Lampreys (Was: Average Life Expectancy in Medieval Times?)
Peter Nyikos
added sci.bio.paleontology and sci.bio.systematics because
of the talk about "phylogenetic systematics". I'm doing
a shorter followup to talk.origins and soc.history.medieval
which is not relevant to the science newsgroups.
mtu...@snipthis.acpub.duke.edu (mel turner) writes:
>In article <jfbV6.1878$rS4....@eagle.america.net>, D._Spence...@aya.yale.edu [D.
>Spencer Hines] wrote...
>>Or ----- do Lampreys and Eels both belong to the Superclass _Agnatha_
>>[jawless fish]
No. I've known this since I was nine years old. I learned
from the children's encyclopedia, _The Book of Knowledge_,
that lampreys and hagfish are very special vertebrates in
a class all their own, according to the systematics
that was prevalent in those days, and that ONLY they
are true jawless fish among living fish.
>> ---- while Lampreys belong to the Class
>>_Cephalospidomorphi_ and Eels to the Class _Osteichthyes_?
Sounds like a worthy but outdated attempt at classification.
>Osteichthys aren't jawless. "True eels" are a large group of
>advanced ray-finned bony fish [Teleostei] that are understood
>to be most closely related to tarpons and bonefish and kin
>[Elopomorpha]
><http://phylogeny.arizona.edu/tree/eukaryotes/animals/chordata/actinopterygii/teleostei.html>
>but then various other slender, elongate fishes are also called
>"eels"
Like the "electric eel".
>"Agnatha" [or Cyclostomata for that matter] aren't a
>recognized group in modern, phylogenetic systematics.
"Phylogenetic systematics" is a self-serving term
adopted by cladists for what Romer termed "vertical
classification" back in 1945, before Hennig even
founded cladistics.
"group" has been co-opted by the cladophiles and
cladomaniacs to be synonymous with "clades". Cladomaniacs
will tolerate no other meaning for the word "group"
and will tolerate no meaning to such traditional
words as "dinosaur" or "reptile" which does not
include all descendants (including birds, of course).
>Hagfishes [also sometimes called "eels"] evidently aren't
>close to lampreys.
Yes, they are a mystery. They may even have arisen
independently from the lower chordates from not only
lampreys but from ALL known fossil vertebrates (craniates).
This is something John Harshman didn't take into account when
he posted a reference to an article about fossil agnathans
which he thought shed light on how vertebrates arose from
lower chordates.
I talk shop like this all the time while I participate
in the two science newsgroups, and Paul Gans simply
cannot comprehend the fact that I could not be
doing it the way I do and still be a creationist.
He and his ally Pat James have doggedly insisted
that I am a creationist without providing a scrap
of evidence--because there is none.
><http://phylogeny.arizona.edu/tree/eukaryotes/animals/chordata/vertebrata.html>
><http://phylogeny.arizona.edu/tree/eukaryotes/animals/chordata/craniata.html>
>"Eel" is really just an English common name [here in the SE
>USA some large elongate salamanders (Amphiuma spp. and Siren spp.
>are also commonly called "eels"]
Is Amphiura the "Congo eel"?
Peter Nyikos -- standard disclaimer --
Professor, Dept. of Mathematics
University of South Carolina
Columbia, SC 29208
Peter Nyikos
>Fair Enough.
>So, continuing with the line of reasoning that you began ---- if
>_Gnathostomata_ [jawed (among other things?)] and _Agnatha_ [jawless
>(among other things?) are Superclasses ---- is it fair to say that is
>where the schism is between Lampreys and Eels?
As good as any. I kind of like the idea of Agnatha being
a superclass, myself.
Gnathostomata is, I believe, a paraphyletic taxon like
Agnatha. This simply means that it doesn't include
all its descendants. For reasons only known to them,
this makes the two groups anathema to what I call "cladophiles":
people who insist that all groups be clades. A clade
is a single species and all creatures descended from it.
Agnatha is believed to have given rise to jawed fishes--both
Romer and Colbert go into how the jaws are believed to have
arisen--and hence to Gnathostomes. I can't recall whether
that group includes all non-Agnathan vertebrates--neither
Romer nor Colbert mention it, and I'd have to look in the
library for more mondern books.
There is a whole newsgroup, sci.bio.sysematics, which
deals with the shifting patterns of classification. Asking
for the *right* classification is
a bit like asking when the Dark Ages ended, or whether
this or that country was steeped in Feudalism at a certain
point in time. Lots of areas of agreement, but lots
of divergence as well.
>That is say that at the Superclass level, Lampreys are _Agnatha_ and
>Eels are _Gnathostomata_?
