On Mon, 4 Mar 2024 10:11:08 -0600, the following appeared in
talk.origins, posted by DB Cates <cates_db@hotmail.com>:

>On 2024-03-03 11:49 PM, Bob Casanova wrote:
>> On Sun, 3 Mar 2024 18:13:12 -0600, the following appeared in
>> talk.origins, posted by DB Cates <cates_db@hotmail.com>:
>>
>>> On 2024-03-03 1:22 PM, Bob Casanova wrote:
>>>> On Sat, 2 Mar 2024 23:45:12 -0600, the following appeared in
>>>> talk.origins, posted by DB Cates <cates_db@hotmail.com>:
>>>>
>>>>> On 2024-03-02 10:56 PM, Bob Casanova wrote:
>>>>>> On Fri, 1 Mar 2024 13:10:52 -0600, the following appeared in
>>>>>> talk.origins, posted by DB Cates <cates_db@hotmail.com>:
>>>>>>
>>>>>>> On 2024-03-01 10:49 AM, Bob Casanova wrote:
>>>>>>>> On Thu, 29 Feb 2024 22:31:16 -0600, the following appeared
>>>>>>>> in talk.origins, posted by DB Cates <cates_db@hotmail.com>:
>>>>>>>>
>>>>>>>>> On 2024-02-29 1:17 PM, Bob Casanova wrote:
>>>>>>>>>> On Thu, 29 Feb 2024 08:05:05 -0800, the following appeared
>>>>>>>>>> in talk.origins, posted by erik simpson
>>>>>>>>>> <eastside.erik@gmail.com>:
>>>>>>>>>>
>>>>>>>>>>> On 2/29/24 3:55 AM, RonO wrote:
>>>>>>>>>>>> On 2/28/2024 5:41 PM, erik simpson wrote:
>>>>>>>>>>>>> On 2/28/24 3:21 PM, RonO wrote:
>>>>>>>>>>>>>> It turns out that the common ancestor that between gibbons and the
>>>>>>>>>>>>>> great apes had an ALU transposon jump into the intron between exon 6
>>>>>>>>>>>>>> and exon 7 of the TBXT gene.  There was already an transposon between
>>>>>>>>>>>>>> exon 5 and exon 6.  Monkeys and apes have the ALU insertion in the
>>>>>>>>>>>>>> intron between exon 5 and exon 6, but the apes have the second ALU
>>>>>>>>>>>>>> insertion in the intron between exons 6 and 7.  So it turns out that
>>>>>>>>>>>>>> apes still have the exon 6 sequence in the TBXT gene, but the two ALU
>>>>>>>>>>>>>> transposon sequences form a stem loop structure in the RNA transcript
>>>>>>>>>>>>>> that messes up processing so exon 6 is skipped and exon 5 is stuck to
>>>>>>>>>>>>>> exon 7 in the final ape mRNA.  So part of what makes us human is due
>>>>>>>>>>>>>> to a transposon insertion mutation into the TBXT gene.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> The insertion happened in the common ancestor of all extant apes, and
>>>>>>>>>>>>>> has been retained by the extant ape lineages.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> https://www.nature.com/articles/s41586-024-07095-8
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> The article is open access.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Ron Okimoto
>>>>>>>>>>>>>>
>>>>>>>>>>>>> Another effect of this modification is also "Moreover, mice expressing
>>>>>>>>>>>>> the exon-skipped Tbxt isoform develop neural tube defects, a condition
>>>>>>>>>>>>> that affects approximately 1 in 1,000 neonates in humans10. Thus,
>>>>>>>>>>>>> tail-loss evolution may have been associated with an adaptive cost of
>>>>>>>>>>>>> the potential for neural tube defects, which continue to affect human
>>>>>>>>>>>>> health today."
>>>>>>>>>>>>>
>>>>>>>>>>>>> Evidently, the advantages of losing the tail outweigh the disadvantage
>>>>>>>>>>>>> of the neural tube defects.
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> What were the advantages?
>>>>>>>>>>>>
>>>>>>>>>>>> Some other simian lineages have lost their tails, but what is the
>>>>>>>>>>>> advantage?
>>>>>>>>>>>>
>>>>>>>>>>>> Apes did become brachiators, but other simian lineages did not, and some
>>>>>>>>>>>> simian lineages that adopted a similar lifestyle for supporting
>>>>>>>>>>>> themselves in the trees, actually developed prehensile tails as a fifth
>>>>>>>>>>>> limb for supporting themselves hanging from branches.
>>>>>>>>>>>>
>>>>>>>>>>>> For birds there was a selective advantage in terms of weight, and the
>>>>>>>>>>>> tailbones degenerated and fused into a small nub.  The tail was not
>>>>>>>>>>>> lost, and birds still have a nub that they call a pygostyle that still
>>>>>>>>>>>> supports the muscles that control the tail movements and so the feathers
>>>>>>>>>>>> associated with the tail.
>>>>>>>>>>>>
>>>>>>>>>>>> Ron Okimoto
>>>>>>>>>>>>
>>>>>>>>>>> I believe the article mentions that bipedalism is speculated to have
>>>>>>>>>>> made bipedalism easier.
>>>>>>>>>>>
>>>>>>>>>> No causal link there... ;-)
>>>>>>>>>>>
>>>>>>>>>>> That could be a just-so story, but mutations
>>>>>>>>>>> that are adopted and fixed within a population must have advantages that
>>>>>>>>>>> outweigh potential advantages.
>>>>>>>>>>>
>>>>>>>>>> Indubitably.
>>>>>>>>>>>
>>>>>>>>> Really? Drift is out?
>>>>>>>>>
>>>>>>>> No. But I didn't say it was; my comment was about advantages
>>>>>>>> vs. potential advantages, the "bird in the hand" idea. I
>>>>>>>> may, of course, be mistaken; I'm not a biologist, nor have I
>>>>>>>> ever played one on TV. And my days of staying in chain
>>>>>>>> motels/hotels are behind me.
>>>>>>>>>
>>>>>>> The math says that neutral mutations become fixed at the mutation rate
>>>>>>> and even slightly deleterious mutation can occasionally become fixed.
>>>>>>>
>>>>>> Not disputed.
>>>>>>>
>>>>>>> and why is it "indubitable" some fixed mutation ("bird in the hand"?)
>>>>>>> have advantages that outweigh that of some mutation that didn't happen?
>>>>>>> (Assuming that "potential advantage" is due to some 'potential mutation')
>>>>>>>
>>>>>> Because an existing advantage outweighs one which doesn't
>>>>>> (yet, or possibly ever) exist? Seems pretty straightforward
>>>>>> to me...
>>>>>>>
>>>>> Why must any fixed mutation have any advantage at all. It might have a
>>>>> small disadvantage, which would be *less* than a non-existent mutation. (:p
>>>>>
>>>> OK, my assumption was that we were talking about beneficial
>>>> mutations/traits; that's what "advantage" means to me. If
>>>> advantage includes deleterious traits (IOW, DISadvantages),
>>>> I'll have to bow out.
>>>
>>> More succinctly (I hope); It seemed to me that that we were talking
>>> about 'fixed mutations' and the 'advantageous' bit is what I was
>>> complaining about.
>>>
>> OK. I keyed on the "advantages" part, which by definition
>> means beneficial changes (although mutations which become
>> fixed aren't usually egregiously disadvantageous or they
>> wouldn't become fixed).
>>>>>
>And I keyed on the *"must"*"have advantages".
>
OK. And since this is going nowhere I can only wish you a
good day. *Not* intended sarcastically.
>
>>>>>>>>>>> Aside from posture I can't think of what
>>>>>>>>>>> the advantages might be. Pants are easier? (Note to literalists: I
>>>>>>>>>>> don't seriously suggest that.)
>>>>>>>>>
>>>>>>>>> --
>>>>>>>
>>>>>>> --
>>>>>
>>>>> --
>>>
>>> --
>
>--
--

On Wed, 28 Feb 2024 17:21:19 -0600, RonO <rokimoto@cox.net> wrote:

>It turns out that the common ancestor that between gibbons and the great
>apes had an ALU transposon jump into the intron between exon 6 and exon
>7 of the TBXT gene. There was already an transposon between exon 5 and
>exon 6. Monkeys and apes have the ALU insertion in the intron between
>exon 5 and exon 6, but the apes have the second ALU insertion in the
>intron between exons 6 and 7. So it turns out that apes still have the
>exon 6 sequence in the TBXT gene, but the two ALU transposon sequences
>form a stem loop structure in the RNA transcript that messes up
>processing so exon 6 is skipped and exon 5 is stuck to exon 7 in the
>final ape mRNA. So part of what makes us human is due to a transposon
>insertion mutation into the TBXT gene.
>
>The insertion happened in the common ancestor of all extant apes, and
>has been retained by the extant ape lineages.
>
>https://www.nature.com/articles/s41586-024-07095-8
>
>The article is open access.
>
>Ron Okimoto

In the following Youtube video, Gutsick Gibbon provides a 33-minute
anthropological perspective about the same article:

<https://www.youtube.com/watch?v=dImLB0ePWR8>

It turns out that losing their tails had happened to at least one
other primate group, between lorises and bushbabies. It would be
interesting to see if the tailless lorises have a similar ALU
transposon in the TBXT gene.

