question about HGT

[whois]

let's take the following quote as a reference to my question.
i am basically wondering how they can determine if an "ancient" gene is HGT:
Available data indicate that no insurmountable barrier to HGT exists, even in complex multicellular eukaryotes. In addition, the discovery of both recent and ancient HGT events in all major eukaryotic groups suggests that HGT has been a regular occurrence throughout the history of eukaryotic evolution.
www.ncbi.nlm.nih.gov/pmc/articles/PMC4033532/

 

[bhsmte]

That is your oppion as net police yet. But would you agree that answering the questions someone has instead of setting them up for straw man is just as appropriate as well?

As a general rule, my observations on this board, lead me to believe, certain posters tend to set themselves up for scrutiny, when they make claims they can not substantiate and they post information, that does not support their claims.

 

[whois]

related to this question is "gene evolution".
if gene do not evolve then how do they get into DNA?
combine this with the apparent immutability of HOX genes and you are going to have to come to one of the following 2 conclusions.
1. each lifeform has a unique origin.
2. life evolved from a pool of organisms, not from a single source.

 

[Squeegee Beckenheim]

let's take the following quote as a reference to my question.
i am basically wondering how they can determine if an "ancient" gene is HGT:

http://www.researchgate.net/publication/10922742_Ancient_Horizontal_Gene_Transfer

Detection of horizontal gene transfer
Horizontal gene transfer (HGT) can be detected using several methods, each with important advantages and
caveats23–26,35,123.
Phylogenetic methods
Phylogenetic trees of proteins or DNA sequences can show incongruent relationships among taxa, which might be the
result of HGT. However, lineage-specific gene losses, CONVERGENCE and unequal mutation rates in different taxa can cause similar effects. Because protein sequences change more slowly than their DNA coding regions, ancient HGT can be best detected by using protein trees, whereas nucleotide trees are better for studying closely related species. Overall,
phylogenetic analysis is the most robust indicator of ancient HGT.

Nucleotide composition analysis

Shifts in nucleotide composition between neighbouring sequences, such as an increase in the frequencies of G•C bases
over A•T bases, could indicate that a gene or non-coding region from another species has been inserted into the genome.
However, it is important to realize that intra-genome regional biases in nucleotide composition can introduce a false
signal. The signal will be degraded as DNA sequences AMELIORATE over time, making ancient HGT difficult to detect.

Unusual species distributions of genes

The presence, in a particular species, of one or more genes that are also found in distant relatives but not in closely related species indicates the occurrence of HGT. If the genes are physically close (for example, if they are in the same operon), HGT might have facilitated the incorporation of a new biochemical pathway. However, this approach does not work for universally occurring genes. Furthermore, the gene order on the chromosome is often poorly conserved even among closely related species. The alternative hypothesis of extensive gene loss in the intervening lineages must also be considered.

Homology
Significant homology of a gene to that of a distantly related species, as determined using the database search tool BLAST
(see online link to National Center for Biotechnology Information) (REF. 29), is a rapid method to detect HGT. However,
BLAST similarity scores do not always accurately indicate evolutionary relationships. In addition, the size and type of the
database can affect the results obtained by this method.

 

[Squeegee Beckenheim]

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

Genes are part of DNA. I don't understand what you mean by "get in to". Are you asking how DNA first formed?

combine this with the apparent immutability of HOX genes and you are going to have to come to one of the following 2 conclusions.
1. each lifeform has a unique origin.
2. life evolved from a pool of organisms, not from a single source.

How do these conclusions logically follow from your premises?

 

[In situ]

I'm sure whois would be happy to explain to anybody who asks.

Whois tried but failed in your case. Granted Whois is sometimes unclear, but that is why one need to read Whois comments a few times and try to figure out what Whois actually mean. It is not always what first comes to mind.

Or, indeed, I'm sure anybody who is curious can use google.

Nobody force you to reply or even read Whois' questions. The overall impression from your reply makes me feel you are trying to push your own opinions and knowledge onto others because you seams to be of the opinion you are entitled to do so? (Don't take me wrong, I am doing the same - but for other reasons).

Because people discussion evolution should understand what evolution is. That should be a bare minimum for any honest discussion of the subject.

It is your opinion that people need to understand the subject they discuss. I agree it might be annoying with such people, and one may think they should know better. But people will continue do regards what you think about it. Because people are entitled to be ignorant, or stupid or lie. You can tell you disagree, you can tell they are ignorant and that they do not understand, you can tell you don't like people with no knowledge discussing a subject, you can tell you dislike intellectual dishonesty etc, but you are not entitled to demand anyone to know anything, not being(acting) stupid.