Yes, but not everyone deals with the Superclass concept. There
is even a movement underfoot to do away with ALL Linnean
categories above the Genus level--sort of like abolishing
all divisions of history into eras like Ancient, Medieval,
Modern.
>[N.B. I realise I'm being quite repetitive and somewhat simplistic here.
>Step by step. I'm simply trying to be as precise as I can and make sure
>that we are singing from the same sheet of music ---- or at least in
>harmony. ---- DSH]
>If all that follows, what would be a similar differentiation between
>_Homo sapiens_ on the one leg and some other creature in a different
>Superclass?
Homo Sapiens, other mammals, reptiles, amphibians, birds,
bony fish, ...these are all in one Superclass. All are
more closely related to each other than lampreys are
to any of them, by several different standards.
And lampreys are, by several standards, the only living things that
are about as far from humans as lampreys are from eels.
>"lenny" <le...@sentex.net> wrote in message
>news:3b25...@news.sentex.net...
>| D. Spencer Hines <D._Spence...@aya.yale.edu> wrote in message
>| news:alhV6.1989$rS4....@eagle.america.net...
>| > Most interesting. Thank you kindly. You are probing at just the
>points
>| > that seem to me as paramount here.
>| >
>| > So, would it be fair to say that confusing Lampreys with Eels is
>| > comparable to confusing Salamanders with Lizards?
>|
>| I think that's reasonable. At least, it's not unreasonable.
>|
>| > I believe Peter Nyikos has already said that and Andrew Groves has
>| > concurred. But, please correct me if I am wrong.
>| >
>| > I am not trying to blaze a path through the wilderness here ----
>just
>| > nail some things down ---- in this very volatile USENET medium,
>where
>| > *Semantic Obfuscation* -- Fraud and Charlatanry so often rule and
>carry
>| > the day ---- with the naive and gullible.
>| >
>| > Continuing ---- would it be fair to say that confusing Lampreys and
>Eels
>| > is *worse* than confusing, say *Frogs* [Amphibia] and *Snakes*
>| > [Reptilia] ---- or *Dogs* [Mammalia] and *Snakes* [Reptilia] ?
>|
>| Probably a little worse--it's hard to say exactly. The higher taxa
>are
>| somewhat arbitrary constructions, so it's hard to be exact about this
>sort
>| of thing. Usually above Class (the difference between a dog and a
>snake)
>| comes Phylum (the difference between a clam and a snake, for example),
>but
>| sometimes there are intermediate taxa like Superclass and Subphylum
>between
>| Class and Phylum. This is further complicated because systematics is
>a very
>| vital field where things are currently changing rather quickly as new
>| information and techniques become available. The text I have ready to
>hand
>| dates from the '80s and is already quite out of date. The
>Cyclostomata
>| (Agnatha) were, at that time, considered a Class of the Subphylum
>| Vertebrata. Agnatha now seems to be considered by many to be a
>Superclass,
>| not because it is now thought to be more different from the
>Gnathostomata
>| than used to be the case, but because the constituents of the
>Agnatha, the
>| lampreys and hagfish, are now thought to be more distantly related
>than once
>| they were and can no longer be contained in the same Class. If
>lampreys and
>| hagfish belong in different Classes, then the group that contains both
>must
>| be a higher taxa, like a Superclass. I think.
About the only thing that now contains both lampreys and
the hagfish in most classifications is the Subphylum Vertebrata,
a.k.a. Craniata. The traditional systematists, who gave us
such entities as the paraphyletic taxon Agnatha, seem to be
lying low at the present time. I don't think any of them
has given us anything new since it was decided that the
hagfish was way out there all by itself.
D. Spencer Hines
about as far from humans as lampreys are from eels."
Peter Nyikos
--------------------
Now THAT is an interesting statement and gets at the sorts of
distinctions I hope we can shred out.
What are those "several standards"?
Comments?
--
D. Spencer Hines
Lux et Veritas et Libertas
"The only thing necessary for the triumph of evil is for good men to do
nothing." -- Attributed to Edmund Burke [1729-1797]
Sol Disinfectus Optimus Est. Peccatoris Justificatio Absque
Paenitentia, Legem Destruit Moralem.
"There are more things in heaven and earth, Horatio, Than are dreamt of
in your philosophy." ---- William Shakespeare [1564-1616] The Tragedy of
Hamlet, Prince of Denmark, Act I, Scene V, Line 166-167
All replies to the newsgroup please. Thank you kindly.
All original material contained herein is copyright and property of the
author. It may be quoted only in discussions on this forum and with an
attribution to the author, unless permission is otherwise expressly
given, in writing.
Vires et Honor
D. Spencer Hines
But then it's MORE than just Jaw and No-Jaw as between Lampreys and
Eels ---- Right?