--
To know less than we don't know is the nature of most knowledge

On 3/9/24 7:16 AM, jillery wrote:
> On Wed, 28 Feb 2024 17:21:19 -0600, RonO <rokimoto@cox.net> wrote:
>
>> It turns out that the common ancestor that between gibbons and the great
>> apes had an ALU transposon jump into the intron between exon 6 and exon
>> 7 of the TBXT gene. There was already an transposon between exon 5 and
>> exon 6. Monkeys and apes have the ALU insertion in the intron between
>> exon 5 and exon 6, but the apes have the second ALU insertion in the
>> intron between exons 6 and 7. So it turns out that apes still have the
>> exon 6 sequence in the TBXT gene, but the two ALU transposon sequences
>> form a stem loop structure in the RNA transcript that messes up
>> processing so exon 6 is skipped and exon 5 is stuck to exon 7 in the
>> final ape mRNA. So part of what makes us human is due to a transposon
>> insertion mutation into the TBXT gene.
>>
>> The insertion happened in the common ancestor of all extant apes, and
>> has been retained by the extant ape lineages.
>>
>> https://www.nature.com/articles/s41586-024-07095-8
>>
>> The article is open access.
>>
>> Ron Okimoto
>
>
> In the following Youtube video, Gutsick Gibbon provides a 33-minute
> anthropological perspective about the same article:
>
> <https://www.youtube.com/watch?v=dImLB0ePWR8>
>
> It turns out that losing their tails had happened to at least one
> other primate group, between lorises and bushbabies. It would be
> interesting to see if the tailless lorises have a similar ALU
> transposon in the TBXT gene.
>
> --
> To know less than we don't know is the nature of most knowledge
>
It seems that the Lorax also is tailless. I doubt it has anything to do
with ALU.

On Sat, 9 Mar 2024 09:45:44 -0800, erik simpson
<eastside.erik@gmail.com> wrote:

>On 3/9/24 7:16 AM, jillery wrote:
>> On Wed, 28 Feb 2024 17:21:19 -0600, RonO <rokimoto@cox.net> wrote:
>>
>>> It turns out that the common ancestor that between gibbons and the great
>>> apes had an ALU transposon jump into the intron between exon 6 and exon
>>> 7 of the TBXT gene. There was already an transposon between exon 5 and
>>> exon 6. Monkeys and apes have the ALU insertion in the intron between
>>> exon 5 and exon 6, but the apes have the second ALU insertion in the
>>> intron between exons 6 and 7. So it turns out that apes still have the
>>> exon 6 sequence in the TBXT gene, but the two ALU transposon sequences
>>> form a stem loop structure in the RNA transcript that messes up
>>> processing so exon 6 is skipped and exon 5 is stuck to exon 7 in the
>>> final ape mRNA. So part of what makes us human is due to a transposon
>>> insertion mutation into the TBXT gene.
>>>
>>> The insertion happened in the common ancestor of all extant apes, and
>>> has been retained by the extant ape lineages.
>>>
>>> https://www.nature.com/articles/s41586-024-07095-8
>>>
>>> The article is open access.
>>>
>>> Ron Okimoto
>>
>>
>> In the following Youtube video, Gutsick Gibbon provides a 33-minute
>> anthropological perspective about the same article:
>>
>> <https://www.youtube.com/watch?v=dImLB0ePWR8>
>>
>> It turns out that losing their tails had happened to at least one
>> other primate group, between lorises and bushbabies. It would be
>> interesting to see if the tailless lorises have a similar ALU
>> transposon in the TBXT gene.
>>
>It seems that the Lorax also is tailless. I doubt it has anything to do
>with ALU.

The Lorax is a clever tale. Perhaps if Dr. Seuss knew more genetics,
his tale could have informed us about being tailless.

--
To know less than we don't know is the nature of most knowledge

On 29/02/2024 16:06, erik simpson wrote:
> On 2/29/24 4:29 AM, FromTheRafters wrote:
>> It happens that RonO formulated :
>>> On 2/28/2024 5:41 PM, erik simpson wrote:
>>>> On 2/28/24 3:21 PM, RonO wrote:
>>>>> It turns out that the common ancestor that between gibbons and the
>>>>> great apes had an ALU transposon jump into the intron between exon
>>>>> 6 and exon 7 of the TBXT gene.  There was already an transposon
>>>>> between exon 5 and exon 6.  Monkeys and apes have the ALU insertion
>>>>> in the intron between exon 5 and exon 6, but the apes have the
>>>>> second ALU insertion in the intron between exons 6 and 7.  So it
>>>>> turns out that apes still have the exon 6 sequence in the TBXT
>>>>> gene, but the two ALU transposon sequences form a stem loop
>>>>> structure in the RNA transcript that messes up processing so exon 6
>>>>> is skipped and exon 5 is stuck to exon 7 in the final ape mRNA.  So
>>>>> part of what makes us human is due to a transposon insertion
>>>>> mutation into the TBXT gene.
>>>>>
>>>>> The insertion happened in the common ancestor of all extant apes,
>>>>> and has been retained by the extant ape lineages.
>>>>>
>>>>> https://www.nature.com/articles/s41586-024-07095-8
>>>>>
>>>>> The article is open access.
>>>>>
>>>>> Ron Okimoto
>>>>>
>>>> Another effect of this modification is also "Moreover, mice
>>>> expressing the exon-skipped Tbxt isoform develop neural tube
>>>> defects, a condition that affects approximately 1 in 1,000 neonates
>>>> in humans10. Thus, tail-loss evolution may have been associated with
>>>> an adaptive cost of the potential for neural tube defects, which
>>>> continue to affect human health today."
>>>>
>>>> Evidently, the advantages of losing the tail outweigh the
>>>> disadvantage of the neural tube defects.
>>>>
>>>
>>> What were the advantages?
>>>
>>> Some other simian lineages have lost their tails, but what is the
>>> advantage?
>>>
>>> Apes did become brachiators, but other simian lineages did not, and
>>> some simian lineages that adopted a similar lifestyle for supporting
>>> themselves in the trees, actually developed prehensile tails as a
>>> fifth limb for supporting themselves hanging from branches.
>>>
>>> For birds there was a selective advantage in terms of weight, and the
>>> tailbones degenerated and fused into a small nub.  The tail was not
>>> lost, and birds still have a nub that they call a pygostyle that
>>> still supports the muscles that control the tail movements and so the
>>> feathers associated with the tail.
>>>
>>> Ron Okimoto
>>
>> I suppose sitting is much easier without a tail.
>>
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417348/
>>
> That can't be it.  My dog has a long tail and has no trouble sitting.

A dog can adjust their tail. The article refers
to a Young man who had one and didn't know what
to do with it, and who indeed was having trouble
sitting with comfort.

I can't read this style of writing well enough
to tell whether doctors removed the tail, or
only adjusted the bones that it was attached to.

