Are these the "SAME GENES"?

[tas8831]

Here, a creationist wrote:

Look at this alleged “same gene” across species...an ALLEGED shared gene...

Human Gene HDLBP (uc002wba.1) a 110-kD protein that specifically binds HDL molecules, which functions in the removal of cellular cholesteral...it is a section 87,092 base pairs long

Rat Gene Hdlbp (NM_172039) which is only 68, 238 base pairs long performs a similar function but apparently not identically.

The allegedly the “SAME GENE” in Yeast, S. cerevisiae Gene SCP160 (YJL080C) functions differently and is primary to cell division, and only has 3,669 base pairs.

Finally, the alleged “SAME GENE” in D. Melongaster, Gene Dp1 (CG5170-RB). Having 9119 base pairs (3 times that of Yeast) seems to do nothing!

Now as fit as the hypothesis based explanation appears, the actual data shows us they actually are nothing alike...they are different in size AND FUNCTION...yet billed as “commonly shared” in the rhetoric.

Well since what I am telling you is true, how did they convince so many?​

I omitted inflammatory and insulting rhetoric from the rest of the that post - and I will not detail my findings regarding the plagiarism in the depiction of those genes here, but I will add that the creationist author of that post later expanded on his assertion, indicating that yes, he felt these could not possibly be the 'SAME GENES' because their sequence lengths were not identical.

When I had mentioned that the sequence length differences could be due to things like different start/stop sites of the sequencing process, etc., my suggestion was dismissed out of hand.

So let us take a look at the human reference gene indicated - Human Gene HDLBP. This gene is also known as the Vigilin gene.

This gene has been sequenced a number of times in humans - different researchers sequenced different parts for different studies, the genome consortia sequenced the chromosomes more than once, etc.

So, here are 2 reports for that gene that I found (there are many more):

CCDS Report for Consensus CDS

and

CCDS Report for Consensus CDS

Keep in mind, those reports are for humans, and for the SAME GENE.

And yet, in the first one, the nucleotide sequence is given as 3708*, and the amino acid sequence is given as 1235.

In the second, the nucleotide sequence is given as 3807, the amino acid sequence given as 1268.

Same gene. Same protein. 2 different gene lengths, 2 different protein lengths, same species.


So, what can we glean from this?

Possibilities:

1. One sequence contains sequencing errors.
2. Both sequences contain sequencing errors.
3. Human SAME GENES are not necessarily identical.
4. Different proteins (i.e., proteins with differing amino acid sequence) can perform the same task
5. People arguing that if genes are not the exact same length as published in various databases and so cannot be the SAME GENES do not understand how to analyze genetic data.
6. People arguing that if genes are not the exact same length as published in various databases and so cannot be the SAME GENES do understand how to analyze genetic data but are content to misrepresent it all in order to score rhetorical points
7 People arguing that if genes are not the exact same length as published in various databases and so cannot be the SAME GENES thought they understood how to analyze genetic data, and upon learning otherwise, sought to save face by doubling down.
8. Combinations of the above.



*these represent the coding sequence only - the longer sequence length indicated in the original post as quoted refers to what is considered the length of the gene including introns and flanking sequence.

 

[Jimmy D]

 

[FrumiousBandersnatch]

Here, a creationist wrote:

Look at this alleged “same gene” across species...an ALLEGED shared gene...

Human Gene HDLBP (uc002wba.1) a 110-kD protein that specifically binds HDL molecules, which functions in the removal of cellular cholesteral...it is a section 87,092 base pairs long

Rat Gene Hdlbp (NM_172039) which is only 68, 238 base pairs long performs a similar function but apparently not identically.

The allegedly the “SAME GENE” in Yeast, S. cerevisiae Gene SCP160 (YJL080C) functions differently and is primary to cell division, and only has 3,669 base pairs.

Finally, the alleged “SAME GENE” in D. Melongaster, Gene Dp1 (CG5170-RB). Having 9119 base pairs (3 times that of Yeast) seems to do nothing!

Now as fit as the hypothesis based explanation appears, the actual data shows us they actually are nothing alike...they are different in size AND FUNCTION...yet billed as “commonly shared” in the rhetoric.

Well since what I am telling you is true, how did they convince so many?​

I omitted inflammatory and insulting rhetoric from the rest of the that post - and I will not detail my findings regarding the plagiarism in the depiction of those genes here, but I will add that the creationist author of that post later expanded on his assertion, indicating that yes, he felt these could not possibly be the 'SAME GENES' because their sequence lengths were not identical.

When I had mentioned that the sequence length differences could be due to things like different start/stop sites of the sequencing process, etc., my suggestion was dismissed out of hand.

So let us take a look at the human reference gene indicated - Human Gene HDLBP. This gene is also known as the Vigilin gene.

This gene has been sequenced a number of times in humans - different researchers sequenced different parts for different studies, the genome consortia sequenced the chromosomes more than once, etc.

So, here are 2 reports for that gene that I found (there are many more):

CCDS Report for Consensus CDS

and

CCDS Report for Consensus CDS

Keep in mind, those reports are for humans, and for the SAME GENE.

