Mysteries of Evolution: Sexual Reproduction; Part A, meiosis

[Peter Nyikos]

All sexual reproduction in eukaryotes has meiosis as its first, essential part.
There are several mysteries about meiosis.
The two most intriguing ones are intimately connected, and
it is difficult to imagine how the second can be seriously tackled
until the first is solved.

Mystery 1: How do the the chromosomes in each homologous pair find each other?

Mystery 2: How did meiosis originate?

Accordingly, in this OP, and in the first post of mine
after that, I will be talking about Mystery 1. But it is Mystery 2
that is really on-topic for what talk.origins was designed for,
so I will soon be talking about it too.

First, a reminder of some basic concepts.
Meiosis involves paired chromosomes, yet the term "sister chromatids"
applies to two copies of the *same* chromosome in the pair.
The paired chromosomes of a homologous pair are called *homologs*.

Already during interphase, each homolog is duplicated,
producing sister chromatids. However, unlike in mitosis, these do not
separate for the first cell division. Instead, each pair of sister
chromatids somehow finds their homolog, also in the form
of sister chromatids at this stage.


How this happens was a mystery eleven years ago, and
I have found no sign that it is any less of a mystery now.


This finding of each other marks the start of Meiosis I,
which consists of the homologs separating from each
other while still in the form of attached sister chromatids.
But prior to this separation there occurs an exchange
of parts of a sister chromatid in one pair with parts
of a sister chromatid in another pair. Meiosis I ends
with the fission of the cell in which the separated
homologs go into daughter cells. Meiosis II is where
the sister chromatids, in turn, go into separate
daughter cells. Details can be found in any respectable
textbook that covers biology in general.


Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu

[Peter Nyikos]

On Wednesday, May 15, 2019 at 4:30:02 PM UTC-4, Peter Nyikos wrote:
> All sexual reproduction in eukaryotes has meiosis as its first, essential part.
> There are several mysteries about meiosis.
> The two most intriguing ones are intimately connected, and
> it is difficult to imagine how the second can be seriously tackled
> until the first is solved.
>
> Mystery 1: How do the the chromosomes in each homologous pair find each other?

I learned about this mystery only this month, from the 2008 edition
of Biology, 8th ed. (Campbell, Reece et al) where MIT Professor
Terry L. Orr-Weaver says the following on pp. 246-7 in the course of an
interview:

What we don't understand at all is how the chromosomes of a homologous
pair find each other. That pairing is unique to meiosis: it doesn't
happen in mitosis. The two strands of DNA
[in each of the sister chromatids of each homolog -- PN]
don't come apart, so although the homologous chromosomes have very
similar DNA sequences, it's not base-pairing that brings the homologous
chromosomes together. Given the relatively gigantic volume of the nucleus
and the huge mass of chromatin in the eukaryotic cell, how do the right
chromosomes find each other? That's the number one mystery about
meiosis.

Orr-Weaver is billed in the book as a member of the National Academy of Sciences and a past president of the Genetics Society of America.
She is currently at Whitehead Institute, Cambridge, MA.


Since I came across this, I've been trying to find any sign of progress
on this, but all I've found so far is detailed explanations of what
happens after the homologs have come together. An example is:

PNAS May 7, 2019 116 (19) 9417-9422; first published April 24, 2019 https://doi.org/10.1073/pnas.1902526116

The abstract can also be found here:

https://www.pnas.org/content/116/19/9417.short

and a pdf is available here for the full article.


Trivia: The article was edited by none other than Terry L. Orr-Weaver.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina

http://www.math.sc.edu/~nyikos

[John Harshman]

Interesting question that had never occurred to me. Can we agree that it
should be obvious that at least some sequence similarity must play a
role, and that this relevant sequence similarity must be distributed
throughout the chromosome? (If it were not, there would be no problem
with pairing in certain types of chromosomal rearrangements.)

[Peter Nyikos]

I took another look at the introduction to the two-page interview,
and she was already there back then:

...the first woman to become a member of the Whitehead Institute
for Biomedical Research.

Kudos to her, and shame on the people who ran it, if it predated
her entry for many years.

> >
> > Since I came across this, I've been trying to find any sign of progress
> > on this, but all I've found so far is detailed explanations of what
> > happens after the homologs have come together. An example is:
> >
> > PNAS May 7, 2019 116 (19) 9417-9422; first published April 24, 2019 https://doi.org/10.1073/pnas.1902526116
> >
> > The abstract can also be found here:
> >
> > https://www.pnas.org/content/116/19/9417.short
> >
> > and a pdf is available here for the full article.
>
> Interesting question that had never occurred to me. Can we agree that it
> should be obvious that at least some sequence similarity must play a
> role,

That certainly is a natural assumption, and it's hard to think
how it would be otherwise, but I know even less about genetics
than the textbook teaches, so I can't really say more than this right now.

> and that this relevant sequence similarity must be distributed
> throughout the chromosome?

I thought this was a consensus, that the loci are almost all identical
but the alleles vary greatly. I've never read anything that challenged
this truism. In that 2008 textbook, for instance, one reads:

Both chromosomes of each [homologous] pair carry genes controlling
the same inherited characters. For example, if a gene for eye
color is situated at a particular locus on a certain chromosome,
then the homolog of that chromosome will also have a gene specifying
eye color at the equivalent locus. [p. 250].

Immediately, however, the text points out "the exception that proves
the rule": whereas the two X chromosomes in the mammalian female
form a homologous pair, the X and Y chromosomes of the male do not.
I couldn't find anything in the textbook about how these two chromosomes
behave in the male during meiosis, but I expect that advanced books can
easily remedy that.


The persistence of the correspondence of loci through eons
of evolution has always seemed like a mystery to me.
[I never doubted it, so powerful is the voice of "consensus".]

However, that's a theme for later in this thread;
I wanted to begin with a publicly acknowledged mystery,
and with its inevitable consequence, Mystery 2.

> (If it were not, there would be no problem
> with pairing in certain types of chromosomal rearrangements.)

Huh? which rearrangements did you have in mind?


Peter Nyikos
Professor of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu

[John Harshman]

Depends on what you mean by that, which is unclear. If I do understand
your meaning, then yes. It's not just a consensus; it's a finding based
on genome sequencing.

But that's not the point. The point is that *relevant* sequence
similarity must be distributed, not just sequence similarity.

> I've never read anything that challenged
> this truism. In that 2008 textbook, for instance, one reads:
>
> Both chromosomes of each [homologous] pair carry genes controlling
> the same inherited characters. For example, if a gene for eye
> color is situated at a particular locus on a certain chromosome,
> then the homolog of that chromosome will also have a gene specifying
> eye color at the equivalent locus. [p. 250].

Again true, but not relevant to my point. One could imagine all-over
sequence homology while the sequence important for pairing would be
only, for example, near the centromeres. My point is that this idea
appears not to be true.

> Immediately, however, the text points out "the exception that proves
> the rule": whereas the two X chromosomes in the mammalian female
> form a homologous pair, the X and Y chromosomes of the male do not.
> I couldn't find anything in the textbook about how these two chromosomes
> behave in the male during meiosis, but I expect that advanced books can
> easily remedy that.

There is a portion of the Y chromosome homologous to a portion of the X
chromosome, the "pseudoautosomal region", and this is that pairs during
meiosis.

> The persistence of the correspondence of loci through eons
> of evolution has always seemed like a mystery to me.
> [I never doubted it, so powerful is the voice of "consensus".]

OK, you lost me on that one. "Correspondence of loci"? At any rate, this
is a digression having nothing to do wit the topic.

> However, that's a theme for later in this thread;
> I wanted to begin with a publicly acknowledged mystery,
> and with its inevitable consequence, Mystery 2.

>> (If it were not, there would be no problem
>> with pairing in certain types of chromosomal rearrangements.)
>
> Huh? which rearrangements did you have in mind?

Large translocations, generally. Also fusions and fissions. Anything
where big pieces of chromosome A in one haploid genome match pieces of
chromosome B (rather than A) in another. Then you get weird pairing of
one chromosome to two others, as in an A/AB triplet. And who knows what
gets dragged off into what gamete when that happens?

[Ernest Major]

On 16/05/2019 05:17, John Harshman wrote:
>> The persistence of the correspondence of loci through eons
>> of evolution has always seemed like a mystery to me.
>> [I never doubted it, so powerful is the voice of "consensus".]
>
> OK, you lost me on that one. "Correspondence of loci"? At any rate, this
> is a digression having nothing to do wit the topic.

He might be asking why diploid genomes remain diploid rather than the
pairs of chromosomes diverging as in bdelloid rotifers. In which case if
appealing to recombination as a means for retaining "correspondence of
loci" is not considered sufficient explanation one could investigate the
mechanisms of diploidisation in polyploids. It seems to me that meiosis
results in a selection pressure for homology between the chromosomes of
a pair. One could also look into the oddities of meiosis in dog roses,
evening primroses and sedges.

Alternatively he could be referring to synteny.

--
alias Ernest Major

[Peter Nyikos]

On Thursday, May 16, 2019 at 2:40:03 AM UTC-4, Ernest Major wrote:
> On 16/05/2019 05:17, John Harshman wrote:
> >> The persistence of the correspondence of loci through eons
> >> of evolution has always seemed like a mystery to me.
> >> [I never doubted it, so powerful is the voice of "consensus".]

> > OK, you lost me on that one. "Correspondence of loci"? At any rate, this
> > is a digression having nothing to do wit the topic.

The topic is Mysteries of Evolution, and specifically how sequence
similarity may well be essential for homologous chromosomes to
find each other. Solidly on-topic by any reasonable standard.

> He might be asking why diploid genomes remain diploid rather than the
> pairs of chromosomes diverging as in bdelloid rotifers.

I am talking about the hypothesized necessity of sequence
similarity, and "correspondence of loci" refers to everything in
the immediately preceding quote and to what I wrote immediately before that.
John just wasn't keeping the context in mind.

> In which case if
> appealing to recombination as a means for retaining "correspondence of
> loci" is not considered sufficient explanation one could investigate the
> mechanisms of diploidisation in polyploids.

I'm in a hurry, so I'll just ask: are those rotifers diploid, or
haploid? Consider also *Giardia*, which does not have matched
chromosomes -- but who would hazard a guess as to whether it
is the haploid (or diploid, or polyploid) descendant of sexually
reproducing protists, or whether it represents a primitive organism
that predated the advent of meiosis?

But back to the topic at hand.

How would recombination work if loci are in different places, and
crossover would result in chromosomes of mismatched length?

My conjecture is that this would be lethal to the offspring,
or at least to their offspring. Can you think of any other explanations?


You seem to think along the same lines:

> It seems to me that meiosis
> results in a selection pressure for homology between the chromosomes of
> a pair. One could also look into the oddities of meiosis in dog roses,
> evening primroses and sedges.

Rather far removed from humans, whose meiosis is under intensive research,
but a start.

>
> Alternatively he could be referring to synteny.

This word is unfamiliar to me and not in the textbook which
I have been referencing.


Got to go now. I have a 9:30 appointment not far from here, but
I need to be on time.


Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
U. of South Carolina at Columbia
http://people.math.sc.edu

[Peter Nyikos]

Before I try to address the formidable question of how meiosis may
have originated, I look at another mystery mentioned by Orr-Weaver in
the interview in _Biology_ 8th ed., by Campbell, Reece et al.

Immediately after the part I quoted in my second post, she said:

And I would say the second big mystery is why humans
are so unbelievably bad at carrying out meiosis.

The interviewer, _Biology_ co-author Janet Reece, asked:

Why makes you say that? Are we worse than fruit flies?

Orr-Weaver replies:

We're about a thousand times worse. Here are some amazing
statistics: Twenty percent of recognized pregnancies end in
spontaneous miscarriage, and out of those at least half are
due to a mistake during meiosis. And for every pregnancy
that proceeds far enough to be recognized, there have been
many that ended without being recognized. So about 10-20%
of the time meiosis doesn't work properly in humans. In
fruit flies, meiosis seems to occur inaccurately only
0.01 - 0.05% of the time. Even mice, which are mammals like
ourselves, do much better than than humans.

Orr-Weaver goes on to say what happens when meiosis does not work
correctly in humans, but these live long enough to be born.
Trisomy 13, 18 and 21 (Down syndrome) are well known examples
of failures of meiosis, although not usually thought of that way.
The first two lead to death in infancy, and even in the case of
Down syndrome,

only a minority of fetuses survive to term. . . . In fact,
errors in meiosis are the leading cause of mental retardation
in the United States. Some scientists argue that, in evolutionary
terms, the human species is able to cope with such a high rate
of meiotic errors because most of the pregnancies are lost
very early.

That last sentence leads to a number of ideas for research by
evolutionary biologists. One is to compare the two statistics
-- frequency of miscarriage and mental defects after birth
due to meiotic errors -- with the corresponding statistics
for other mammals. These may be hard to find on primates,
especially the great apes, because of protests by PETA
and other animal rights groups, but it might be easy to find
out the rate of Trisomy 21 and its effects on these animals.

The statisics also pose a problem for creationists. Some may
be like global warming denialists, alleging that the numerical
figures above are bogus. Others may bite the bullet by embracing them
and claiming that this is evidence that God punished animals
less severely for Adam's original sin than he did humans; and
that this is what one might expect of a just and merciful God.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--

U. of South Carolina in Columbia
http://people.math.sc.edu

[John Harshman]

On 5/16/19 3:03 PM, Peter Nyikos wrote:
> Before I try to address the formidable question of how meiosis may
> have originated, I look at another mystery mentioned by Orr-Weaver in
> the interview in _Biology_ 8th ed., by Campbell, Reece et al.
>
> Immediately after the part I quoted in my second post, she said:
>
> And I would say the second big mystery is why humans
> are so unbelievably bad at carrying out meiosis.
>
> The interviewer, _Biology_ co-author Janet Reece, asked:
>
> Why makes you say that? Are we worse than fruit flies?
>
> Orr-Weaver replies:
>
> We're about a thousand times worse. Here are some amazing
> statistics: Twenty percent of recognized pregnancies end in
> spontaneous miscarriage, and out of those at least half are
> due to a mistake during meiosis. And for every pregnancy
> that proceeds far enough to be recognized, there have been
> many that ended without being recognized. So about 10-20%
> of the time meiosis doesn't work properly in humans. In
> fruit flies, meiosis seems to occur inaccurately only
> 0.01 - 0.05% of the time. Even mice, which are mammals like
> ourselves, do much better than than humans.

One wonders how the number of chromosomes and their lengths correlate
with problems in meiosis. Also frequency of chromosomal mutations. I
seem to recall that Drosophila have a reduced frequency of crossing over
too.

[Peter Nyikos]

> >> role, and that this relevant sequence similarity must be distributed
> >> throughout the chromosome?

I thought I knew what you meant by this, but now you've added some
comments about it that I have a hard time figuring out. I've snipped all
intervening material to focus on the additions.
...

> The point is that *relevant* sequence
> similarity must be distributed, not just sequence similarity.

...

> One could imagine all-over
> sequence homology while the sequence important for pairing would be
> only, for example, near the centromeres. My point is that this idea
> appears not to be true.

Do you mean that some subset -- called "relevant" -- of the sequence
for the homologous chromosomes is necessary for them to "find each other,"
and it doesn't matter what similarity happens outside this relevant subset?

And do you mean that every sufficiently large subsequence (like, maybe,
every subsequence longer than one-tenth of the whole chromosome) should
contain some part of the relevant subset?

[By "subsequence" I mean an uninterrupted section of the chromosome:
as you move along the chromosome from beginning to end, you never get
off a subsequence, once you are on it, until you reach its end.]

...

> There is a portion of the Y chromosome homologous to a portion of the X
> chromosome, the "pseudoautosomal region", and this is that pairs during
> meiosis.

Now it sounds like the relevant sequence is NOT distributed through the
Y chromosome, but is concentrated in one region.

...

> >> (If it were not, there would be no problem
> >> with pairing in certain types of chromosomal rearrangements.)

> > Huh? which rearrangements did you have in mind?

In light of what you wrote next, it would seem that you meant
to say "there would be a problem," instead of "there would
be no problem". Correct?

> Large translocations, generally. Also fusions and fissions. Anything
> where big pieces of chromosome A in one haploid genome match pieces of
> chromosome B (rather than A) in another. Then you get weird pairing of
> one chromosome to two others, as in an A/AB triplet. And who knows what
> gets dragged off into what gamete when that happens?

Peter Nyikos

[John Harshman]

Yes, that's an idea. Of course we don't know. All we know is that
whatever portion of the sequence is relevant must be distributed at
various places throughout the chromosome, not just one location. The
relevant portion might be "all of it", but we don't know that.

> And do you mean that every sufficiently large subsequence (like, maybe,
> every subsequence longer than one-tenth of the whole chromosome) should
> contain some part of the relevant subset?

Yes.

> [By "subsequence" I mean an uninterrupted section of the chromosome:
> as you move along the chromosome from beginning to end, you never get
> off a subsequence, once you are on it, until you reach its end.]
>
> ...
>> There is a portion of the Y chromosome homologous to a portion of the X
>> chromosome, the "pseudoautosomal region", and this is that pairs during
>> meiosis.
>
> Now it sounds like the relevant sequence is NOT distributed through the
> Y chromosome, but is concentrated in one region.

That's right. But the humans sex chromosomes are unusual in that way.

>>>> (If it were not, there would be no problem
>>>> with pairing in certain types of chromosomal rearrangements.)
>
>>> Huh? which rearrangements did you have in mind?
>
> In light of what you wrote next, it would seem that you meant
> to say "there would be a problem," instead of "there would
> be no problem". Correct?

No. I meant that there would not be a problem, as I said. As it is, the
problem happens that if a chromosome has a rearrangement and ends up
half A and half B, for example, its A half will pair with chromosome A
and its B half with chromosome B, and thus we get a problematic bundle
of pieces that will not segregate properly in meiosis. But if the
sequence responsible for pairing were located in a single spot, the
chromosome would pair with either A or B, whichever part contained the
relevant sequence. No problem.

[Peter Nyikos]

I didn't want to go on my usual weekend posting break before
saying some words about:

Mystery 2: How did meiosis originate?

At our present state of knowledge, this is such a formidable mystery
that it seems best to approach it, before seriously addressing it,
with questions like the following:

Mystery 3: Did meiosis predate the LCA of living eukaryotes?

Here LCA stands for Last Common Ancestor. This is quite distinct
from asking whether the first eukaryote had meiosis.
What makes it distinct is that we are dealing with
the great-granddaddy of all ghost taxa.

The gap in complexity between any prokaryote and the simplest living
eukaryote is enormous. So even a billion years might have elapsed
between the first eukaryotes and that LCA,
with all the intermediate forms vanishing without a trace: no
real chance of ever finding even their fossils.


Before going further, let us recall the actual definition of "eukaryote."
The following is taken from the biology text I keep using:

eukaryotic cell: A type of cell with a membrane-enclosed nucleus
and membrane-enclosed organelles.

Note that there is no mention of meiosis or even mitosis; nor of
endosymbionts (mitochondria and plastids) even though they are
examples of organelles.


It now seems well established that all eukaryotes undergo mitosis
and that they have mitochondria or the remnants of mitochondria.
On the other hand, there are many eukaryotes, including a few
vertebrates, that do not reproduce sexually. However, almost all
of these (including all the vertebrate examples) are easily
seen to have evolved from organisms that underwent meiosis in
some part of their life cycle.

A possible exception that is rather well known because it is
the most common protist that is parasitic on humans: *Giardia lamblia*.
It is also widely believed to be one of the most primitive. It was
once thought to lack mitochondria but it is now believed to have
evolved from eukaryotes with mitochondria.

It has a peculiar mode of reproduction: two equal-sized nuclei,
both of which divide, with the two halves going to two daughter cells.
This obviously has some features in common with meiosis, and it would
be interesting to see some up to date literature on how the two
might be related. If it could be shown that Giardia's mode is
the more primitive, we would have a negative answer to Mystery 3
and perhaps a significant advance in the direction of Mystery 2.


Unfortunately, my most promising lead so far has led to a temporary
dead end. It is here:

https://microbewiki.kenyon.edu/index.php/Giardia_lamblia#Description_and_significance

And here is the relevant excerpt:

The Giardia lamblia genome project at the Marine Biological Laboratory in Masshuttes, in which shotgun sequencing is used to obtain the full genome of G. lamblia, is currently under way. Annotated genome assembly is released regularly and is made available to researchers worldwide. The analysis of gene function is done currently in collaboration with Dr. Frances Gillin at UCSD molecular pathology. This study is of great significance in evolutionary biology, as it will provide insight into the history of G. lamblia': its relation with the mitochondria, and its role in serving as the bridge between prokaryotes and eukaryotes.

The link to the project is in the second through fifth words of
the excerpt, but it leads to the Marine Biological
Laboratory at U. Chicago and "Page not found." Looking elsewhere,
using those words, led me to:

The Giardia genome project database
FEMS Microbiology Letters 189 (2000) 271-273
Elsevier

It's certainly optimistic about finding the craved bridge between
prokaryotes and eukaryotes, but the home page it gives for the
project, www.mbl.edu/Giardia takes one the same "Page not found"
at U. Chicago.


TGIF

Peter Nyikos
Professor, Dept. of Mathematics

U. of South Carolina -- standard disclaimer--
http://people.math.sc.edu

[John Harshman]

On 5/17/19 6:29 PM, Peter Nyikos wrote:
> I didn't want to go on my usual weekend posting break before
> saying some words about:
>
> Mystery 2: How did meiosis originate?
>
> At our present state of knowledge, this is such a formidable mystery
> that it seems best to approach it, before seriously addressing it,
> with questions like the following:
>
> Mystery 3: Did meiosis predate the LCA of living eukaryotes?

Yes, obviously, unless you want to propose that meiosis arose multiple
times convergently.

> Here LCA stands for Last Common Ancestor. This is quite distinct
> from asking whether the first eukaryote had meiosis.
> What makes it distinct is that we are dealing with
> the great-granddaddy of all ghost taxa.
>
> The gap in complexity between any prokaryote and the simplest living
> eukaryote is enormous. So even a billion years might have elapsed
> between the first eukaryotes and that LCA,
> with all the intermediate forms vanishing without a trace: no
> real chance of ever finding even their fossils.
>
>
> Before going further, let us recall the actual definition of "eukaryote."
> The following is taken from the biology text I keep using:
>
> eukaryotic cell: A type of cell with a membrane-enclosed nucleus
> and membrane-enclosed organelles.
>
> Note that there is no mention of meiosis or even mitosis; nor of
> endosymbionts (mitochondria and plastids) even though they are
> examples of organelles.

No, they're examples of membrane-bound organelles. In fact they're the
major examples thereof. Note that the definition is a bit problematic,
referring to two potentially independent characters that probably arose
at quite different times. The "first eukaryote" would be the species in
which the last of those characters arose. Further, it wouldn't have
happened in one shot, so how do you decide when the character is
complete enough?

Don't know about that, but it appears that Giardia and other diplomonads
are embedded within a larger group Fornicata, most of whose members have
the usual single nucleus. So Giardia isn't a basal eukaryote and its
characteristics are not primitive.

https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-8-205

[Oxyaena]

On 5/15/2019 4:27 PM, Peter Nyikos wrote:
[snip]

>
>
> How this happens was a mystery eleven years ago, and
> I have found no sign that it is any less of a mystery now.

https://www.ncbi.nlm.nih.gov/pubmed/26811992

Maybe it's because you haven't looked hard enough. Big surprise there.


[snip]

[Peter Nyikos]

On Friday, May 17, 2019 at 11:35:03 PM UTC-4, John Harshman wrote:
> On 5/17/19 6:29 PM, Peter Nyikos wrote:
> > I didn't want to go on my usual weekend posting break before
> > saying some words about:
> >
> > Mystery 2: How did meiosis originate?
> >
> > At our present state of knowledge, this is such a formidable mystery
> > that it seems best to approach it, before seriously addressing it,
> > with questions like the following:
> >
> > Mystery 3: Did meiosis predate the LCA of living eukaryotes?
>
> Yes, obviously, unless you want to propose that meiosis arose multiple
> times convergently.

Your comment assumes a nonexistent shared understanding, and is not
conducive to fruitful discussion.

You are "obviously" assuming that the tree of Domain Eukarya has been
successfully rooted in a way that has "obviously" found general
acceptance. And for that, you need a source substantially more
recent than the 2007 paper that is the only article you've
referenced here (at the end of this post, in a similar context).

By the way, I would no sooner propose that meiosis, as described
in the OP, arose convergently than I would propose that flight
remiges arose in two separate lineages which originally lacked
so much as "dinofuzz."


<snip comments to which you did not respond, about the huge
gap between prokaryotes and eukaryotes probably being a temporal
one as well as a structural/genetic one>

> > Before going further, let us recall the actual definition of "eukaryote."
> > The following is taken from the biology text I keep using:
> >
> > eukaryotic cell: A type of cell with a membrane-enclosed nucleus
> > and membrane-enclosed organelles.
> >
> > Note that there is no mention of meiosis or even mitosis; nor of
> > endosymbionts (mitochondria and plastids) even though they are
> > examples of organelles.
>
> No, they're examples of membrane-bound organelles.

To be precise: multiply membrane-bound organelles.

In contrast to organelles of the endomembrane system,
mitochondria have two membranes separating their innermost space
from the cytosol, and chloroplasts typically have three.
--_Biology_, 8th ed. Campbell, Reece et al, (2008) p. 109

> In fact they're the major examples thereof.

"the major" is subjective. On p. 123 [*ibid*], the endoplasmic
reticulum is described as having "membrane-bounded tubules and sacs,"
and vacuoles are described as "Large membrane-bounded vesicle[s] in plants."

> Note that the definition is a bit problematic,
> referring to two potentially independent characters that probably arose
> at quite different times.

Nothing problematic about it: it doesn't refer to *just* two things,
see above.


<snip GIGO for the sake of brevity>

> > It now seems well established that all eukaryotes undergo mitosis
> > and that they have mitochondria or the remnants of mitochondria.

OOps, I'm glad I hedged with "seems". There is one eukaryote that
is believed to lack all trace of mitochondria: *Monocercomonoides*:

https://www.cell.com/current-biology/fulltext/S0960-9822(16)30263-9

> > On the other hand, there are many eukaryotes, including a few
> > vertebrates, that do not reproduce sexually. However, almost all
> > of these (including all the vertebrate examples) are easily
> > seen to have evolved from organisms that underwent meiosis in
> > some part of their life cycle.
> >
> > A possible exception that is rather well known because it is
> > the most common protist that is parasitic on humans: *Giardia lamblia*.

However, there are many asexually reproducing eukaryotes; for
example, there seems to be no sexual reproduction in the clade Excavata,
which includes *Giardia*. [*ibid*, p. 578].

Fornicata doesn't seem to be recognized at present, unlike Excavata,
which is one of the five "supergroups" in the hypothesis adopted
in the 2008 text [*ibid*].
You are relying on a 2007 paper below.

> So Giardia isn't a basal eukaryote and its
> characteristics are not primitive.
>
> https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-8-205

Contrary to your cocksure claim, this 2007 article is mostly about
the polyphyletic status of what was once thought to be a clade
of single-nucleus eukaryotes. The authors argue that they
arose convergently within the diplomonads.

Also, the 2008 textbook I reference above says the following on p. 577:

The ongoing changes in our understanding of the phylogeny of
protists pose challenges to students and instructors alike.
Hypotheses about these relationships are a hotbed of scientific
activity, changing rapidly as new data cause previous ideas
to be modified or discarded. In this chapter, our discussion
is organized around one current hypothesis: the five supergroups
of eukaryotes shown in Figure 28.3, on the next two pages.
Because the root of the eukaryotic tree is not known, all
five supergroups are shown as diverging simultaneously
from a common ancestor -- something that we know is not correct,
but we do not know which organisms were the first to diverge from the others.


Peter Nyikos

Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu

PS You aren't pulling your weight on this thread, John. You and Oxyaena
together haven't been as helpful as Ernest Major was in just his
one post, and he hasn't participated since then.

[Walter Bushell]

In article <bKOdnYr1jb3d4ULB...@giganews.com>,

John Harshman <jhar...@pacbell.net> wrote:

>
> Don't know about that, but it appears that Giardia and other diplomonads
> are embedded within a larger group Fornicata, most of whose members have
> the usual single nucleus. So Giardia isn't a basal eukaryote and its
> characteristics are not primitive.
>
> https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-8-205
> >

Good grief, all the members of that group fornicate?

--
Never attribute to stupidity that which can be explained by greed. Me.

[Peter Nyikos]

On Monday, May 20, 2019 at 9:30:03 AM UTC-4, Walter Bushell wrote:
> In article <bKOdnYr1jb3d4ULB...@giganews.com>,
> John Harshman <jhar...@pacbell.net> wrote:
>
> >
> > Don't know about that, but it appears that Giardia and other diplomonads
> > are embedded within a larger group Fornicata, most of whose members have
> > the usual single nucleus. So Giardia isn't a basal eukaryote and its
> > characteristics are not primitive.
> >
> > https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-8-205
> > >
>
> Good grief, all the members of that group fornicate?

Stop hiding your light under a bushel, Walter, and try contributing
on-topic to this thread.

I mean it seriously, Walter. I hope the whole context of my pun makes that clear. You DO recognize the allusion to the Sermon on the Mount, don't you?