--
D. Spencer Hines
Lux et Veritas et Libertas
"The only thing necessary for the triumph of evil is for good men to do
nothing." -- Attributed to Edmund Burke [1729-1797]
Sol Disinfectus Optimus Est. Peccatoris Justificatio Absque
Paenitentia, Legem Destruit Moralem.
"There are more things in heaven and earth, Horatio, Than are dreamt of
in your philosophy." ---- William Shakespeare [1564-1616] The Tragedy of
Hamlet, Prince of Denmark, Act I, Scene V, Line 166-167
All replies to the newsgroup please. Thank you kindly.
All original material contained herein is copyright and property of the
author. It may be quoted only in discussions on this forum and with an
attribution to the author, unless permission is otherwise expressly
given, in writing.
Vires et Honor
"D. Spencer Hines" <D._Spence...@aya.yale.edu> wrote in message
news:MtuV6.2097$rS4....@eagle.america.net...
Andy Groves
>
> mtu...@snipthis.acpub.duke.edu (mel turner) writes:
<snip>
> >Hagfishes [also sometimes called "eels"] evidently aren't
> >close to lampreys.
>
> Yes, they are a mystery. They may even have arisen
> independently from the lower chordates from not only
> lampreys but from ALL known fossil vertebrates (craniates).
The implication fom the two studies below is that hagfish and lampreys
are monophyletic,
and that hagfish (Myxinoidea) have lost certain morphological
characteristics secondarily.
Some limited data suggest that hagfish may have some craniofacial
placodes; I don't know if anyone has
looked to see if they have a rudimentary neural crest.
Science 1992 Aug 7;257(5071):787-9
Evidence from 18S ribosomal RNA sequences that lampreys and hagfishes
form a natural group.
Stock DW, Whitt GS.
Lampreys and hagfishes (cyclostomes) traditionally were considered to
be a natural (monophyletic) group. Recently, the consensus of
opinion, based largely on morphological analyses, has shifted to a
view that lampreys are more closely related to jawed vertebrates
(gnathostomes) than to hagfishes. Phylogenetic comparisons of 18S
ribosomal RNA sequences from two hagfishes, two lampreys, a
tunicate, a lancelet, and a number of gnathostomes support the
monophyly of the cyclostomes. These data force a reassessment of
several features of early vertebrate evolution.
Mol Biol Evol 1998 Dec;15(12):1706-18
28S and 18S rDNA sequences support the monophyly of lampreys and
hagfishes.
Mallatt J, Sullivan J.
Resolving the interrelationships of three major extant lineages of
vertebrates (hagfishes, lampreys, and gnathostomes) is a particularly
important issue in evolution, because the basal resolution critically
influences our understanding of primitive vertebrate characters. A
consensus has emerged over the last 20 years that lampreys are the
sister group to the gnathostomes and the hagfishes represent an
ancient, basal lineage. This hypothesis has essentially displaced the
classical hypothesis of monophyly of the cyclostomes (lampreys
plus hagfishes). To test these hypotheses, we compared nearly complete
ribosomal DNA sequences from each of these major lineages,
as well as those from a cephalochordate and a urochordate, which
represent a paraphyletic outgroup for assessing the basal vertebrate
relationships. For this comparison, 92%-99% complete 28S rDNA
sequences were obtained from the lancelet Branchiostoma floridae,
the hagfish Eptatretus stouti, the lamprey Petromyzon marinus, and
cartilaginous fishes Hydrolagus colliei and Squalus acanthias and
were then analyzed with previously reported 28S and 18S rDNA sequences
from other chordates. We conducted conventional
(nonparametric) bootstrap analyses, under maximum-likelihood,
parsimony, and minimum-evolution (using LogDet distances) criteria,
of both 28S and 18S rDNA sequences considered separately and combined.
All these analyses provide moderate to very strong support
for the monophyly of the cyclostomes. Furthermore, the currently
accepted hypothesis of a lamprey-gnathostome clade is moderately
rejected by the Kishino-Hasegawa test (P = 0.099) and resoundingly
rejected by parametric bootstrap tests (P < 0.01) in favor of
monophyly of living cyclostomes. Another significant finding is that
the hagfish E. stouti has the longest 28S rDNA gene known in
any organism (> 5,200 nt).
Andy
T. Mike Keesey
> Gnathostomata is, I believe, a paraphyletic taxon like
> Agnatha. This simply means that it doesn't include
> all its descendants. For reasons only known to them,
> this makes the two groups anathema to what I call "cladophiles":
> people who insist that all groups be clades. A clade
> is a single species and all creatures descended from it.
_Gnathostomata_ is a clade, not a paraphyletic group.