And yet, in the first one, the nucleotide sequence is given as 3708*, and the amino acid sequence is given as 1235.

In the second, the nucleotide sequence is given as 3807, the amino acid sequence given as 1268.

Same gene. Same protein. 2 different gene lengths, 2 different protein lengths, same species.


So, what can we glean from this?

Possibilities:

1. One sequence contains sequencing errors.
2. Both sequences contain sequencing errors.
3. Human SAME GENES are not necessarily identical.
4. Different proteins (i.e., proteins with differing amino acid sequence) can perform the same task
5. People arguing that if genes are not the exact same length as published in various databases and so cannot be the SAME GENES do not understand how to analyze genetic data.
6. People arguing that if genes are not the exact same length as published in various databases and so cannot be the SAME GENES do understand how to analyze genetic data but are content to misrepresent it all in order to score rhetorical points
7 People arguing that if genes are not the exact same length as published in various databases and so cannot be the SAME GENES thought they understood how to analyze genetic data, and upon learning otherwise, sought to save face by doubling down.
8. Combinations of the above.



*these represent the coding sequence only - the longer sequence length indicated in the original post as quoted refers to what is considered the length of the gene including introns and flanking sequence.

Seems to me that the obvious question is, in what sense are they the same gene(s)? i.e. what does 'the same' mean in this context?

 

[tas8831]

Seems to me that the obvious question is, in what sense are they the same gene(s)? i.e. what does 'the same' mean in this context?

Homologous. But creationists do not accept homology.

 

[sfs]

Homologous.

As shown by comparison of the sequence. If you just blast one of the longer human exons, you'll find obvious hits in the rat and fruit fly genes. (Yeast is too distantly related for trivial methods to work.)

 

[FrumiousBandersnatch]

Homologous. But creationists do not accept homology.

Homologous in what respect?

(playing 'man on the Clapham omnibus' here)

 

[tas8831]

Homologous in what respect?

(playing 'man on the Clapham omnibus' here)

via shared ancestry.

 

[FrumiousBandersnatch]

via shared ancestry.

OK, so although the gene sequences are different and their products are different, we know they're 'the same' gene because they clearly derive from a common ancestral gene (presumably in the same location and with sequences common to both) ?

Just trying to clarify.

 

[tas8831]

OK, so although the gene sequences are different and their products are different, we know they're 'the same' gene because they clearly derive from a common ancestral gene (presumably in the same location and with sequences common to both) ?

Just trying to clarify.

Well... They are both humans, so I sort of guess that humans have a common ancestor.

But these cannot be the 'same genes' according to creationists, because their reported sequences are not identical lengths.

 

[FrumiousBandersnatch]

Well... They are both humans, so I sort of guess that humans have a common ancestor.

Maybe I've misunderstood the issue; I'm trying to establish what makes two genes, that have different sequences and produce different products, the 'same' gene. If it was only that they're both human genes, then we could call any two human genes 'the same'.

So I'm asking what makes them identifiably the same gene - is it a shared location in the genome and some shared sequences (or an ancestral gene in that location with sequences that appear in both derived genes) ?

But these cannot be the 'same genes' according to creationists, because their reported sequences are not identical lengths.

In that case it's reasonable for creationists to ask what makes them the same, which is what I've been trying to discover.

 

[tas8831]

Maybe I've misunderstood the issue; I'm trying to establish what makes two genes, that have different sequences and produce different products, the 'same' gene. If it was only that they're both human genes, then we could call any two human genes 'the same'.

They are both identified as HDLBP. They both occupy the same locus.

So I'm asking what makes them identifiably the same gene - is it a shared location in the genome and some shared sequences (or an ancestral gene in that location with sequences that appear in both derived genes) ?

In that case it's reasonable for creationists to ask what makes them the same, which is what I've been trying to discover.

The only difference between them is the length of the sequence. Upon doing an EMBOSS comparison, they are identical except for an indel in one of them.

I suspect, but have not checked, that the aa sequence described for each was generated via an algorithm as opposed to an actual assay, accounting for the aa sequence differences.

My actual point was that it is not reasonable to judge whether or not genes in compared taxa are the 'SAME GENES' (to borrow pshun's depiction of them) based solely on their published sequence length, which is what he was basing his conclusion on (the there really are no homologous genes).

 

[FrumiousBandersnatch]

They are both identified as HDLBP. They both occupy the same locus.

The only difference between them is the length of the sequence. Upon doing an EMBOSS comparison, they are identical except for an indel in one of them.

I suspect, but have not checked, that the aa sequence described for each was generated via an algorithm as opposed to an actual assay, accounting for the aa sequence differences.

OK, thanks, that explains it all pretty clearly. I don't see a reasonable argument for them not being considered the same gene.

My actual point was that it is not reasonable to judge whether or not genes in compared taxa are the 'SAME GENES' (to borrow pshun's depiction of them) based solely on their published sequence length, which is what he was basing his conclusion on (the there really are no homologous genes).

Yes, quite; I just wanted to clarify precisely what it means to be called 'the same' gene in this context, so it would be obvious why they were considered to be the same gene.

Thanks for your patience!