Peter Nyikos

[John Harshman]

On 5/20/19 6:03 AM, Peter Nyikos wrote:
> On Friday, May 17, 2019 at 11:35:03 PM UTC-4, John Harshman wrote:
>> On 5/17/19 6:29 PM, Peter Nyikos wrote:
>>> I didn't want to go on my usual weekend posting break before
>>> saying some words about:
>>>
>>> Mystery 2: How did meiosis originate?
>>>
>>> At our present state of knowledge, this is such a formidable mystery
>>> that it seems best to approach it, before seriously addressing it,
>>> with questions like the following:
>>>
>>> Mystery 3: Did meiosis predate the LCA of living eukaryotes?
>>
>> Yes, obviously, unless you want to propose that meiosis arose multiple
>> times convergently.
>
> Your comment assumes a nonexistent shared understanding, and is not
> conducive to fruitful discussion.
>
> You are "obviously" assuming that the tree of Domain Eukarya has been
> successfully rooted in a way that has "obviously" found general
> acceptance. And for that, you need a source substantially more
> recent than the 2007 paper that is the only article you've
> referenced here (at the end of this post, in a similar context).
>
> By the way, I would no sooner propose that meiosis, as described
> in the OP, arose convergently than I would propose that flight
> remiges arose in two separate lineages which originally lacked
> so much as "dinofuzz."

So we are agreed at least that if Giardia is located within a large
group of eukaryotes that have regular meiosis, it's not relevant to the
evolution of meiosis. The remaining contention would be about the tree
itself. Giardia was once presumed to be a basal eukaryote, but I see no
recent revivals of that claim. What do you find?

> <snip comments to which you did not respond, about the huge
> gap between prokaryotes and eukaryotes probably being a temporal
> one as well as a structural/genetic one>

It doesn't seem relevant to a discussion of meiosis, so I saw no reason
to discuss it.

>>> Before going further, let us recall the actual definition of "eukaryote."
>>> The following is taken from the biology text I keep using:
>>>
>>> eukaryotic cell: A type of cell with a membrane-enclosed nucleus
>>> and membrane-enclosed organelles.
>>>
>>> Note that there is no mention of meiosis or even mitosis; nor of
>>> endosymbionts (mitochondria and plastids) even though they are
>>> examples of organelles.
>>
>> No, they're examples of membrane-bound organelles.
>
> To be precise: multiply membrane-bound organelles.
>
> In contrast to organelles of the endomembrane system,
> mitochondria have two membranes separating their innermost space
> from the cytosol, and chloroplasts typically have three.
> --_Biology_, 8th ed. Campbell, Reece et al, (2008) p. 109
>
>> In fact they're the major examples thereof.
>
> "the major" is subjective. On p. 123 [*ibid*], the endoplasmic
> reticulum is described as having "membrane-bounded tubules and sacs,"
> and vacuoles are described as "Large membrane-bounded vesicle[s] in plants."

Yes, those are membrane-bound organelles too. But it's the mitochondria
that are most often mentioned in that context.

>> Note that the definition is a bit problematic,
>> referring to two potentially independent characters that probably arose
>> at quite different times.
>
> Nothing problematic about it: it doesn't refer to *just* two things,
> see above.

The more things it refers to, the more problematic.

>>> It now seems well established that all eukaryotes undergo mitosis
>>> and that they have mitochondria or the remnants of mitochondria.
>
> OOps, I'm glad I hedged with "seems". There is one eukaryote that
> is believed to lack all trace of mitochondria: *Monocercomonoides*:
>
> https://www.cell.com/current-biology/fulltext/S0960-9822(16)30263-9

Primitively or secondarily? What is the phylogenetic position of
Monocercomonoides? Based on a quick google, it seems that secondary loss
is the parsiminious position.

>>> On the other hand, there are many eukaryotes, including a few
>>> vertebrates, that do not reproduce sexually. However, almost all
>>> of these (including all the vertebrate examples) are easily
>>> seen to have evolved from organisms that underwent meiosis in
>>> some part of their life cycle.
>>>
>>> A possible exception that is rather well known because it is
>>> the most common protist that is parasitic on humans: *Giardia lamblia*.
>
> However, there are many asexually reproducing eukaryotes; for
> example, there seems to be no sexual reproduction in the clade Excavata,
> which includes *Giardia*. [*ibid*, p. 578].

But there is meiosis, right?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048101/

What do you mean by "recognized at present"? Recognized by whom?
Fornicata is a subdivision of Excavata. Here, for example:

http://tolweb.org/Eukaryotes/3

>> So Giardia isn't a basal eukaryote and its
>> characteristics are not primitive.
>>
>> https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-8-205
>
> Contrary to your cocksure claim, this 2007 article is mostly about
> the polyphyletic status of what was once thought to be a clade
> of single-nucleus eukaryotes. The authors argue that they
> arose convergently within the diplomonads.

Try not to characterize others' statements with needless pejoratives.
There's no point to it and it introduces hostility to what should be a
simple scientific discussion.

The article may be mostly about one thing, but it supports what I'm
claiming also, which is the point.

> Also, the 2008 textbook I reference above says the following on p. 577:
>
> The ongoing changes in our understanding of the phylogeny of
> protists pose challenges to students and instructors alike.
> Hypotheses about these relationships are a hotbed of scientific
> activity, changing rapidly as new data cause previous ideas
> to be modified or discarded. In this chapter, our discussion
> is organized around one current hypothesis: the five supergroups
> of eukaryotes shown in Figure 28.3, on the next two pages.
> Because the root of the eukaryotic tree is not known, all
> five supergroups are shown as diverging simultaneously
> from a common ancestor -- something that we know is not correct,
> but we do not know which organisms were the first to diverge from the others.

Not a problem, since Fornicata is a clade within Excavata, and nesting
within excavates is enough to make the point. There has also been some
progress since 2008. A 2008 textbook in general wouldn't even be
expected to reference papers from 2007.

Here are a few more recent references:

https://www.pnas.org/content/106/10/3859

https://cshperspectives.cshlp.org/content/6/5/a016147.full

You will note that even Excavata is not the sister group of other
eukaryotes, and thus its odd characteristics are not parsimoniously to
be construed as primitive.

[Peter Nyikos]

On Monday, May 20, 2019 at 11:40:03 AM UTC-4, John Harshman wrote:
> On 5/20/19 6:03 AM, Peter Nyikos wrote:
> > On Friday, May 17, 2019 at 11:35:03 PM UTC-4, John Harshman wrote:
> >> On 5/17/19 6:29 PM, Peter Nyikos wrote:

> >>> Mystery 3: Did meiosis predate the LCA of living eukaryotes?
> >>
> >> Yes, obviously, unless you want to propose that meiosis arose multiple
> >> times convergently.
> >
> > Your comment assumes a nonexistent shared understanding, and is not
> > conducive to fruitful discussion.
> >
> > You are "obviously" assuming that the tree of Domain Eukarya has been
> > successfully rooted in a way that has "obviously" found general
> > acceptance. And for that, you need a source substantially more
> > recent than the 2007 paper that is the only article you've
> > referenced here (at the end of this post, in a similar context).
> >
> > By the way, I would no sooner propose that meiosis, as described
> > in the OP, arose convergently than I would propose that flight
> > remiges arose in two separate lineages which originally lacked
> > so much as "dinofuzz."
>
> So we are agreed at least that if Giardia is located within a large
> group of eukaryotes that have regular meiosis, it's not relevant to the
> evolution of meiosis.

We could have agreed on that when I was still in high school.
But that's beside any point either of us was making.

And it does nothing to ameliorate the fact that you made
gratuitous assumptions while calling things "obvious" that
depended on those assumptions.

> The remaining contention would be about the tree
> itself. Giardia was once presumed to be a basal eukaryote, but I see no
> recent revivals of that claim. What do you find?

Nothing along those lines. But I've found a far more promising
possibility: the jakobids. And it is for the opposite reason:
its mitochondria preserve more of the bacterial genome than any
other eukaryotes.

https://en.wikipedia.org/wiki/Jakobid

Had I known about them when I started this thread, I would
have considered them to be the best bet from the beginning.
Can you see why?


<big snip of things that we might decide to discuss later>

> > However, there are many asexually reproducing eukaryotes; for
> > example, there seems to be no sexual reproduction in the clade Excavata,
> > which includes *Giardia*. [*ibid*, p. 578].
>
> But there is meiosis, right?

Why do you ask me, when the source you give only talks about
the existence of "homologs of meiotic genes" and "meiosis-specific
proteins" and similar related matters?

> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048101/

The word "meiotic" in the title is misleading. I've seen loose talk
like this which even attributes the beginning of meiosis to
prokaryotes.


Anyway, this might not be relevant where Jakobida is concerned.
Read on.


<moderate snip of things we might discuss later>

> >> Don't know about that, but it appears that Giardia and other diplomonads
> >> are embedded within a larger group Fornicata, most of whose members have
> >> the usual single nucleus.
> >
> > Fornicata doesn't seem to be recognized at present, unlike Excavata,
> > which is one of the five "supergroups" in the hypothesis adopted
> > in the 2008 text [*ibid*].
> > You are relying on a 2007 paper below.
>
> What do you mean by "recognized at present"? Recognized by whom?
> Fornicata is a subdivision of Excavata. Here, for example:
>
> http://tolweb.org/Eukaryotes/3

Dated 2007. 'Nuff said?

> >> So Giardia isn't a basal eukaryote and its
> >> characteristics are not primitive.
> >>
> >> https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-8-205
> >
> > Contrary to your cocksure claim, this 2007 article is mostly about
> > the polyphyletic status of what was once thought to be a clade
> > of single-nucleus eukaryotes. The authors argue that they
> > arose convergently within the diplomonads.
>
> Try not to characterize others' statements with needless pejoratives.

Try not to assume things you can't back up, while calling
the conclusions "obvious." And be a man, and take what's
coming to you without whining.

<snip>

>
> > Also, the 2008 textbook I reference above says the following on p. 577:
> >
> > The ongoing changes in our understanding of the phylogeny of
> > protists pose challenges to students and instructors alike.
> > Hypotheses about these relationships are a hotbed of scientific
> > activity, changing rapidly as new data cause previous ideas
> > to be modified or discarded. In this chapter, our discussion
> > is organized around one current hypothesis: the five supergroups
> > of eukaryotes shown in Figure 28.3, on the next two pages.
> > Because the root of the eukaryotic tree is not known, all
> > five supergroups are shown as diverging simultaneously
> > from a common ancestor -- something that we know is not correct,
> > but we do not know which organisms were the first to diverge from the others.
>
> Not a problem,

The hotbed is a problem, and it still exists.


<snip minutiae>

> Here are a few more recent references:
>
> https://www.pnas.org/content/106/10/3859

> https://cshperspectives.cshlp.org/content/6/5/a016147.full
>
> You will note that even Excavata is not the sister group of other
> eukaryotes,

The first article, dated 2011, "reforms" it into one of three "supergroups"
in an unresolved trichotomy, by eliminating dubious "members."

The second article admits that efforts to root the eukaryotic
tree have been unsuccessful. One of six possible roots is
the one that makes the reformed Excavata one of the two branches
of the first split.

Going along Excavata in the tree of life they give, I see
that the first split looks like an unresolved tetrachotomy,
with one branch including Jakobids and other asexually
reproducing protists.

> and thus its odd characteristics are not parsimoniously to
> be construed as primitive.

What have you decided to be "its odd characteristics," and why?

Try not to be so cryptic. It's what landed you in trouble
at the beginning of this post.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--

Univ. of South Carolina at Columbia
http://people.math.sc.edu

[John Harshman]

I think we have now established that my gratuitous assumption, by which
I am gratuitously assuming you mean that the tree has been rooted
sufficiently that Giardia/diplomonads is not the sister group of all
other eukaryotes, is correct.

>> The remaining contention would be about the tree
>> itself. Giardia was once presumed to be a basal eukaryote, but I see no
>> recent revivals of that claim. What do you find?
>
> Nothing along those lines. But I've found a far more promising
> possibility: the jakobids. And it is for the opposite reason:
> its mitochondria preserve more of the bacterial genome than any
> other eukaryotes.
>
> https://en.wikipedia.org/wiki/Jakobid
>
> Had I known about them when I started this thread, I would
> have considered them to be the best bet from the beginning.
> Can you see why?

In fact I can't. According to the article, they're nested deep within
Excavata and their odd features are, once more, probably not primitive.
Further, the way in which they are odd has nothing to do with meiosis.
So could you explain?

>>> However, there are many asexually reproducing eukaryotes; for
>>> example, there seems to be no sexual reproduction in the clade Excavata,
>>> which includes *Giardia*. [*ibid*, p. 578].
>>
>> But there is meiosis, right?
>
> Why do you ask me, when the source you give only talks about
> the existence of "homologs of meiotic genes" and "meiosis-specific
> proteins" and similar related matters?

Apparently even Giardia shows evidence of occasional gene exchange among
individuals, though again it apparently hasn't been directly observed.

>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048101/
>
> The word "meiotic" in the title is misleading. I've seen loose talk
> like this which even attributes the beginning of meiosis to
> prokaryotes.
>
>
> Anyway, this might not be relevant where Jakobida is concerned.
> Read on.
>
>
> <moderate snip of things we might discuss later>
>
>
>>>> Don't know about that, but it appears that Giardia and other diplomonads
>>>> are embedded within a larger group Fornicata, most of whose members have
>>>> the usual single nucleus.
>>>
>>> Fornicata doesn't seem to be recognized at present, unlike Excavata,
>>> which is one of the five "supergroups" in the hypothesis adopted
>>> in the 2008 text [*ibid*].
>>> You are relying on a 2007 paper below.
>>
>> What do you mean by "recognized at present"? Recognized by whom?
>> Fornicata is a subdivision of Excavata. Here, for example:
>>
>> http://tolweb.org/Eukaryotes/3
>
> Dated 2007. 'Nuff said?

2009, actually. And as far as I can tell it's still current.

>>>> So Giardia isn't a basal eukaryote and its
>>>> characteristics are not primitive.
>>>>
>>>> https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-8-205
>>>
>>> Contrary to your cocksure claim, this 2007 article is mostly about
>>> the polyphyletic status of what was once thought to be a clade
>>> of single-nucleus eukaryotes. The authors argue that they
>>> arose convergently within the diplomonads.
>>
>> Try not to characterize others' statements with needless pejoratives.
>
> Try not to assume things you can't back up, while calling
> the conclusions "obvious." And be a man, and take what's
> coming to you without whining.

More needless pejoratives.

>>> Also, the 2008 textbook I reference above says the following on p. 577:
>>>
>>> The ongoing changes in our understanding of the phylogeny of
>>> protists pose challenges to students and instructors alike.
>>> Hypotheses about these relationships are a hotbed of scientific
>>> activity, changing rapidly as new data cause previous ideas
>>> to be modified or discarded. In this chapter, our discussion
>>> is organized around one current hypothesis: the five supergroups
>>> of eukaryotes shown in Figure 28.3, on the next two pages.
>>> Because the root of the eukaryotic tree is not known, all
>>> five supergroups are shown as diverging simultaneously
>>> from a common ancestor -- something that we know is not correct,
>>> but we do not know which organisms were the first to diverge from the others.
>>
>> Not a problem,
>
> The hotbed is a problem, and it still exists.

Sure, but there are many issues in that hotbed that have been resolved,
and one of them is the monophyly of Excavata.

>> Here are a few more recent references:
>>
>> https://www.pnas.org/content/106/10/3859
>
>> https://cshperspectives.cshlp.org/content/6/5/a016147.full
>>
>> You will note that even Excavata is not the sister group of other
>> eukaryotes,
>
> The first article, dated 2011, "reforms" it into one of three "supergroups"
> in an unresolved trichotomy, by eliminating dubious "members."
>
> The second article admits that efforts to root the eukaryotic
> tree have been unsuccessful. One of six possible roots is
> the one that makes the reformed Excavata one of the two branches
> of the first split.

True, though that isn't the rooting the author thinks has the best
support. And even so, it makes neither diplomonads nor jakobids the
sister group of other eukaryotes.

> Going along Excavata in the tree of life they give, I see
> that the first split looks like an unresolved tetrachotomy,
> with one branch including Jakobids and other asexually
> reproducing protists.

True. (Incidentally, the proper spelling is "tetratomy".)

>> and thus its odd characteristics are not parsimoniously to
>> be construed as primitive.
>
> What have you decided to be "its odd characteristics," and why?

I refer to the characteristics you have mentioned, the ones that are
your reason for bringing up Giardia in the first place, the double
nucleus and such. Since these are characteristics of diplomonads, which
lie within excavates, and other excavates do not share these features,
they are not features of primitive eukaryotes.

> Try not to be so cryptic. It's what landed you in trouble
> at the beginning of this post.

I was in trouble?

[Peter Nyikos]

Of course, what you are "gratuitously assuming" is false. What I was
referring to, obviously, is your blanket statement
that the LCA of Eukarya had meiosis, qualified only by the "obvious assumption" that the tree of Eukarya had been firmly rooted.

And by "referring to, obviously..." I mean that anyone who carefully
reads what has transpired between us can easily see it.

The paragraph to which I am responding is too full of baloney to be
worth unraveling. Kindly re-state it if you want me to agree on
some part of it with you.

>
> >> The remaining contention would be about the tree
> >> itself. Giardia was once presumed to be a basal eukaryote, but I see no
> >> recent revivals of that claim. What do you find?
> >
> > Nothing along those lines. But I've found a far more promising
> > possibility: the jakobids. And it is for the opposite reason:
> > its mitochondria preserve more of the bacterial genome than any
> > other eukaryotes.
> >
> > https://en.wikipedia.org/wiki/Jakobid
> >
> > Had I known about them when I started this thread, I would
> > have considered them to be the best bet from the beginning.
> > Can you see why?
>
> In fact I can't. According to the article, they're nested deep within
> Excavata

Which article would that be? the 2014 article that you posted last time
around? "According to the article" is a distortion of that article;
see below.

> and their odd features are, once more, probably not primitive.

"once more" assumes a falsehood. The post to which you are
replying is the only place on the whole internet on which I've
written about the Jakobids.

And what do you mean by "odd features"? I gave one all-embracing one:
go back and re-read it.

>Further, the way in which they are odd has nothing to do with meiosis.
> So could you explain?

Could you explain your switch from plural to singular here?

In partial answer to your question: you seem to think
that phylogenetic trees are the be-all and end-all of systematics.
But the tree does not give an adequate reason for rejecting various
states as primitive, because it is always a compromise between
a huge number of pieces of conflicting evidence.



<snip of things we can discuss later, if we see a need for it>

> >>>> So Giardia isn't a basal eukaryote and its
> >>>> characteristics are not primitive.
> >>>>
> >>>> https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-8-205
> >>>
> >>> Contrary to your cocksure claim, this 2007 article is mostly about
> >>> the polyphyletic status of what was once thought to be a clade
> >>> of single-nucleus eukaryotes. The authors argue that they
> >>> arose convergently within the diplomonads.
> >>
> >> Try not to characterize others' statements with needless pejoratives.
> >
> > Try not to assume things you can't back up, while calling
> > the conclusions "obvious." And be a man, and take what's
> > coming to you without whining.
>
> More needless pejoratives.

"whining" is the only pejorative, and I believe it is warranted.
Care to dispute the matter?

>
> >>> Also, the 2008 textbook I reference above says the following on p. 577:
> >>>
> >>> The ongoing changes in our understanding of the phylogeny of
> >>> protists pose challenges to students and instructors alike.
> >>> Hypotheses about these relationships are a hotbed of scientific
> >>> activity, changing rapidly as new data cause previous ideas
> >>> to be modified or discarded. In this chapter, our discussion
> >>> is organized around one current hypothesis: the five supergroups
> >>> of eukaryotes shown in Figure 28.3, on the next two pages.
> >>> Because the root of the eukaryotic tree is not known, all
> >>> five supergroups are shown as diverging simultaneously
> >>> from a common ancestor -- something that we know is not correct,
> >>> but we do not know which organisms were the first to diverge from the others.
> >>
> >> Not a problem,
> >
> > The hotbed is a problem, and it still exists.
>
> Sure, but there are many issues in that hotbed that have been resolved,
> and one of them is the monophyly of Excavata.

No, that isn't one of them. The second article you reference below,
dated 2014, leaves open the possibility that it is paraphyletic.
Keep reading.

>
> >> Here are a few more recent references:
> >>
> >> https://www.pnas.org/content/106/10/3859
> >
> >> https://cshperspectives.cshlp.org/content/6/5/a016147.full
> >>
> >> You will note that even Excavata is not the sister group of other
> >> eukaryotes,
> >
> > The first article, dated 2011, "reforms" it into one of three "supergroups"
> > in an unresolved trichotomy, by eliminating dubious "members."
> >
> > The second article admits that efforts to root the eukaryotic
> > tree have been unsuccessful. One of six possible roots is
> > the one that makes the reformed Excavata one of the two branches
> > of the first split.
>
> True, though that isn't the rooting the author thinks has the best
> support.

Fabien Burki is sufficiently unsure of his choice that he
lists five possible alternatives. He shows an admirable
degree of scientific caution all through the long and
thorough article. It's something you would do well to emulate
as best you can.

> And even so, it makes neither diplomonads nor jakobids the
> sister group of other eukaryotes.

Sink me. So they are.

But if you look out *that* window...

-- Percy, in the title role of "The Scarlet Pimpernel,"
at the climactic turn of events in the 1982 film.

The relevant "window" here is the tree of life provided in
your 2014 reference:

https://cshperspectives.cshlp.org/content/6/5/a016147/F1.large.jpg

And if you "look out that window," you will see, close to the edge,
one of the five dotted arrows that mark possible rootings of
the tree of Eukarya. On one branch off that split, there are just
three taxa: euglenids, diplonemids, and kinetoblastids.

On the other branch, representing ALL other eukaryotes, the jakobids
are the second of two basal taxa: the jakobids are the
sister group of all the rest.

The first to branch off after the original split is a group called "heteroloboseans",
and they are not mentioned in the text of the article, nor in the
references. I have been unable to find out anything about them.
There are groups with similar names, but I have found none
of them to even remotely corresponds to the placement this group has
on this tree. But unless they have meiosis -- real meiosis, not
just some factors unique to it in extant organisms -- there
is no support for your claim there.

>
> > Going along Excavata in the tree of life they give, I see
> > that the first split looks like an unresolved tetrachotomy,
> > with one branch including Jakobids and other asexually
> > reproducing protists.
>
> True. (Incidentally, the proper spelling is "tetratomy".)

This changes if the tree is rooted in the place I described
this time around. The tetratomy now has all non-excavates
replacing Excavata as the fourth branch emanating from that point.


Unlike Percy's final victory over Chauvelin in the 1982 film, my
conclusion is more modest: I am quite happy about the hypothesis
that this is where the root belongs. And, at the rate you are going,
I don't think I'll need to abandon it for quite some time, if ever.

Of course, that assumes that I don't find out otherwise from
someone less lazy than yourself. [Caution: you have admitted
to being lazy in the past, and there is ample evidence of that.]

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--

University of South Carolina
http://people.math.sc.edu

PS If you know much of anything about any version of The Scarlet
Pimpernel, you can probably find a pun implicit in what I've written here,
even though it is backwards from my hypothesis.

[John Harshman]

It doesn't need to be firmly rooted if all the possible roots fail to
put diplomonads next to the root. Would you agree?

>>>> The remaining contention would be about the tree
>>>> itself. Giardia was once presumed to be a basal eukaryote, but I see no
>>>> recent revivals of that claim. What do you find?
>>>
>>> Nothing along those lines. But I've found a far more promising
>>> possibility: the jakobids. And it is for the opposite reason:
>>> its mitochondria preserve more of the bacterial genome than any
>>> other eukaryotes.
>>>
>>> https://en.wikipedia.org/wiki/Jakobid
>>>
>>> Had I known about them when I started this thread, I would
>>> have considered them to be the best bet from the beginning.
>>> Can you see why?
>>
>> In fact I can't. According to the article, they're nested deep within
>> Excavata
>
> Which article would that be? the 2014 article that you posted last time
> around? "According to the article" is a distortion of that article;
> see below.

No. According to the Wikipedia article you linked just above.

>> and their odd features are, once more, probably not primitive.
>
> "once more" assumes a falsehood. The post to which you are
> replying is the only place on the whole internet on which I've
> written about the Jakobids.

I refer to your previous candidate for primitive eukaryote, Giardia.

> And what do you mean by "odd features"? I gave one all-embracing one:
> go back and re-read it.

Fine. "Odd feature", then.

>> Further, the way in which they are odd has nothing to do with meiosis.
>> So could you explain?
>
> Could you explain your switch from plural to singular here?

They have a number of odd features, of which you mentioned one. I bow to
your preference for the singular.

> In partial answer to your question: you seem to think
> that phylogenetic trees are the be-all and end-all of systematics.
> But the tree does not give an adequate reason for rejecting various
> states as primitive, because it is always a compromise between
> a huge number of pieces of conflicting evidence.

Not sure what you mean by that. Do you mean that the tree itself is
uncertain and therefore not a basis for character inference, or do you
mean that not even a certain tree is such a basis? If the former, I
think we know enough to be reasonably certain about enough parts of the
tree for the present purpose. If the latter, it's true that the
principle of parsimony can be violated, we have also agreed that meiosis
is unlikely to have evolved twice; if our choice is between multiple
losses and multiple gains, we should generally prefer multiple losses.

>>>>>> So Giardia isn't a basal eukaryote and its
>>>>>> characteristics are not primitive.
>>>>>>
>>>>>> https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-8-205
>>>>>
>>>>> Contrary to your cocksure claim, this 2007 article is mostly about
>>>>> the polyphyletic status of what was once thought to be a clade
>>>>> of single-nucleus eukaryotes. The authors argue that they
>>>>> arose convergently within the diplomonads.

>>>>> Also, the 2008 textbook I reference above says the following on p. 577:
>>>>>
>>>>> The ongoing changes in our understanding of the phylogeny of
>>>>> protists pose challenges to students and instructors alike.
>>>>> Hypotheses about these relationships are a hotbed of scientific
>>>>> activity, changing rapidly as new data cause previous ideas
>>>>> to be modified or discarded. In this chapter, our discussion
>>>>> is organized around one current hypothesis: the five supergroups
>>>>> of eukaryotes shown in Figure 28.3, on the next two pages.
>>>>> Because the root of the eukaryotic tree is not known, all
>>>>> five supergroups are shown as diverging simultaneously
>>>>> from a common ancestor -- something that we know is not correct,
>>>>> but we do not know which organisms were the first to diverge from the others.
>>>>
>>>> Not a problem,
>>>
>>> The hotbed is a problem, and it still exists.
>>
>> Sure, but there are many issues in that hotbed that have been resolved,
>> and one of them is the monophyly of Excavata.
>
> No, that isn't one of them. The second article you reference below,
> dated 2014, leaves open the possibility that it is paraphyletic.
> Keep reading.

That possibility is just mentioned as a claim by somebody else. More
importantly, paraphyly doesn't matter if both basal branches have
meiosis somewhere on them.

>>>> Here are a few more recent references:
>>>>
>>>> https://www.pnas.org/content/106/10/3859
>>>
>>>> https://cshperspectives.cshlp.org/content/6/5/a016147.full
>>>>
>>>> You will note that even Excavata is not the sister group of other
>>>> eukaryotes,
>>>
>>> The first article, dated 2011, "reforms" it into one of three "supergroups"
>>> in an unresolved trichotomy, by eliminating dubious "members."
>>>
>>> The second article admits that efforts to root the eukaryotic
>>> tree have been unsuccessful. One of six possible roots is
>>> the one that makes the reformed Excavata one of the two branches
>>> of the first split.
>>
>> True, though that isn't the rooting the author thinks has the best
>> support.
>
> Fabien Burki is sufficiently unsure of his choice that he
> lists five possible alternatives. He shows an admirable
> degree of scientific caution all through the long and
> thorough article. It's something you would do well to emulate
> as best you can.

Nevertheless, he has a preferred rooting.

>> And even so, it makes neither diplomonads nor jakobids the
>> sister group of other eukaryotes.
>
> Sink me. So they are.
>
> But if you look out *that* window...
>
> -- Percy, in the title role of "The Scarlet Pimpernel,"
> at the climactic turn of events in the 1982 film.
>
> The relevant "window" here is the tree of life provided in
> your 2014 reference:
>
> https://cshperspectives.cshlp.org/content/6/5/a016147/F1.large.jpg
>
> And if you "look out that window," you will see, close to the edge,
> one of the five dotted arrows that mark possible rootings of
> the tree of Eukarya. On one branch off that split, there are just
> three taxa: euglenids, diplonemids, and kinetoblastids.
>
> On the other branch, representing ALL other eukaryotes, the jakobids
> are the second of two basal taxa: the jakobids are the
> sister group of all the rest.
>
> The first to branch off after the original split is a group called "heteroloboseans",
> and they are not mentioned in the text of the article, nor in the
> references. I have been unable to find out anything about them.
> There are groups with similar names, but I have found none
> of them to even remotely corresponds to the placement this group has
> on this tree. But unless they have meiosis -- real meiosis, not
> just some factors unique to it in extant organisms -- there
> is no support for your claim there.

Can we agree that both the rooting and the taxa around the base are not
important to the question if there are taxa with meiosis on both sides
of the root? (This would be the case if we agree that meiosis is
unlikely to have arisen twice; thus taxa without it must be explained by
loss. Only if one of the two basal branches were completely lacking
meiosis would we postulate that meiosis was not present in the common
ancestor.)

A little google finds this:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517231/

I direct your attention especially to Fig. 2.