On 01/03/2024 05:31, DB Cates wrote:
> On 2024-02-29 1:17 PM, Bob Casanova wrote:
>> On Thu, 29 Feb 2024 08:05:05 -0800, the following appeared
>> in talk.origins, posted by erik simpson
>> <eastside.erik@gmail.com>:
>>
>>> On 2/29/24 3:55 AM, RonO wrote:
>>>> On 2/28/2024 5:41 PM, erik simpson wrote:
>>>>> On 2/28/24 3:21 PM, RonO wrote:
>>>>>> It turns out that the common ancestor that between gibbons and the
>>>>>> great apes had an ALU transposon jump into the intron between exon 6
>>>>>> and exon 7 of the TBXT gene.  There was already an transposon between
>>>>>> exon 5 and exon 6.  Monkeys and apes have the ALU insertion in the
>>>>>> intron between exon 5 and exon 6, but the apes have the second ALU
>>>>>> insertion in the intron between exons 6 and 7.  So it turns out that
>>>>>> apes still have the exon 6 sequence in the TBXT gene, but the two ALU
>>>>>> transposon sequences form a stem loop structure in the RNA transcript
>>>>>> that messes up processing so exon 6 is skipped and exon 5 is stuck to
>>>>>> exon 7 in the final ape mRNA.  So part of what makes us human is due
>>>>>> to a transposon insertion mutation into the TBXT gene.
>>>>>>
>>>>>> The insertion happened in the common ancestor of all extant apes, and
>>>>>> has been retained by the extant ape lineages.
>>>>>>
>>>>>> https://www.nature.com/articles/s41586-024-07095-8
>>>>>>
>>>>>> The article is open access.
>>>>>>
>>>>>> Ron Okimoto
>>>>>>
>>>>> Another effect of this modification is also "Moreover, mice expressing
>>>>> the exon-skipped Tbxt isoform develop neural tube defects, a condition
>>>>> that affects approximately 1 in 1,000 neonates in humans10. Thus,
>>>>> tail-loss evolution may have been associated with an adaptive cost of
>>>>> the potential for neural tube defects, which continue to affect human
>>>>> health today."
>>>>>
>>>>> Evidently, the advantages of losing the tail outweigh the disadvantage
>>>>> of the neural tube defects.
>>>>>
>>>>
>>>> What were the advantages?
>>>>
>>>> Some other simian lineages have lost their tails, but what is the
>>>> advantage?
>>>>
>>>> Apes did become brachiators, but other simian lineages did not, and
>>>> some
>>>> simian lineages that adopted a similar lifestyle for supporting
>>>> themselves in the trees, actually developed prehensile tails as a fifth
>>>> limb for supporting themselves hanging from branches.
>>>>
>>>> For birds there was a selective advantage in terms of weight, and the
>>>> tailbones degenerated and fused into a small nub.  The tail was not
>>>> lost, and birds still have a nub that they call a pygostyle that still
>>>> supports the muscles that control the tail movements and so the
>>>> feathers
>>>> associated with the tail.
>>>>
>>>> Ron Okimoto
>>>>
>>> I believe the article mentions that bipedalism is speculated to have
>>> made bipedalism easier.
>>>
>> No causal link there... ;-)
>>>
>>> That could be a just-so story, but mutations
>>> that are adopted and fixed within a population must have advantages that
>>> outweigh potential advantages.
>>>
>> Indubitably.
>>>
> Really? Drift is out?
>

I don't know if drift is ever out but is it particularly plausible in
the case of tail loss, something that seems really rare in tetrapods?
Like, what lineages actually lost their tails - like, really lost, not
"reduced" or "replaced by a non-bony appendage that serves a taily
function": frogs, apes, manx cats... bears are maybe on their way... who
else?

Not to mention the article suggests tail loss could be associated with
neural tube defects, which would definitely make drift much less likely.

>>> Aside from posture I can't think of what
>>> the advantages might be.  Pants are easier? (Note to literalists: I
>>> don't seriously suggest that.)
>

On 09/03/2024 18:45, erik simpson wrote:
> On 3/9/24 7:16 AM, jillery wrote:
>> On Wed, 28 Feb 2024 17:21:19 -0600, RonO <rokimoto@cox.net> wrote:
>>
>>> It turns out that the common ancestor that between gibbons and the great
>>> apes had an ALU transposon jump into the intron between exon 6 and exon
>>> 7 of the TBXT gene.  There was already an transposon between exon 5 and
>>> exon 6.  Monkeys and apes have the ALU insertion in the intron between
>>> exon 5 and exon 6, but the apes have the second ALU insertion in the
>>> intron between exons 6 and 7.  So it turns out that apes still have the
>>> exon 6 sequence in the TBXT gene, but the two ALU transposon sequences
>>> form a stem loop structure in the RNA transcript that messes up
>>> processing so exon 6 is skipped and exon 5 is stuck to exon 7 in the
>>> final ape mRNA.  So part of what makes us human is due to a transposon
>>> insertion mutation into the TBXT gene.
>>>
>>> The insertion happened in the common ancestor of all extant apes, and
>>> has been retained by the extant ape lineages.
>>>
>>> https://www.nature.com/articles/s41586-024-07095-8
>>>
>>> The article is open access.
>>>
>>> Ron Okimoto
>>
>>
>> In the following Youtube video, Gutsick Gibbon provides a 33-minute
>> anthropological perspective about the same article:
>>
>> <https://www.youtube.com/watch?v=dImLB0ePWR8>
>>
>> It turns out that losing their tails had happened to at least one
>> other primate group, between lorises and bushbabies.  It would be
>> interesting to see if the tailless lorises have a similar ALU
>> transposon in the TBXT gene.
>>
>> --
>> To know less than we don't know is the nature of most knowledge
>>
> It seems that the Lorax also is tailless.  I doubt it has anything to do
> with ALU.
>

Isn't the Lorax an ape though? Even a hominid, as it has hands AND feet
- but I suppose the latter might be the kind of trait that could evolve
convergently in any ape group that becomes ground-based & bipedal.

On 2024-04-05 3:56 AM, Arkalen wrote:
> On 01/03/2024 05:31, DB Cates wrote:
>> On 2024-02-29 1:17 PM, Bob Casanova wrote:
>>> On Thu, 29 Feb 2024 08:05:05 -0800, the following appeared
>>> in talk.origins, posted by erik simpson
>>> <eastside.erik@gmail.com>:
>>>
>>>> On 2/29/24 3:55 AM, RonO wrote:
>>>>> On 2/28/2024 5:41 PM, erik simpson wrote:
>>>>>> On 2/28/24 3:21 PM, RonO wrote:
>>>>>>> It turns out that the common ancestor that between gibbons and the
>>>>>>> great apes had an ALU transposon jump into the intron between exon 6
>>>>>>> and exon 7 of the TBXT gene.  There was already an transposon
>>>>>>> between
>>>>>>> exon 5 and exon 6.  Monkeys and apes have the ALU insertion in the
>>>>>>> intron between exon 5 and exon 6, but the apes have the second ALU
>>>>>>> insertion in the intron between exons 6 and 7.  So it turns out that
>>>>>>> apes still have the exon 6 sequence in the TBXT gene, but the two
>>>>>>> ALU
>>>>>>> transposon sequences form a stem loop structure in the RNA
>>>>>>> transcript
>>>>>>> that messes up processing so exon 6 is skipped and exon 5 is
>>>>>>> stuck to
>>>>>>> exon 7 in the final ape mRNA.  So part of what makes us human is due
>>>>>>> to a transposon insertion mutation into the TBXT gene.
>>>>>>>
>>>>>>> The insertion happened in the common ancestor of all extant apes,
>>>>>>> and
>>>>>>> has been retained by the extant ape lineages.
>>>>>>>
>>>>>>> https://www.nature.com/articles/s41586-024-07095-8
>>>>>>>
>>>>>>> The article is open access.
>>>>>>>
>>>>>>> Ron Okimoto
>>>>>>>
>>>>>> Another effect of this modification is also "Moreover, mice
>>>>>> expressing
>>>>>> the exon-skipped Tbxt isoform develop neural tube defects, a
>>>>>> condition
>>>>>> that affects approximately 1 in 1,000 neonates in humans10. Thus,
>>>>>> tail-loss evolution may have been associated with an adaptive cost of
>>>>>> the potential for neural tube defects, which continue to affect human
>>>>>> health today."
>>>>>>
>>>>>> Evidently, the advantages of losing the tail outweigh the
>>>>>> disadvantage
>>>>>> of the neural tube defects.
>>>>>>
>>>>>
>>>>> What were the advantages?
>>>>>
>>>>> Some other simian lineages have lost their tails, but what is the
>>>>> advantage?
>>>>>
>>>>> Apes did become brachiators, but other simian lineages did not, and
>>>>> some
>>>>> simian lineages that adopted a similar lifestyle for supporting
>>>>> themselves in the trees, actually developed prehensile tails as a
>>>>> fifth
>>>>> limb for supporting themselves hanging from branches.
>>>>>
>>>>> For birds there was a selective advantage in terms of weight, and the
>>>>> tailbones degenerated and fused into a small nub.  The tail was not
>>>>> lost, and birds still have a nub that they call a pygostyle that still
>>>>> supports the muscles that control the tail movements and so the
>>>>> feathers
>>>>> associated with the tail.
>>>>>
>>>>> Ron Okimoto
>>>>>
>>>> I believe the article mentions that bipedalism is speculated to have
>>>> made bipedalism easier.
>>>>
>>> No causal link there... ;-)
>>>>
>>>> That could be a just-so story, but mutations
>>>> that are adopted and fixed within a population must have advantages
>>>> that
>>>> outweigh potential advantages.
>>>>
>>> Indubitably.
>>>>
>> Really? Drift is out?
>>
>
> I don't know if drift is ever out but is it particularly plausible in
> the case of tail loss, something that seems really rare in tetrapods?
> Like, what lineages actually lost their tails - like, really lost, not
> "reduced" or "replaced by a non-bony appendage that serves a taily
> function": frogs, apes, manx cats... bears are maybe on their way... who
> else?
>
Well, my reply was not specific to the 'tailless' idea but rather to the
more general statement "mutations that are adopted and fixed within a
population must have advantages that outweigh potential advantages." and
the "Indubitably." reply.
However, you seem to making the claim that 'rare' fixed mutations are
less likely to be due to drift. It would seem to me that common (over
many lineages) fixed mutations, even if not identical but responsible
for very similar morphology, are almost certainly due to selection. Rare
fixed mutations that have not been *demonstrated* to be associated with
enhanced reproductive success are more likely to be due to drift.

