insertion), a single base pair can be added, or two, or three, or twenty, or one million.

so these are inserted rather than appended?

If the insertion occurs in coding sequence, any number of bases added that is not a multiple of three will be a frame-shift mutation, which has a high probability of disrupting the function of the gene and which will usually be deleterious and weeded out by purifying selection.

okay, this answers my question.
i wasn't exactly sure how DNA acquired extra information.
so anything less than a full codon would most likely be detrimental (if added in a coding sequence)?

 

[whois]

I say Whois is a creationist.

you would be wrong.
although i'm fairly open minded about alternative ideas.

 

[In situ]

related to this question is "gene evolution".
if gene do not evolve then how do they get into DNA?

Genes do evolve.

combine this with the apparent immutability of HOX genes and you are going to have to come to one of the following 2 conclusions.

HOX genes are certainly not immutable.

1. each lifeform has a unique origin.

I dunno about you, but my brother has the same parents as me.

2. life evolved from a pool of organisms, not from a single source.

And where did this pool come from?

 

[sfs]

like transposons maybe?

No, a transposon is copies from one place in the genome to another. Some transposons are deleted from their old site, which would mean a deletion from the old site and an insertion at the new. Other remain at the old site and are copied into a new site, which is just an insertion.

so these are inserted rather than appended?

They're typically inserted somewhere into an existing chromosome, yes. They could be inserted into the middle of an existing gene, added to either end of the gene, or (most commonly) into DNA that is not part of a gene.

so anything less than a full codon would most likely be detrimental (if added in a coding sequence)?

Correct. There are exceptions, as with many things in biology.

 

[In situ]

you would be wrong.
although i'm fairly open minded about alternative ideas.

Do you accept the basic ideas of the theory of evolution which says that things evolve over time and thus causes the species differentiation and variations we observe?

 

[In situ]

any number of bases added that is not a multiple of three will be a frame-shift mutation, which has a high probability of disrupting the function of the gene and which will usually be deleterious and weeded out by purifying selection.

My understanding of insert mutations is that to open a gap in the strand for an insert is much less likely than just a substitute. However once a gap is open, it is just as likely to add 1, 3 or 42, 1000, 100000 or whatever number of bases available for insert.

 

[whois]

They're typically inserted somewhere into an existing chromosome, yes. They could be inserted into the middle of an existing gene, added to either end of the gene, or (most commonly) into DNA that is not part of a gene.

okay.
let see if i got this right.
we have the following coding sequence
ABCDEF:GHI
the colon is an inserted base pair.
we now have
ABCDEFXXX
where the x's are undetermined due to the unknown base pair insertion.

Correct. There are exceptions, as with many things in biology.

so genes aren't always triplets?

 

[sfs]

My understanding of insert mutations is that to open a gap in the strand for an insert is much less likely than just a substitute. However once a gap is open, it is just as likely to add 1, 3 or 42, 1000, 100000 or whatever number of bases available for insert.

Depends on the organism. I think for humans insertions and deletions combined are about a fifth as common as substitutions. Any number of bases can be added, but the probability decreases with length. Long insertions are rare.

 

[sfs]

okay.
let see if i got this right.
we have the following coding sequence
ABCDEF:GHI
the colon is an inserted base pair.
we now have
ABCDEFXXX
where the x's are undetermined due to the unknown base pair insertion.

I'm not sure what you're describing. Suppose the original sequence is
...TGTCTTTGAGTCGATGA
where the blue represents sequence coding for amino acids, the red is the stop codon that ends the gene's coding sequence, and the black is noncoding. This sequence codes for a protein ending in the amino acids ...[cystine][leucine]. Suppose a single base, A, is inserted. Depending on where it is inserted, it will have the following effects:

...TGATCTTTGAGTCGATGA: The insertion creates a premature stop codon (TGA), and the last two amino acids are lost from the protein. This is a frameshift.