>>> Going along Excavata in the tree of life they give, I see
>>> that the first split looks like an unresolved tetrachotomy,
>>> with one branch including Jakobids and other asexually
>>> reproducing protists.
>>
>> True. (Incidentally, the proper spelling is "tetratomy".)
>
> This changes if the tree is rooted in the place I described
> this time around. The tetratomy now has all non-excavates
> replacing Excavata as the fourth branch emanating from that point.
>
>
> Unlike Percy's final victory over Chauvelin in the 1982 film, my
> conclusion is more modest: I am quite happy about the hypothesis
> that this is where the root belongs. And, at the rate you are going,
> I don't think I'll need to abandon it for quite some time, if ever.

It would be up to you to provide evidence for that root. Its mention in
a paper that prefers another rooting is not very good evidence. Still,
can we agree that the important question is whether there is meiosis on
both sides of the root, whatever that root may be?

> PS If you know much of anything about any version of The Scarlet
> Pimpernel, you can probably find a pun implicit in what I've written here,
> even though it is backwards from my hypothesis.

This is another pointless digression, which I again ask you to avoid.
FYI, I have never read the book or seen any of the various film
adaptations, and I have never heard of the one you describe here.

[Don Cates]

You might prefer "The Brown Pumpernickel"
<https://www.youtube.com/watch?v=8U1AM5dVR70>

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

[Charles Brenner]

And mice have less than half the cross-over rate (per Mb) of humans.

The correlation between cross-over rate in a species and reproductive success seems to support the hypothesis that cross-overs are an important cause of inaccurate homolog pairing during meiosis, and that the cross-over rate is consequently an evolutionary compromise between the disadvantages of reproductive failure and the advantages of genetic variety.

Is there a general theme in biology and genetics that the most intricate and complicated beneficial capabilities tend to have a flip side of fragility and unpleasant effects when they go off the rails?

[Peter Nyikos]

On Friday, May 24, 2019 at 11:30:03 AM UTC-4, Charles Brenner wrote:

Wow, Charles, it's great to see you post again! I do hope you hang around
this thread for a while.

Do you know of any scientific papers which study this correlation
over a wide range of species?

It certainly stands to reason. I even asked Ernest Major the following:

How would recombination work if loci are in different places, and
crossover would result in chromosomes of mismatched length?

My conjecture is that this would be lethal to the offspring,
or at least to their offspring. Can you think of any other explanations?

Unfortunately, Ernest only popped into this thread for one post
and I never got any answers. Might you be able to enlighten us?

> and that the cross-over rate is consequently an evolutionary compromise between the disadvantages of reproductive failure and the advantages of genetic variety.

A closely related theme is the well known factoid that asexual
reproduction more "fit" than sexual, and the Wiki entry even
calls this a "major puzzle".

https://en.wikipedia.org/wiki/Sexual_reproduction

When I was planning this thread, I toyed with the idea of
leaving off "meiosis" at the end of the Subject line, but then
decided that the theme of meiosis could be badly out-competed by
this better known topic.

> Is there a general theme in biology and genetics that the most intricate and complicated beneficial capabilities tend to have a flip side of fragility and unpleasant effects when they go off the rails?

That too stands to reason, but in this day of specialization, I don't
think many research papers address this topic. IF neither Isaak Asimov
nor Stephen Jay Gould nor Carl Sagan wrote on this topic, I don't
think the popular literature of biology and genetics will be of help either.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--

University of South Carolina
http://people.math.sc.edu

PS I'll be taking a posting break of three days for the Memorial Day
weekend, and during that time I might be able to look through my old
paperbacks to see what is said on the topic.

[Peter Nyikos]

This stupid prank of yours did nothing but waste both of our times.

> > Of course, what you are "gratuitously assuming" is false. What I was
> > referring to, obviously, is your blanket statement
> > that the LCA of Eukarya had meiosis, qualified only by the "obvious assumption" that the tree of Eukarya had been firmly rooted.

> It doesn't need to be firmly rooted if all the possible roots fail to
> put diplomonads next to the root. Would you agree?

If you had written this instead of your stupid prank, you would know
already that the answer to this is as before: I would have agreed
back in high school.

> >>>> The remaining contention would be about the tree
> >>>> itself. Giardia was once presumed to be a basal eukaryote, but I see no
> >>>> recent revivals of that claim. What do you find?
> >>>
> >>> Nothing along those lines. But I've found a far more promising
> >>> possibility: the jakobids. And it is for the opposite reason:
> >>> its mitochondria preserve more of the bacterial genome than any
> >>> other eukaryotes.
> >>>
> >>> https://en.wikipedia.org/wiki/Jakobid
> >>>
> >>> Had I known about them when I started this thread, I would
> >>> have considered them to be the best bet from the beginning.
> >>> Can you see why?
> >>
> >> In fact I can't. According to the article, they're nested deep within
> >> Excavata
> >
> > Which article would that be? the 2014 article that you posted last time
> > around? "According to the article" is a distortion of that article;
> > see below.
>
> No. According to the Wikipedia article you linked just above.

I see nothing there to that effect. Is this another prank of yours?

> >> and their odd features are, once more, probably not primitive.
> >
> > "once more" assumes a falsehood. The post to which you are
> > replying is the only place on the whole internet on which I've
> > written about the Jakobids.
>
> I refer to your previous candidate for primitive eukaryote, Giardia.

For reasons only you understand, since we stopped talking about
it as soon as I posted the url for the Jakobids.

I can't be wasting any more time on your pranks today. The rest
of my posts to t.o. today will be replies to people who manage to stay
focused on communication, like Charles Brenner on this thread,
even though a lot of them are posting off-topic, on other threads.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu

PS I'll return to the rest of your post on Tuesday, after a three day
weekend break from posting, including Memorial Day.

[John Harshman]

Please stop accusing me of stupid pranks. I never play pranks on you,
since you lack a sense of humor.

>>>>>> The remaining contention would be about the tree
>>>>>> itself. Giardia was once presumed to be a basal eukaryote, but I see no
>>>>>> recent revivals of that claim. What do you find?
>>>>>
>>>>> Nothing along those lines. But I've found a far more promising
>>>>> possibility: the jakobids. And it is for the opposite reason:
>>>>> its mitochondria preserve more of the bacterial genome than any
>>>>> other eukaryotes.
>>>>>
>>>>> https://en.wikipedia.org/wiki/Jakobid
>>>>>
>>>>> Had I known about them when I started this thread, I would
>>>>> have considered them to be the best bet from the beginning.
>>>>> Can you see why?
>>>>
>>>> In fact I can't. According to the article, they're nested deep within
>>>> Excavata
>>>
>>> Which article would that be? the 2014 article that you posted last time
>>> around? "According to the article" is a distortion of that article;
>>> see below.
>>
>> No. According to the Wikipedia article you linked just above.
>
> I see nothing there to that effect. Is this another prank of yours?

"Molecular phylogenetic evidence suggests strongly that jakobids are
most closely related to Heterolobosea (Percolozoa) and Euglenozoa.[6]"

Reference 6, coincidentally, is that first paper I cited.

>>>> and their odd features are, once more, probably not primitive.
>>>
>>> "once more" assumes a falsehood. The post to which you are
>>> replying is the only place on the whole internet on which I've
>>> written about the Jakobids.
>>
>> I refer to your previous candidate for primitive eukaryote, Giardia.
>
> For reasons only you understand, since we stopped talking about
> it as soon as I posted the url for the Jakobids.

Yes, that's why it's *previous*. That's why I said *once more*.

> I can't be wasting any more time on your pranks today. The rest
> of my posts to t.o. today will be replies to people who manage to stay
> focused on communication, like Charles Brenner on this thread,
> even though a lot of them are posting off-topic, on other threads.

Brenner is your new buddy, but you never responded to my post that he
discussed, and which he, unlike you, thought was interesting. You are
allowing your antipathies to guide your actions, which cripples your
ability to discuss anything rationally with me.

[Charles Brenner]

On Friday, May 24, 2019 at 2:05:03 PM UTC-7, Peter Nyikos wrote:
> On Friday, May 24, 2019 at 11:30:03 AM UTC-4, Charles Brenner wrote:
>
> Wow, Charles, it's great to see you post again! I do hope you hang around
> this thread for a while.

Thank you Peter. Slight connection: Sorgenfrey, your advisor's advisor, was an emeritus figure at UCLA when I was doing my PhD. I didn't know him but I understood he had (probably since WWII) a nice house in a Santa Monica canyon.

> > On Thursday, May 16, 2019 at 4:25:03 PM UTC-7, John Harshman wrote:
> > > On 5/16/19 3:03 PM, Peter Nyikos wrote:
> > > > Before I try to address the formidable question of how meiosis may
> > > > have originated, I look at another mystery mentioned by Orr-Weaver in
> > > > the interview in _Biology_ 8th ed., by Campbell, Reece et al.
> > > >
> > > > Immediately after the part I quoted in my second post, she said:
> > > >
> > > > And I would say the second big mystery is why humans
> > > > are so unbelievably bad at carrying out meiosis.
> > > >
> > > > The interviewer, _Biology_ co-author Janet Reece, asked:

Jane. Fine cellist. She gave me a copy of the book but I can't find it.

> > > > Why makes you say that? Are we worse than fruit flies?
> > > >
> > > > Orr-Weaver replies:
> > > >
> > > > We're about a thousand times worse. Here are some amazing
> > > > statistics: Twenty percent of recognized pregnancies end in
> > > > spontaneous miscarriage, and out of those at least half are
> > > > due to a mistake during meiosis. And for every pregnancy
> > > > that proceeds far enough to be recognized, there have been
> > > > many that ended without being recognized. So about 10-20%
> > > > of the time meiosis doesn't work properly in humans. In
> > > > fruit flies, meiosis seems to occur inaccurately only
> > > > 0.01 - 0.05% of the time. Even mice, which are mammals like
> > > > ourselves, do much better than than humans.
> > >
> > > One wonders how the number of chromosomes and their lengths correlate
> > > with problems in meiosis. Also frequency of chromosomal mutations. I
> > > seem to recall that Drosophila have a reduced frequency of crossing over
> > > too.
> >
> > And mice have less than half the cross-over rate (per Mb) of humans.
> >
> > The correlation between cross-over rate in a species and reproductive success seems to support the hypothesis that cross-overs are an important cause of inaccurate homolog pairing during meiosis,
>
> Do you know of any scientific papers which study this correlation
> over a wide range of species?

No.

> It certainly stands to reason. I even asked Ernest Major the following:
>
> How would recombination work if loci are in different places, and
> crossover would result in chromosomes of mismatched length?

My tangential understanding of recombination hot-spot evolution tells me that it is too subtle for a non-biologist dabbler like myself to seriously understand. But for example "Reciprocal crossover asymmetry and meiotic drive in a human recombination hot spot" (Jeffreys & Neumann) seems to say that hot-spots are transient which might mean that either through luck or somehow by selection, opportunities for mismatched length get cleaned away by evolution.

> My conjecture is that this would be lethal to the offspring,
> or at least to their offspring. Can you think of any other explanations?

> Unfortunately, Ernest only popped into this thread for one post
> and I never got any answers. Might you be able to enlighten us?

Explanation other than that asymmetrical crossover evolved to prevent survival?

> > and that the cross-over rate is consequently an evolutionary compromise between the disadvantages of reproductive failure and the advantages of genetic variety.
>
> A closely related theme is the well known factoid that asexual
> reproduction more "fit" than sexual, and the Wiki entry even
> calls this a "major puzzle".
>
> https://en.wikipedia.org/wiki/Sexual_reproduction

Yes, seems like a piece of the same story.

[Peter Nyikos]

How ELSE would you characterize your time-wasting use of "gratuitously
assuming"?

> I never play pranks on you,
> since you lack a sense of humor.

I have never seen you give credible evidence for this perennial
put-down of yours. Your last attempt to give some, earlier
this year, was so abysmally stupid that it suggests you've been
running a deliberate scam all these years.

>
> >>>>>> The remaining contention would be about the tree
> >>>>>> itself. Giardia was once presumed to be a basal eukaryote, but I see no
> >>>>>> recent revivals of that claim. What do you find?
> >>>>>
> >>>>> Nothing along those lines. But I've found a far more promising
> >>>>> possibility: the jakobids. And it is for the opposite reason:
> >>>>> its mitochondria preserve more of the bacterial genome than any
> >>>>> other eukaryotes.
> >>>>>
> >>>>> https://en.wikipedia.org/wiki/Jakobid
> >>>>>
> >>>>> Had I known about them when I started this thread, I would
> >>>>> have considered them to be the best bet from the beginning.
> >>>>> Can you see why?
> >>>>
> >>>> In fact I can't. According to the article, they're nested deep within
> >>>> Excavata
> >>>
> >>> Which article would that be? the 2014 article that you posted last time
> >>> around? "According to the article" is a distortion of that article;
> >>> see below.
> >>
> >> No. According to the Wikipedia article you linked just above.
> >
> > I see nothing there to that effect. Is this another prank of yours?

Either that, or you were trying so hard to be cryptic, you wound
up uttering a deliberate falsehood.

> "Molecular phylogenetic evidence suggests strongly that jakobids are
> most closely related to Heterolobosea (Percolozoa) and Euglenozoa.[6]"
>
> Reference 6, coincidentally, is that first paper I cited.

And it is the REAL reference you should have cited instead of
the Wikipedia article. Note the following excerpt from [6]:

The Jakobida clade, including Andalucia, branched robustly
as the sister group to a clade comprising Heterolobosea + Euglenozoa.

See if you can untangle what follows, if you want to exonerate
the anonymous Wikipedia author of misreading [6].

> >>>> and their odd features are, once more, probably not primitive.
> >>>
> >>> "once more" assumes a falsehood. The post to which you are
> >>> replying is the only place on the whole internet on which I've
> >>> written about the Jakobids.
> >>
> >> I refer to your previous candidate for primitive eukaryote, Giardia.
> >
> > For reasons only you understand, since we stopped talking about
> > it as soon as I posted the url for the Jakobids.
>
> Yes, that's why it's *previous*. That's why I said *once more*.

Is German your first language? The standard English term is *here too*.
Or you could have said, "just as in Giardia," if you had wanted to be
as clear as you keep demanding that I be.

> > I can't be wasting any more time on your pranks today. The rest
> > of my posts to t.o. today will be replies to people who manage to stay
> > focused on communication, like Charles Brenner on this thread,
> > even though a lot of them are posting off-topic, on other threads.
>
> Brenner is your new buddy,

Do you have any idea how insecure this makes you sound?

I never jump to this kind of conclusion until many posts strongly
indicate that people are consistently treating each other with
blatant favoritism. Until then, I address the actions, not
the relationships, e.g. "You are shackling yourself to ______________'s
dishonest comment."

Hell, Brenner hadn't even replied to me until after you jumped to
this irrational conclusion. I can't even recall whether he EVER
replied to any of my posts before now. If he did, it had to be quite a
number of years ago.

> but you never responded to my post that he
> discussed,

He gave concrete information, unlike your highly tentative and
uncertain thing that put all the onus on readers who more than
you do on the subject.

And you never entered into a discussion with him, nor did you
reply to the detailed reply I gave him.

> and which he, unlike you, thought was interesting.

Now you are pretending to be able to read his mind. He obviously
thought the TOPIC was interesting, but that's a different issue.

> You are
> allowing your antipathies to guide your actions, which cripples your
> ability to discuss anything rationally with me.

Stop trolling. Your inexplicable antipathy towards me dates back
to the very day I returned to sci.bio.paleontology and talk.origins
after almost a decade of absence from both. I put up with your
obnoxious behavior for at least a year, until you made some
*demonstrably* dishonest and hypocritical statements.

What you call my "antipathy" is my criticism of one display after another
over the years of dishonesty, hypocrisy, cowardice, or just plain
obnoxiousness. Displays of obnoxiousness by you run through
much of the post to which I am replying.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--

[Peter Nyikos]

On Saturday, May 25, 2019 at 4:55:03 PM UTC-4, Charles Brenner wrote:
> On Friday, May 24, 2019 at 2:05:03 PM UTC-7, Peter Nyikos wrote:
> > On Friday, May 24, 2019 at 11:30:03 AM UTC-4, Charles Brenner wrote:
> >
> > Wow, Charles, it's great to see you post again! I do hope you hang around
> > this thread for a while.
>
> Thank you Peter. Slight connection: Sorgenfrey, your advisor's advisor, was an emeritus figure at UCLA when I was doing my PhD.

How about that! Was your PhD in mathematics, too?

>I didn't know him but I understood he had (probably since WWII) a nice house in a Santa Monica canyon.

My first time in southern California was at a Spring Topology Conference
in Riverside, 1980. Alas, Sorgenfrey wasn't there -- he might have passed
away before then -- and I never got to meet him.

>
> > > On Thursday, May 16, 2019 at 4:25:03 PM UTC-7, John Harshman wrote:
> > > > On 5/16/19 3:03 PM, Peter Nyikos wrote:
> > > > > Before I try to address the formidable question of how meiosis may
> > > > > have originated, I look at another mystery mentioned by Orr-Weaver in
> > > > > the interview in _Biology_ 8th ed., by Campbell, Reece et al.
> > > > >
> > > > > Immediately after the part I quoted in my second post, she said:
> > > > >
> > > > > And I would say the second big mystery is why humans
> > > > > are so unbelievably bad at carrying out meiosis.
> > > > >
> > > > > The interviewer, _Biology_ co-author Janet Reece, asked:
>
> Jane. Fine cellist. She gave me a copy of the book but I can't find it.

Where did you get to meet her?

> > > > > Why makes you say that? Are we worse than fruit flies?
> > > > >
> > > > > Orr-Weaver replies:
> > > > >
> > > > > We're about a thousand times worse. Here are some amazing
> > > > > statistics: Twenty percent of recognized pregnancies end in
> > > > > spontaneous miscarriage, and out of those at least half are
> > > > > due to a mistake during meiosis. And for every pregnancy
> > > > > that proceeds far enough to be recognized, there have been
> > > > > many that ended without being recognized. So about 10-20%
> > > > > of the time meiosis doesn't work properly in humans. In
> > > > > fruit flies, meiosis seems to occur inaccurately only
> > > > > 0.01 - 0.05% of the time. Even mice, which are mammals like
> > > > > ourselves, do much better than than humans.
> > > >
> > > > One wonders how the number of chromosomes and their lengths correlate
> > > > with problems in meiosis. Also frequency of chromosomal mutations. I
> > > > seem to recall that Drosophila have a reduced frequency of crossing over
> > > > too.
> > >
> > > And mice have less than half the cross-over rate (per Mb) of humans.

Where did you learn about this? And do you know the cross-over rate
for Drosophila?

> > > The correlation between cross-over rate in a species and reproductive success seems to support the hypothesis that cross-overs are an important cause of inaccurate homolog pairing during meiosis,
> >
> > Do you know of any scientific papers which study this correlation
> > over a wide range of species?
>
> No.

I just might get up the courage to ask Prof. Orr-Weaver herself.
I would mostly focus on her "number one" mystery, and the closely
related "Mystery 2" of my OP, and Mystery 3.

> > It certainly stands to reason. I even asked Ernest Major the following:
> >
> > How would recombination work if loci are in different places, and
> > crossover would result in chromosomes of mismatched length?
>
> My tangential understanding of recombination hot-spot evolution tells me that it is too subtle for a non-biologist dabbler like myself to seriously understand. But for example "Reciprocal crossover asymmetry and meiotic drive in a human recombination hot spot" (Jeffreys & Neumann) seems to say that hot-spots are transient which might mean that either through luck or somehow by selection, opportunities for mismatched length get cleaned away by evolution.
>
> > My conjecture is that this would be lethal to the offspring,
> > or at least to their offspring. Can you think of any other explanations?
>
> > Unfortunately, Ernest only popped into this thread for one post
> > and I never got any answers. Might you be able to enlighten us?
>
> Explanation other than that asymmetrical crossover evolved to prevent survival?

That's a bit too teleological. Science moved away from "final cause"
long ago.

> > > and that the cross-over rate is consequently an evolutionary compromise between the disadvantages of reproductive failure and the advantages of genetic variety.
> >
> > A closely related theme is the well known factoid that asexual

> > reproduction [is] more "fit" than sexual, and the Wiki entry even

> > calls this a "major puzzle".
> >
> > https://en.wikipedia.org/wiki/Sexual_reproduction
>
> Yes, seems like a piece of the same story.

I haven't been pursuing either topic since I first replied to you.
My attention has been riveted on the problem of whether the LCA
of Eukarya had meiosis. It's getting to be a fascinating detective
story. Would you like a synopsis of its twists and turns up to now,
or would you prefer just to watch and see what transpires between
John and myself during the rest of this week?

John is rather obnoxious, but he's come up with some fascinating
references, so I put up with his shenanigans the way a bear puts up with
bee stings to get at some delicious honey.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--

[John Harshman]

Perhaps you should just stop characterizing. It would save time and
effort that you could then devote to on-topic discussion.

>> I never play pranks on you,
>> since you lack a sense of humor.
>
> I have never seen you give credible evidence for this perennial
> put-down of yours. Your last attempt to give some, earlier
> this year, was so abysmally stupid that it suggests you've been
> running a deliberate scam all these years.

It's not the sort of thing that can be demonstrated to you. Everyone
else gets it, though. But this too is a time-wasting digression.

Why would I want to exonerate anyone of anything here? Doesn't your
quote exactly math what Wikipedia says? I'm not understanding your
objection.

>>>>>> and their odd features are, once more, probably not primitive.
>>>>>
>>>>> "once more" assumes a falsehood. The post to which you are
>>>>> replying is the only place on the whole internet on which I've
>>>>> written about the Jakobids.
>>>>
>>>> I refer to your previous candidate for primitive eukaryote, Giardia.
>>>
>>> For reasons only you understand, since we stopped talking about
>>> it as soon as I posted the url for the Jakobids.
>>
>> Yes, that's why it's *previous*. That's why I said *once more*.
>
> Is German your first language? The standard English term is *here too*.
> Or you could have said, "just as in Giardia," if you had wanted to be
> as clear as you keep demanding that I be.

More off-topic crap. "Once more" is standard English. I've explained
what I meant. Please stop.

>>> I can't be wasting any more time on your pranks today. The rest
>>> of my posts to t.o. today will be replies to people who manage to stay
>>> focused on communication, like Charles Brenner on this thread,
>>> even though a lot of them are posting off-topic, on other threads.
>>
>> Brenner is your new buddy,
>
> Do you have any idea how insecure this makes you sound?

Yes, but it probably conflicts with your idea.

Ack. There's nothing on-topic at all in this post. I've wasted my time
in reading it.

[Charles Brenner]

On Tuesday, May 28, 2019 at 7:45:03 AM UTC-7, Peter Nyikos wrote:
> On Saturday, May 25, 2019 at 4:55:03 PM UTC-4, Charles Brenner wrote:
> > On Friday, May 24, 2019 at 2:05:03 PM UTC-7, Peter Nyikos wrote:
> > > On Friday, May 24, 2019 at 11:30:03 AM UTC-4, Charles Brenner wrote:
> > >
> > > Wow, Charles, it's great to see you post again! I do hope you hang around
> > > this thread for a while.
> >
> > Thank you Peter. Slight connection: Sorgenfrey, your advisor's advisor, was an emeritus figure at UCLA when I was doing my PhD.
>
> How about that! Was your PhD in mathematics, too?
>
> >I didn't know him but I understood he had (probably since WWII) a nice house in a Santa Monica canyon.
>
> My first time in southern California was at a Spring Topology Conference
> in Riverside, 1980. Alas, Sorgenfrey wasn't there -- he might have passed
> away before then -- and I never got to meet him.

He was alive. I'm surprised you're not aware of the Math Genealogy Project. You have at your internet fingertips a wonderful tree of information including thesis, advisor, and students about every mathematician since before Gauss. By back-of-the-envelope calculation that includes you and me.

> > > > On Thursday, May 16, 2019 at 4:25:03 PM UTC-7, John Harshman wrote:
> > > > > On 5/16/19 3:03 PM, Peter Nyikos wrote:
> > > > > > Before I try to address the formidable question of how meiosis may
> > > > > > have originated, I look at another mystery mentioned by Orr-Weaver in
> > > > > > the interview in _Biology_ 8th ed., by Campbell, Reece et al.
> > > > > >
> > > > > > Immediately after the part I quoted in my second post, she said:
> > > > > >
> > > > > > And I would say the second big mystery is why humans
> > > > > > are so unbelievably bad at carrying out meiosis.
> > > > > >
> > > > > > The interviewer, _Biology_ co-author Janet Reece, asked:
> >
> > Jane. Fine cellist. She gave me a copy of the book but I can't find it.
>
> Where did you get to meet her?

Chamber music evening at a friend's house. And no, I'm not good enough to sit in. I do have expertise about some chapter in the book though, reviewing which got me the offer of a copy which I cashed in on.

> > > > > > Why makes you say that? Are we worse than fruit flies?
> > > > > >
> > > > > > Orr-Weaver replies:
> > > > > >
> > > > > > We're about a thousand times worse. Here are some amazing
> > > > > > statistics: Twenty percent of recognized pregnancies end in
> > > > > > spontaneous miscarriage, and out of those at least half are
> > > > > > due to a mistake during meiosis. And for every pregnancy
> > > > > > that proceeds far enough to be recognized, there have been
> > > > > > many that ended without being recognized. So about 10-20%
> > > > > > of the time meiosis doesn't work properly in humans. In
> > > > > > fruit flies, meiosis seems to occur inaccurately only
> > > > > > 0.01 - 0.05% of the time. Even mice, which are mammals like
> > > > > > ourselves, do much better than than humans.
> > > > >
> > > > > One wonders how the number of chromosomes and their lengths correlate
> > > > > with problems in meiosis. Also frequency of chromosomal mutations. I
> > > > > seem to recall that Drosophila have a reduced frequency of crossing over
> > > > > too.
> > > >
> > > > And mice have less than half the cross-over rate (per Mb) of humans.
>
> Where did you learn about this?

sidebar in the Jeffreys paper I cited

> And do you know the cross-over rate for Drosophila?

We can work it out from Orr-Weaver's comment and the human rate which is I heard is 30 per human genome.

> > > > The correlation between cross-over rate in a species and reproductive success seems to support the hypothesis that cross-overs are an important cause of inaccurate homolog pairing during meiosis,

Now we get to a classic instance of my caution that "a little knowledge is a dangerous thing" for science dilettantes. Per Jeffreys the truth is the exact opposite of my surmise. Homologues recognize each other by single-strand invasions between chromosomes and crossover is an essential part of the recognition process.

> > > Do you know of any scientific papers which study this correlation
> > > over a wide range of species?
> >
> > No.
>
> I just might get up the courage to ask Prof. Orr-Weaver herself.
> I would mostly focus on her "number one" mystery, and the closely
> related "Mystery 2" of my OP, and Mystery 3.
>
>
> > > It certainly stands to reason. I even asked Ernest Major the following:
> > >
> > > How would recombination work if loci are in different places, and
> > > crossover would result in chromosomes of mismatched length?
> >
> > My tangential understanding of recombination hot-spot evolution tells me that it is too subtle for a non-biologist dabbler like myself to seriously understand. But for example "Reciprocal crossover asymmetry and meiotic drive in a human recombination hot spot" (Jeffreys & Neumann) seems to say that hot-spots are transient which might mean that either through luck or somehow by selection, opportunities for mismatched length get cleaned away by evolution.

> > > My conjecture is that this would be lethal to the offspring,
> > > or at least to their offspring. Can you think of any other explanations?

> > Explanation other than that asymmetrical crossover evolved to prevent survival?
>
> That's a bit too teleological. Science moved away from "final cause"
> long ago.

I was joshing you by taking your use of the word "explanation", which makes no sense to me in context, literally.

> John ...'s come up with some fascinating references
not to mention knowledge and insight; he is a genuine scientist.

[Peter Nyikos]

On Tuesday, May 28, 2019 at 3:45:03 PM UTC-4, Charles Brenner wrote:
> On Tuesday, May 28, 2019 at 7:45:03 AM UTC-7, Peter Nyikos wrote:
> > On Saturday, May 25, 2019 at 4:55:03 PM UTC-4, Charles Brenner wrote:
> > > On Friday, May 24, 2019 at 2:05:03 PM UTC-7, Peter Nyikos wrote:
> > > > On Friday, May 24, 2019 at 11:30:03 AM UTC-4, Charles Brenner wrote:
> > > >
> > > > Wow, Charles, it's great to see you post again! I do hope you hang around
> > > > this thread for a while.
> > >
> > > Thank you Peter. Slight connection: Sorgenfrey, your advisor's advisor, was an emeritus figure at UCLA when I was doing my PhD.
> >
> > How about that! Was your PhD in mathematics, too?
> >
> > >I didn't know him but I understood he had (probably since WWII) a nice house in a Santa Monica canyon.
> >
> > My first time in southern California was at a Spring Topology Conference
> > in Riverside, 1980. Alas, Sorgenfrey wasn't there -- he might have passed
> > away before then -- and I never got to meet him.
>
> He was alive. I'm surprised you're not aware of the Math Genealogy Project.

I know lots about it, but I don't pay much attention to times of
deaths. Mary Ellen Rudin and Sibe Mardesic are special cases because
both of them died just before math conferences, and I can look
up the dates of those. Also, there has been a special issue of
Notices of the AMS with a great feature on Mary Ellen's life and math.
I contributed a page to it as did quite a few other set-theoretic
topologists.

> You have at your internet fingertips a wonderful tree of information including thesis, advisor, and students about every mathematician since before Gauss. By back-of-the-envelope calculation that includes you and me.