> Not to mention the article suggests tail loss could be associated with
> neural tube defects, which would definitely make drift much less likely.
>
Could you be more explicit here?

>>>> Aside from posture I can't think of what
>>>> the advantages might be.  Pants are easier? (Note to literalists: I
>>>> don't seriously suggest that.)
>>
>

--
--
Don Cates ("he's a cunning rascal" PN)

On 05/04/2024 22:07, DB Cates wrote:
>
>> Not to mention the article suggests tail loss could be associated with
>> neural tube defects, which would definitely make drift much less likely.
>>
> Could you be more explicit here?

I think that the idea is that a mutation associated with neural tube
defects is under strong enough negative selection that it would be fixed
by drift, and therefore there must be a countervailing selective
advantage to the mutation (and also selection for compensatory mutations
preventing the neural tube defects).

On the other had, the mutation has been shown to be associated with
neural tube defects in one genetic background. Assuming that the
association carries over to other genetic backgrounds is a leap.

--
alias Ernest Major

On Fri, 5 Apr 2024 11:01:34 +0200, Arkalen <arkalen@proton.me> wrote:

>On 09/03/2024 18:45, erik simpson wrote:
>> On 3/9/24 7:16 AM, jillery wrote:
>>> On Wed, 28 Feb 2024 17:21:19 -0600, RonO <rokimoto@cox.net> wrote:
>>>
>>>> It turns out that the common ancestor that between gibbons and the great
>>>> apes had an ALU transposon jump into the intron between exon 6 and exon
>>>> 7 of the TBXT gene.  There was already an transposon between exon 5 and
>>>> exon 6.  Monkeys and apes have the ALU insertion in the intron between
>>>> exon 5 and exon 6, but the apes have the second ALU insertion in the
>>>> intron between exons 6 and 7.  So it turns out that apes still have the
>>>> exon 6 sequence in the TBXT gene, but the two ALU transposon sequences
>>>> form a stem loop structure in the RNA transcript that messes up
>>>> processing so exon 6 is skipped and exon 5 is stuck to exon 7 in the
>>>> final ape mRNA.  So part of what makes us human is due to a transposon
>>>> insertion mutation into the TBXT gene.
>>>>
>>>> The insertion happened in the common ancestor of all extant apes, and
>>>> has been retained by the extant ape lineages.
>>>>
>>>> https://www.nature.com/articles/s41586-024-07095-8
>>>>
>>>> The article is open access.
>>>>
>>>> Ron Okimoto
>>>
>>>
>>> In the following Youtube video, Gutsick Gibbon provides a 33-minute
>>> anthropological perspective about the same article:
>>>
>>> <https://www.youtube.com/watch?v=dImLB0ePWR8>
>>>
>>> It turns out that losing their tails had happened to at least one
>>> other primate group, between lorises and bushbabies.  It would be
>>> interesting to see if the tailless lorises have a similar ALU
>>> transposon in the TBXT gene.
>>>
>>>
>> It seems that the Lorax also is tailless.  I doubt it has anything to do
>> with ALU.
>>
>
>Isn't the Lorax an ape though? Even a hominid, as it has hands AND feet
>- but I suppose the latter might be the kind of trait that could evolve
>convergently in any ape group that becomes ground-based & bipedal.

Apparently it depends on if Dr. Seuss drew the Lorax with shoes.

--
To know less than we don't know is the nature of most knowledge

On 05/04/2024 23:07, DB Cates wrote:
> On 2024-04-05 3:56 AM, Arkalen wrote:
>> On 01/03/2024 05:31, DB Cates wrote:
>>> On 2024-02-29 1:17 PM, Bob Casanova wrote:
>>>> On Thu, 29 Feb 2024 08:05:05 -0800, the following appeared
>>>> in talk.origins, posted by erik simpson
>>>> <eastside.erik@gmail.com>:
>>>>
>>>>> On 2/29/24 3:55 AM, RonO wrote:
>>>>>> On 2/28/2024 5:41 PM, erik simpson wrote:
>>>>>>> On 2/28/24 3:21 PM, RonO wrote:
>>>>>>>> It turns out that the common ancestor that between gibbons and the
>>>>>>>> great apes had an ALU transposon jump into the intron between
>>>>>>>> exon 6
>>>>>>>> and exon 7 of the TBXT gene.  There was already an transposon
>>>>>>>> between
>>>>>>>> exon 5 and exon 6.  Monkeys and apes have the ALU insertion in the
>>>>>>>> intron between exon 5 and exon 6, but the apes have the second ALU
>>>>>>>> insertion in the intron between exons 6 and 7.  So it turns out
>>>>>>>> that
>>>>>>>> apes still have the exon 6 sequence in the TBXT gene, but the
>>>>>>>> two ALU
>>>>>>>> transposon sequences form a stem loop structure in the RNA
>>>>>>>> transcript
>>>>>>>> that messes up processing so exon 6 is skipped and exon 5 is
>>>>>>>> stuck to
>>>>>>>> exon 7 in the final ape mRNA.  So part of what makes us human is
>>>>>>>> due
>>>>>>>> to a transposon insertion mutation into the TBXT gene.
>>>>>>>>
>>>>>>>> The insertion happened in the common ancestor of all extant
>>>>>>>> apes, and
>>>>>>>> has been retained by the extant ape lineages.
>>>>>>>>
>>>>>>>> https://www.nature.com/articles/s41586-024-07095-8
>>>>>>>>
>>>>>>>> The article is open access.
>>>>>>>>
>>>>>>>> Ron Okimoto
>>>>>>>>
>>>>>>> Another effect of this modification is also "Moreover, mice
>>>>>>> expressing
>>>>>>> the exon-skipped Tbxt isoform develop neural tube defects, a
>>>>>>> condition
>>>>>>> that affects approximately 1 in 1,000 neonates in humans10. Thus,
>>>>>>> tail-loss evolution may have been associated with an adaptive
>>>>>>> cost of
>>>>>>> the potential for neural tube defects, which continue to affect
>>>>>>> human
>>>>>>> health today."
>>>>>>>
>>>>>>> Evidently, the advantages of losing the tail outweigh the
>>>>>>> disadvantage
>>>>>>> of the neural tube defects.
>>>>>>>
>>>>>>
>>>>>> What were the advantages?
>>>>>>
>>>>>> Some other simian lineages have lost their tails, but what is the
>>>>>> advantage?
>>>>>>
>>>>>> Apes did become brachiators, but other simian lineages did not,
>>>>>> and some
>>>>>> simian lineages that adopted a similar lifestyle for supporting
>>>>>> themselves in the trees, actually developed prehensile tails as a
>>>>>> fifth
>>>>>> limb for supporting themselves hanging from branches.
>>>>>>
>>>>>> For birds there was a selective advantage in terms of weight, and the
>>>>>> tailbones degenerated and fused into a small nub.  The tail was not
>>>>>> lost, and birds still have a nub that they call a pygostyle that
>>>>>> still
>>>>>> supports the muscles that control the tail movements and so the
>>>>>> feathers
>>>>>> associated with the tail.
>>>>>>
>>>>>> Ron Okimoto
>>>>>>
>>>>> I believe the article mentions that bipedalism is speculated to have
>>>>> made bipedalism easier.
>>>>>
>>>> No causal link there... ;-)
>>>>>
>>>>> That could be a just-so story, but mutations
>>>>> that are adopted and fixed within a population must have advantages
>>>>> that
>>>>> outweigh potential advantages.
>>>>>
>>>> Indubitably.
>>>>>
>>> Really? Drift is out?
>>>
>>
>> I don't know if drift is ever out but is it particularly plausible in
>> the case of tail loss, something that seems really rare in tetrapods?
>> Like, what lineages actually lost their tails - like, really lost, not
>> "reduced" or "replaced by a non-bony appendage that serves a taily
>> function": frogs, apes, manx cats... bears are maybe on their way...
>> who else?
>>
> Well, my reply was not specific to the 'tailless' idea but rather to the
> more general statement "mutations that are adopted and fixed within a
> population must have advantages that outweigh potential advantages." and
> the "Indubitably." reply.