Why is that?

It is for the simple reason that a knowledge threshold then need to be set. But why should that threshold be set just below your level of knowledge? What if somebody suggest the threshold to be set a bit above your level of knowledge? I don't think you would like that, right?
The second reason is; what if you are wrong? If you don't like to listen to people who knows nothing, or have other opinions or seam to have insane ideas about reality, or claims you are plain and utterly wrong, then it begs the question why you are here in the first place?

And anybody who is genuinely and honestly seeking to learn about the subject should be happy to be corrected when they make a mistake. That is, after all, how you learn.

I agree, but that is another issue.

I don't see any other mistakes in the OP which require correcting. If you can see one, I'd appreciate you pointing it out.

I already pointed this out two times; this is the third and last time I try:

The usage of the word of 'scientists' in the question is inappropriate (it implicitly refers to biologists - but if one like to cut hairs one can complain about that as well). I didn't really care about it, but when I saw your effort to police Whois and create a straw man it became an issue to me. It wasn't fair what you did, none of it was... it is a matter of justice to me.

 

[In situ]

If there is to be a discussion about scientific issues, then everybody involved in the discussion should a) use the correct terminology, and b) understand what that terminology means.

That is your opinion yes. I disagrees with your oppinion.

 

[bhsmte]

That is your opinion yes. I disagrees with your oppinion.

Why do you think it is a bad thing, to have any discussion about science matters, include a discussion about correct terminology and their meaning?

I would think, this would make the discussion more fruitful.

 

[Squeegee Beckenheim]

Whois tried but failed in your case.

whois has not tried to explain HGT to anybody in this thread. And I already know what it is and do not need it explained.

I think you're confused.

Nobody force you to reply or even read Whois' questions.

Can the same logic not be applied to you and my posts? At least I was correcting an important, fundamental error, and then trying to get the right context from which to answer the questions asked, rather than just telling someone off.

The overall impression from your reply makes me feel you are trying to push your own opinions and knowledge onto others because you seams to be of the opinion you are entitled to do so? (Don't take me wrong, I am doing the same - but for other reasons).

That evolution is something that happens at the population level rather than to an individual gene is not an opinion. And what is wrong with trying to share knowledge? Especially if you're sharing it with someone who wants to know more about that particular subject.

It is your opinion that people need to understand the subject they discuss.

It's the only possible way to have informed discussion, surely?

But people will continue do regards what you think about it.

I have never implied differently. And, if people do post from a position of ignorance then I will provide the correct information, if I can. That way, if they are so inclined, they can learn and become informed about the subject (as can people reading the thread).

I find it odd that you appear to be arguing against the idea of people learning things.

Why is that?

I don't know. It's your straw man. You made it up. You tell me why.

What if somebody suggest the threshold to be set a bit above your level of knowledge? I don't think you would like that, right?

Personally, I love learning things. If people correct me when I've made a mistake I think it's great. I end up a little more educated for it, and education is a wonderful thing. Knowledge is a wonderful thing, and I appreciate people sharing theirs with me.

I honestly can't imagine why anybody would think differently. Why would anybody prefer to remain ignorant? Especially on a subject that they're interested in learning about. That just makes no sense.

The second reason is; what if you are wrong?

Then I would hope someone would correct me.

In this case, however, I am not wrong. Evolution is not something that happens to individual genes, it is something that happens to populations.

I agree, but that is another issue.

No, it's exactly the issue we're discussing. whois started a thread seeking to learn about evolution. In the OP of that thread, he made a fundamental mistake. I corrected that mistake.

I already pointed this out two times; this is the third and last time I try:

The usage of the word of 'scientists' in the question is inappropriate (it implicitly refers to biologists - but if one like to cut hairs one can complain about that as well).

Firstly, the word "scientists" doesn't appear in the OP. Or, indeed, anywhere in this thread until you specifically mentioned it in this post.

Secondly, why would it be a mistake to refer to people who do science as scientists?

You've completely lost me with this argument. I honestly have no clue what mistake you think there is in the OP, other than the misuse of the word "evolution".

It wasn't fair what you did, none of it was... it is a matter of justice to me.

And yet in this same post you said that you agreed that it's good to correct people's
mistakes.

I have no idea what your argument is at this point. It's incoherent.