I keep forgetting whether my Erdos number is two, or three:
I've co-authored some papers with Istvan Juhasz, but I can't
recall whether he co-authored one with Erdos. For sure, he and Hajnal
had lots of joint papers, as did Hajnal and Erdos.

You cited "Jeffreys & Neumann." Which paper is that?

> > And do you know the cross-over rate for Drosophila?
>
> We can work it out from Orr-Weaver's comment and the human rate which is I heard is 30 per human genome.

Thanks, but are you sure almost all errors of meiosis are due
to faulty cross-over? Harshman was obviously unaware of that.

>
> > > > > The correlation between cross-over rate in a species and reproductive success seems to support the hypothesis that cross-overs are an important cause of inaccurate homolog pairing during meiosis,
>
> Now we get to a classic instance of my caution that "a little knowledge is a dangerous thing" for science dilettantes. Per Jeffreys the truth is the exact opposite of my surmise. Homologues recognize each other by single-strand invasions between chromosomes and crossover is an essential part of the recognition process.

Hmmmm... You sound almost as though Jeffreys had solved Orr-Weavers'
"number one mystery of meiosis". (How do the right
chromosomes find each other?) What distinction do you draw
between "find" and "recognize"?

> > > > Do you know of any scientific papers which study this correlation
> > > > over a wide range of species?
> > >
> > > No.
> >
> > I just might get up the courage to ask Prof. Orr-Weaver herself.
> > I would mostly focus on her "number one" mystery, and the closely
> > related "Mystery 2" of my OP, and Mystery 3.
> >
> >
> > > > It certainly stands to reason. I even asked Ernest Major the following:
> > > >
> > > > How would recombination work if loci are in different places, and
> > > > crossover would result in chromosomes of mismatched length?
> > >
> > > My tangential understanding of recombination hot-spot evolution tells me that it is too subtle for a non-biologist dabbler like myself to seriously understand. But for example "Reciprocal crossover asymmetry and meiotic drive in a human recombination hot spot" (Jeffreys & Neumann) seems to say that hot-spots are transient which might mean that either through luck or somehow by selection, opportunities for mismatched length get cleaned away by evolution.
>
> > > > My conjecture is that this would be lethal to the offspring,
> > > > or at least to their offspring. Can you think of any other explanations?
>
> > > Explanation other than that asymmetrical crossover evolved to prevent survival?
> >
> > That's a bit too teleological. Science moved away from "final cause"
> > long ago.
>
> I was joshing you by taking your use of the word "explanation", which makes no sense to me in context, literally.
>
> > John ...'s come up with some fascinating references
> not to mention knowledge and insight; he is a genuine scientist.

Knowledge I grant, but he is far too confident about all kinds of
things, especially some of the latest hypotheses, to be what I would call
a genuine scientist. Certainly he is a far cry from being a naturalist.

Also, John has a "we go with what we got" attitude about things
for which evidence is almost wholly lacking. When two papers
came out about a few molecules that are unique to animals among
extant organisms being found in some Ediacaran fauna,
and claimed on that basis that the Ediacaran fauna were animals,
John liked the idea far more than I think is warranted.

This took place in sci.bio.paleontology several months ago.
If you are curious about Ediacarans, I can find it for you.
When the Ediacarans were first discovered, it was assumed that they were
all animals, but now there are only a few on which biologists are close
to agreement, the best known being Kimberella.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--

Univ. of South Carolina in Columbia
http://people.math.sc.edu

[Peter Nyikos]

On Friday, May 24, 2019 at 9:50:03 AM UTC-4, John Harshman wrote:
> On 5/23/19 8:46 AM, Peter Nyikos wrote:
> > On Wednesday, May 22, 2019 at 9:40:03 AM UTC-4, John Harshman wrote:
> >> On 5/22/19 4:48 AM, Peter Nyikos wrote:
> >>> On Monday, May 20, 2019 at 11:40:03 AM UTC-4, John Harshman wrote:
> >>>> On 5/20/19 6:03 AM, Peter Nyikos wrote:
> >>>>> On Friday, May 17, 2019 at 11:35:03 PM UTC-4, John Harshman wrote:
> >>>>>> On 5/17/19 6:29 PM, Peter Nyikos wrote:
> >>>
> >>>>>>> Mystery 3: Did meiosis predate the LCA of living eukaryotes?
> >>>>>>
> >>>>>> Yes, obviously, unless you want to propose that meiosis arose multiple
> >>>>>> times convergently.

We still lack enough data to justify your "obviously" here, and
it looks like it may be that way for a good long time to come.

I've snipped the part we've argued about these last two days.
Your claim at the end of your arrogant post that there was
nothing on-topic by me in it is completely false. If, despite
what I quoted about the Jakobids in (6), you are
happy about what the Wikipedia entry said about reference [6]
then you need to exonerate yourself of having misread the
Wikipedia entry and thus having wasted our time by coyly withholding
false "information".


Picking up the part of your post which I haven't addressed yet:

> >> Further, the way in which [the Jakobids] are odd has nothing to do with meiosis.
> >> So could you explain?


<snip for focus>

> > In partial answer to your question: you seem to think
> > that phylogenetic trees are the be-all and end-all of systematics.
> > But the tree does not give an adequate reason for rejecting various
> > states as primitive, because it is always a compromise between
> > a huge number of pieces of conflicting evidence.
>
> Not sure what you mean by that. Do you mean that the tree itself is
> uncertain and therefore not a basis for character inference,

Not necessarily.

> or do you mean that not even a certain tree is such a basis?

Yes, but try to stay focused. The issue is whether a given
character is primitive or derived. In the case of the Jakobids,
the "peculiar" character is their retention of a bigger part of
the bacterial genome in their mitochondria than in other eukaryotes.

> If the former, I
> think we know enough to be reasonably certain about enough parts of the
> tree for the present purpose. If the latter, it's true that the
> principle of parsimony can be violated, we have also agreed that meiosis
> is unlikely to have evolved twice; if our choice is between multiple

> losses and multiple gains, we should generally prefer multiple losWses.

Yes, and so I would argue that the "peculiar" character of the Jakobids
is primitive, no matter where in the tree of Eukarya they are situated.
And so the probability of meiosis being primitive goes up, unless you
want to argue that retention of the two has no correlation whatsoever.

>
> >>>>>> So Giardia isn't a basal eukaryote and its
> >>>>>> characteristics are not primitive.
> >>>>>>
> >>>>>> https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-8-205
> >>>>>
> >>>>> Contrary to your cocksure claim, this 2007 article is mostly about
> >>>>> the polyphyletic status of what was once thought to be a clade
> >>>>> of single-nucleus eukaryotes. The authors argue that they
> >>>>> arose convergently within the diplomonads.

It's nice to see, by your unmarked snip here, that you no longer
contest the designation "cocksure."

> >>>>> Also, the 2008 textbook I reference above says the following on p. 577:
> >>>>>
> >>>>> The ongoing changes in our understanding of the phylogeny of
> >>>>> protists pose challenges to students and instructors alike.
> >>>>> Hypotheses about these relationships are a hotbed of scientific
> >>>>> activity, changing rapidly as new data cause previous ideas
> >>>>> to be modified or discarded. In this chapter, our discussion
> >>>>> is organized around one current hypothesis: the five supergroups
> >>>>> of eukaryotes shown in Figure 28.3, on the next two pages.
> >>>>> Because the root of the eukaryotic tree is not known, all
> >>>>> five supergroups are shown as diverging simultaneously
> >>>>> from a common ancestor -- something that we know is not correct,
> >>>>> but we do not know which organisms were the first to diverge from the others.
> >>>>
> >>>> Not a problem,
> >>>
> >>> The hotbed is a problem, and it still exists.
> >>
> >> Sure, but there are many issues in that hotbed that have been resolved,
> >> and one of them is the monophyly of Excavata.
> >
> > No, that isn't one of them. The second article you reference below,
> > dated 2014, leaves open the possibility that it is paraphyletic.
> > Keep reading.
>
> That possibility is just mentioned as a claim by somebody else.

That "someone else" is myself, arguing with impeccable logic from the
rooting of the tree which I've hypothesized below.


<snip of something on which we have repeatedly agreed before>

> >>>> Here are a few more recent references:

Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups" (7 authors, 2009):
> >>>> https://www.pnas.org/content/106/10/3859

The Eukaryotic Tree of Life from a Global Phylogenomic Perspective, by Fabien Burki (2014):

> >>>> https://cshperspectives.cshlp.org/content/6/5/a016147.full
> >>>>
> >>>> You will note that even Excavata is not the sister group of other
> >>>> eukaryotes,
> >>>

> >>> The first article "reforms" it into one of three "supergroups"

> >>> in an unresolved trichotomy, by eliminating dubious "members."
> >>>
> >>> The second article admits that efforts to root the eukaryotic
> >>> tree have been unsuccessful. One of six possible roots is
> >>> the one that makes the reformed Excavata one of the two branches
> >>> of the first split.
> >>
> >> True, though that isn't the rooting the author thinks has the best
> >> support.
> >
> > Fabien Burki is sufficiently unsure of his choice that he
> > lists five possible alternatives. He shows an admirable
> > degree of scientific caution all through the long and
> > thorough article. It's something you would do well to emulate
> > as best you can.
>
> Nevertheless, he has a preferred rooting.

So? the next reference you give below, dated 2015, also gives six
possible rootings, but only one of them coincides with any of the
six given by the 2014 reference. In particular, they differ
in their "preferred" rooting as to where they place Malawinomonadida.

Under the circumstances, including the fact that these papers
are a mere year apart, and the fact that the latter cites the
former several times, we cannot be sure any rooting will stand
the test of time in the next decade.


> >> And even so, it makes neiwther diplomonads nor jakobids the

> >> sister group of other eukaryotes.

[...]

> >
> > https://cshperspectives.cshlp.org/content/6/5/a016147/F1.large.jpg
> >
> > And if you "look out that window," you will see, close to the edge,
> > one of the five dotted arrows that mark possible rootings of
> > the tree of Eukarya. On one branch off that split, there are just
> > three taxa: euglenids, diplonemids, and kinetoblastids.
> >
> > On the other branch, representing ALL other eukaryotes, the jakobids
> > are the second of two basal taxa: the jakobids are the
> > sister group of all the rest.

<snip for focus>


Here is that 2015 paper:

"Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life," by three authors (2015):

> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517231/
>
> I direct your attention especially to Fig. 2.

Yes, and with a minor detail it gives the same huge split that
I give above. And it has another possible rooting in which
the Euglenozoa split off from **ALL** other eukaryotes.

And in both cases, the whole issue of primitiveness of meiosis
revolves around one detail: does *Trypanosoma* *brucei* undergo
meiosis?


And now the plot starts to thicken. The 2015 paper says "meiosis and gametes were only detected very recently (10, 11)" in this species.

10. Peacock L, et al. Identification of the meiotic life cycle stage of *Trypanosoma* *brucei* in the tsetse fly. Proc Natl Acad Sci USA. 2011;108(9):3671–3676. [PMC free article] [PubMed] [Google Scholar]
11. Peacock L, Bailey M, Carrington M, Gibson W. Meiosis and haploid gametes
in the pathogen *Trypanosoma* *brucei*. Curr Biol. 2014;24(2):181–186. [PMC free article] [PubMed] [Google Scholar]

However, the first only speaks of "homologs of meiotic genes in the T. brucei genome" and "threef unctionally distinct, meiosis-specific proteins". The second also talks about such things, and contains photographs of various pairs and groups of trypanosomes "exchanging cytoplasmic material." However,
there is no photographic evidence of meiosis, nor is there a single picture
that identifies any chromosome.

The plot really thickens with the following "embargoed"
[whatever that means] article, which seems to call the first Peacock
paper and much of the second into question:

"‘Meiotic genes’ are constitutively expressed in an asexual amoeba and are
not necessarily involved in sexual reproduction," Sutherland K. Maciver,
Zisis Koutsogiannis, Alvaro de Obeso Fernández del Valle Biol Lett. 2019
Mar; 15(3): 20180871. Published online 2019 Mar 6.
doi: 10.1098/rsbl.2018.0871 PMCID: PMC6451372
Currently embargoed: Free in PMC on Mar 1, 2020; PubMed

I have been able to access the abstract using the doi reference, and it ends with:

We contend that they are only involved in meiosis in other
organisms that indulge in sexual reproduction and that homologous
recombination is important in asexual protists as a guard against
the accumulation of mutations. We also suggest that asexual
reproduction is the ancestral state.

IOW, Peacock et. al. may have run afoul of a favorite argument
against Behe by anti-ID zealots, by confusing factors exapted in
meiosis with the existence of meiosis itself.

Peter Nyikos
Professor, Dept. of Mathematics

Univ. of South Carolina -- standard disclaimer--
http://people.math.sc.edu

[Peter Nyikos]

A pair of corrections, and a bit of perspective on things.

Correction: goes down.

> unless you
> want to argue that retention of the two has no correlation whatsoever.

Correction: retention of much bacterial genome in the
mitochondria and of asexual reproduction.


The hypothesis I defend is in agreement with the most
recent hypothesis we've found:


<snip to get to end>

> "‘Meiotic genes’ are constitutively expressed in an asexual amoeba and are
> not necessarily involved in sexual reproduction," Sutherland K. Maciver,
> Zisis Koutsogiannis, Alvaro de Obeso Fernández del Valle Biol Lett. 2019
> Mar; 15(3): 20180871. Published online 2019 Mar 6.
> doi: 10.1098/rsbl.2018.0871 PMCID: PMC6451372
> Currently embargoed: Free in PMC on Mar 1, 2020; PubMed
>
> I have been able to access the abstract using the doi reference, and it ends with:
>
> We contend that they are only involved in meiosis in other
> organisms that indulge in sexual reproduction and that homologous
> recombination is important in asexual protists as a guard against
> the accumulation of mutations. We also suggest that asexual
> reproduction is the ancestral state.

I realize that the hypothesis I defend is controversial until the
status of this "embargoed" paper is resolved, and will probably
remain controversial thereafter. But I approach this issue,
as I do so many others, under the same kind of principle that prevails
in courts of law: justice is best served, on the whole, if sharply
opposing sides are argued for, and a jury has a chance to hear both sides.
I do believe Harshman will continue to take the opposing side on this issue,
and that is all to the good.

On this issue, as on all strictly scientific issues, the jury is the
scientific community, not the highly unrepresentative regulars of
talk.origins. Our arguments here stand or fall as the scientific community
would judge, and so it behooves us to do our best to use
arguments that are sound enough to stand tall in that community.

[John Harshman]

On 5/28/19 4:44 PM, Peter Nyikos wrote:
> On Friday, May 24, 2019 at 9:50:03 AM UTC-4, John Harshman wrote:
>> On 5/23/19 8:46 AM, Peter Nyikos wrote:
>>> On Wednesday, May 22, 2019 at 9:40:03 AM UTC-4, John Harshman wrote:
>>>> On 5/22/19 4:48 AM, Peter Nyikos wrote:
>>>>> On Monday, May 20, 2019 at 11:40:03 AM UTC-4, John Harshman wrote:
>>>>>> On 5/20/19 6:03 AM, Peter Nyikos wrote:
>>>>>>> On Friday, May 17, 2019 at 11:35:03 PM UTC-4, John Harshman wrote:
>>>>>>>> On 5/17/19 6:29 PM, Peter Nyikos wrote:
>>>>>
>>>>>>>>> Mystery 3: Did meiosis predate the LCA of living eukaryotes?
>>>>>>>>
>>>>>>>> Yes, obviously, unless you want to propose that meiosis arose multiple
>>>>>>>> times convergently.
>
> We still lack enough data to justify your "obviously" here, and
> it looks like it may be that way for a good long time to come.
>
> I've snipped the part we've argued about these last two days.
> Your claim at the end of your arrogant post that there was
> nothing on-topic by me in it is completely false. If, despite
> what I quoted about the Jakobids in (6), you are
> happy about what the Wikipedia entry said about reference [6]
> then you need to exonerate yourself of having misread the
> Wikipedia entry and thus having wasted our time by coyly withholding
> false "information".

If I'm intended to understand what you're saying there, you will need to
explain.

> Picking up the part of your post which I haven't addressed yet:
>
>>>> Further, the way in which [the Jakobids] are odd has nothing to do with meiosis.
>>>> So could you explain?

> <snip for focus>
>
>>> In partial answer to your question: you seem to think
>>> that phylogenetic trees are the be-all and end-all of systematics.
>>> But the tree does not give an adequate reason for rejecting various
>>> states as primitive, because it is always a compromise between
>>> a huge number of pieces of conflicting evidence.
>>
>> Not sure what you mean by that. Do you mean that the tree itself is
>> uncertain and therefore not a basis for character inference,
>
> Not necessarily.
>
>> or do you mean that not even a certain tree is such a basis?
>
> Yes, but try to stay focused. The issue is whether a given
> character is primitive or derived. In the case of the Jakobids,
> the "peculiar" character is their retention of a bigger part of
> the bacterial genome in their mitochondria than in other eukaryotes.

Have we fundamentally changed the subject from meiosis then? If not,
what does this have to do with that subject?

It's been suggested that the jakobid mt genome is derived, though
horizontal transfer. The other possibility is that it's primitive but
that other lineages have transferred those genes to the nucleus
convergently.

>> If the former, I
>> think we know enough to be reasonably certain about enough parts of the
>> tree for the present purpose. If the latter, it's true that the
>> principle of parsimony can be violated, we have also agreed that meiosis
>> is unlikely to have evolved twice; if our choice is between multiple
>> losses and multiple gains, we should generally prefer multiple losWses.
>
> Yes, and so I would argue that the "peculiar" character of the Jakobids
> is primitive, no matter where in the tree of Eukarya they are situated.
> And so the probability of meiosis being primitive goes up, unless you
> want to argue that retention of the two has no correlation whatsoever.

I don't understand your argument, if you actually intend there to be
one. It seems incoherent at present. Perhaps you should expand on what
you mean by all this. Present a series of clear statements to support
your claim.

>>>>>>>> So Giardia isn't a basal eukaryote and its
>>>>>>>> characteristics are not primitive.
>>>>>>>>
>>>>>>>> https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-8-205
>>>>>>>
>>>>>>> Contrary to your cocksure claim, this 2007 article is mostly about
>>>>>>> the polyphyletic status of what was once thought to be a clade
>>>>>>> of single-nucleus eukaryotes. The authors argue that they
>>>>>>> arose convergently within the diplomonads.
>
> It's nice to see, by your unmarked snip here, that you no longer
> contest the designation "cocksure."

Please stop.

>>>>>>> Also, the 2008 textbook I reference above says the following on p. 577:
>>>>>>>
>>>>>>> The ongoing changes in our understanding of the phylogeny of
>>>>>>> protists pose challenges to students and instructors alike.
>>>>>>> Hypotheses about these relationships are a hotbed of scientific
>>>>>>> activity, changing rapidly as new data cause previous ideas
>>>>>>> to be modified or discarded. In this chapter, our discussion
>>>>>>> is organized around one current hypothesis: the five supergroups
>>>>>>> of eukaryotes shown in Figure 28.3, on the next two pages.
>>>>>>> Because the root of the eukaryotic tree is not known, all
>>>>>>> five supergroups are shown as diverging simultaneously
>>>>>>> from a common ancestor -- something that we know is not correct,
>>>>>>> but we do not know which organisms were the first to diverge from the others.
>>>>>>
>>>>>> Not a problem,
>>>>>
>>>>> The hotbed is a problem, and it still exists.
>>>>
>>>> Sure, but there are many issues in that hotbed that have been resolved,
>>>> and one of them is the monophyly of Excavata.
>>>
>>> No, that isn't one of them. The second article you reference below,
>>> dated 2014, leaves open the possibility that it is paraphyletic.
>>> Keep reading.
>>
>> That possibility is just mentioned as a claim by somebody else.
>
> That "someone else" is myself, arguing with impeccable logic from the
> rooting of the tree which I've hypothesized below.

Not true. The someone else is the person(s) who proposed the alternative
rooting, as mentioned in the article.

By the way, using the adjective "impeccable" doesn't make your argument
any better.

I think you don't quite understand what "rooting" means. It's separate
from topology.

> Under the circumstances, including the fact that these papers
> are a mere year apart, and the fact that the latter cites the
> former several times, we cannot be sure any rooting will stand
> the test of time in the next decade.

Agreed. The rooting is not completely clear. But it doesn't have to be
in order to make my point.

>>>> And even so, it makes neiwther diplomonads nor jakobids the
>>>> sister group of other eukaryotes.
> [...]
>>>
>>> https://cshperspectives.cshlp.org/content/6/5/a016147/F1.large.jpg
>>>
>>> And if you "look out that window," you will see, close to the edge,
>>> one of the five dotted arrows that mark possible rootings of
>>> the tree of Eukarya. On one branch off that split, there are just
>>> three taxa: euglenids, diplonemids, and kinetoblastids.
>>>
>>> On the other branch, representing ALL other eukaryotes, the jakobids
>>> are the second of two basal taxa: the jakobids are the
>>> sister group of all the rest.
>
>
> <snip for focus>
>
>
> Here is that 2015 paper:
>
> "Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life," by three authors (2015):
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517231/
>>
>> I direct your attention especially to Fig. 2.
>
> Yes, and with a minor detail it gives the same huge split that
> I give above. And it has another possible rooting in which
> the Euglenozoa split off from **ALL** other eukaryotes.

The root in this case is not relevant, since regardless of the root
position there is meiosis on both sides of the basal branching.

> And in both cases, the whole issue of primitiveness of meiosis
> revolves around one detail: does *Trypanosoma* *brucei* undergo
> meiosis?

No, it doesn't. It's enough that meiosis is known on both sides of
whatever you think is the basal split. Given the rooting you mention
above, it's only necessary that there be meiosis in some euglenozoan,
any euglenozoan. While it's true that Trypanosoma is the only
euglenozoan mentioned in the text, you shouldn't assume that it's the
only one known to do meiosis.

> And now the plot starts to thicken. The 2015 paper says "meiosis and gametes were only detected very recently (10, 11)" in this species.
>
> 10. Peacock L, et al. Identification of the meiotic life cycle stage of *Trypanosoma* *brucei* in the tsetse fly. Proc Natl Acad Sci USA. 2011;108(9):3671–3676. [PMC free article] [PubMed] [Google Scholar]
> 11. Peacock L, Bailey M, Carrington M, Gibson W. Meiosis and haploid gametes
> in the pathogen *Trypanosoma* *brucei*. Curr Biol. 2014;24(2):181–186. [PMC free article] [PubMed] [Google Scholar]
>
> However, the first only speaks of "homologs of meiotic genes in the T. brucei genome" and "threef unctionally distinct, meiosis-specific proteins".

No, that's not all it speaks of. It says they are expressed at a
particular time, right before cellular fusion. This is when we would
expect meiosis to happen, but not other suggested functions of those genes.

> The second also talks about such things, and contains photographs of various pairs and groups of trypanosomes "exchanging cytoplasmic material." > However,
> there is no photographic evidence of meiosis, nor is there a single picture
> that identifies any chromosome.
>
> The plot really thickens with the following "embargoed"
> [whatever that means] article, which seems to call the first Peacock
> paper and much of the second into question:

Embargoed articles are usually those you aren't allowed to see before
official publication. In this case it seems to be one that's been
published but that you have to pay for until a certain date, when it
becomes free.

> "‘Meiotic genes’ are constitutively expressed in an asexual amoeba and are
> not necessarily involved in sexual reproduction," Sutherland K. Maciver,
> Zisis Koutsogiannis, Alvaro de Obeso Fernández del Valle Biol Lett. 2019
> Mar; 15(3): 20180871. Published online 2019 Mar 6.
> doi: 10.1098/rsbl.2018.0871 PMCID: PMC6451372
> Currently embargoed: Free in PMC on Mar 1, 2020; PubMed

> I have been able to access the abstract using the doi reference, and it ends with:
>
> We contend that they are only involved in meiosis in other
> organisms that indulge in sexual reproduction and that homologous
> recombination is important in asexual protists as a guard against
> the accumulation of mutations. We also suggest that asexual
> reproduction is the ancestral state.
>
> IOW, Peacock et. al. may have run afoul of a favorite argument
> against Behe by anti-ID zealots, by confusing factors exapted in
> meiosis with the existence of meiosis itself.

I don't think that's the case, since the figure has separate indications
for meiosis and for meiotic genes. But they don't go into enough detail
on the actual sources of the data represented in the figure. It's
possible that the figure is wrong. If it's wrong, one can't draw good
inferences from it.

However, this asexual amoeba can't be an example of primitive asexuality
unless you want to have meiosis evolving multiple times, which we agree
is implausible. This is not good evidence that homologous recombination
is the primitive role of the genes.

[John Harshman]

That's a big correction. Can you see why I couldn't understand your
argument? But I still don't see why that should be relevant.

>> unless you
>> want to argue that retention of the two has no correlation whatsoever.
>
> Correction: retention of much bacterial genome in the
> mitochondria and of asexual reproduction.

Why should there be any correlation?

> The hypothesis I defend is in agreement with the most
> recent hypothesis we've found:
>
>
> <snip to get to end>
>
>
>> "‘Meiotic genes’ are constitutively expressed in an asexual amoeba and are
>> not necessarily involved in sexual reproduction," Sutherland K. Maciver,
>> Zisis Koutsogiannis, Alvaro de Obeso Fernández del Valle Biol Lett. 2019
>> Mar; 15(3): 20180871. Published online 2019 Mar 6.
>> doi: 10.1098/rsbl.2018.0871 PMCID: PMC6451372
>> Currently embargoed: Free in PMC on Mar 1, 2020; PubMed
>>
>> I have been able to access the abstract using the doi reference, and it ends with:
>>
>> We contend that they are only involved in meiosis in other
>> organisms that indulge in sexual reproduction and that homologous
>> recombination is important in asexual protists as a guard against
>> the accumulation of mutations. We also suggest that asexual
>> reproduction is the ancestral state.

I don't think that follows at all and is unlikely if this "amoeba" is in
fact an amoebozoan. One would have to assume multiple evolutions of
meiosis to make that work. More likely, it's evidence that a) they have
found a reason for retention of the proteins in asexual organisms and b)
they may have found a pre-LECA, pre-meiosis role for those genes that
tells us something about the evolution of meiosis, but not that the LECA
lacked meiosis.

> I realize that the hypothesis I defend is controversial until the
> status of this "embargoed" paper is resolved, and will probably
> remain controversial thereafter. But I approach this issue,
> as I do so many others, under the same kind of principle that prevails
> in courts of law: justice is best served, on the whole, if sharply
> opposing sides are argued for, and a jury has a chance to hear both sides.
> I do believe Harshman will continue to take the opposing side on this issue,
> and that is all to the good.
>
> On this issue, as on all strictly scientific issues, the jury is the
> scientific community, not the highly unrepresentative regulars of
> talk.origins. Our arguments here stand or fall as the scientific community
> would judge, and so it behooves us to do our best to use
> arguments that are sound enough to stand tall in that community.

You bet.

[Ernest Major]

On 29/05/2019 05:05, John Harshman wrote:
>
> Have we fundamentally changed the subject from meiosis then? If not,
> what does this have to do with that subject?
>
> It's been suggested that the jakobid mt genome is derived, though
> horizontal transfer. The other possibility is that it's primitive but
> that other lineages have transferred those genes to the nucleus
> convergently.

As you now doubt know, there is a pattern of organellear genes being
consecutively lost, mostly by transfer to the nucleus, but also
absolutely in lineages that gave up aerobic metabolism (mitochondria) or
photosynthesis (plasmids), so there is to all intents and purposes a
ratchet of reducing mitochondrial gene content. This means that there
will be an eukaryote lineage with the largest gene content, but this
could be anywhere in the tree.

Unless one is a Lamarckian, one recognises that all lineages are mosaics
of ancestral and derived traits.

Hence the jakobid mitochondrial genone presents to justification for
identifying jakobids as primitive or "basal". While jakobids have the
largest known mitochondria gene content, some of their relatively close
relatives have much smaller mitochondrial gene contents, while the
lineage with the second largest mitochondrial gene content is Diphylleia
(the protist, not the plant), which is part of a group which is sister
to unikonts, and the lineage with the third largest (Ancoracysta) is
sister to Haptista.

The Archezoa hypothesis is long dead - the various groups placed there
have been found to be primitively mitochondriate, and their basal
placement in nrRNA trees to be an artefact of long branch attraction,
and perhaps convergence. (I speculate that there is selection pressure
for divergence between mitochondrial and nuclear ribosomes, to reduce
the risk of cross-interference, which is relaxed in secondarily
amitochondriate lineages.)

Subsequently the estimated eukaryote root has been placed in various
placed, but almost always with plants on one side of the root, and
animals on the other. Such topologies imply that either meiosis in
plants and animals are convergent, or that their last common ancestor
was capable of meiosis. Earlier excavates were placed on the plant side
of the root, but more recently there have been proposals that excavates
lies on both sides of the root, which would make them a
para/polyphyletic group lacking the derived characters that define the
other supergroups. That doesn't make them primitive; it just means that
the derived characters of the various excavate lineages are less striking.

Some trees place parts of Excavata (Discoba) as basal to the
plant-animal split, but I haven't seen anything proposing excavates as a
whole are basal. This means that the absence of observed sexuality in
the excavates as a whole cannot be used to draw any conclusions about
the eukaryote LCA - even before it is noted that in several other
lineages sexuality wasn't observed until very recently (this is a case
where absence of evidence isn't evidence of absence), that recombination
does occur in Giardia (but as far as I know it hasn't been demonstrated
to be sexual rather than parasexual), and that genes involved in meiosis
are commonly found in lineages not known to be sexual, including Jakobida.