Fair enough, I'd missed that context and I agree it was a reasonable
response to that sentence in isolation.

> However, you seem to making the claim that 'rare' fixed mutations are
> less likely to be due to drift. It would seem to me that common (over
> many lineages) fixed mutations, even if not identical but responsible
> for very similar morphology, are almost certainly due to selection. Rare
> fixed mutations that have not been *demonstrated* to be associated with
> enhanced reproductive success are more likely to be due to drift.
>

I'm not sure whether by "rare" mutation you mean "rarely found" or
"rarely occurs". In terms of "rarely occurs", such mutations are
definitely much less likely to get fixed by drift than by natural
selection, because drift depends almost purely on statistics and those
are by definition not in favor of rare occurrences.

In terms of "rarely found" I don't think I'd say that; in principle both
drift and selection can result in rare traits or common ones via
different dynamics.

The reason I think it speaks to drift in this case is *how rare* it is
over *how large* a population. Basically the possibilities seem to be:

- the base rate of occurrence of this mutation is extremely low - much
lower than that of mutations causing limb loss for example. It's
possible enough that the genetics & developmental pathways of tails in
tetrapods make it so but it strikes me as implausible, and the mutation
described in the article doesn't look like an unusually unlikely one.

- the base rate of occurrence of this mutation is higher than the number
of time it got fixed suggests, which in turn suggests the mutation is
deleterious for almost all tetrapods - either because their tails are
universally useful, or because this is a tricky developmental pathway to
mess with without negative impacts.

If the second is true then that leaves two non-mutually-exclusive
options for why it got fixed in the few cases it did: it was
particularly beneficial in those groups, or it wasn't deleterious for
them the way it is for other tetrapods. While the second *does* mean the
trait could arise via drift, the fact it's not deleterious for them when
it is for *all other tetrapods* is itself an oddity that demands
explanation beyond "drift".

In the three clades I listed (still haven't thought of others, still
interested to see if anyone does) tail loss seems pretty clearly
selective in frogs and pretty clearly due to drift in Manx cats but that
latter case almost "proves the rule" - we have a clear founder effect, a
very recent trait in a small population that we can doubt would persist
over geologic time, and in a species that humans haven't been provably
messing with as blatantly as dogs but still somewhat. I've never heard
of a notable bottleneck in early ape evolutionary history but it's
possible this isn't the kind of thing there would be much evidence for
or against this far out; the other two factors however are definitely
out for apes.

Actually this made me realize another reason to doubt the "base
likelihood happens to match up to 3 in all tetrapods" option: the fact
frogs went tail-less so much earlier than apes or Manx cats. Like, the
base rate is either high enough that the mutation would occur early in
tetrapod history in a then-much-lower-and-less-diverse population and be
available for selection to work on, OR it's low enough that it would
never drift to fixation once in non-amphibian tetrapods until apes.
Those are radically different base rates ! It's not impossible to be
fair, genetics change and the base rate could have been different in
early tetrapods vs amniotes for example. But those are some assumptions
we're adding there.

On 2024-04-06 2:55 AM, Arkalen wrote:
> On 05/04/2024 23:07, DB Cates wrote:
>> On 2024-04-05 3:56 AM, Arkalen wrote:
>>> On 01/03/2024 05:31, DB Cates wrote:
>>>> On 2024-02-29 1:17 PM, Bob Casanova wrote:
>>>>> On Thu, 29 Feb 2024 08:05:05 -0800, the following appeared
>>>>> in talk.origins, posted by erik simpson
>>>>> <eastside.erik@gmail.com>:
>>>>>
>>>>>> On 2/29/24 3:55 AM, RonO wrote:
>>>>>>> On 2/28/2024 5:41 PM, erik simpson wrote:
>>>>>>>> On 2/28/24 3:21 PM, RonO wrote:
>>>>>>>>> It turns out that the common ancestor that between gibbons and the
>>>>>>>>> great apes had an ALU transposon jump into the intron between
>>>>>>>>> exon 6
>>>>>>>>> and exon 7 of the TBXT gene.  There was already an transposon
>>>>>>>>> between
>>>>>>>>> exon 5 and exon 6.  Monkeys and apes have the ALU insertion in the
>>>>>>>>> intron between exon 5 and exon 6, but the apes have the second ALU
>>>>>>>>> insertion in the intron between exons 6 and 7.  So it turns out
>>>>>>>>> that
>>>>>>>>> apes still have the exon 6 sequence in the TBXT gene, but the
>>>>>>>>> two ALU
>>>>>>>>> transposon sequences form a stem loop structure in the RNA
>>>>>>>>> transcript
>>>>>>>>> that messes up processing so exon 6 is skipped and exon 5 is
>>>>>>>>> stuck to
>>>>>>>>> exon 7 in the final ape mRNA.  So part of what makes us human
>>>>>>>>> is due
>>>>>>>>> to a transposon insertion mutation into the TBXT gene.
>>>>>>>>>
>>>>>>>>> The insertion happened in the common ancestor of all extant
>>>>>>>>> apes, and
>>>>>>>>> has been retained by the extant ape lineages.
>>>>>>>>>
>>>>>>>>> https://www.nature.com/articles/s41586-024-07095-8
>>>>>>>>>
>>>>>>>>> The article is open access.
>>>>>>>>>
>>>>>>>>> Ron Okimoto
>>>>>>>>>
>>>>>>>> Another effect of this modification is also "Moreover, mice
>>>>>>>> expressing
>>>>>>>> the exon-skipped Tbxt isoform develop neural tube defects, a
>>>>>>>> condition
>>>>>>>> that affects approximately 1 in 1,000 neonates in humans10. Thus,
>>>>>>>> tail-loss evolution may have been associated with an adaptive
>>>>>>>> cost of
>>>>>>>> the potential for neural tube defects, which continue to affect
>>>>>>>> human
>>>>>>>> health today."
>>>>>>>>
>>>>>>>> Evidently, the advantages of losing the tail outweigh the
>>>>>>>> disadvantage
>>>>>>>> of the neural tube defects.
>>>>>>>>
>>>>>>>
>>>>>>> What were the advantages?
>>>>>>>
>>>>>>> Some other simian lineages have lost their tails, but what is the
>>>>>>> advantage?
>>>>>>>
>>>>>>> Apes did become brachiators, but other simian lineages did not,
>>>>>>> and some
>>>>>>> simian lineages that adopted a similar lifestyle for supporting
>>>>>>> themselves in the trees, actually developed prehensile tails as a
>>>>>>> fifth
>>>>>>> limb for supporting themselves hanging from branches.
>>>>>>>
>>>>>>> For birds there was a selective advantage in terms of weight, and
>>>>>>> the
>>>>>>> tailbones degenerated and fused into a small nub.  The tail was not
>>>>>>> lost, and birds still have a nub that they call a pygostyle that
>>>>>>> still
>>>>>>> supports the muscles that control the tail movements and so the
>>>>>>> feathers
>>>>>>> associated with the tail.
>>>>>>>
>>>>>>> Ron Okimoto
>>>>>>>
>>>>>> I believe the article mentions that bipedalism is speculated to have
>>>>>> made bipedalism easier.
>>>>>>
>>>>> No causal link there... ;-)
>>>>>>
>>>>>> That could be a just-so story, but mutations
>>>>>> that are adopted and fixed within a population must have
>>>>>> advantages that
>>>>>> outweigh potential advantages.
>>>>>>
>>>>> Indubitably.
>>>>>>
>>>> Really? Drift is out?
>>>>
>>>
>>> I don't know if drift is ever out but is it particularly plausible in
>>> the case of tail loss, something that seems really rare in tetrapods?
>>> Like, what lineages actually lost their tails - like, really lost,
>>> not "reduced" or "replaced by a non-bony appendage that serves a
>>> taily function": frogs, apes, manx cats... bears are maybe on their
>>> way... who else?
>>>
>> Well, my reply was not specific to the 'tailless' idea but rather to the
>> more general statement "mutations that are adopted and fixed within a
>> population must have advantages that outweigh potential advantages." and
>> the "Indubitably." reply.
>
> Fair enough, I'd missed that context and I agree it was a reasonable
> response to that sentence in isolation.
>
>> However, you seem to making the claim that 'rare' fixed mutations are
>> less likely to be due to drift. It would seem to me that common (over
>> many lineages) fixed mutations, even if not identical but responsible
>> for very similar morphology, are almost certainly due to selection. Rare
>> fixed mutations that have not been *demonstrated* to be associated with
>> enhanced reproductive success are more likely to be due to drift.
>>
>
> I'm not sure whether by "rare" mutation you mean "rarely found" or
> "rarely occurs".