 

[In situ]

You believe that people who make fundamental mistakes about evolution are better off not knowing that they're making such mistakes?

No. I believe in a different pedagogic than you do.

I've not set whois up for anything, let alone a straw man.

Okay, but that was my impression, since you appeard not to respond to what Whois wrote.

Before any meaningful answers to his questions are possible, it's necessary to know what knowledge he already has and why he is asking

Well, my impression of Whois is; nothing admittinlgy that would confirm with science and contradict the bible. But that is no news for any creationist - because that is why they are creationist in the first place, would you not agree?

The OP appears to be starting from the assumption

I don't know what the OP's assumptions are and I don't care. I only respond to what is written so far. If there is something else we will find out, be sure about that.... It is not like we need to clean up this before lunch, right?

If I knew whether or not ....

How long have you actually dealt with creationists?

 

[bhsmte]

No. I believe in a different pedagogic than you do.



Okay, but that was my impression, since you appeard not to respond to what Whois wrote.



Well, my impression of Whois is; nothing admittinlgy that would confirm with science and contradict the bible. But that is no news for any creationist - because that is why they are creationist in the first place, would you not agree?



I don't know what the OP's assumptions are and I don't care. I only respond to what is written so far. If there is something else we will find out, be sure about that.... It is not like we need to clean up this before lunch, right?



How long have you actually dealt with creationists?

Are you saying whois is a creationist?

Whois has claimed, a concept of a God is ludicrous, if I recall correctly.

Now, whois, is clearly anti evolution and this is not difficult to comprehend, based on the selective quotes the poster uses and how the poster has constantly been tripped up in the fact, the quotes when taken in full context, don't support the posters position.

 

[In situ]

let's take the following quote as a reference to my question.
i am basically wondering how they can determine if an "ancient" gene is HG

I already told you; if it is an apple then it is an apple (HGT) and not a pear (mutation). I am sure you know what granting is, HGT is like granting. Do you understand now or do I need to take the analogy further?

 

[Squeegee Beckenheim]

How long have you actually dealt with creationists?

Right, first you seem to be telling me off because I'm not treating whois as if he's genuinely seeking information, and now you're telling me off for giving him the benefit of the doubt and treating him as if he's genuinely seeking information.

I don't think even you know what it is that you're having a go at me for.

Whatever the case may be, I'm done with this. It's tiresome, you aren't saying anything that makes any kind of sense, and it's wholly off-topic for the thread. I won't reply to you on this subject again.

 

[In situ]

Are you saying whois is a creationist?

Yes, I believe I wrote that, or did I miss to be fully clear on that point?

whois, is clearly anti evolution

Then the alternative is creation, hence creationist. Or do you have a third alternative?

and this is not difficult to comprehend, based on the selective quotes the poster uses and how the poster has constantly been tripped up in the fact, the quotes when taken in full context, don't support the posters position.

Well, lets leave the psychoanalysis for the psychologists, and keep it simple; if you don't think life came around by natural means then you must think it came around by unnatural means. Do you agree?

 

[sfs]

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.

 

[Squeegee Beckenheim]

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.

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

 

[In situ]

Whatever the case may be, I'm done with this. It's tiresome, you aren't saying anything that makes any kind of sense, and it's wholly off-topic for the thread. I won't reply to you on this subject again.

I agree. Let's drop it.

 

[In situ]

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

First you say you don't know what the op knows no you say you know that the op know what the op says. Make up your mind please.

 

[sfs]

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

I just looked up "rhodopsin evolution" on Google Scholar, and found the following titles, among many others:
"The structural evolution of a P2Y-like G-protein-coupled receptor"
"Molecular evolution of the rhodopsin gene of marine lamprey, Petromyzon marinus"
"Rhodopsin molecular evolution in mammals inhabiting low light environments"
"The evolution and structure of aminergic G protein-coupled receptors."
"Evolution of rhodopsin ion pumps in haloarchaea"
"Molecular evolution of bat color vision genes"
"Molecular evolution of human visual pigment genes."

The list goes on, and that's just for one small family of genes. This is absolutely standard terminology in molecular evolution.

 

[bhsmte]

Yes, I believe I wrote that, or did I miss to be fully clear on that point?



Then the alternative is creation, hence creationist. Or do you have a third alternative?



Well, lets leave the psychoanalysis for the psychologists, and keep it simple; if you don't think life came around by natural means then you must think it came around by unnatural means. Do you agree?

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

Unless they believe, aliens did the creating.