--
alias Ernest Major

[John Harshman]

Good news: there is observed sexuality in excavates, and not just genes
associated with meiosis. The best I've seen so far is the expression of
meiotic genes just before cellular fusion in trypanosomes. But there is
apparently observed sex in other excavates too. Check out some of the
papers we've been arguing over, particularly this one:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517231/#d35e355

[Peter Nyikos]

On Wednesday, May 29, 2019 at 12:10:03 AM UTC-4, John Harshman wrote:
> On 5/28/19 4:44 PM, Peter Nyikos wrote:
> > On Friday, May 24, 2019 at 9:50:03 AM UTC-4, John Harshman wrote:
> >> On 5/23/19 8:46 AM, Peter Nyikos wrote:
> >>> On Wednesday, May 22, 2019 at 9:40:03 AM UTC-4, John Harshman wrote:
> >>>> On 5/22/19 4:48 AM, Peter Nyikos wrote:
> >>>>> On Monday, May 20, 2019 at 11:40:03 AM UTC-4, John Harshman wrote:
> >>>>>> On 5/20/19 6:03 AM, Peter Nyikos wrote:
> >>>>>>> On Friday, May 17, 2019 at 11:35:03 PM UTC-4, John Harshman wrote:
> >>>>>>>> On 5/17/19 6:29 PM, Peter Nyikos wrote:
> >>>>>
> >>>>>>>>> Mystery 3: Did meiosis predate the LCA of living eukaryotes?
> >>>>>>>>
> >>>>>>>> Yes, obviously, unless you want to propose that meiosis arose multiple
> >>>>>>>> times convergently.

This cocksure comment of yours is echoed twice by you below,
and yet the following comment by me still applies:

> > We still lack enough data to justify your "obviously" here, and
> > it looks like it may be that way for a good long time to come.

<snip for focus>

> > Picking up the part of your post which I haven't addressed yet:
> >
> >>>> Further, the way in which [the Jakobids] are odd has nothing to do with meiosis.
> >>>> So could you explain?
>

> > <snip for focus>.

> >
> >>> In partial answer to your question: you seem to think
> >>> that phylogenetic trees are the be-all and end-all of systematics.
> >>> But the tree does not give an adequate reason for rejecting various
> >>> states as primitive, because it is always a compromise between
> >>> a huge number of pieces of conflicting evidence.
> >>
> >> Not sure what you mean by that. Do you mean that the tree itself is
> >> uncertain and therefore not a basis for character inference,
> >
> > Not necessarily.
> >
> >> or do you mean that not even a certain tree is such a basis?
> >
> > Yes, but try to stay focused. The issue is whether a given
> > character is primitive or derived. In the case of the Jakobids,
> > the "peculiar" character is their retention of a bigger part of
> > the bacterial genome in their mitochondria than in other eukaryotes.
>
> Have we fundamentally changed the subject from meiosis then? If not,
> what does this have to do with that subject?

I think it is worth discussing both, because it appears that
the following two statements are increasingly tending towards
becoming the conventional wisdom:

A. The LCA of extant eukaryotes had mitochondria.

B. The LCA of extant eukaryotes had meiosis.

Close study of the various phylogenetic trees, especially of
differences between where the rootings (including alternative ones)
are hypothesized to be, might shed light on both questions
simultaneously.


It's getting late, so I am snipping a lot that I'll be discussing
later, some of it next week.

The placement of that one critter could be relevant to both A
and B. It seems to lack all sign of ever having had mitochondria,
and I've seen no suggestion that it undergoes meiosis.

> I think you don't quite understand what "rooting" means. It's separate
> from topology.

What is behind this bolt out of the blue? It doesn't
have any connection with anything I wrote anywhere, and the second sentence
is something I've known about since I learned the concept of rooting,
back in the 1990's in sci.bio.paleontology.

>
> > Under the circumstances, including the fact that these papers
> > are a mere year apart, and the fact that the latter cites the
> > former several times, we cannot be sure any rooting will stand
> > the test of time in the next decade.
>
> Agreed. The rooting is not completely clear. But it doesn't have to be
> in order to make my point.

Stop being obscure and spell out what this "point" is; and
I hope it isn't something we've already agreed on several times.

> >>>> And even so, it makes neiwther diplomonads nor jakobids the
> >>>> sister group of other eukaryotes.
> > [...]
> >>>
> >>> https://cshperspectives.cshlp.org/content/6/5/a016147/F1.large.jpg
> >>>
> >>> And if you "look out that window," you will see, close to the edge,
> >>> one of the five dotted arrows that mark possible rootings of
> >>> the tree of Eukarya. On one branch off that split, there are just
> >>> three taxa: euglenids, diplonemids, and kinetoblastids.
> >>>
> >>> On the other branch, representing ALL other eukaryotes, the jakobids
> >>> are the second of two basal taxa: the jakobids are the
> >>> sister group of all the rest.
> >
> >
> > <snip for focus>
> >
> >
> > Here is that 2015 paper:
> >
> > "Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life," by three authors (2015):
> >> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517231/
> >>
> >> I direct your attention especially to Fig. 2.
> >
> > Yes, and with a minor detail it gives the same huge split that
> > I give above. And it has another possible rooting in which
> > the Euglenozoa split off from **ALL** other eukaryotes.
>
> The root in this case is not relevant, since regardless of the root
> position there is meiosis on both sides of the basal branching.

More cocksureness from you, without you giving a smidgin of
evidence for it here or below.

> > And in both cases, the whole issue of primitiveness of meiosis
> > revolves around one detail: does *Trypanosoma* *brucei* undergo
> > meiosis?
>
> No, it doesn't.

In the 2015 paper, it does.

> It's enough that meiosis is known on both sides of
> whatever you think is the basal split. Given the rooting you mention
> above, it's only necessary that there be meiosis in some euglenozoan,
> any euglenozoan.

Stop belaboring the obvious, and instead let us know whether
you know something that you don't seem to know.

> While it's true that Trypanosoma is the only
> euglenozoan mentioned in the text, you shouldn't assume that it's the
> only one known to do meiosis.

Are you categorically claiming above that there ARE some others known?
Or do you have some reason to think that what you write below
proves that Trypanosoma *does* have meiosis?

>
> > And now the plot starts to thicken. The 2015 paper says "meiosis and gametes were only detected very recently (10, 11)" in this species.
> >
> > 10. Peacock L, et al. Identification of the meiotic life cycle stage of *Trypanosoma* *brucei* in the tsetse fly. Proc Natl Acad Sci USA. 2011;108(9):3671–3676. [PMC free article] [PubMed] [Google Scholar]
> > 11. Peacock L, Bailey M, Carrington M, Gibson W. Meiosis and haploid gametes
> > in the pathogen *Trypanosoma* *brucei*. Curr Biol. 2014;24(2):181–186. [PMC free article] [PubMed] [Google Scholar]
> >

> > However, the first only speaks of "homologs of meiotic genes in the T. brucei genome" and "three functionally distinct, meiosis-specific proteins".

>
> No, that's not all it speaks of. It says they are expressed at a
> particular time, right before cellular fusion.

At which time cytoplasm is exchanged, according to the second article.
Where are the chromosomes in all this? Can you find any clue in
either paper?

> This is when we would
> expect meiosis to happen,

In humans, meiosis II is spurred by penetration. What other source
do you have for this expectation?

> but not other suggested functions of those genes.

Do you include the ones mentioned in the embargoed 2019 article
among the "others"? Why or why not?

>
> > The second also talks about such things, and contains photographs of various pairs and groups of trypanosomes "exchanging cytoplasmic material." > However,
> > there is no photographic evidence of meiosis, nor is there a single picture
> > that identifies any chromosome.

Your failure to address this comment suggests that you were
bluffing above; this is where one would expect you to either
produce proof of meiosis in Trypanosoma or to produce another
euglenozoan that has meiosis.

> > The plot really thickens with the following "embargoed"
> > [whatever that means] article, which seems to call the first Peacock
> > paper and much of the second into question:
>
> Embargoed articles are usually those you aren't allowed to see before
> official publication. In this case it seems to be one that's been
> published but that you have to pay for until a certain date, when it
> becomes free.
>
> > "‘Meiotic genes’ are constitutively expressed in an asexual amoeba and are
> > not necessarily involved in sexual reproduction," Sutherland K. Maciver,
> > Zisis Koutsogiannis, Alvaro de Obeso Fernández del Valle Biol Lett. 2019
> > Mar; 15(3): 20180871. Published online 2019 Mar 6.
> > doi: 10.1098/rsbl.2018.0871 PMCID: PMC6451372
> > Currently embargoed: Free in PMC on Mar 1, 2020; PubMed
>
> > I have been able to access the abstract using the doi reference, and it ends with:
> >
> > We contend that they are only involved in meiosis in other
> > organisms that indulge in sexual reproduction and that homologous
> > recombination is important in asexual protists as a guard against
> > the accumulation of mutations. We also suggest that asexual
> > reproduction is the ancestral state.
> >
> > IOW, Peacock et. al. may have run afoul of a favorite argument
> > against Behe by anti-ID zealots, by confusing factors exapted in
> > meiosis with the existence of meiosis itself.
>
> I don't think that's the case,

But your attempt to justify this skepticism is extremely underwhelming.

> since the figure has separate indications
> for meiosis and for meiotic genes.

If you are talking about that Fig 2 in that 2015 paper, I'm way
ahead of you. I saw euglenozoans credited with "sex known"
but the only evidence I saw for it in the text was in Trypanosoma.
That's why I said what I did about "revolves around one detail".

> But they don't go into enough detail
> on the actual sources of the data represented in the figure. It's
> possible that the figure is wrong. If it's wrong, one can't draw good
> inferences from it.

Huge backpedal from what looks now like a bluff, noted. Also from
your sending me specifically to fig. 2 in your earlier post,
as if it cleared up any doubts about meiosis being on both branches
of any divide.

> However, this asexual amoeba can't be an example of primitive asexuality
> unless you want to have meiosis evolving multiple times, which we agree
> is implausible.

This cocksure comment is an echo of the one at the top of this
post. No explanation provided, of course.

> This is not good evidence that homologous recombination
> is the primitive role of the genes.

Let's just wait till we see this article before you make
comments like this, shall we?


Peter Nyikos

Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina

http://www.math.sc.edu/~nyikos

PS In this second half of your post, you've been devolving from
*Homo* *sapiens* *sapiens* into *Homo* *sapiens* *polemica*.
Does promoting fruitful discussion bore you?

[John Harshman]

On 5/29/19 9:11 PM, Peter Nyikos wrote:
> On Wednesday, May 29, 2019 at 12:10:03 AM UTC-4, John Harshman wrote:
>> On 5/28/19 4:44 PM, Peter Nyikos wrote:
>>> On Friday, May 24, 2019 at 9:50:03 AM UTC-4, John Harshman wrote:
>>>> On 5/23/19 8:46 AM, Peter Nyikos wrote:
>>>>> On Wednesday, May 22, 2019 at 9:40:03 AM UTC-4, John Harshman wrote:
>>>>>> On 5/22/19 4:48 AM, Peter Nyikos wrote:
>>>>>>> On Monday, May 20, 2019 at 11:40:03 AM UTC-4, John Harshman wrote:
>>>>>>>> On 5/20/19 6:03 AM, Peter Nyikos wrote:
>>>>>>>>> On Friday, May 17, 2019 at 11:35:03 PM UTC-4, John Harshman wrote:
>>>>>>>>>> On 5/17/19 6:29 PM, Peter Nyikos wrote:
>>>>>>>
>>>>>>>>>>> Mystery 3: Did meiosis predate the LCA of living eukaryotes?
>>>>>>>>>>
>>>>>>>>>> Yes, obviously, unless you want to propose that meiosis arose multiple
>>>>>>>>>> times convergently.
>
> This cocksure comment of yours is echoed twice by you below,
> and yet the following comment by me still applies:
>
>>> We still lack enough data to justify your "obviously" here, and
>>> it looks like it may be that way for a good long time to come.

But we do appear to have enough data.

It might, but you should agree that the two questions have nothing to do
with each other. They are not linked as you seem to have claimed
earlier. They are both interesting. The answer to neither seems to
depend much on rooting, for the same reason: both mitochondria and
meiosis are so widely distributed in eukaryotes that no rooting will
fail to put taxa possessing them on both sides of the root.

So? This is only relevant if the root lies within or directly adjacent
to Malawinomonadida. Is any suggested rooting of that sort?

>> I think you don't quite understand what "rooting" means. It's separate
>> from topology.
>
> What is behind this bolt out of the blue? It doesn't
> have any connection with anything I wrote anywhere, and the second sentence
> is something I've known about since I learned the concept of rooting,
> back in the 1990's in sci.bio.paleontology.

What you say above suggests that you don't understand the concept,
though it might be something else you don't understand. Can't tell.

>>> Under the circumstances, including the fact that these papers
>>> are a mere year apart, and the fact that the latter cites the
>>> former several times, we cannot be sure any rooting will stand
>>> the test of time in the next decade.
>>
>> Agreed. The rooting is not completely clear. But it doesn't have to be
>> in order to make my point.
>
> Stop being obscure and spell out what this "point" is; and
> I hope it isn't something we've already agreed on several times.

I have spelled it out several times: none of the roots make it
parsimonious for the LECA to lack meiosis.

>>>>>> And even so, it makes neiwther diplomonads nor jakobids the
>>>>>> sister group of other eukaryotes.
>>> [...]
>>>>>
>>>>> https://cshperspectives.cshlp.org/content/6/5/a016147/F1.large.jpg
>>>>>
>>>>> And if you "look out that window," you will see, close to the edge,
>>>>> one of the five dotted arrows that mark possible rootings of
>>>>> the tree of Eukarya. On one branch off that split, there are just
>>>>> three taxa: euglenids, diplonemids, and kinetoblastids.
>>>>>
>>>>> On the other branch, representing ALL other eukaryotes, the jakobids
>>>>> are the second of two basal taxa: the jakobids are the
>>>>> sister group of all the rest.
>>>
>>>
>>> <snip for focus>
>>>
>>>
>>> Here is that 2015 paper:
>>>
>>> "Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life," by three authors (2015):
>>>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517231/
>>>>
>>>> I direct your attention especially to Fig. 2.
>>>
>>> Yes, and with a minor detail it gives the same huge split that
>>> I give above. And it has another possible rooting in which
>>> the Euglenozoa split off from **ALL** other eukaryotes.
>>
>> The root in this case is not relevant, since regardless of the root
>> position there is meiosis on both sides of the basal branching.
>
> More cocksureness from you, without you giving a smidgin of
> evidence for it here or below.

I'm confused as to why the evidence I give below is not to be considered
evidence.

>>> And in both cases, the whole issue of primitiveness of meiosis
>>> revolves around one detail: does *Trypanosoma* *brucei* undergo
>>> meiosis?
>>
>> No, it doesn't.
>
> In the 2015 paper, it does.

I don't think it does, as I have tried to argue below.

>> It's enough that meiosis is known on both sides of
>> whatever you think is the basal split. Given the rooting you mention
>> above, it's only necessary that there be meiosis in some euglenozoan,
>> any euglenozoan.
>
> Stop belaboring the obvious, and instead let us know whether
> you know something that you don't seem to know.

What would that something be?

>> While it's true that Trypanosoma is the only
>> euglenozoan mentioned in the text, you shouldn't assume that it's the
>> only one known to do meiosis.
>
> Are you categorically claiming above that there ARE some others known?
> Or do you have some reason to think that what you write below
> proves that Trypanosoma *does* have meiosis?

1. No.

2. You should know that "proves" isn't a word we use. I'll say that the
evidence is quite strong.

>>> And now the plot starts to thicken. The 2015 paper says "meiosis and gametes were only detected very recently (10, 11)" in this species.
>>>
>>> 10. Peacock L, et al. Identification of the meiotic life cycle stage of *Trypanosoma* *brucei* in the tsetse fly. Proc Natl Acad Sci USA. 2011;108(9):3671–3676. [PMC free article] [PubMed] [Google Scholar]
>>> 11. Peacock L, Bailey M, Carrington M, Gibson W. Meiosis and haploid gametes
>>> in the pathogen *Trypanosoma* *brucei*. Curr Biol. 2014;24(2):181–186. [PMC free article] [PubMed] [Google Scholar]
>>>
>>> However, the first only speaks of "homologs of meiotic genes in the T. brucei genome" and "three functionally distinct, meiosis-specific proteins".
>>
>> No, that's not all it speaks of. It says they are expressed at a
>> particular time, right before cellular fusion.
>
> At which time cytoplasm is exchanged, according to the second article.
> Where are the chromosomes in all this? Can you find any clue in
> either paper?

This is cellular fusion, not just exchange of cytoplasm.

>> This is when we would
>> expect meiosis to happen,
>
> In humans, meiosis II is spurred by penetration. What other source
> do you have for this expectation?

Now you're just being contentious. What's being formed here is analogous
to a zygote.

>> but not other suggested functions of those genes.
>
> Do you include the ones mentioned in the embargoed 2019 article
> among the "others"? Why or why not?

Yes. I don't know of any other suggested functions than those.

>>> The second also talks about such things, and contains photographs of various pairs and groups of trypanosomes "exchanging cytoplasmic material." > However,
>>> there is no photographic evidence of meiosis, nor is there a single picture
>>> that identifies any chromosome.
>
> Your failure to address this comment suggests that you were
> bluffing above; this is where one would expect you to either
> produce proof of meiosis in Trypanosoma or to produce another
> euglenozoan that has meiosis.

I consider the evidence already mentioned good enough. Why are you
insisting on a photograph of...of what, exactly?

It does unless you claim that the figure is wrong. Are you indeed making
that claim? In what way is it wrong.

>> However, this asexual amoeba can't be an example of primitive asexuality
>> unless you want to have meiosis evolving multiple times, which we agree
>> is implausible.
>
> This cocksure comment is an echo of the one at the top of this
> post. No explanation provided, of course.

Why is an explanation necessary? What is the phylogenetic position of
this amoeba (again, presumably an amoebozoan) that could make it
credibly primitive in its asexuality?

>> This is not good evidence that homologous recombination
>> is the primitive role of the genes.
>
> Let's just wait till we see this article before you make
> comments like this, shall we?

No. All that's necessary is to know what this "amoeba" is.

> PS In this second half of your post, you've been devolving from
> *Homo* *sapiens* *sapiens* into *Homo* *sapiens* *polemica*.
> Does promoting fruitful discussion bore you?

Do you call that comment promoting fruitful discussion? I don't. It
serves no purpose other than to insult me.

[Ernest Major]

On 30/05/2019 06:52, John Harshman wrote:
>>>> So? the next reference you give below, dated 2015, also gives six
>>>> possible rootings, but only one of them coincides with any of the
>>>> six given by the 2014 reference. In particular, they differ
>>>> in their "preferred" rooting as to where they place Malawinomonadida.
>>
>> The placement of that one critter could be relevant to both A
>> and B. It seems to lack all sign of ever having had mitochondria,
>> and I've seen no suggestion that it undergoes meiosis.
>
> So? This is only relevant if the root lies within or directly adjacent
> to Malawinomonadida. Is any suggested rooting of that sort?

I presume that the problem with rooting eukaryotes is that the outgroups
aren't very close (and that eukaryotes are rather derived in several
ways). But, as you understand, that doesn't mean that all rootings
aren't equally plausible.

For an analogy, if we had a mammalian tree, and no outgroups, we (you
and I at least) would place the root between Homo sapiens and the rest
of Mammalia. Rate heterogenity is a thing, but it's not reasonable to
pick a root which results in a 30-fold rate variation when there's a
root which gives a 3-fold rate variation. Or to reduce it to the
completely absurd, placing the root of eukaryotes beween Arabidopsis
thaliana and the remainder of eukaryotes.

--
alias Ernest Major

[Peter Nyikos]

On Thursday, May 30, 2019 at 1:55:03 AM UTC-4, John Harshman wrote:
> On 5/29/19 9:11 PM, Peter Nyikos wrote:
> > On Wednesday, May 29, 2019 at 12:10:03 AM UTC-4, John Harshman wrote:
> >> On 5/28/19 4:44 PM, Peter Nyikos wrote:
> >>> On Friday, May 24, 2019 at 9:50:03 AM UTC-4, John Harshman wrote:
> >>>> On 5/23/19 8:46 AM, Peter Nyikos wrote:
> >>>>> On Wednesday, May 22, 2019 at 9:40:03 AM UTC-4, John Harshman wrote:
> >>>>>> On 5/22/19 4:48 AM, Peter Nyikos wrote:
> >>>>>>> On Monday, May 20, 2019 at 11:40:03 AM UTC-4, John Harshman wrote:
> >>>>>>>> On 5/20/19 6:03 AM, Peter Nyikos wrote:
> >>>>>>>>> On Friday, May 17, 2019 at 11:35:03 PM UTC-4, John Harshman wrote:
> >>>>>>>>>> On 5/17/19 6:29 PM, Peter Nyikos wrote:
> >>>>>>>
> >>>>>>>>>>> Mystery 3: Did meiosis predate the LCA of living eukaryotes?
> >>>>>>>>>>
> >>>>>>>>>> Yes, obviously, unless you want to propose that meiosis arose multiple
> >>>>>>>>>> times convergently.
> >
> > This cocksure comment of yours is echoed twice by you below,
> > and yet the following comment by me still applies:
> >
> >>> We still lack enough data to justify your "obviously" here, and
> >>> it looks like it may be that way for a good long time to come.
>
> But we do appear to have enough data.

You are not talking like a scientist here, but like a
polemicist. Your evidence for this claim is pathetically weak,
even in the part I postponed talking about at the end.

Your animosity towards me is causing you to spurn a beautiful
chance to shed light on Mystery 2 -- How did meiosis originate?
We could be exploring the various factors that might have been
exapted to produce full-fledged Meiosis I and Meiosis II.

Instead, your dogmatic position that the factors identified
give sufficient evidence that they were already present,
is torpedoing any hope of us doing this together.

I can be about 5% as obdurate as you have been in your last
few replies to me, and so I will not agree to this one thing.
As to why not, see my next comment.

> They are not linked as you seem to have claimed earlier.

I muffed the explanation because I didn't want to go into
a long detailed essay. But if the word "omnimal" rings
a bell with you -- it's about the "starring" animal
in an old science fiction story, one of the best examples of
"evolutionary theory fiction" ever -- I may not have to take
long about it.

> They are both interesting. The answer to neither seems to
> depend much on rooting, for the same reason: both mitochondria and
> meiosis are so widely distributed in eukaryotes that no rooting will
> fail to put taxa possessing them on both sides of the root.

This is just another variation on your earlier cocksure statement,
where meiosis is concerned; as for mitochondria, see below about
Malawinomonadida.

>
> > It's getting late, so I am snipping a lot that I'll be discussing
> > later, some of it next week.
> >
> >
> >>>>>>>> Here are a few more recent references:
> >>>
> >>> Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups" (7 authors, 2009):
> >>>>>>>> https://www.pnas.org/content/106/10/3859
> >>>
> >>> The Eukaryotic Tree of Life from a Global Phylogenomic Perspective, by Fabien Burki (2014):
> >>>>>>>> https://cshperspectives.cshlp.org/content/6/5/a016147.full
> >>>>>>>>
> >>>>>>>> You will note that even Excavata is not the sister group of other
> >>>>>>>> eukaryotes,
> >>>>>>>
> >>>>>>> The first article "reforms" it into one of three "supergroups"
> >>>>>>> in an unresolved trichotomy, by eliminating dubious "members."
> >>>>>>>
> >>>>>>> The second article admits that efforts to root the eukaryotic
> >>>>>>> tree have been unsuccessful. One of six possible roots is
> >>>>>>> the one that makes the reformed Excavata one of the two branches
> >>>>>>> of the first split.
> >>>>>>
> >>>>>> True, though that isn't the rooting the author thinks has the best
> >>>>>> support.
> >>>>>
> >>>>> Fabien Burki is sufficiently unsure of his choice that he
> >>>>> lists five possible alternatives. He shows an admirable
> >>>>> degree of scientific caution all through the long and
> >>>>> thorough article. It's something you would do well to emulate
> >>>>> as best you can.

You keep spurning this suggestion and continuing along your
dogmatic track like a horse with blinders.

> >>>> Nevertheless, he has a preferred rooting.
> >>>
> >>> So? the next reference you give below, dated 2015, also gives six
> >>> possible rootings, but only one of them coincides with any of the
> >>> six given by the 2014 reference. In particular, they differ
> >>> in their "preferred" rooting as to where they place Malawinomonadida.
> >
> > The placement of that one critter could be relevant to both A
> > and B. It seems to lack all sign of ever having had mitochondria,
> > and I've seen no suggestion that it undergoes meiosis.
>
> So? This is only relevant if the root lies within or directly adjacent
> to Malawinomonadida.

"Within" is impossible, due to the ban on paraphyletic taxa.

> Is any suggested rooting of that sort?

It's the next best thing to M. being the sister taxon of all other
Eukaryotes in the 2015 paper, and I think you know that.
After all, it was you who prematurely suggested that Fig 2
of the 2015 paper settled the "both branches" issue in your favor.

Fig. 1 of the 2014 paper is almost as good.

> >> I think you don't quite understand what "rooting" means. It's separate
> >> from topology.
> >
> > What is behind this bolt out of the blue? It doesn't
> > have any connection with anything I wrote anywhere, and the second sentence
> > is something I've known about since I learned the concept of rooting,
> > back in the 1990's in sci.bio.paleontology.
>
> What you say above suggests that you don't understand the concept,

Like hell it does. Quote what you claim to be suggesting it,
or retract.

> though it might be something else you don't understand. Can't tell.

I think readers will be able to tell that you are bluffing here if
you try to meet the challenge I have given you just now.

Unfortunately, they will either be toadies of yours who will be
willing to post any crap in support of you, or people who know it is
dangerous to "mess with you" because of the existence of toadies like
Oxyaena and Erik Simpson in both talk.origins and sci.bio.paleontology.

Some of the non-toadies may think I am coming down way too hard on you,
but that's because they won't know that your bolt-out-of-the-blue
crap is of the same genre as something infinitely worse: a claim in
s.b.p. last year that you "think" I believe something that would make
me shockingly misogynistic if I even came close to believing it.

At the time you made this hateful claim, I gave
a very detailed explanation why, **IF** you were sincere, you
were suffering from at least a moderate case of Alzheimer's.

Your arrogant treatment of this lifeline, and the revelation
that you are probably at least a decade younger than I,
have now convinced me to formally charge you with having
shamelessly lied about what you claimed to "think".

How do you plead, guilty or not guilty? Snipping this
revelation of our clash last year will be tantamount
to a plea of *nolo* *contendere*.


Remainder deleted, to be replied to later.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--

[Peter Nyikos]

On Thursday, May 30, 2019 at 3:55:02 AM UTC-4, Ernest Major wrote:
> On 30/05/2019 06:52, John Harshman wrote:
> >>>> So? the next reference you give below, dated 2015, also gives six
> >>>> possible rootings, but only one of them coincides with any of the
> >>>> six given by the 2014 reference. In particular, they differ
> >>>> in their "preferred" rooting as to where they place Malawinomonadida.
> >>
> >> The placement of that one critter could be relevant to both A
> >> and B. It seems to lack all sign of ever having had mitochondria,
> >> and I've seen no suggestion that it undergoes meiosis.
> >
> > So? This is only relevant if the root lies within or directly adjacent
> > to Malawinomonadida. Is any suggested rooting of that sort?

As I told John less than an hour ago, Fig. 2 of the 2015
paper gives pretty much the next best thing.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517231/

The degree of uncertainty it shows suggests the possibility that
some more recent, or future tree, might actually show
what John is asking about.

By the way, do you know of any more recent trees as thorough
as the one in that 2015 paper or the 2014 paper,

https://cshperspectives.cshlp.org/content/6/5/a016147.full#F1

> I presume that the problem with rooting eukaryotes is that the outgroups
> aren't very close (and that eukaryotes are rather derived in several
> ways). But, as you understand, that doesn't mean that all rootings
> aren't equally plausible.

Maybe John does understand it, but he gave no hint of that
in his replies to me.

Oh, wait, did you mean "are" instead of "aren't"? Your talk
of rate heterogeneity suggests that. Even so, read on.

> For an analogy, if we had a mammalian tree, and no outgroups, we (you
> and I at least) would place the root between Homo sapiens and the rest
> of Mammalia.

HUH? Why not where it is now: between Monotremata and the
rest of Mammalia? Even if monotremes were the only vertebrates
which are oviparous and have very different shoulder girdles
than the rest of mammalia, that would already be a strong
argument for the present rooting.

> Rate heterogenity is a thing, but it's not reasonable to
> pick a root which results in a 30-fold rate variation when there's a
> root which gives a 3-fold rate variation.

Please explain why this doesn't apply to monotremata
vs rest of mammalia.

Come to think of it, perhaps this was one reason for the
reckless hypothesis which put marsupials on one branch
of mammalia and monotremes and placentals on the other
branch. Called the "marsupionta hypotesis", it actually
resulted in a number of peer-reviewed papers.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--

U. of So. Carolina at Columbia
http://people.math.sc.edu

[Oxyaena]

In the category of "Judge, Jury, and Executioner"

> have now convinced me to formally charge you with having

> shamelessly lied about what you claimed to "think" > How do you plead, guilty or not guilty?