We have a miscommunication. I was referring to *fixed* mutations only,
not mutations in general. I don't think there are such things as "rare
mutations". There are some biases and special circumstances, but I think
it can be stated that mutations occur randomly without too much
violation of reality. The total number of mutations extant in a given
population depends on mutation rate, genome size, and population size in
any cases meaning that every possible mutation happens regularly over
time. The *really* bad ones are eliminated early and are never observed.
Most are neutral or near neutral and are, at a very low probability,
randomly (biased by things like proximity to highly conserved areas)
fixed by drift. A significant number are deleterious and are eliminated
before fixation by selection and a small number are useful in the extant
environment and are positively selected and have a higher rate of fixation.

So my argument is that any *particular* mutation that becomes fixed in
one or a few populations is more likely to be due to drift while one
that becomes fixed in many diverse populations is much more likely to be
due to selection. This also applies to different mutations that have the
same or similar phenotypic effects.

In terms of "rarely occurs", such mutations are
> definitely much less likely to get fixed by drift than by natural
> selection, because drift depends almost purely on statistics and those
> are by definition not in favor of rare occurrences.
>
> In terms of "rarely found" I don't think I'd say that; in principle both
> drift and selection can result in rare traits or common ones via
> different dynamics.
>
>
> The reason I think it speaks to drift in this case is *how rare* it is
> over *how large* a population. Basically the possibilities seem to be:
>
> - the base rate of occurrence of this mutation is extremely low - much
> lower than that of mutations causing limb loss for example. It's
> possible enough that the genetics & developmental pathways of tails in
> tetrapods make it so but it strikes me as implausible, and the mutation
> described in the article doesn't look like an unusually unlikely one.
>
>
> - the base rate of occurrence of this mutation is higher than the number
> of time it got fixed suggests, which in turn suggests the mutation is
> deleterious for almost all tetrapods - either because their tails are
> universally useful, or because this is a tricky developmental pathway to
> mess with without negative impacts.
>
>
> If the second is true then that leaves two non-mutually-exclusive
> options for why it got fixed in the few cases it did: it was
> particularly beneficial in those groups, or it wasn't deleterious for
> them the way it is for other tetrapods. While the second *does* mean the
> trait could arise via drift, the fact it's not deleterious for them when
> it is for *all other tetrapods* is itself an oddity that demands
> explanation beyond "drift".
>
>
> In the three clades I listed (still haven't thought of others, still
> interested to see if anyone does) tail loss seems pretty clearly
> selective in frogs and pretty clearly due to drift in Manx cats but that
> latter case almost "proves the rule" - we have a clear founder effect, a
> very recent trait in a small population that we can doubt would persist
> over geologic time, and in a species that humans haven't been provably
> messing with as blatantly as dogs but still somewhat. I've never heard
> of a notable bottleneck in early ape evolutionary history but it's
> possible this isn't the kind of thing there would be much evidence for
> or against this far out; the other two factors however are definitely
> out for apes.
>
>
> Actually this made me realize another reason to doubt the "base
> likelihood happens to match up to 3 in all tetrapods" option: the fact
> frogs went tail-less so much earlier than apes or Manx cats. Like, the
> base rate is either high enough that the mutation would occur early in
> tetrapod history in a then-much-lower-and-less-diverse population and be
> available for selection to work on, OR it's low enough that it would
> never drift to fixation once in non-amphibian tetrapods until apes.
> Those are radically different base rates ! It's not impossible to be
> fair, genetics change and the base rate could have been different in
> early tetrapods vs amniotes for example. But those are some assumptions
> we're adding there.
>
>
>>
>>> Not to mention the article suggests tail loss could be associated
>>> with neural tube defects, which would definitely make drift much less
>>> likely.
>>>
>> Could you be more explicit here?
>>
>
> It would make the trait deleterious, and while mildly deleterious traits
> can fix through drift it's kind of core to the point of natural
> selection that the probability of this happening drops sharply the more
> deleterious the trait is (founder effects aside).
>
Okay, tell me where I'm wrong here and if I'm not wrong, justify your
conclusion.
It seems to me that you are claiming that association with a severely
deleterious effect would prevent fixation by drift but selection in the
same circumstances would work.
Selection will fix a severely deleterious mutation??
>
>>>>>> Aside from posture I can't think of what
>>>>>> the advantages might be.  Pants are easier? (Note to literalists: I
>>>>>> don't seriously suggest that.)
>>>>
>>>
>>
>

On 2024-04-05 5:05 PM, Ernest Major wrote:
> On 05/04/2024 22:07, DB Cates wrote:
>>
>>> Not to mention the article suggests tail loss could be associated
>>> with neural tube defects, which would definitely make drift much less
>>> likely.
>>>
>> Could you be more explicit here?
>
> I think that the idea is that a mutation associated with neural tube
> defects is under strong enough negative selection that it would be fixed
> by drift, and therefore there must be a countervailing selective
> advantage to the mutation (and also selection for compensatory mutations
> preventing the neural tube defects).
>
Okay, I can see the force of the argument in theory but I'm having a
great deal of trouble understanding how it could realistically operate
in practice.

> On the other had, the mutation has been shown to be associated with
> neural tube defects in one genetic background. Assuming that the
> association carries over to other genetic backgrounds is a leap.
>

--
--
Don Cates ("he's a cunning rascal" PN)