...TGTCTTATGAGTCGATGA: The insertion disrupts the existing stop codon (TGA -> ATG), and the sequence now reads like this: ...TGTCTTATGAGTCGATGA, and the end of the protein now is ...[cystine][leucine][methionine][serine][arginine]; three amino acids have been added. This is also a frameshift.

...TGTCTTTGAGTCGAATGA: The insertion occurs outside the coding region, and does not affect the protein's structure.

so genes aren't always triplets?

No, protein-coding genes are always coded by three-base codons. What I meant is that a frameshift mutation needn't be deleterious. If it occurs near the end of a gene, it might cause the loss of a few amino acids that don't do much of anything. Or it might cause a truncated protein that does something new, or might cause the loss of a protein that's actually harmful in the present environment. The latter two in particular would be unusual, but they could happen.

 

[In situ]

so these are inserted rather than appended?

If you have a circular genome, like in bacterium, then it must necessary be an insert.

i wasn't exactly sure how DNA acquired extra information.

Any form of mutations might cause a change in what is expressed as the final product. However, I don't know what it is supposed to mean to add "extra information" into DNA.

so anything less than a full codon would most likely be detrimental (if added in a coding sequence)?

It depends on which gene it is, how many genes there is of that type, in which environment the organism live and what type the organism is.

But in essence:

The probability to alter the secondary folding structure is close to 100% (almost guaranteed) in case of a frame shift. If so, the probability that the tertiary folding structure will end up being similar to the none-mutated protein or enzyme is very slim - or non-existing. It will be something new made.

But making new stuff does not imply detrimental effects. It just mean the gene will express some different stuff compared to before.

This may or may not harm the cells - if that particular gene is critical for survival or development then yes it will be detrimental, but not all genes are. Some genes comes in multiple copies, breaking one may not effect you at all, unless the product created by the mutant gene interfere in some bad way with the pathways in the cell - or it can just as well do nothing but just accumulate junk in the cell which may or may not cause harm. But the new product may also cause some beneficial effect!

All changes are not bad - many are neutral - some rare are beneficial and if that happen selection has an opportunity to select for them. Also notice, what is detrimental in one environment might be beneficial in another. And what might be detrimental in one organisms might be beneficial in another organism.

It is not a clear cut yes or no answer. But yes in most cases it is not a good idea with a frame shift....but certain you can never be.

 

[In situ]

Depends on the organism. I think for humans insertions and deletions combined are about a fifth as common as substitutions. Any number of bases can be added, but the probability decreases with length. Long insertions are rare.

Yea, course but as a general rule. Once cut open, the cost of adding 1 or 1 million base pairs is the same, or do a retrovirus with shorter DNA has a benefit over those with longer, i.e. once the virus penetrated the cell is the insert probability still correlated to insert length?

 

[In situ]

I think I say TATATA now....

 

[Justatruthseeker]

Well said! The best definition of evolution is "a change in the frequency of alleles in a population over time."

Which is just a natural occurrence between mating taxa. Despite the claimed 50 mutations per birth - all Asians remain Asians and will always remain Asian. As all Africans will remain African. And when two infraspecific taxa mate - is variation observed within the species. Asian mates with African and produces an Afro-Asian. Husky mates with Mastiff and produces a Chinook.

The only change in the alleles that cause variation among the species is the natural recombination of genomes and new dominant and recessive traits from two different infraspecific taxa within a species. T-Rex remained T-Rex as did every other you care to name.

There are no missing transitional species - because half of what you call separate species in the fossil record was not. They are merely different infraspecific taxa within a species. As Husky is a different infraspecific taxa than Mastiff. As Asian is from African.

 

[sfs]

Yea, course but as a general rule. Once cut open, the cost of adding 1 or 1 million base pairs is the same, or do a retrovirus with shorter DNA has a benefit over those with longer, i.e. once the virus penetrated the cell is the insert probability still correlated to insert length?

Different mechanisms produce different sizes of insertions and deletions (indels). For example, replication slippage will produce short indels in short tandem repeats; see this paper for a rundown on known mechanisms for short indels. Transposons will produce medium sized insertions, while large indels can be produced by DNA repair mechanisms; see here for another summary.