--
"I'd rather be the son of an ape than be descended from a man afraid to
face the truth." - TH Huxley

https://peradectes.wordpress.com/

[erik simpson]

You better watch out
You better not cry
Better not pout
I'm telling you why
Santa Claus is coming to town

He's making a list,
And checking it twice;
Gonna find out Who's naughty and nice.
Santa Claus is coming to town

He sees you when you're sleeping
He knows when you're awake
He knows if you've been bad or good
So be good for goodness sake!

(J. Fred Coots, Henry Gillespie (c) 1934)

[jillery]

On Thu, 30 May 2019 12:49:10 -0400, Oxyaena <oxy...@creo.dont> wrote:

>
>In the category of "Judge, Jury, and Executioner"
>
>> have now convinced me to formally charge you with having
>> shamelessly lied about what you claimed to "think" > How do you plead, guilty or not guilty?

Judge Roy Bean strikes again!

--
I disapprove of what you say, but I will defend to the death your right to say it.

Evelyn Beatrice Hall
Attributed to Voltaire

[Oxyaena]

Peter disses me for being "tight lipped" but I know he'll be the type of
asshole to doxx me in harmful ways to get a leg up if I make even *one*
slip up, so this song is incredibly prescient when it comes to Peter.

[Oxyaena]

On 5/30/2019 1:00 PM, jillery wrote:
> On Thu, 30 May 2019 12:49:10 -0400, Oxyaena <oxy...@creo.dont> wrote:
>
>>
>> In the category of "Judge, Jury, and Executioner"
>>
>>> have now convinced me to formally charge you with having
>>> shamelessly lied about what you claimed to "think" > How do you plead, guilty or not guilty?
>
>
> Judge Roy Bean strikes again!
>

I wonder if this will hold up in court.

[Ernest Major]

Yes, that's a mistype, probably caused by recomposing the sentence on
the fly while typing - I'm a sufficiently slow typist that I can
recompose sentences several times over while typing them. I would have
hoped that that it was obvious that this was a mistype.

>
>
>> For an analogy, if we had a mammalian tree, and no outgroups, we (you
>> and I at least) would place the root between Homo sapiens and the rest
>> of Mammalia.
>
> HUH? Why not where it is now: between Monotremata and the
> rest of Mammalia? Even if monotremes were the only vertebrates
> which are oviparous and have very different shoulder girdles
> than the rest of mammalia, that would already be a strong
> argument for the present rooting.

That's another mistype - missing negative syndrome caused by typing much
slower than I think. s/would/wouldn't/. I would have hoped that this
would have been obvious.

>
>
>> Rate heterogenity is a thing, but it's not reasonable to
>> pick a root which results in a 30-fold rate variation when there's a
>> root which gives a 3-fold rate variation.
>
> Please explain why this doesn't apply to monotremata
> vs rest of mammalia.
>
> Come to think of it, perhaps this was one reason for the
> reckless hypothesis which put marsupials on one branch
> of mammalia and monotremes and placentals on the other
> branch. Called the "marsupionta hypotesis", it actually
> resulted in a number of peer-reviewed papers.

Marsupionta united monotremes and marsupials, not monotremes and
placentals. It was one of a number of early results from mtDNA
sequencing that were incorrect - if I understand correctly as a result
of artefacts resulting from base composition biases.

>
>
> Peter Nyikos
> Professor, Dept. of Mathematics -- standard disclaimer--
> U. of So. Carolina at Columbia
> http://people.math.sc.edu
>
>
>> Or to reduce it to the
>> completely absurd, placing the root of eukaryotes beween Arabidopsis
>> thaliana and the remainder of eukaryotes.
>

--
alias Ernest Major

[John Harshman]

On 5/30/19 8:44 AM, Peter Nyikos wrote:
> Even if monotremes were the only vertebrates
> which are oviparous and have very different shoulder girdles
> than the rest of mammalia, that would already be a strong
> argument for the present rooting.

Not without an outgroup it isn't. Egglaying and odd shoulder girdles
would as easily be apomorphic as plesiomorphic, absent an outgroup to
root the characters.

[John Harshman]

On 5/30/19 7:49 AM, Peter Nyikos wrote:
> On Thursday, May 30, 2019 at 1:55:03 AM UTC-4, John Harshman wrote:
>> On 5/29/19 9:11 PM, Peter Nyikos wrote:
>>> On Wednesday, May 29, 2019 at 12:10:03 AM UTC-4, John Harshman wrote:
>>>> On 5/28/19 4:44 PM, Peter Nyikos wrote:
>>>>> On Friday, May 24, 2019 at 9:50:03 AM UTC-4, John Harshman wrote:
>>>>>> On 5/23/19 8:46 AM, Peter Nyikos wrote:
>>>>>>> On Wednesday, May 22, 2019 at 9:40:03 AM UTC-4, John Harshman wrote:
>>>>>>>> On 5/22/19 4:48 AM, Peter Nyikos wrote:
>>>>>>>>> On Monday, May 20, 2019 at 11:40:03 AM UTC-4, John Harshman wrote:
>>>>>>>>>> On 5/20/19 6:03 AM, Peter Nyikos wrote:
>>>>>>>>>>> On Friday, May 17, 2019 at 11:35:03 PM UTC-4, John Harshman wrote:
>>>>>>>>>>>> On 5/17/19 6:29 PM, Peter Nyikos wrote:
>>>>>>>>>
>>>>>>>>>>>>> Mystery 3: Did meiosis predate the LCA of living eukaryotes?
>>>>>>>>>>>>
>>>>>>>>>>>> Yes, obviously, unless you want to propose that meiosis arose multiple
>>>>>>>>>>>> times convergently.
>>>
>>> This cocksure comment of yours is echoed twice by you below,
>>> and yet the following comment by me still applies:
>>>
>>>>> We still lack enough data to justify your "obviously" here, and
>>>>> it looks like it may be that way for a good long time to come.
>>
>> But we do appear to have enough data.

I'm just going to start just snipping out all the off-topic and
insulting bits.

I will not agree to this one thing.

>> They are not linked as you seem to have claimed earlier.

>> They are both interesting. The answer to neither seems to
>> depend much on rooting, for the same reason: both mitochondria and
>> meiosis are so widely distributed in eukaryotes that no rooting will
>> fail to put taxa possessing them on both sides of the root.

>>> It's getting late, so I am snipping a lot that I'll be discussing
>>> later, some of it next week.
>>>
>>>
>>>>>>>>>> Here are a few more recent references:
>>>>>
>>>>> Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups" (7 authors, 2009):
>>>>>>>>>> https://www.pnas.org/content/106/10/3859
>>>>>
>>>>> The Eukaryotic Tree of Life from a Global Phylogenomic Perspective, by Fabien Burki (2014):
>>>>>>>>>> https://cshperspectives.cshlp.org/content/6/5/a016147.full
>>>>>>>>>>
>>>>>>>>>> You will note that even Excavata is not the sister group of other
>>>>>>>>>> eukaryotes,
>>>>>>>>>
>>>>>>>>> The first article "reforms" it into one of three "supergroups"
>>>>>>>>> in an unresolved trichotomy, by eliminating dubious "members."
>>>>>>>>>
>>>>>>>>> The second article admits that efforts to root the eukaryotic
>>>>>>>>> tree have been unsuccessful. One of six possible roots is
>>>>>>>>> the one that makes the reformed Excavata one of the two branches
>>>>>>>>> of the first split.
>>>>>>>>
>>>>>>>> True, though that isn't the rooting the author thinks has the best
>>>>>>>> support.
>>>>>>>
>>>>>>> Fabien Burki is sufficiently unsure of his choice that he
>>>>>>> lists five possible alternatives. He shows an admirable
>>>>>>> degree of scientific caution all through the long and
>>>>>>> thorough article. It's something you would do well to emulate
>>>>>>> as best you can.

>>>>>> Nevertheless, he has a preferred rooting.
>>>>>
>>>>> So? the next reference you give below, dated 2015, also gives six
>>>>> possible rootings, but only one of them coincides with any of the
>>>>> six given by the 2014 reference. In particular, they differ
>>>>> in their "preferred" rooting as to where they place Malawinomonadida.
>>>
>>> The placement of that one critter could be relevant to both A
>>> and B. It seems to lack all sign of ever having had mitochondria,
>>> and I've seen no suggestion that it undergoes meiosis.
>>
>> So? This is only relevant if the root lies within or directly adjacent
>> to Malawinomonadida.
>
> "Within" is impossible, due to the ban on paraphyletic taxa.

Then let's say "within the (in that case) paraphyletic and therefore
nonexistent group Malawimonadida".

>> Is any suggested rooting of that sort?
>
> It's the next best thing to M. being the sister taxon of all other
> Eukaryotes in the 2015 paper, and I think you know that.

> After all, it was you who suggested that Fig 2

> of the 2015 paper settled the "both branches" issue in your favor.

Ah, but "the next best thing" isn't good enough. "The next best thing"
puts meiosis on both sides of the root.

> Fig. 1 of the 2014 paper is almost as good.

"Almost" just doesn't count. The rooting either makes ancestral meiosis
parsimonious (meiosis on both sides), unparsimonious (meiosis nested
within non-meiosis), or undetermined (meiosis on one side but not the
other).

>>>> I think you don't quite understand what "rooting" means. It's separate
>>>> from topology.
>>>
>>> What is behind this bolt out of the blue? It doesn't
>>> have any connection with anything I wrote anywhere, and the second sentence
>>> is something I've known about since I learned the concept of rooting,
>>> back in the 1990's in sci.bio.paleontology.
>>
>> What you say above suggests that you don't understand the concept,
>
> Like hell it does. Quote what you claim to be suggesting it,
> or retract.

"The placement of that one critter could be relevant to both A and B."

That's what I'm trying to figure out and what suggested that you don't
understand rooting.

>> though it might be something else you don't understand. Can't tell.

You suggested at least twice above (though I snipped as irrelevant) that
you were going to explain this point, but you never did. It would be
good if you did explain. Or did I fail to recognize it as an explanation?

[Peter Nyikos]

On Thursday, May 30, 2019 at 4:10:03 PM UTC-4, John Harshman wrote:
> On 5/30/19 8:44 AM, Peter Nyikos wrote:
> > Even if monotremes were the only vertebrates
> > which are oviparous and have very different shoulder girdles
> > than the rest of mammalia, that would already be a strong
> > argument for the present rooting.

> Not without an outgroup it isn't.

Yes, it is, because I am talking about a choice between
alternatives, GIVEN that there is no outgroup. You deleted Ernest
Major's remark to which the above was a rejoinder:

>>For an analogy, if we had a mammalian tree, and no outgroups, we
>> (you and I at least) would place the root between Homo sapiens
>> and the rest of Mammalia.

He was talking to you. Do you agree with his characterization
of what you would do? If so, I'd love to hear your reasoning,
because I am sure I could shoot you down in a far more
convincing way than your silly effort to shoot me down:

> Egglaying and odd shoulder girdles
> would as easily be apomorphic as plesiomorphic, absent an outgroup to
> root the characters.

You've got to be kidding! getting from the shoulder girdle
of all other mammals to the one of monotremes is much harder
than the opposite direction. We AGREED that it is harder
to add new parts than to lose old parts.

You might as well say:

Mitosis could as easily be apomorphic as plesimorphic.
IOW, meiosis could be as easily plesimorphic as apomorphic.

That's assuming one developed from the other. Or do you
prefer a third alternative, that both developed independently
from a common ancestral state?

Funny thing, though: it's almost a no-brainer to imagine
a way mitosis could have evolved from meiosis. The drawback
is that it makes it even harder to imagine how meiosis
could have evolved, if that were the case. It's a classic
case of kicking the can down the road where you'd rather
kick it up the road.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--

University of South Carolina
http://www.math.sc.edu/~nyikos

PS I couldn't decipher what Ernest wrote about his claim about
you and he putting the root by Homo sapiens after I countered
with the one thing you left in above. I'll query him tomorrow:
my wife just got back from a long trip and we need quality
time together. It was hard enough to squeeze time out
for this post.

[John Harshman]

On 5/30/19 6:57 PM, Peter Nyikos wrote:
> On Thursday, May 30, 2019 at 4:10:03 PM UTC-4, John Harshman wrote:
>> On 5/30/19 8:44 AM, Peter Nyikos wrote:
>>> Even if monotremes were the only vertebrates
>>> which are oviparous and have very different shoulder girdles
>>> than the rest of mammalia, that would already be a strong
>>> argument for the present rooting.
>
>> Not without an outgroup it isn't.
>
> Yes, it is, because I am talking about a choice between
> alternatives, GIVEN that there is no outgroup. You deleted Ernest
> Major's remark to which the above was a rejoinder:
>
>>> For an analogy, if we had a mammalian tree, and no outgroups, we
>>> (you and I at least) would place the root between Homo sapiens
>>> and the rest of Mammalia.
>
> He was talking to you. Do you agree with his characterization
> of what you would do? If so, I'd love to hear your reasoning,
> because I am sure I could shoot you down in a far more
> convincing way than your silly effort to shoot me down:

He meant "would not", I suspect. He's talking about midpoint rooting or
at least not-too-far-from-midpoint rooting. This has nothing to do with
character states, which is what you seem to be talking about.

>> Egglaying and odd shoulder girdles
>> would as easily be apomorphic as plesiomorphic, absent an outgroup to
>> root the characters.
>
> You've got to be kidding! getting from the shoulder girdle
> of all other mammals to the one of monotremes is much harder
> than the opposite direction. We AGREED that it is harder
> to add new parts than to lose old parts.

That's an assumption that I would not make, absent an outgroup.

> You might as well say:
>
> Mitosis could as easily be apomorphic as plesimorphic.
> IOW, meiosis could be as easily plesimorphic as apomorphic.

Why not?

> That's assuming one developed from the other. Or do you
> prefer a third alternative, that both developed independently
> from a common ancestral state?
>
> Funny thing, though: it's almost a no-brainer to imagine
> a way mitosis could have evolved from meiosis. The drawback
> is that it makes it even harder to imagine how meiosis
> could have evolved, if that were the case. It's a classic
> case of kicking the can down the road where you'd rather
> kick it up the road.

After all, you have claimed that it's easier to remove than to add, and
meiosis is more complicated than mitosis.

> PS I couldn't decipher what Ernest wrote about his claim about
> you and he putting the root by Homo sapiens after I countered
> with the one thing you left in above. I'll query him tomorrow:
> my wife just got back from a long trip and we need quality
> time together. It was hard enough to squeeze time out
> for this post.

Again, he meant "would not" rather than "would".

[Bob Casanova]

On Thu, 30 May 2019 18:57:23 -0700 (PDT), the following
appeared in talk.origins, posted by Peter Nyikos
<nyik...@gmail.com>:

>On Thursday, May 30, 2019 at 4:10:03 PM UTC-4, John Harshman wrote:
>> On 5/30/19 8:44 AM, Peter Nyikos wrote:
>> > Even if monotremes were the only vertebrates
>> > which are oviparous and have very different shoulder girdles
>> > than the rest of mammalia, that would already be a strong
>> > argument for the present rooting.
>
>> Not without an outgroup it isn't.
>
>Yes, it is, because I am talking about a choice between
>alternatives, GIVEN that there is no outgroup. You deleted Ernest
>Major's remark to which the above was a rejoinder:
>
>>>For an analogy, if we had a mammalian tree, and no outgroups, we
>>> (you and I at least) would place the root between Homo sapiens
>>> and the rest of Mammalia.
>
>He was talking to you. Do you agree with his characterization
>of what you would do? If so, I'd love to hear your reasoning,
>because I am sure I could shoot you down in a far more
>convincing way than your silly effort to shoot me down:
>
>
>> Egglaying and odd shoulder girdles
>> would as easily be apomorphic as plesiomorphic, absent an outgroup to
>> root the characters.
>
>You've got to be kidding! getting from the shoulder girdle
>of all other mammals to the one of monotremes is much harder
>than the opposite direction. We AGREED that it is harder
>to add new parts than to lose old parts.

I suspect that would strongly depend on whether there was a
strong negative selection pressure involved WRT the "old
parts", and/or a strong positive selection pressure WRT the
development of "new parts".

>You might as well say:
>
> Mitosis could as easily be apomorphic as plesimorphic.
> IOW, meiosis could be as easily plesimorphic as apomorphic.
>
>That's assuming one developed from the other. Or do you
>prefer a third alternative, that both developed independently
>from a common ancestral state?
>
>Funny thing, though: it's almost a no-brainer to imagine
>a way mitosis could have evolved from meiosis. The drawback
>is that it makes it even harder to imagine how meiosis
>could have evolved, if that were the case. It's a classic
>case of kicking the can down the road where you'd rather
>kick it up the road.
>
>
>Peter Nyikos
>Professor, Dept. of Mathematics -- standard disclaimer--
>University of South Carolina
>http://www.math.sc.edu/~nyikos
>
>PS I couldn't decipher what Ernest wrote about his claim about
>you and he putting the root by Homo sapiens after I countered
>with the one thing you left in above. I'll query him tomorrow:
>my wife just got back from a long trip and we need quality
>time together. It was hard enough to squeeze time out
>for this post.

--

Bob C.

"The most exciting phrase to hear in science,
the one that heralds new discoveries, is not
'Eureka!' but 'That's funny...'"

- Isaac Asimov

[Peter Nyikos]

On Thursday, May 30, 2019 at 1:05:04 PM UTC-4, jillery wrote:
> On Thu, 30 May 2019 12:49:10 -0400, Oxyaena <oxy...@creo.dont> wrote:
>
> >
> >In the category of "Judge, Jury, and Executioner"

This is so openly and transparently dishonest that I think Oxyaena
was trying to goad me into breaking my boycott. But you've
saved me from having to ignore it, jillery.

> >> have now convinced me to formally charge you with having
> >> shamelessly lied about what you claimed to "think"
> >> How do you plead, guilty or not guilty?


>
> Judge Roy Bean strikes again!

You've shackled yourself to Oxyaena's lie.


Obviously, I am only playing the role of a plaintiff and his lawyer. Or, at best from the POV of Oxyaena, the DA.
The final question is a formality that is left for a judge to
utter by custom, but has nothing to do with anything a jury
has to do, let alone an executioner. And the real role of a judge,
sentencing, is not even hinted at.


It is a sad commentary on the state of talk.origins that I am the
only person who ever points out such obvious reasonings, and
a powerful testimony to the truth of what I said about
what "messing with [Harshman]" is apt to lead to.

Namely, it is apt to bring the wrath of Oxyaena and Erik
-- and now you -- down on the head of the "messer".
For starters, 'e could be charged with "sucking up to the peter," and the attack would go downhill from there.

And the wrath bears no resemblance to righteous wrath; it is a pure imposition of "might makes right".


Peter Nyikos

[Oxyaena]

On 5/31/2019 12:58 PM, Peter Nyikos wrote:
[snip stupidity]

Don't you have anything better to do than to act like a complete dipshit
on the internet?

[jillery]

On Fri, 31 May 2019 09:58:55 -0700 (PDT), Peter Nyikos
<nyik...@gmail.com> wrote:

>On Thursday, May 30, 2019 at 1:05:04 PM UTC-4, jillery wrote:
>> On Thu, 30 May 2019 12:49:10 -0400, Oxyaena <oxy...@creo.dont> wrote:
>>
>> >
>> >In the category of "Judge, Jury, and Executioner"
>
>This is so openly and transparently dishonest that I think Oxyaena
>was trying to goad me into breaking my boycott. But you've
>saved me from having to ignore it, jillery.

Of course, since your boycott is self-imposed and self-maintained, you
didn't have to ignore it. And you didn't. Is anybody surprised.

<snip remaining self-serving spew>

[Peter Nyikos]

On Thursday, May 30, 2019 at 10:30:02 PM UTC-4, John Harshman wrote:
> On 5/30/19 6:57 PM, Peter Nyikos wrote:
> > On Thursday, May 30, 2019 at 4:10:03 PM UTC-4, John Harshman wrote:
> >> On 5/30/19 8:44 AM, Peter Nyikos wrote:
> >>> Even if monotremes were the only vertebrates
> >>> which are oviparous and have very different shoulder girdles
> >>> than the rest of mammalia, that would already be a strong
> >>> argument for the present rooting.
> >
> >> Not without an outgroup it isn't.
> >
> > Yes, it is, because I am talking about a choice between
> > alternatives, GIVEN that there is no outgroup. You deleted Ernest
> > Major's remark to which the above was a rejoinder:
> >
> >>> For an analogy, if we had a mammalian tree, and no outgroups, we
> >>> (you and I at least) would place the root between Homo sapiens
> >>> and the rest of Mammalia.
> >
> > He was talking to you. Do you agree with his characterization
> > of what you would do? If so, I'd love to hear your reasoning,
> > because I am sure I could shoot you down in a far more
> > convincing way than your silly effort to shoot me down:
>
> He meant "would not", I suspect. He's talking about midpoint rooting or
> at least not-too-far-from-midpoint rooting.

How do you define "midpoint" and why should this be important?
You certainly DO seem to lean heavily on this ill-defined
principle.

> This has nothing to do with
> character states, which is what you seem to be talking about.

Character states what phylogenetic trees are based on, and
those in turn become the be-all and end-all of what
counts as apomorphic and what counts as plesimorphic.
And so you happily picked up the ball and ran with it:

> >> Egglaying and odd shoulder girdles
> >> would as easily be apomorphic as plesiomorphic, absent an outgroup to
> >> root the characters.
> >
> > You've got to be kidding! getting from the shoulder girdle
> > of all other mammals to the one of monotremes is much harder
> > than the opposite direction. We AGREED that it is harder
> > to add new parts than to lose old parts.

In fact, I agreed to something YOU wrote:

if our choice is between multiple losses and
multiple gains, we should generally prefer multiple losWses.

> That's an assumption that I would not make, absent an outgroup.

Outgroups were not mentioned when you made that claim, so
you need to explain this.

In particular, you need to explain why we cannot
agree, in the absence of an outgroup, that it
is less likely that two pairs of bones, the interclavicles
and the procoracoids, were gained by the monotremes,
than it is that they were lost by the non-monotremes.

Also, why we cannot agree that it is less likely
to evolve AWAY from prenatal parasitism
by adding yolk to the umbilical vesicle and a shell
and protective membrane outside the chorion, than
it is to evolve into obligate prenatal parasitism
by losing these things.

> > You might as well say:
> >
> > Mitosis could as easily be apomorphic as plesimorphic.
> > IOW, meiosis could be as easily plesimorphic as apomorphic.
>
> Why not?

You certainly are consistent HERE! Knowing that there is
no nearby known outgroup to (crown) Eukarya, and believing that
its LCA had both mitosis and meiosis, you have no trouble with
the interesting opinion that both alternatives are equally likely.
But keep reading.

> > That's assuming one developed from the other. Or do you
> > prefer a third alternative, that both developed independently
> > from a common ancestral state?

Why didn't you address this question? Given your apparent
indifference to the alternatives I gave, one would think that you
would have no trouble considering all three alternatives
to be equally likely.

> > Funny thing, though: it's almost a no-brainer to imagine
> > a way mitosis could have evolved from meiosis. The drawback
> > is that it makes it even harder to imagine how meiosis
> > could have evolved, if that were the case. It's a classic
> > case of kicking the can down the road where you'd rather
> > kick it up the road.
>
> After all, you have claimed that it's easier to remove than to add,

I agreed with what YOU wrote.

> and meiosis is more complicated than mitosis.

"After all" is very misleading. You are ignoring the fact
that there is MUCH MORE being added if meiosis cannot build
on mitosis, than if it can.


You need to stop and think about what you write, far
more often than you have been doing. Your way makes for very
inefficient communication.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--

U. of So. Carolina in Columbia
http://people.math.sc.edu

[Peter Nyikos]

On Thursday, May 30, 2019 at 4:10:03 PM UTC-4, Ernest Major wrote:
> On 30/05/2019 16:44, Peter Nyikos wrote:
> > On Thursday, May 30, 2019 at 3:55:02 AM UTC-4, Ernest Major wrote:
> >> On 30/05/2019 06:52, John Harshman wrote:
> >>>>>> So? the next reference you give below, dated 2015, also gives six
> >>>>>> possible rootings, but only one of them coincides with any of the
> >>>>>> six given by the 2014 reference. In particular, they differ
> >>>>>> in their "preferred" rooting as to where they place Malawinomonadida.
> >>>>
> >>>> The placement of that one critter could be relevant to both A
> >>>> and B. It seems to lack all sign of ever having had mitochondria,
> >>>> and I've seen no suggestion that it undergoes meiosis.
> >>>
> >>> So? This is only relevant if the root lies within or directly adjacent
> >>> to Malawinomonadida. Is any suggested rooting of that sort?
> >
> > As I told John less than an hour ago, Fig. 2 of the 2015
> > paper gives pretty much the next best thing.
> >
> > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517231/
> >
> > The degree of uncertainty it shows suggests the possibility that
> > some more recent, or future tree, might actually show
> > what John is asking about.
> >
> > By the way, do you know of any more recent trees as thorough
> > as the one in that 2015 paper or the 2014 paper,
> >
> > https://cshperspectives.cshlp.org/content/6/5/a016147.full#F1

I take it from your silence here that you know of no such
trees, Ernest. Correct me if I am wrong.

> >
> >> I presume that the problem with rooting eukaryotes is that the outgroups
> >> aren't very close (and that eukaryotes are rather derived in several
> >> ways). But, as you understand, that doesn't mean that all rootings
> >> aren't equally plausible.
> >
> > Maybe John does understand it, but he gave no hint of that
> > in his replies to me.
> >
> > Oh, wait, did you mean "are" instead of "aren't"? Your talk
> > of rate heterogeneity suggests that. Even so, read on.
>
> Yes, that's a mistype, probably caused by recomposing the sentence on
> the fly while typing - I'm a sufficiently slow typist that I can
> recompose sentences several times over while typing them.

I am a touch typist and a rather
quick one at that, but I know what you mean: I am sufficiently
*cautious* enough to frequently recompose sentences, but
then I can be too hasty due to having so little free time
compared to what I would like to have.

> I would have hoped that that it was obvious that this was a mistype.

It's become clear now. MY problem is that the sequel misled me:

> >> For an analogy, if we had a mammalian tree, and no outgroups, we (you
> >> and I at least) would place the root between Homo sapiens and the rest
> >> of Mammalia.

Here it is clear that you meant, "would NOT place". But I
was unfamiliar with the principle of "Rate heterogeneity,"

and so I wrote:

> > HUH? Why not where it is now: between Monotremata and the
> > rest of Mammalia? Even if monotremes were the only vertebrates
> > which are oviparous and have very different shoulder girdles
> > than the rest of mammalia, that would already be a strong
> > argument for the present rooting.

<snip for focus>

> >> Rate heterogenity is a thing, but it's not reasonable to
> >> pick a root which results in a 30-fold rate variation when there's a
> >> root which gives a 3-fold rate variation.
> >
> > Please explain why this doesn't apply to monotremata
> > vs rest of mammalia.

Apparently it WOULD apply, were there no close outgroups, from the
way Harshman seems to lay great store by it.
I went into detail with him about this less than an hour ago.


But is it actually used by research biologists, rather than
just philosophers of science? To me it seems just a
rule of thumb in the absence of the kind of evidence
that makes for successful research papers. In fact, to me it seems
even shakier than Ockham's razor, which also serves that purpose.

> > Come to think of it, perhaps this was one reason for the
> > reckless hypothesis which put marsupials on one branch
> > of mammalia and monotremes and placentals on the other
> > branch. Called the "marsupionta hypotesis", it actually
> > resulted in a number of peer-reviewed papers.
>
> Marsupionta united monotremes and marsupials, not monotremes and
> placentals.

Thanks for the correction. My main point still stands,
of course.

> It was one of a number of early results from mtDNA
> sequencing that were incorrect - if I understand correctly as a result
> of artefacts resulting from base composition biases.

mtDNA is a very small, and probably biased, sample of
all the molecular evidence available. I don't think
it is much of an improvement over the use of Rate heterogeneity.

> >> Or to reduce it to the
> >> completely absurd, placing the root of eukaryotes beween Arabidopsis
> >> thaliana and the remainder of eukaryotes.

Just be glad monotremes include not only the platypus
but also the echidnas! :-)

Peter Nyikos
Professor, Dept. of Mathematics

U. of So. Carolina -- standard disclaimer--
http://people.math.sc.edu

[Ernest Major]

http://www3.botany.ubc.ca/keeling/PDF/16Burki.pdf

You are aware of Google Scholar Search?

Google Scholar gives approaching 2,000 papers referring to midpoint
rooting, though of course some will be spurious instances from the
titles of referenced paper. A 2007 paper, cited 164 times, reviews the
method

https://s3.amazonaws.com/academia.edu.documents/31905962/Hess___Russo_2007.pdf

>
>>> Come to think of it, perhaps this was one reason for the
>>> reckless hypothesis which put marsupials on one branch
>>> of mammalia and monotremes and placentals on the other
>>> branch. Called the "marsupionta hypotesis", it actually
>>> resulted in a number of peer-reviewed papers.
>>
>> Marsupionta united monotremes and marsupials, not monotremes and
>> placentals.
>
> Thanks for the correction. My main point still stands,
> of course.
>
>
>> It was one of a number of early results from mtDNA
>> sequencing that were incorrect - if I understand correctly as a result
>> of artefacts resulting from base composition biases.
>
> mtDNA is a very small, and probably biased, sample of
> all the molecular evidence available. I don't think
> it is much of an improvement over the use of Rate heterogeneity.