On 07/04/2024 00:16, DB Cates wrote:
> On 2024-04-06 2:55 AM, Arkalen wrote:
>> On 05/04/2024 23:07, DB Cates wrote:
>>> On 2024-04-05 3:56 AM, Arkalen wrote:
>>>> On 01/03/2024 05:31, DB Cates wrote:
>>>>> On 2024-02-29 1:17 PM, Bob Casanova wrote:
>>>>>> On Thu, 29 Feb 2024 08:05:05 -0800, the following appeared
>>>>>> in talk.origins, posted by erik simpson
>>>>>> <eastside.erik@gmail.com>:
>>>>>>
>>>>>>> On 2/29/24 3:55 AM, RonO wrote:
>>>>>>>> On 2/28/2024 5:41 PM, erik simpson wrote:
>>>>>>>>> On 2/28/24 3:21 PM, RonO wrote:
>>>>>>>>>> It turns out that the common ancestor that between gibbons and
>>>>>>>>>> the
>>>>>>>>>> great apes had an ALU transposon jump into the intron between
>>>>>>>>>> exon 6
>>>>>>>>>> and exon 7 of the TBXT gene.  There was already an transposon
>>>>>>>>>> between
>>>>>>>>>> exon 5 and exon 6.  Monkeys and apes have the ALU insertion in
>>>>>>>>>> the
>>>>>>>>>> intron between exon 5 and exon 6, but the apes have the second
>>>>>>>>>> ALU
>>>>>>>>>> insertion in the intron between exons 6 and 7.  So it turns
>>>>>>>>>> out that
>>>>>>>>>> apes still have the exon 6 sequence in the TBXT gene, but the
>>>>>>>>>> two ALU
>>>>>>>>>> transposon sequences form a stem loop structure in the RNA
>>>>>>>>>> transcript
>>>>>>>>>> that messes up processing so exon 6 is skipped and exon 5 is
>>>>>>>>>> stuck to
>>>>>>>>>> exon 7 in the final ape mRNA.  So part of what makes us human
>>>>>>>>>> is due
>>>>>>>>>> to a transposon insertion mutation into the TBXT gene.
>>>>>>>>>>
>>>>>>>>>> The insertion happened in the common ancestor of all extant
>>>>>>>>>> apes, and
>>>>>>>>>> has been retained by the extant ape lineages.
>>>>>>>>>>
>>>>>>>>>> https://www.nature.com/articles/s41586-024-07095-8
>>>>>>>>>>
>>>>>>>>>> The article is open access.
>>>>>>>>>>
>>>>>>>>>> Ron Okimoto
>>>>>>>>>>
>>>>>>>>> Another effect of this modification is also "Moreover, mice
>>>>>>>>> expressing
>>>>>>>>> the exon-skipped Tbxt isoform develop neural tube defects, a
>>>>>>>>> condition
>>>>>>>>> that affects approximately 1 in 1,000 neonates in humans10. Thus,
>>>>>>>>> tail-loss evolution may have been associated with an adaptive
>>>>>>>>> cost of
>>>>>>>>> the potential for neural tube defects, which continue to affect
>>>>>>>>> human
>>>>>>>>> health today."
>>>>>>>>>
>>>>>>>>> Evidently, the advantages of losing the tail outweigh the
>>>>>>>>> disadvantage
>>>>>>>>> of the neural tube defects.
>>>>>>>>>
>>>>>>>>
>>>>>>>> What were the advantages?
>>>>>>>>
>>>>>>>> Some other simian lineages have lost their tails, but what is the
>>>>>>>> advantage?
>>>>>>>>
>>>>>>>> Apes did become brachiators, but other simian lineages did not,
>>>>>>>> and some
>>>>>>>> simian lineages that adopted a similar lifestyle for supporting
>>>>>>>> themselves in the trees, actually developed prehensile tails as
>>>>>>>> a fifth
>>>>>>>> limb for supporting themselves hanging from branches.
>>>>>>>>
>>>>>>>> For birds there was a selective advantage in terms of weight,
>>>>>>>> and the
>>>>>>>> tailbones degenerated and fused into a small nub.  The tail was not
>>>>>>>> lost, and birds still have a nub that they call a pygostyle that
>>>>>>>> still
>>>>>>>> supports the muscles that control the tail movements and so the
>>>>>>>> feathers
>>>>>>>> associated with the tail.
>>>>>>>>
>>>>>>>> Ron Okimoto
>>>>>>>>
>>>>>>> I believe the article mentions that bipedalism is speculated to have
>>>>>>> made bipedalism easier.
>>>>>>>
>>>>>> No causal link there... ;-)
>>>>>>>
>>>>>>> That could be a just-so story, but mutations
>>>>>>> that are adopted and fixed within a population must have
>>>>>>> advantages that
>>>>>>> outweigh potential advantages.
>>>>>>>
>>>>>> Indubitably.
>>>>>>>
>>>>> Really? Drift is out?
>>>>>
>>>>
>>>> I don't know if drift is ever out but is it particularly plausible
>>>> in the case of tail loss, something that seems really rare in
>>>> tetrapods? Like, what lineages actually lost their tails - like,
>>>> really lost, not "reduced" or "replaced by a non-bony appendage that
>>>> serves a taily function": frogs, apes, manx cats... bears are maybe
>>>> on their way... who else?
>>>>
>>> Well, my reply was not specific to the 'tailless' idea but rather to the
>>> more general statement "mutations that are adopted and fixed within a
>>> population must have advantages that outweigh potential advantages." and
>>> the "Indubitably." reply.
>>
>> Fair enough, I'd missed that context and I agree it was a reasonable
>> response to that sentence in isolation.
>>
>>> However, you seem to making the claim that 'rare' fixed mutations are
>>> less likely to be due to drift. It would seem to me that common (over
>>> many lineages) fixed mutations, even if not identical but responsible
>>> for very similar morphology, are almost certainly due to selection. Rare
>>> fixed mutations that have not been *demonstrated* to be associated with
>>> enhanced reproductive success are more likely to be due to drift.
>>>
>>
>> I'm not sure whether by "rare" mutation you mean "rarely found" or
>> "rarely occurs".
>
> We have a miscommunication. I was referring to *fixed* mutations only,
> not mutations in general. I don't think there are such things as "rare
> mutations". There are some biases and special circumstances, but I think
> it can be stated that mutations occur randomly without too much
> violation of reality. The total number of mutations extant in a given
> population depends on mutation rate, genome size, and population size in
> any cases meaning that every possible mutation happens regularly over
> time. The *really* bad ones are eliminated early and are never observed.
> Most are neutral or near neutral and are, at a very low probability,
> randomly (biased by things like proximity to highly conserved areas)
> fixed by drift. A significant number are deleterious and are eliminated
> before fixation by selection and a small number are useful in the extant
> environment and are positively selected and have a higher rate of fixation.
>
> So my argument is that any *particular* mutation that becomes fixed in
> one or a few populations is more likely to be due to drift while one
> that becomes fixed in many diverse populations is much more likely to be
> due to selection. This also applies to different mutations that have the
> same or similar phenotypic effects.
>

I'm not sure I completely follow/agree but I might be being biased by
the fact I came into this talking about a phenotypic trait not a
mutation and that gets back to how the whole thing started with a
misunderstanding anyway, and it might be best to leave it at that.

On 2024-04-06 7:37 PM, Arkalen wrote:
> On 07/04/2024 00:16, DB Cates wrote:
>> On 2024-04-06 2:55 AM, Arkalen wrote:
>>> On 05/04/2024 23:07, DB Cates wrote:
>>>> On 2024-04-05 3:56 AM, Arkalen wrote:
>>>>> On 01/03/2024 05:31, DB Cates wrote:
>>>>>> On 2024-02-29 1:17 PM, Bob Casanova wrote:
>>>>>>> On Thu, 29 Feb 2024 08:05:05 -0800, the following appeared
>>>>>>> in talk.origins, posted by erik simpson
>>>>>>> <eastside.erik@gmail.com>:
>>>>>>>
>>>>>>>> On 2/29/24 3:55 AM, RonO wrote:
>>>>>>>>> On 2/28/2024 5:41 PM, erik simpson wrote:
>>>>>>>>>> On 2/28/24 3:21 PM, RonO wrote:
>>>>>>>>>>> It turns out that the common ancestor that between gibbons
>>>>>>>>>>> and the
>>>>>>>>>>> great apes had an ALU transposon jump into the intron between
>>>>>>>>>>> exon 6
>>>>>>>>>>> and exon 7 of the TBXT gene.  There was already an transposon
>>>>>>>>>>> between
>>>>>>>>>>> exon 5 and exon 6.  Monkeys and apes have the ALU insertion
>>>>>>>>>>> in the
>>>>>>>>>>> intron between exon 5 and exon 6, but the apes have the
>>>>>>>>>>> second ALU
>>>>>>>>>>> insertion in the intron between exons 6 and 7.  So it turns
>>>>>>>>>>> out that
>>>>>>>>>>> apes still have the exon 6 sequence in the TBXT gene, but the
>>>>>>>>>>> two ALU
>>>>>>>>>>> transposon sequences form a stem loop structure in the RNA
>>>>>>>>>>> transcript
>>>>>>>>>>> that messes up processing so exon 6 is skipped and exon 5 is
>>>>>>>>>>> stuck to
>>>>>>>>>>> exon 7 in the final ape mRNA.  So part of what makes us human
>>>>>>>>>>> is due
>>>>>>>>>>> to a transposon insertion mutation into the TBXT gene.
>>>>>>>>>>>
>>>>>>>>>>> The insertion happened in the common ancestor of all extant
>>>>>>>>>>> apes, and
>>>>>>>>>>> has been retained by the extant ape lineages.
>>>>>>>>>>>
>>>>>>>>>>> https://www.nature.com/articles/s41586-024-07095-8
>>>>>>>>>>>
>>>>>>>>>>> The article is open access.
>>>>>>>>>>>
>>>>>>>>>>> Ron Okimoto
>>>>>>>>>>>
>>>>>>>>>> Another effect of this modification is also "Moreover, mice
>>>>>>>>>> expressing
>>>>>>>>>> the exon-skipped Tbxt isoform develop neural tube defects, a
>>>>>>>>>> condition
>>>>>>>>>> that affects approximately 1 in 1,000 neonates in humans10. Thus,
>>>>>>>>>> tail-loss evolution may have been associated with an adaptive
>>>>>>>>>> cost of
>>>>>>>>>> the potential for neural tube defects, which continue to
>>>>>>>>>> affect human
>>>>>>>>>> health today."
>>>>>>>>>>
>>>>>>>>>> Evidently, the advantages of losing the tail outweigh the
>>>>>>>>>> disadvantage
>>>>>>>>>> of the neural tube defects.
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> What were the advantages?
>>>>>>>>>
>>>>>>>>> Some other simian lineages have lost their tails, but what is the
>>>>>>>>> advantage?
>>>>>>>>>
>>>>>>>>> Apes did become brachiators, but other simian lineages did not,
>>>>>>>>> and some
>>>>>>>>> simian lineages that adopted a similar lifestyle for supporting
>>>>>>>>> themselves in the trees, actually developed prehensile tails as
>>>>>>>>> a fifth
>>>>>>>>> limb for supporting themselves hanging from branches.
>>>>>>>>>
>>>>>>>>> For birds there was a selective advantage in terms of weight,
>>>>>>>>> and the
>>>>>>>>> tailbones degenerated and fused into a small nub.  The tail was
>>>>>>>>> not
>>>>>>>>> lost, and birds still have a nub that they call a pygostyle
>>>>>>>>> that still
>>>>>>>>> supports the muscles that control the tail movements and so the
>>>>>>>>> feathers
>>>>>>>>> associated with the tail.
>>>>>>>>>
>>>>>>>>> Ron Okimoto
>>>>>>>>>
>>>>>>>> I believe the article mentions that bipedalism is speculated to
>>>>>>>> have
>>>>>>>> made bipedalism easier.
>>>>>>>>
>>>>>>> No causal link there... ;-)
>>>>>>>>
>>>>>>>> That could be a just-so story, but mutations
>>>>>>>> that are adopted and fixed within a population must have
>>>>>>>> advantages that
>>>>>>>> outweigh potential advantages.
>>>>>>>>
>>>>>>> Indubitably.
>>>>>>>>
>>>>>> Really? Drift is out?
>>>>>>
>>>>>
>>>>> I don't know if drift is ever out but is it particularly plausible
>>>>> in the case of tail loss, something that seems really rare in
>>>>> tetrapods? Like, what lineages actually lost their tails - like,
>>>>> really lost, not "reduced" or "replaced by a non-bony appendage
>>>>> that serves a taily function": frogs, apes, manx cats... bears are
>>>>> maybe on their way... who else?
>>>>>
>>>> Well, my reply was not specific to the 'tailless' idea but rather to
>>>> the
>>>> more general statement "mutations that are adopted and fixed within
>>>> a population must have advantages that outweigh potential
>>>> advantages." and
>>>> the "Indubitably." reply.
>>>
>>> Fair enough, I'd missed that context and I agree it was a reasonable
>>> response to that sentence in isolation.
>>>
>>>> However, you seem to making the claim that 'rare' fixed mutations are
>>>> less likely to be due to drift. It would seem to me that common
>>>> (over many lineages) fixed mutations, even if not identical but
>>>> responsible
>>>> for very similar morphology, are almost certainly due to selection.
>>>> Rare
>>>> fixed mutations that have not been *demonstrated* to be associated with
>>>> enhanced reproductive success are more likely to be due to drift.
>>>>
>>>
>>> I'm not sure whether by "rare" mutation you mean "rarely found" or
>>> "rarely occurs".
>>
>> We have a miscommunication. I was referring to *fixed* mutations only,
>> not mutations in general. I don't think there are such things as "rare
>> mutations". There are some biases and special circumstances, but I
>> think it can be stated that mutations occur randomly without too much
>> violation of reality. The total number of mutations extant in a given
>> population depends on mutation rate, genome size, and population size
>> in any cases meaning that every possible mutation happens regularly
>> over time. The *really* bad ones are eliminated early and are never
>> observed. Most are neutral or near neutral and are, at a very low
>> probability, randomly (biased by things like proximity to highly
>> conserved areas) fixed by drift. A significant number are deleterious
>> and are eliminated before fixation by selection and a small number are
>> useful in the extant environment and are positively selected and have
>> a higher rate of fixation.
>>
>> So my argument is that any *particular* mutation that becomes fixed in
>> one or a few populations is more likely to be due to drift while one
>> that becomes fixed in many diverse populations is much more likely to
>> be due to selection. This also applies to different mutations that
>> have the same or similar phenotypic effects.
>>
>
> I'm not sure I completely follow/agree but I might be being biased by
> the fact I came into this talking about a phenotypic trait not a
> mutation and that gets back to how the whole thing started with a
> misunderstanding anyway, and it might be best to leave it at that.

On 4/5/24 10:43 PM, jillery wrote:
> On Fri, 5 Apr 2024 11:01:34 +0200, Arkalen <arkalen@proton.me> wrote:
>
>> On 09/03/2024 18:45, erik simpson wrote:
>>> On 3/9/24 7:16 AM, jillery wrote:
>>>> On Wed, 28 Feb 2024 17:21:19 -0600, RonO <rokimoto@cox.net> wrote:
>>>>
>>>>> It turns out that the common ancestor that between gibbons and the great
>>>>> apes had an ALU transposon jump into the intron between exon 6 and exon
>>>>> 7 of the TBXT gene.  There was already an transposon between exon 5 and
>>>>> exon 6.  Monkeys and apes have the ALU insertion in the intron between
>>>>> exon 5 and exon 6, but the apes have the second ALU insertion in the
>>>>> intron between exons 6 and 7.  So it turns out that apes still have the
>>>>> exon 6 sequence in the TBXT gene, but the two ALU transposon sequences
>>>>> form a stem loop structure in the RNA transcript that messes up
>>>>> processing so exon 6 is skipped and exon 5 is stuck to exon 7 in the
>>>>> final ape mRNA.  So part of what makes us human is due to a transposon
>>>>> insertion mutation into the TBXT gene.
>>>>>
>>>>> The insertion happened in the common ancestor of all extant apes, and
>>>>> has been retained by the extant ape lineages.
>>>>>
>>>>> https://www.nature.com/articles/s41586-024-07095-8
>>>>>
>>>>> The article is open access.
>>>>>
>>>>> Ron Okimoto
>>>>
>>>>
>>>> In the following Youtube video, Gutsick Gibbon provides a 33-minute
>>>> anthropological perspective about the same article:
>>>>
>>>> <https://www.youtube.com/watch?v=dImLB0ePWR8>
>>>>
>>>> It turns out that losing their tails had happened to at least one
>>>> other primate group, between lorises and bushbabies.  It would be
>>>> interesting to see if the tailless lorises have a similar ALU
>>>> transposon in the TBXT gene.
>>>>
>>>>
>>> It seems that the Lorax also is tailless.  I doubt it has anything to do
>>> with ALU.
>>>
>>
>> Isn't the Lorax an ape though? Even a hominid, as it has hands AND feet
>> - but I suppose the latter might be the kind of trait that could evolve
>> convergently in any ape group that becomes ground-based & bipedal.
>
>
> Apparently it depends on if Dr. Seuss drew the Lorax with shoes.
>
> --
> To know less than we don't know is the nature of most knowledge
>
The Lorax has magnificent mustaches, but is apparently unclothed. It
may be modeled after an African monkey
https://www.smithsonianmag.com/science-nature/new-research-suggests-dr-seuss-modeled-lorax-on-this-real-life-monkey-180969692/