Back in the old days sequencing was much slower, and people were
perforced constrained to using small samples of DNA. There was no as far
as I know no a priori reason to expect mtDNA to be particularly biased,
and it had the advantages that it occurs in larger copy numbers than
most nuclear DNA, and, I suspect, that mitochondria can be separated
from the rest of the cell using a centrifuge.

The other notorious error from mtDNA sequencing was placing hedgehogs as
basal in placentals or at least boreotherians - they're now back with
shrews and moles.

Rate heterogenity isn't used for rooting. Rate heterogenity is the
reason why midpoint rooting (John provided the technical term) is not a
wholly reliable method of finding the true root. Another problem is that
the apparent rate in a subclade depends on the dependency of taxon
sampling in that clade - in a well sampled clade the individual branch
lengths are shorter than in a poorly sampled clade, and a greater
proportion of reversals at a particular base pair will be captured -
this has the effect that the sums of branch lengths for terminal taxa in
well sampled clades are greater. No doubt all this can be corrected for,
but it means that it's not as simple as picking the root which minimises
the mean distance of terminal taxa from the root. (MEGA 4 uses a cruder
form of midpoint rooting - "the root of an unrooted tree is placed at
the mid-point of the longest distance between two taxa in a tree".)

More generally, I believe that improved taxon sampling is generally more
effective in improving trees than throwing more base pairs at the problem.

>
>
>>>> Or to reduce it to the
>>>> completely absurd, placing the root of eukaryotes beween Arabidopsis
>>>> thaliana and the remainder of eukaryotes.
>
> Just be glad monotremes include not only the platypus
> but also the echidnas! :-)
>
>
> Peter Nyikos
> Professor, Dept. of Mathematics
> U. of So. Carolina -- standard disclaimer--
> http://people.math.sc.edu
>

--
alias Ernest Major

[Peter Nyikos]

On Monday, June 3, 2019 at 12:35:03 PM UTC-4, Ernest Major wrote:
> On 03/06/2019 15:11, Peter Nyikos wrote:
> > On Thursday, May 30, 2019 at 4:10:03 PM UTC-4, Ernest Major wrote:
> >> On 30/05/2019 16:44, Peter Nyikos wrote:
> >>> On Thursday, May 30, 2019 at 3:55:02 AM UTC-4, Ernest Major wrote:
> >>>> On 30/05/2019 06:52, John Harshman wrote:
> >>>>>>>> So? the next reference you give below, dated 2015, also gives six
> >>>>>>>> possible rootings, but only one of them coincides with any of the
> >>>>>>>> six given by the 2014 reference. In particular, they differ
> >>>>>>>> in their "preferred" rooting as to where they place Malawinomonadida.
> >>>>>>
> >>>>>> The placement of that one critter could be relevant to both A
> >>>>>> and B. It seems to lack all sign of ever having had mitochondria,
> >>>>>> and I've seen no suggestion that it undergoes meiosis.
> >>>>>
> >>>>> So? This is only relevant if the root lies within or directly adjacent
> >>>>> to Malawinomonadida. Is any suggested rooting of that sort?
> >>>
> >>> As I told John less than an hour ago, Fig. 2 of the 2015
> >>> paper gives pretty much the next best thing.
> >>>
> >>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517231/
> >>>
> >>> The degree of uncertainty it shows suggests the possibility that
> >>> some more recent, or future tree, might actually show
> >>> what John is asking about.

The tree you linked for me below, Ernest, does not eliminate this
possibility. More importantly, it does not eliminate the
alternative rootings which make it possible, at our
present state of knowlege, that the LCA of Eukarya did
*not* undergo meiosis.

> >>> By the way, do you know of any more recent trees as thorough
> >>> as the one in that 2015 paper or the 2014 paper,
> >>>
> >>> https://cshperspectives.cshlp.org/content/6/5/a016147.full#F1
> >
> > I take it from your silence here that you know of no such
> > trees, Ernest. Correct me if I am wrong.
>
> http://www3.botany.ubc.ca/keeling/PDF/16Burki.pdf

It's less than a year after Fabien Burki's solo job that I've been
discussing with John,

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517231/

On Figure 1 of this multiply co-authored paper, the caption ends:

The tree is drawn rooted between Obazoa, Amoebozoa,
Collodictyon, Malawimonas and the rest of eukaryotes
after [42], though we note that the position of the root
is under active debate.

Reference [42] evidently used bacterial proteins -- a very
distant outgroup. Considering the enormous gap between the
structure and mode of reproduction of the simplest eukaryotes
and the most complex prokaryotes, we could easily be looking
at Eukarya as a "ghost taxon" of a billion years duration.

As to the comment about the position of the root: unlike in
Fabien Burki's solo 2015 paper, no alternatives under active
consideration are given. But the main divisions are essentially
the same. [Note: The tree in the solo paper is upside down with
respect to this one.] I say "solo" because Burki is one of
the co-authors of this later paper.

> You are aware of Google Scholar Search?

I am, but I haven't used it yet.


Bottom line: absent more recent trees, my comments to
John about two of the alternative roots of Eukarya still stand:
their support for the LCA of Eukarya having meiosis hinges on the
issue of whether Trypanosoma really undergoes Meiosis I
and Meiosis II or merely some evolutionary precursor.

I've been trying to get a real discussion on this with John
going, but progress in that direction is very slow.



Concluded in next post, to be done shortly after I see that this one has posted.

[Peter Nyikos]

On Monday, June 3, 2019 at 12:35:03 PM UTC-4, Ernest Major wrote:
> On 03/06/2019 15:11, Peter Nyikos wrote:
> > On Thursday, May 30, 2019 at 4:10:03 PM UTC-4, Ernest Major wrote:
> >> On 30/05/2019 16:44, Peter Nyikos wrote:
> >>> On Thursday, May 30, 2019 at 3:55:02 AM UTC-4, Ernest Major wrote:


> >>>> I presume that the problem with rooting eukaryotes is that the outgroups
> >>>> aren't very close (and that eukaryotes are rather derived in several
> >>>> ways). But, as you understand, that doesn't mean that all rootings

> >>>> [are] equally plausible.

For once, the expression "Fixed it for you" really applies.
[Usually, it's a taunt, as you probably know.]


<snip for focus>

> >>>> For an analogy, if we had a mammalian tree, and no outgroups, we (you

> >>>> and I at least) would [not] place the root between Homo sapiens and the rest
> >>>> of Mammalia.

Also fixed for you, and now I fix it for myself:

> >>> [How about] where it is now: between Monotremata and the

> >>> rest of Mammalia? Even if monotremes were the only vertebrates
> >>> which are oviparous and have very different shoulder girdles
> >>> than the rest of mammalia, that would already be a strong
> >>> argument for the present rooting.
> >
> > <snip for focus>
> >
> >>>> Rate heterogenity is a thing, but it's not reasonable to
> >>>> pick a root which results in a 30-fold rate variation when there's a
> >>>> root which gives a 3-fold rate variation.
> >>>
> >>> Please explain why this doesn't apply to monotremata
> >>> vs rest of mammalia.
> >
> > Apparently it WOULD apply, were there no close outgroups, from the
> > way Harshman seems to lay great store by it.
> > I went into detail with him about this less than an hour ago.
> >
> >
> > But is it actually used by research biologists, rather than
> > just philosophers of science? To me it seems just a
> > rule of thumb in the absence of the kind of evidence
> > that makes for successful research papers. In fact, to me it seems
> > even shakier than Ockham's razor, which also serves that purpose.


> Google Scholar gives approaching 2,000 papers referring to
> midpoint rooting,

Any way to trim that down to relevant papers?

> though of course some will be spurious instances from the
> titles of referenced paper. A 2007 paper, cited 164 times, reviews the
> method
>
> https://s3.amazonaws.com/academia.edu.documents/31905962/Hess___Russo_2007.pdf

Even when stretched out over one line, this returns an error message. I've tried trimming the triple underline after Hess to
single, and double, and I've tried eliminating the part after the
last slash, but it's no go.

> >>> Come to think of it, perhaps this was one reason for the
> >>> reckless hypothesis which put marsupials on one branch
> >>> of mammalia and monotremes and placentals on the other
> >>> branch. Called the "marsupionta hypotesis", it actually
> >>> resulted in a number of peer-reviewed papers.
> >>
> >> Marsupionta united monotremes and marsupials, not monotremes and
> >> placentals.
> >
> > Thanks for the correction. My main point still stands,
> > of course.
> >
> >
> >> It was one of a number of early results from mtDNA
> >> sequencing that were incorrect - if I understand correctly as a result
> >> of artefacts resulting from base composition biases.
> >
> > mtDNA is a very small, and probably biased, sample of
> > all the molecular evidence available. I don't think
> > it is much of an improvement over the use of Rate heterogeneity.
>
> Back in the old days sequencing was much slower, and people were
> perforced constrained to using small samples of DNA. There was no as far
> as I know no a priori reason to expect mtDNA to be particularly biased,

One reason is that many of the still-active mitochondrial enzymes
are now coded in the nuclear genome. This applies to the all-important
aa-tRNA sythetases, which are thus shielded from the devastating
feedback loops that would otherwise accompany changes in the
genetic code of the mitochondria.

I spotted this danger when I first really understood the
protein translation mechanism, and read that mitochondria have
such a different genetic code from the standard one.
Mystified by it, I asked a biochemist friend here at the
original USC, and he told me about the "shielding."

> and it had the advantages that it occurs in larger copy numbers than
> most nuclear DNA, and, I suspect, that mitochondria can be separated
> from the rest of the cell using a centrifuge.
>
> The other notorious error from mtDNA sequencing was placing hedgehogs as
> basal in placentals or at least boreotherians - they're now back with
> shrews and moles.

Interesting history. I wonder whether these trees of Eukarya
are completely free of ignorant choice of "basal" members.

> Rate heterogenity isn't used for rooting. Rate heterogenity is the
> reason why midpoint rooting (John provided the technical term) is not a
> wholly reliable method of finding the true root.

"wholly" is too generous; look at monotremes vs. the rest of
mammalia -- or, worse yet, the "superclass" Sarcopterygii, split between
*Latimeria chalumnae* and all the rest, including all tetrapods.

If it weren't for fossil fish, this would be our picture
no matter what the outgroup. But fossil protists are exactly
what we lack in all those trees from 2015 thru 2016.


<snip of things to be discussed later, if we both so decide>

> >>>> Or to reduce it to the
> >>>> completely absurd, placing the root of eukaryotes beween Arabidopsis
> >>>> thaliana and the remainder of eukaryotes.

I hope there are more reasons for calling this "completely
absurd" than for the *Latimeria* example.

> > Just be glad monotremes include not only the platypus
> > but also the echidnas! :-)


Peter Nyikos

Professor, Dept. of Mathematics -- standard disclaimer--
Univ. of So. Carolina at Columbia
http://www.math.sc.edu/~nyikos

> alias Ernest Major

[John Harshman]

I do not understand why this should lead to expectation of bias in mtDNA
data. Can you explain?

> I spotted this danger when I first really understood the
> protein translation mechanism, and read that mitochondria have
> such a different genetic code from the standard one.
> Mystified by it, I asked a biochemist friend here at the
> original USC, and he told me about the "shielding."

>> and it had the advantages that it occurs in larger copy numbers than
>> most nuclear DNA, and, I suspect, that mitochondria can be separated
>> from the rest of the cell using a centrifuge.
>>
>> The other notorious error from mtDNA sequencing was placing hedgehogs as
>> basal in placentals or at least boreotherians - they're now back with
>> shrews and moles.
>
> Interesting history. I wonder whether these trees of Eukarya
> are completely free of ignorant choice of "basal" members.

Choice is not involved, either with regard to hedgehogs or "basal"
eukaryotes. It's just where they happen to come out in analyses.

>> Rate heterogenity isn't used for rooting. Rate heterogenity is the
>> reason why midpoint rooting (John provided the technical term) is not a
>> wholly reliable method of finding the true root.
>
> "wholly" is too generous; look at monotremes vs. the rest of
> mammalia -- or, worse yet, the "superclass" Sarcopterygii, split between
> *Latimeria chalumnae* and all the rest, including all tetrapods.

Are you talking about midpoint rooting for a morphological tree? I don't
think anyone has done that or suggested that it be done.

> If it weren't for fossil fish, this would be our picture
> no matter what the outgroup. But fossil protists are exactly
> what we lack in all those trees from 2015 thru 2016.

It isn't clear what you're saying. Is it that Latimeria is not the
living outgroup to other living sarcopterygians? What do fossils do to
illuminate this question?

> <snip of things to be discussed later, if we both so decide>
>
>
>>>>>> Or to reduce it to the
>>>>>> completely absurd, placing the root of eukaryotes beween Arabidopsis
>>>>>> thaliana and the remainder of eukaryotes.
>
> I hope there are more reasons for calling this "completely
> absurd" than for the *Latimeria* example.

What's absurd about the Latimeria example? I don't understand your point.

[erik simpson]

The Hess & Russo paper is here:

https://www2.gwu.edu/~clade/bisc%20207/Hess%20%26%20de%20Moraes%20Russo,%202007%20(Midpoint%20rooting).pdf

[John Harshman]

Not enamored with that paper. They used data of a particularly limited
sort: mtDNA sequences of congeneric tetrapods, and they used only
neighbor-joining trees. One should be cautious in extending the results
beyond that narrow window.

[Peter Nyikos]

On Saturday, June 1, 2019 at 8:35:03 AM UTC-4, jillery wrote:
> On Fri, 31 May 2019 09:58:55 -0700 (PDT), Peter Nyikos
> <nyik...@gmail.com> wrote:
>
> >On Thursday, May 30, 2019 at 1:05:04 PM UTC-4, jillery wrote:
> >> On Thu, 30 May 2019 12:49:10 -0400, Oxyaena <oxy...@creo.dont> wrote:
> >>
> >> >
> >> >In the category of "Judge, Jury, and Executioner"
> >
> >This is so openly and transparently dishonest that I think Oxyaena
> >was trying to goad me into breaking my boycott. But you've
> >saved me from having to ignore it, jillery.
>
>
> Of course, since your boycott is self-imposed and self-maintained,

...as is every killfile I've ever known of, except those "self-imposed" -- but not self-maintained as boycotts --
by your loyal ally Oxyaena. Hers kept "timing out" within
a day before she managed to fix them, and it never seemed to occur to her to exercise a little self-discipline and act AS THOUGH
the boycotts were still in force.

> you
> didn't have to ignore it. And you didn't. Is anybody surprised.

Nor was anyone surprised when Oxyaena, with one of her killfiles
still in existence, swooped down on a post by me in s.b.p.
and replied to it directly.

Nor was anyone surprised when Oxyaena encouraged Harshman right about at the same time
to killfile me, extolling the advantages of having me killfiled.

That was more in the way of "bragging" about a boycott than
I have ever done, but you are permanently married to double
standards, so this revelation will probably result in
even closer bonding between the two of you.


<snip remaining Oxyaena-serving spew>


Peter Nyikos

[Peter Nyikos]

On Friday, May 31, 2019 at 12:40:03 PM UTC-4, Bob Casanova wrote:
> On Thu, 30 May 2019 18:57:23 -0700 (PDT), the following
> appeared in talk.origins, posted by Peter Nyikos
> <nyik...@gmail.com>:
>
> >On Thursday, May 30, 2019 at 4:10:03 PM UTC-4, John Harshman wrote:

> >> Egglaying and odd shoulder girdles
> >> would as easily be apomorphic as plesiomorphic, absent an outgroup to
> >> root the characters.
> >
> >You've got to be kidding! getting from the shoulder girdle
> >of all other mammals to the one of monotremes is much harder
> >than the opposite direction. We AGREED that it is harder
> >to add new parts than to lose old parts.
>
> I suspect that would strongly depend on whether there was a
> strong negative selection pressure involved WRT the "old
> parts", and/or a strong positive selection pressure WRT the
> development of "new parts".

I never thought I would see the day when you would
sound like Dr. Dr. Kleinman.

Won't he be proud. :-) :-)


Peter Nyikos

[Alan Kleinman MD PhD]

On Tuesday, June 4, 2019 at 6:45:02 PM UTC-7, Peter Nyikos wrote:
> On Friday, May 31, 2019 at 12:40:03 PM UTC-4, Bob Casanova wrote:
> > On Thu, 30 May 2019 18:57:23 -0700 (PDT), the following
> > appeared in talk.origins, posted by Peter Nyikos
> > <nyik...@gmail.com>:
> >
> > >On Thursday, May 30, 2019 at 4:10:03 PM UTC-4, John Harshman wrote:
>
> > >> Egglaying and odd shoulder girdles
> > >> would as easily be apomorphic as plesiomorphic, absent an outgroup to
> > >> root the characters.
> > >
> > >You've got to be kidding! getting from the shoulder girdle
> > >of all other mammals to the one of monotremes is much harder
> > >than the opposite direction. We AGREED that it is harder
> > >to add new parts than to lose old parts.
> >
> > I suspect that would strongly depend on whether there was a
> > strong negative selection pressure involved WRT the "old
> > parts", and/or a strong positive selection pressure WRT the
> > development of "new parts".
>
> I never thought I would see the day when you would
> sound like Dr. Dr. Kleinman.

Get the wax out of your ears Professor Nomathos. Only dim bulbs would see selection pressures as positive or negative. Selection pressures always kill or impair the replication of some or all members of a population.

[jillery]

On Tue, 4 Jun 2019 11:00:52 -0700 (PDT), Peter Nyikos

<nyik...@gmail.com> wrote:

>On Saturday, June 1, 2019 at 8:35:03 AM UTC-4, jillery wrote:
>> On Fri, 31 May 2019 09:58:55 -0700 (PDT), Peter Nyikos
>> <nyik...@gmail.com> wrote:
>>
>> >On Thursday, May 30, 2019 at 1:05:04 PM UTC-4, jillery wrote:
>> >> On Thu, 30 May 2019 12:49:10 -0400, Oxyaena <oxy...@creo.dont> wrote:
>> >>
>> >> >
>> >> >In the category of "Judge, Jury, and Executioner"
>> >
>> >This is so openly and transparently dishonest that I think Oxyaena
>> >was trying to goad me into breaking my boycott. But you've
>> >saved me from having to ignore it, jillery.
>>
>>
>> Of course, since your boycott is self-imposed and self-maintained,
>
>...as is every killfile I've ever known of,

Killfiles typically prevent the display of posts which fit a specified
filter. Once implemented, a killfile's actions are entirely
automatic, with no further intervention required by the user.

The above is a feature GG does not provide. Instead, to implement
your boycott, for each post, you, Nyikos, must explicitly decide to
ignore or reply to each post, which is functionally no different that
what all posters usually do. So your boycott is not automatic, but
instead is imposed and maintained by yourself on a case-by-case basis.
Not sure how you *still* don't understand this.

<snip remaining spew>

[jillery]

On Tue, 4 Jun 2019 18:58:55 -0700 (PDT), Alan Kleinman MD PhD
<klei...@sti.net> wrote:


>Get the wax out of your ears Professor Nomathos. Only dim bulbs would see selection pressures as positive or negative. Selection pressures always kill or impair the replication of some or all members of a population.

Since you accept there are beneficial and harmful genes, you
necessarily accept there are beneficial and harmful selection
pressures, in order to define some genes beneficial and some genes
harmful.

[Peter Nyikos]

On Tuesday, June 4, 2019 at 10:00:02 PM UTC-4, Alan Kleinman MD PhD wrote:
> On Tuesday, June 4, 2019 at 6:45:02 PM UTC-7, Peter Nyikos wrote:
> > On Friday, May 31, 2019 at 12:40:03 PM UTC-4, Bob Casanova wrote:
> > > On Thu, 30 May 2019 18:57:23 -0700 (PDT), the following
> > > appeared in talk.origins, posted by Peter Nyikos
> > > <nyik...@gmail.com>:
> > >
> > > >On Thursday, May 30, 2019 at 4:10:03 PM UTC-4, John Harshman wrote:
> >
> > > >> Egglaying and odd shoulder girdles
> > > >> would as easily be apomorphic as plesiomorphic, absent an outgroup to
> > > >> root the characters.
> > > >
> > > >You've got to be kidding! getting from the shoulder girdle
> > > >of all other mammals to the one of monotremes is much harder
> > > >than the opposite direction. We AGREED that it is harder
> > > >to add new parts than to lose old parts.
> > >
> > > I suspect that would strongly depend on whether there was a
> > > strong negative selection pressure involved WRT the "old
> > > parts", and/or a strong positive selection pressure WRT the
> > > development of "new parts".
> >
> > I never thought I would see the day when you would
> > sound like Dr. Dr. Kleinman.

> Get the wax out of your ears Professor [Nyikos]. Only dim bulbs would see selection pressures as positive or negative.

Bob was too much of a dimbulb to respond to this, so I will.
It is useful to think of any environmental factor that
increases the fitness of a variety as a positive selection
pressure.

IOW, you are quibbling about semantics, Dr. Dr. anti-Korzybski. :-)

But seriously, I do believe the dimbulb has coined a useful
bit of terminology, and jillery has given a good reason
why it is useful.

> Selection pressures always kill or impair the replication of some or all members of a population.

By your definition of the term.

Are you sure that all biologists heretofore have defined it your way?
If so, the dimbulb has serendepitously made just as valuable a
contribution to evolutionary theory as you made with your excruciatingly
elementary 2014 and 2016 papers which were published in a
reputable journal.

> >
> > Won't he be proud. :-) :-)

Hey, Bob made a step in your direction. Don't be a killjoy --
tell us all how proud you are of his accomplishment.

[Alan Kleinman MD PhD]

Has Professor Nomathos ever grown a garden? Is feeding your plants a positive selection pressure or is it simply removing starvation? If you want to improve fitness of a replicator, remove selection conditions. This allows the less fit variants to reproduce which couldn't under the previous selection conditions and allows the more fit variants to reproduce in greater numbers.

>
> IOW, you are quibbling about semantics, Dr. Dr. anti-Korzybski. :-)

You really should try to get your semantics to coincide with the physics if you want people to understand what you are saying. And saying that you are going to feed your plants in the garden is a positive selection pressure is not going to accomplish that.

>
> But seriously, I do believe the dimbulb has coined a useful
> bit of terminology, and jillery has given a good reason
> why it is useful.

My, my, a true believer.

>
>
> > Selection pressures always kill or impair the replication of some or all members of a population.
>
> By your definition of the term.
>
> Are you sure that all biologists heretofore have defined it your way?
> If so, the dimbulb has serendepitously made just as valuable a
> contribution to evolutionary theory as you made with your excruciatingly
> elementary 2014 and 2016 papers which were published in a
> reputable journal.

https://en.wikipedia.org/wiki/Evolutionary_pressure
And don't blame me if the mathematics of evolutionary adaptation is excruciatingly elementary. In hindsight, it should be as plain as the nose on your face. All you have to understand to do this math is understand what a selection pressure is, what the random trial is for improving fitness to that selection pressure is, and what the probability of that event occurring is for that random trial. It's really not that hard.

>
>
> > >
> > > Won't he be proud. :-) :-)
>
> Hey, Bob made a step in your direction. Don't be a killjoy --
> tell us all how proud you are of his accomplishment.

If dimmy is looking for an ataboy, he needs to go back to his statistic text and read the introductory chapters on probability theory. Once he understands these chapters, then maybe he'll get something out of his statistics courses.

[Peter Nyikos]

On Tuesday, June 4, 2019 at 10:50:02 PM UTC-4, jillery wrote:
> On Tue, 4 Jun 2019 11:00:52 -0700 (PDT), Peter Nyikos
> <nyik...@gmail.com> wrote:
>
> >On Saturday, June 1, 2019 at 8:35:03 AM UTC-4, jillery wrote:
> >> On Fri, 31 May 2019 09:58:55 -0700 (PDT), Peter Nyikos
> >> <nyik...@gmail.com> wrote:
> >>
> >> >On Thursday, May 30, 2019 at 1:05:04 PM UTC-4, jillery wrote:
> >> >> On Thu, 30 May 2019 12:49:10 -0400, Oxyaena <oxy...@creo.dont> wrote:
> >> >>
> >> >> >
> >> >> >In the category of "Judge, Jury, and Executioner"
> >> >
> >> >This is so openly and transparently dishonest that I think Oxyaena
> >> >was trying to goad me into breaking my boycott. But you've
> >> >saved me from having to ignore it, jillery.

And you've "saved yourself" from dealing with its transparent
dishonesty by ignoring it along with your "Roy Bean" support
of it.

The "saving" came in the form of snipping the rebuttal,
and also snipping the very thing about which Oxyaena was
transparently lying:

have now convinced me to formally charge you with having

shamelessly lied about what you claimed to "think".

How do you plead, guilty or not guilty?

The whole snip was marked by a thoroughly dishonest description:

<snip remaining self-serving spew>

Those are your words, jillery, illustrating how thoroughly dishonest
your use of "spew" can be.

It almost invariably refers to text that justifiably puts you or your friends
in a bad light.

You did it below, too.

> >> Of course, since your boycott is self-imposed and self-maintained,
> >
> >...as is every killfile I've ever known of,
>
> Killfiles typically prevent the display of posts which fit a specified
> filter. Once implemented, a killfile's actions are entirely
> automatic, with no further intervention required by the user.

You are conveniently ignoring the actual behavior of the
killfiles of your loyal ally Oxyaena, which kept expiring
after one day and kept having to be renewed.

My method completely eliminates such problems. It is also
a vast improvement on other killfile related behaviors by Oxyaena
once she surmounted that difficulty. I related them to you,
but you Oxyaena-servingly snipped it at the end.

>
> The above is a feature GG does not provide. Instead, to implement
> your boycott, for each post, you, Nyikos, must explicitly decide to
> ignore or reply to each post, which is functionally no different that
> what all posters usually do.

Your pedantic spiel ignores the fact that the only times I reply
to a post by either Oxyaena or Simpson is ONCE on each thread where
I participate. And I don't even need to think about the content
of the post to which I am formally replying.


Hence your "each post" is a grotesque falsehood, and
your whole spiel here collapses without it.

> So your boycott is not automatic, but
> instead is imposed and maintained by yourself on a case-by-case basis.
> Not sure how you *still* don't understand this.

You should realize that there is no reason to "understand" a figment of
your adversarial-since-2011 imagination.

The same applies to all your uses of "Not sure how you *still* don't
understand this" that I can recall.


Now comes your flagrantly Oxyaena-serving snip:

> <snip remaining spew>

See above about what "spew" really means here, too.


Peter Nyikos

[Peter Nyikos]

On Wednesday, June 5, 2019 at 10:15:03 AM UTC-4, Alan Kleinman MD PhD wrote:

... something to which I have replied here:

https://groups.google.com/d/msg/talk.origins/kp-7_EfHeqE/gNC9WLNsAQAJ
Subject: Kleinman's Concept of Selection Pressures
Date: Wed, 5 Jun 2019 12:00:07 -0700 (PDT)
Message-ID: <ebac86f4-52de-4030...@googlegroups.com>

Peter Nyikos

[jillery]

On Wed, 5 Jun 2019 11:03:14 -0700 (PDT), Peter Nyikos
<nyik...@gmail.com> wrote:


<snip self-serving spew for focus>

>The whole snip was marked by a thoroughly dishonest description:
>
> <snip remaining self-serving spew>

You're entitled to your opinion. Everybody has one.

<snip remaining self-serving spew>

[Peter Nyikos]

On Tuesday, June 4, 2019 at 12:10:04 PM UTC-4, John Harshman wrote:

<snip for focus>

> >>>>> Come to think of it, perhaps this was one reason for the
> >>>>> reckless hypothesis which put marsupials on one branch
> >>>>> of mammalia and monotremes and placentals on the other
> >>>>> branch. Called the "marsupionta hypotesis", it actually
> >>>>> resulted in a number of peer-reviewed papers.
> >>>>
> >>>> Marsupionta united monotremes and marsupials, not monotremes and
> >>>> placentals.
> >>>
> >>> Thanks for the correction. My main point still stands,
> >>> of course.
> >>>
> >>>
> >>>> It was one of a number of early results from mtDNA
> >>>> sequencing that were incorrect - if I understand correctly as a result
> >>>> of artefacts resulting from base composition biases.
> >>>
> >>> mtDNA is a very small, and probably biased, sample of
> >>> all the molecular evidence available. I don't think
> >>> it is much of an improvement over the use of Rate heterogeneity.
> >>
> >> Back in the old days sequencing was much slower, and people were
> >> perforced constrained to using small samples of DNA. There was no as far
> >> as I know no a priori reason to expect mtDNA to be particularly biased,
> >
> > One reason is that many of the still-active mitochondrial enzymes
> > are now coded in the nuclear genome. This applies to the all-important
> > aa-tRNA sythetases, which are thus shielded from the devastating
> > feedback loops that would otherwise accompany changes in the
> > genetic code of the mitochondria.

> I do not understand why this should lead to expectation of bias in mtDNA
> data. Can you explain?

I can, but I hope Ernest will understand what I'm getting
at without my explaining further.

> > I spotted this danger when I first really understood the
> > protein translation mechanism, and read that mitochondria have
> > such a different genetic code from the standard one.
> > Mystified by it, I asked a biochemist friend here at the
> > original USC, and he told me about the "shielding."
>
> >> and it had the advantages that it occurs in larger copy numbers than
> >> most nuclear DNA, and, I suspect, that mitochondria can be separated
> >> from the rest of the cell using a centrifuge.
> >>
> >> The other notorious error from mtDNA sequencing was placing hedgehogs as
> >> basal in placentals or at least boreotherians - they're now back with
> >> shrews and moles.
> >
> > Interesting history. I wonder whether these trees of Eukarya
> > are completely free of ignorant choice of "basal" members.
>

> Choice is not involved, either with regard to hedgehogs or "basal"
> eukaryotes. It's just where they happen to come out in analyses.

Reference?

>
> >> Rate heterogenity isn't used for rooting. Rate heterogenity is the
> >> reason why midpoint rooting (John provided the technical term) is not a
> >> wholly reliable method of finding the true root.
> >
> > "wholly" is too generous; look at monotremes vs. the rest of
> > mammalia -- or, worse yet, the "superclass" Sarcopterygii, split between
> > *Latimeria chalumnae* and all the rest, including all tetrapods.
>

> Are you talking about midpoint rooting for a morphological tree?

Why "morphological"? I made no mention of that.

> I don't
> think anyone has done that or suggested that it be done.

Maybe that is because you have yet to reply to the
following post:


https://groups.google.com/d/msg/talk.origins/QWR6N--M754/uPZ-QoWhCAAJ
Subject: Re: Mysteries of Evolution: Sexual Reproduction; Part A, meiosis
Date: Mon, 3 Jun 2019 06:30:27 -0700 (PDT)
Message-ID: <47a21535-9712-4f88...@googlegroups.com>

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina

http://people.math.sc.edu/nyikos

PS this was piggybacked because two attempts at direct replies failed.

[John Harshman]

Why wouldn't you care about me and anyone else reading this
understanding what you mean?

>>> I spotted this danger when I first really understood the
>>> protein translation mechanism, and read that mitochondria have
>>> such a different genetic code from the standard one.
>>> Mystified by it, I asked a biochemist friend here at the
>>> original USC, and he told me about the "shielding."
>>
>>>> and it had the advantages that it occurs in larger copy numbers than
>>>> most nuclear DNA, and, I suspect, that mitochondria can be separated
>>>> from the rest of the cell using a centrifuge.
>>>>
>>>> The other notorious error from mtDNA sequencing was placing hedgehogs as
>>>> basal in placentals or at least boreotherians - they're now back with
>>>> shrews and moles.
>>>
>>> Interesting history. I wonder whether these trees of Eukarya
>>> are completely free of ignorant choice of "basal" members.
>>
>> Choice is not involved, either with regard to hedgehogs or "basal"
>> eukaryotes. It's just where they happen to come out in analyses.
>
> Reference?

All that's required is basic understanding of what Ernest was talking
about. Hedgehog came out basal in an analysis because the algorithm and
data used put it (erroneously) close to the outgroup. Nobody planned it.
Same with eukaryotes.

>>>> Rate heterogenity isn't used for rooting. Rate heterogenity is the
>>>> reason why midpoint rooting (John provided the technical term) is not a
>>>> wholly reliable method of finding the true root.
>>>
>>> "wholly" is too generous; look at monotremes vs. the rest of
>>> mammalia -- or, worse yet, the "superclass" Sarcopterygii, split between
>>> *Latimeria chalumnae* and all the rest, including all tetrapods.
>>
>> Are you talking about midpoint rooting for a morphological tree?
>
> Why "morphological"? I made no mention of that.

Then I don't know what you're talking about. Could you explain, or do
you have no interest in that either?

>> I don't
>> think anyone has done that or suggested that it be done.
>
> Maybe that is because you have yet to reply to the
> following post:

I did, but it seems to have been lost in the ozone. I have replied
again. However, I don't see the connection. Once more, could you explain?

[Peter Nyikos]

On Wednesday, June 5, 2019 at 5:15:03 PM UTC-4, jillery wrote:
> On Wed, 5 Jun 2019 11:03:14 -0700 (PDT), Peter Nyikos
> <nyik...@gmail.com> wrote:
>
>
> <snip self-serving spew for focus>
>
>
> >The whole snip was marked by a thoroughly dishonest description:
> >
> > <snip remaining self-serving spew>
>
>
> You're entitled to your opinion. Everybody has one.

Coming from YOU, this counts as total, utter inability to counter
anything I wrote, together with what you wrote next:


> <snip remaining self-serving spew>


I expect you to draw on all your formidable talents as a propagandist and
polemicist to set up a smokescreen to hide your burial of your head in the sand.

However, you have to also reckon with a post I did on another thread
that delivers a searing indictment of your behavior on your preceding post
on the thread we are on now. Here it is:

___________________________ begin included post________________

On Monday, June 3, 2019 at 9:35:02 PM UTC-4, jillery wrote:
> On Mon, 3 Jun 2019 12:11:40 -0700 (PDT), Peter Nyikos
> <nyik...@gmail.com> wrote:
>
> >On Monday, June 3, 2019 at 2:00:04 PM UTC-4, jillery wrote:
> >> On Mon, 3 Jun 2019 09:39:39 -0700 (PDT), Peter Nyikos
> >> <nyik...@gmail.com> wrote:
> >>
> >> >Jillery enormously cared when she first lied that I had broken
> >> >one of the two;
> >>
> >>
> >> Prove that I lied or retract.
> >
> >You claimed I had broken it, and did not retract the claim
> >when I demonstrated its falsity.
>
>
> Cite the post where I claimed you had broken it.

If I do, will you snip the evidence and post:

<snip remaining self-serving spew>

?


> >I call that a *prima* *facie* case for you having lied.
>
>
> Of course you do, because you use self-serving definitions of words.

...glass houses...stones.

Case in point: your self-serving, Oxyaena-serving definition
of "spew":

https://groups.google.com/d/msg/talk.origins/QWR6N--M754/7eYujW1pAQAJ
Subject: Jillery's use of "spew" unmasked WAS: Re: Chez Watt was Re: Mysteries of Evolution: ...
Date: Wed, 5 Jun 2019 11:03:14 -0700 (PDT)
Message-ID: <c12979f1-2413-4a2f...@googlegroups.com>

If you run true to form, you will snip this link in reply,
with a snip-n-deceive like the one I quote above from it.

>
>
> >If you retract the claim, I will retract the accusation that it was a lie.
>
>
> Cite the post where you proved my alleged claim false.

If I do it, will you snip the evidence and write:

<snip remaining spew>
?

This, and the similar snip-n-deceive above, are taken
directly from the linked post, where I explain what was
actually snipped and why it was flagrantly Oxyaena-serving
and jillery-serving.


Do you ever wonder why I call you "the most dangerously dishonest
regular in talk.origins" and Oxyaena "the most ruthlessly dishonest
regular in talk.origins"? Or do you secretly accept these as
"compliments" and as reassurances that you and Oxyaena are doing all the
"right" self-serving things?


Peter Nyikos

========================================= end of post archived
at
https://groups.google.com/d/msg/talk.origins/uGkhekFCaxY/HnCbDzGxAQAJ
Subject: Re: OT: Homophobia and Related Concepts and Memes ATTN: Burkhard
Date: Thu, 6 Jun 2019 08:58:35 -0700 (PDT)
Message-ID: <413bf356-e510-48c4...@googlegroups.com>

By the way, the post I linked in the archived post is none other
than the one to which you are replying. Readers can check for themselves
to see just how deeply you have buried your head in the sand.


Peter Nyikos

[jillery]

On Thu, 6 Jun 2019 11:39:55 -0700 (PDT), Peter Nyikos
<nyik...@gmail.com> wrote:

>On Wednesday, June 5, 2019 at 5:15:03 PM UTC-4, jillery wrote:
>> On Wed, 5 Jun 2019 11:03:14 -0700 (PDT), Peter Nyikos
>> <nyik...@gmail.com> wrote:
>>
>>
>> <snip self-serving spew for focus>
>>
>>
>> >The whole snip was marked by a thoroughly dishonest description:
>> >
>> > <snip remaining self-serving spew>
>>
>>
>> You're entitled to your opinion. Everybody has one.
>
>Coming from YOU, this counts as total, utter inability to counter
>anything I wrote, together with what you wrote next:

Of course, there's no need to counter your self-serving spew. I
merely note it as it occurs.


<snip your remaining self-serving spew>

[Peter Nyikos]

On Thursday, June 6, 2019 at 3:50:04 PM UTC-4, jillery wrote:
> On Thu, 6 Jun 2019 11:39:55 -0700 (PDT), Peter Nyikos
> <nyik...@gmail.com> wrote:
>
> >On Wednesday, June 5, 2019 at 5:15:03 PM UTC-4, jillery wrote:
> >> On Wed, 5 Jun 2019 11:03:14 -0700 (PDT), Peter Nyikos
> >> <nyik...@gmail.com> wrote:
> >>
> >>
> >> <snip self-serving spew for focus>
> >>
> >>
> >> >The whole snip was marked by a thoroughly dishonest description:
> >> >
> >> > <snip remaining self-serving spew>
> >>
> >>
> >> You're entitled to your opinion. Everybody has one.
> >
> >Coming from YOU, this counts as total, utter inability to counter
> >anything I wrote, together with what you wrote next:

>>><snip remaining self-serving spew>

> Of course, there's no need to counter your self-serving spew. I
> merely note it as it occurs.

Now that your private, self-serving and Oxyaena-serving
definition of "spew" has been thoroughly unmasked, this formulaic,
Casanova-channeling comment by you just underscores
your total inability to rebut anything I wrote.

Also, your use of "note" is a weak substitute for leaving in what
I wrote, then calling it a "lie" without any attempt to show it is
a lie, and bragging in later posts that you've "documented"
innumerable "lies" by me, when the "documentation" simply
consisted of what I had written and of your TbBA that what I wrote was a lie.


TbBA = Truth by Blatant Assertion

>
> <snip your remaining self-serving spew>

Now that the self-serving, Oxyaena-serving meaning of this formulaic
one-liner of yours has been laid bare, nobody needs to pay
the slightest heed to it. And I doubt that anyone, including yourself
and your loyal allies Oxyaena and Casanova, does pay any heed to it.


In the immortal words of Casanova,

HAND.


Peter Nyikos

PS In fact, HANW (W = Weekend).

TGIF.

[Peter Nyikos]

On Wednesday, May 29, 2019 at 9:20:03 AM UTC-4, John Harshman wrote:
> On 5/29/19 1:40 AM, Ernest Major wrote:
> > On 29/05/2019 05:05, John Harshman wrote:
> >>
> >> Have we fundamentally changed the subject from meiosis then? If not,
> >> what does this have to do with that subject?
> >>
> >> It's been suggested that the jakobid mt genome is derived, though
> >> horizontal transfer. The other possibility is that it's primitive but
> >> that other lineages have transferred those genes to the nucleus
> >> convergently.
> >
> > As you now doubt know, there is a pattern of organellear genes being
> > consecutively lost, mostly by transfer to the nucleus, but also
> > absolutely in lineages that gave up aerobic metabolism (mitochondria) or
> > photosynthesis (plasmids), so there is to all intents and purposes a
> > ratchet of reducing mitochondrial gene content. This means that there
> > will be an eukaryote lineage with the largest gene content, but this
> > could be anywhere in the tree.
> >
> > Unless one is a Lamarckian, one recognises that all lineages are mosaics
> > of ancestral and derived traits.
> >
> > Hence the jakobid mitochondrial genone presents to justification for
> > identifying jakobids as primitive or "basal". While jakobids have the
> > largest known mitochondria gene content, some of their relatively close
> > relatives have much smaller mitochondrial gene contents, while the
> > lineage with the second largest mitochondrial gene content is Diphylleia
> > (the protist, not the plant), which is part of a group which is sister
> > to unikonts, and the lineage with the third largest (Ancoracysta) is
> > sister to Haptista.
> >
> > The Archezoa hypothesis is long dead - the various groups placed there
> > have been found to be primitively mitochondriate, and their basal
> > placement in nrRNA trees to be an artefact of long branch attraction,
> > and perhaps convergence. (I speculate that there is selection pressure
> > for divergence between mitochondrial and nuclear ribosomes, to reduce
> > the risk of cross-interference, which is relaxed in secondarily
> > amitochondriate lineages.)
> >
> > Subsequently the estimated eukaryote root has been placed in various
> > placed, but almost always with plants on one side of the root, and
> > animals on the other. Such topologies imply that either meiosis in
> > plants and animals are convergent, or that their last common ancestor
> > was capable of meiosis. Earlier excavates were placed on the plant side
> > of the root, but more recently there have been proposals that excavates
> > lies on both sides of the root, which would make them a
> > para/polyphyletic group lacking the derived characters that define the
> > other supergroups. That doesn't make them primitive;

I glossed over this part of Ernest's very helpful exposition. If Excavata were
polyphyletic, the last bit would not need explanation. But if it is
paraphyletic instead, then we need evidence that various characters
are NOT primitive if they are shared by excavates that branched off
before all other eukaryotes.


> > it just means that
> > the derived characters of the various excavate lineages are less striking.

Ernest hasn't posted in four days, and I'm taking a two-day break
for the weekend as usual, so I'm asking you, John, whether you
agree with this last statement, and why. I don't see offhand why this would
be true if Excavata is paraphyletic.


> > Some trees place parts of Excavata (Discoba) as basal to the
> > plant-animal split,

... and some alternate rootings of the tree of Eukarya place some of
them as basal to all of Eukarya.

This happened with two of the alternate rootings in the 2015 paper
you link below, John, and with one of the alternate rootings
of the tree in the 2014 paper that you linked in an earlier post.


> > but I haven't seen anything proposing excavates as a
> > whole are basal.

If there are excavates on both sides of the first fork, this might
indicate the paraphyly of Excavata with the right topology. The topology
in the 2015 paper does this when one uses the alternate rooting
that puts Euglenoza on one fork and all the rest of Eukarya on the other.
There are excavates on the other side of the fork, including the Jakobids,
that precede the crown group of all non-excavate Eukarya, given this
rooting.


> > This means that the absence of observed sexuality in
> > the excavates as a whole cannot be used to draw any conclusions about
> > the eukaryote LCA - even before it is noted that in several other
> > lineages sexuality wasn't observed until very recently (this is a case
> > where absence of evidence isn't evidence of absence), that recombination
> > does occur in Giardia (but as far as I know it hasn't been demonstrated
> > to be sexual rather than parasexual), and that genes involved in meiosis
> > are commonly found in lineages not known to be sexual, including Jakobida.

"genes involved in meiosis" may have been exapted from genes that were
active in various precursors of full fledged meiosis (including I and II).


Now we come to where you came in, John:

> Good news: there is observed sexuality in excavates, and not just genes
> associated with meiosis.

Do you know what Ernest meant by "parasexual"? And what do you
include under "sexuality"?

I ask because the article you are linking draws an interesting
and crucial distinction:

A detailed account on gamete mating, including cell and nuclear fusion,
was published only for a single species (Chroomonas acuta) (22), whereas
meiosis has still not been reported.


> The best I've seen so far is the expression of
> meiotic genes just before cellular fusion in trypanosomes.

Of what does this "cellular fusion" consist? I couldn't see
much of an explanation in the article you've linked.


> But there is
> apparently observed sex in other excavates too.

Now you are getting informal, talking about "sex". To what
parts of the article are you referring?


> Check out some of the
> papers we've been arguing over, particularly this one:
>
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517231/#d35e355

I've checked it out, see above. Now what?

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--

Univ. of So. Carolina in Columbia
http://www.math.sc.edu/~nyikos

[Oxyaena]

On 6/7/2019 11:32 AM, Peter Nyikos wrote:
[snip shrieking]

Kindly refrain from mentioning my name in these one-sided shouting
matches of yours, thanks.

--
"That which is asserted without evidence can be dismissed without
evidence." - The Hitch

https://peradectes.wordpress.com/

[Bob Casanova]

On Fri, 7 Jun 2019 13:12:22 -0400, the following appeared in
talk.origins, posted by Oxyaena <oxy...@in.valid>:

>On 6/7/2019 11:32 AM, Peter Nyikos wrote:

>[snip shrieking]
>
>Kindly refrain from mentioning my name in these one-sided shouting
>matches of yours, thanks.

Yeah, *that* is likely to happen...
--

Bob C.

"The most exciting phrase to hear in science,
the one that heralds new discoveries, is not
'Eureka!' but 'That's funny...'"

- Isaac Asimov

[Peter Nyikos]

On Friday, June 7, 2019 at 3:00:03 PM UTC-4, Bob Casanova wrote:
> On Fri, 7 Jun 2019 13:12:22 -0400, the following appeared in
> talk.origins, posted by Oxyaena <oxy...@in.valid>:
>
> >On 6/7/2019 11:32 AM, Peter Nyikos wrote:
>
> >[snip shrieking]

Oxyaena becomes a pathological liar when she gets into one of the poles
of her bipolar behavior. This snip-n-deceive of hers illustrates that.

> >Kindly refrain from mentioning my name in these one-sided shouting
> >matches of yours, thanks.
>
> Yeah, *that* is likely to happen...

Especially on sub-threads where the first blow was struck by
Oxyaena. Jillery pinch-hit for her again and again,
destroying any credibility left of her use of "spew."


Oxyaena had devastated her own credibility in her OP of the "Chez Watt..."
subthread by her illogical and obviously intentional
equating of a plea at the beginning of a trial
with the proceedings of the trial and one of its possible aftermaths.

As jillery pinch-hit for Oxyaena again and again,
and I kept using the term "Oxyaena-serving,"
Oxyaena "sat there like a bump on a log," as some of my elementary school
teachers put it, until the devastation of jillery's
credibility was more than even Oxyaena could bear to see.

And that was when Oxyaena finally made her presence felt
again with the post to which you are replying. Her cryptic
reference to statements she didn't dare to leave in,
and the snip-n-deceive with which she snipped them,
are the only hints you have from Oxyaena of that devastation.

I do believe that YOU don't want to get your hands dirty with
doing something neither jillery nor Oxyaena has dared to do:
meet the damning evidence head-on instead of snipping it
and lying about what had been snipped.


HANW.


Peter Nyikos

[*Hemidactylus*]

Try Sanka:

https://youtu.be/7MjY8vo8vDU

[erik simpson]

Won't work. Better try laudanum, or even straight smack.

[Peter Nyikos]

Starbucks Decaf is infinitely superior in flavor, although it
cannot come up to the standard of a great non-decaffeinated coffee.


> https://youtu.be/7MjY8vo8vDU

I'm afraid it is too late in life for you try to understand what
morality is all about. You are a classic example of someone stuck at what
Kierkegaard called the first, esthetic stage. You can cerebrate all kinds
of papers in the philosophy of ethics, but will probably never
experience what William Barrett calls "the bite of the ethical"
in _Irrational Man_.

As a result, mere rudeness becomes the main yardstick by which
you judge my actions, and the gross evil analyzed by my "rude" words
up there means nothing to you.


And so, to keep this post from becoming completely incomprehensible
to you, I put in that plug for Starbucks Decaf.

Actually, I use other, equally good brands at home in my drip coffeemaker
[sorry, no plug for either the brands of coffee or the coffeemaker]
and I usually mix Regular and Decaf about 50-50. But I assume
you are more familiar with Starbucks than with them.


Peter Nyikos

PS Not that I expect it to matter to you, but I talked about you a short
while ago here:

https://groups.google.com/d/msg/talk.origins/uGkhekFCaxY/H9_KM2gKAgAJ

Subject: Re: OT: Homophobia and Related Concepts and Memes ATTN: Burkhard

Lines: 49
Date: Fri, 7 Jun 2019 12:11:31 -0700 (PDT)
Message-ID: <7b6b38cc-0f8f-40e3...@googlegroups.com>

[jillery]

On Fri, 7 Jun 2019 08:32:11 -0700 (PDT), Peter Nyikos

<nyik...@gmail.com> wrote:

>On Thursday, June 6, 2019 at 3:50:04 PM UTC-4, jillery wrote:
>> On Thu, 6 Jun 2019 11:39:55 -0700 (PDT), Peter Nyikos
>> <nyik...@gmail.com> wrote:
>>
>> >On Wednesday, June 5, 2019 at 5:15:03 PM UTC-4, jillery wrote:
>> >> On Wed, 5 Jun 2019 11:03:14 -0700 (PDT), Peter Nyikos
>> >> <nyik...@gmail.com> wrote:
>> >>
>> >>
>> >> <snip self-serving spew for focus>
>> >>
>> >>
>> >> >The whole snip was marked by a thoroughly dishonest description:
>> >> >
>> >> > <snip remaining self-serving spew>
>> >>
>> >>
>> >> You're entitled to your opinion. Everybody has one.
>> >
>> >Coming from YOU, this counts as total, utter inability to counter
>> >anything I wrote, together with what you wrote next:
>
>>>><snip remaining self-serving spew>
>
>
>> Of course, there's no need to counter your self-serving spew. I
>> merely note it as it occurs.
>
>Now that your private, self-serving and Oxyaena-serving
>definition of "spew" has been thoroughly unmasked,

Cite where you thoroughly unmasked what you describe above, in
contrast to what you almost always do, to merely repeat your Big Lies
on top of Big Lies to cover up earlier Big Lies.


<snip remaining self-serving spew>

[jillery]

On Fri, 7 Jun 2019 13:49:02 -0700 (PDT), Peter Nyikos
<nyik...@gmail.com> wrote:


The following video illustrates the spirit of Nyikos the peter's post
below:

<https://www.youtube.com/watch?v=Fitxofd7kOA>

[jillery]

Even better, Nyikos the peter should try Diatabs:

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

[erik simpson]

Awesome! How did you find that?

[*Hemidactylus*]

There are times when I might find that handy to quell those senses of
urgency. I don’t want to crash a plane and become a source of interest for
cannibals. Are they conversing in Tagalog?

[erik simpson]

Tagalog is definitely not one of my languages (I have very few anyway), but it's
using the Roman alphabet, so that's a good guess.

[John Harshman]

I'm not quite sure what Ernest was saying. But if excavates are
paraphyletic AND animals and plants (or anything with meiosis) are on
different sides of the root, it doesn't matter where the root is or how
many excavates are on different sides of it. Meiosis would be present at
the root unless one postulates multiple independent origins.

>>> Some trees place parts of Excavata (Discoba) as basal to the
>>> plant-animal split,
>
> ... and some alternate rootings of the tree of Eukarya place some of
> them as basal to all of Eukarya.
>
> This happened with two of the alternate rootings in the 2015 paper
> you link below, John, and with one of the alternate rootings
> of the tree in the 2014 paper that you linked in an earlier post.
>
>
>>> but I haven't seen anything proposing excavates as a
>>> whole are basal.
>
> If there are excavates on both sides of the first fork, this might
> indicate the paraphyly of Excavata with the right topology. The topology
> in the 2015 paper does this when one uses the alternate rooting
> that puts Euglenoza on one fork and all the rest of Eukarya on the other.
> There are excavates on the other side of the fork, including the Jakobids,
> that precede the crown group of all non-excavate Eukarya, given this
> rooting.

If Euglenozoans have meiosis, which the evidence indicates they do, then
the root doesn't matter there either.

>>> This means that the absence of observed sexuality in
>>> the excavates as a whole cannot be used to draw any conclusions about
>>> the eukaryote LCA - even before it is noted that in several other
>>> lineages sexuality wasn't observed until very recently (this is a case
>>> where absence of evidence isn't evidence of absence), that recombination
>>> does occur in Giardia (but as far as I know it hasn't been demonstrated
>>> to be sexual rather than parasexual), and that genes involved in meiosis
>>> are commonly found in lineages not known to be sexual, including Jakobida.
>
> "genes involved in meiosis" may have been exapted from genes that were
> active in various precursors of full fledged meiosis (including I and II).

True, for all we know. Yes there is more evidence of meiosis than the
presence of genes.

> Now we come to where you came in, John:
>
>> Good news: there is observed sexuality in excavates, and not just genes
>> associated with meiosis.
>
> Do you know what Ernest meant by "parasexual"? And what do you
> include under "sexuality"?

I refer to fusion of full genomes from two different cells. I don't know
what "parasexual" means.

> I ask because the article you are linking draws an interesting
> and crucial distinction:
>
> A detailed account on gamete mating, including cell and nuclear fusion,
> was published only for a single species (Chroomonas acuta) (22), whereas
> meiosis has still not been reported.

I'd look at (22) for an explanation.

>> The best I've seen so far is the expression of
>> meiotic genes just before cellular fusion in trypanosomes.
>
> Of what does this "cellular fusion" consist? I couldn't see
> much of an explanation in the article you've linked.

I assume it's what it says: two cells fuse and combine their genomes.

>> But there is
>> apparently observed sex in other excavates too.
>
> Now you are getting informal, talking about "sex". To what
> parts of the article are you referring?

I'm referring to the figure we've been talking about.

>> Check out some of the
>> papers we've been arguing over, particularly this one:
>>
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517231/#d35e355
>
> I've checked it out, see above. Now what?

We're getting beyond my knowledge. Did you look at (22)? Here's the
abstract:

By means of various electron microscopic techniques, the ultrastructure
of fusing gametes in a cryptomonad is described for the first time. The
isolate used in this study is bisexual, and vegetative cells may act as
isogametes. Plasmogamy usually is initiated at the posterior end of one
gamete and the mild‐ventral region of the other gamete. A posterior,
pointed protuberance may be a specialized mating structure which
initiates the fusion process. Fusion proceeds toward the anterior end,
forming a quadriflagellate cell which becomes spherical and settles to
the bottom of the culture flask. The quadriflagellate, spherical cell
contains two nuclear‐nucleomorph‐chloroplast complexes which remain
intact throughout karyogamy. During karyogamy the nuclei are positioned
close to each other and become lobed on the sides where fusion takes
place. At the points where the lobes touch, the nuclear membranes break
down and direct karyogamy is initiated. Nuclear fusion continues and
eventually a single zygotic nucleus is formed. The zygote nucleus and
the two nucleomorphs and chloroplasts become enclosed in a common
periplastidial compartment. The nucleomorphs, however, remain apart and
do not fuse. Meiosis presumably is zygotic, but the stages of
post‐karyogamy remain to be elucidated.

[Oxyaena]

On 6/7/2019 4:49 PM, Peter Nyikos wrote:
[snip dick-waving]

Did you even read the request?

[Bob Casanova]

On Fri, 7 Jun 2019 14:08:23 -0700 (PDT), the following
appeared in talk.origins, posted by erik simpson
<eastsi...@gmail.com>:

Or fentanyl. I'd suggest starting with 100mg.

[Bob Casanova]

On Fri, 07 Jun 2019 17:41:53 -0400, the following appeared
in talk.origins, posted by jillery <69jp...@gmail.com>:

>On Fri, 7 Jun 2019 08:32:11 -0700 (PDT), Peter Nyikos
><nyik...@gmail.com> wrote:
>
>>On Thursday, June 6, 2019 at 3:50:04 PM UTC-4, jillery wrote:
>>> On Thu, 6 Jun 2019 11:39:55 -0700 (PDT), Peter Nyikos
>>> <nyik...@gmail.com> wrote:
>>>
>>> >On Wednesday, June 5, 2019 at 5:15:03 PM UTC-4, jillery wrote:
>>> >> On Wed, 5 Jun 2019 11:03:14 -0700 (PDT), Peter Nyikos
>>> >> <nyik...@gmail.com> wrote:
>>> >>
>>> >>
>>> >> <snip self-serving spew for focus>
>>> >>
>>> >>
>>> >> >The whole snip was marked by a thoroughly dishonest description:
>>> >> >
>>> >> > <snip remaining self-serving spew>
>>> >>
>>> >>
>>> >> You're entitled to your opinion. Everybody has one.
>>> >
>>> >Coming from YOU, this counts as total, utter inability to counter
>>> >anything I wrote, together with what you wrote next:
>>
>>>>><snip remaining self-serving spew>
>>
>>
>>> Of course, there's no need to counter your self-serving spew. I
>>> merely note it as it occurs.
>>
>>Now that your private, self-serving and Oxyaena-serving
>>definition of "spew" has been thoroughly unmasked,
>
>
>Cite where you thoroughly unmasked what you describe above, in
>contrast to what you almost always do, to merely repeat your Big Lies
>on top of Big Lies to cover up earlier Big Lies.

It's all right there in his imagination, in Glorious Living
Color (TM). You can't see it?

><snip remaining self-serving spew>
--

[Bob Casanova]

On Fri, 7 Jun 2019 13:49:02 -0700 (PDT), the following
appeared in talk.origins, posted by Peter Nyikos
<nyik...@gmail.com>:

>On Friday, June 7, 2019 at 3:00:03 PM UTC-4, Bob Casanova wrote:
>> On Fri, 7 Jun 2019 13:12:22 -0400, the following appeared in
>> talk.origins, posted by Oxyaena <oxy...@in.valid>:
>>
>> >On 6/7/2019 11:32 AM, Peter Nyikos wrote:
>>
>> >[snip shrieking]
>
>Oxyaena becomes a pathological liar when she gets into one of the poles
>of her bipolar behavior. This snip-n-deceive of hers illustrates that.
>
>
>> >Kindly refrain from mentioning my name in these one-sided shouting
>> >matches of yours, thanks.
>>
>> Yeah, *that* is likely to happen...

>Especially on sub-threads <blah, blah, blah...>

<snip additional paranoiac shrieking, dragging in even more
of Peter's alleged "co-conspirators">

As I noted...

[Bob Casanova]

On Fri, 7 Jun 2019 22:42:42 -0400, the following appeared in

talk.origins, posted by Oxyaena <oxy...@in.valid>:

>On 6/7/2019 4:49 PM, Peter Nyikos wrote:
>[snip dick-waving]
>
>Did you even read the request?

He did, and ignored it as usual in favor of more paranoid
ranting.