> Yes, but not everyone deals with the Superclass concept. There
> is even a movement underfoot to do away with ALL Linnean
> categories above the Genus level--sort of like abolishing
> all divisions of history into eras like Ancient, Medieval,
> Modern.
Actually, some of us would also like to do away with genera someday,
although that would be a difficult operation... (It would most likely
involve converting genera to clades, so that there would only be two types
of biological taxa -- clades and species. See
http://www.ohiou.edu/phylocode/)
A cladistic classification of _Vertebrata_:
http://dinosauricon.com/taxa/vertebrata.html
> And lampreys are, by several standards, the only living things that
> are about as far from humans as lampreys are from eels.
Difficult to quantify that....
_____________________________________________________________________________
T. MICHAEL KEESEY
Home Page <http://dinosauricon.com/keesey>
The Dinosauricon <http://dinosauricon.com>
personal <kee...@bigfoot.com> --> <t...@dinosauricon.com>
Dinosauricon-related <dino...@dinosauricon.com>
AOL Instant Messenger <Ric Blayze>
ICQ <77314901>
Yahoo! Messenger <Mighty Odinn>
Andy Groves
> Jaw ---- and No-Jaw, of course ---- and then it gets interesting.
>
> But then it's MORE than just Jaw and No-Jaw as between Lampreys and
> Eels ---- Right?
Right.
Jaws.
True bone (don't be confused by cartilagenous fish. They have some
true bone).
True teeth
and
Paired fins with pelvic and pectoral girdles.
I will wager that 10 other biologists will give you 10 other lists,
but there you are......
Andy
mel turner
gro...@cco.caltech.edu [Andy Groves] wrote...
>Peter Nyikos <nyi...@math.sc.edu> wrote in message
news:<2001061212...@kappa.math.sc.edu>...
>> mtu...@snipthis.acpub.duke.edu (mel turner) writes:
><snip>
>
>>>Hagfishes [also sometimes called "eels"] evidently aren't
>>>close to lampreys.
>> Yes, they are a mystery. They may even have arisen
>> independently from the lower chordates from not only
>> lampreys
Right, that was my impression from the literature & such sites as
http://phylogeny.arizona.edu/tree/eukaryotes/animals/chordata/craniata.html
http://phylogeny.arizona.edu/tree/eukaryotes/animals/chordata/vertebrata.html
http://www.geocities.com/CapeCanaveral/Hall/1636/craniata.html
http://www.geocities.com/CapeCanaveral/Hall/1636/clades.html
>> but from ALL known fossil vertebrates (craniates).
[Although IIRC there are one or more probable fossil hagfish
relatives known]
>The implication fom the two studies below is that hagfish and lampreys
>are monophyletic,
>and that hagfish (Myxinoidea) have lost certain morphological
>characteristics secondarily.
Very interesting!
>Some limited data suggest that hagfish may have some craniofacial
>placodes; I don't know if anyone has
>looked to see if they have a rudimentary neural crest.
>Science 1992 Aug 7;257(5071):787-9
>Evidence from 18S ribosomal RNA sequences that lampreys and hagfishes
>form a natural group.
>Stock DW, Whitt GS.
>Lampreys and hagfishes (cyclostomes) traditionally were considered to
>be a natural (monophyletic) group. Recently, the consensus of
>opinion, based largely on morphological analyses, has shifted to a
>view that lampreys are more closely related to jawed vertebrates
>(gnathostomes) than to hagfishes. Phylogenetic comparisons of 18S
>ribosomal RNA sequences from two hagfishes, two lampreys, a
>tunicate, a lancelet, and a number of gnathostomes support the
>monophyly of the cyclostomes. These data force a reassessment of
>several features of early vertebrate evolution.
>Mol Biol Evol 1998 Dec;15(12):1706-18
>28S and 18S rDNA sequences support the monophyly of lampreys and
>hagfishes.
>Mallatt J, Sullivan J.
[snip]
>All these analyses provide moderate to very strong support
>for the monophyly of the cyclostomes. Furthermore, the currently
>accepted hypothesis of a lamprey-gnathostome clade is moderately
>rejected by the Kishino-Hasegawa test (P = 0.099) and resoundingly
>rejected by parametric bootstrap tests (P < 0.01) in favor of
>monophyly of living cyclostomes. Another significant finding is that
>the hagfish E. stouti has the longest 28S rDNA gene known in
>any organism (> 5,200 nt).
A search finds the above as well as
TI: The complete nucleotide sequence of the mitochondrial DNA of the
agnathan Lampetra fluviatilis: Bearings on the phylogeny of
cyclostomes.
AU: Delarbre-Christiane; Escriva-Hector; Gallut-Cyril;
Barriel-Veronique; Kourilsky-Philippe; Janvier-Philippe;
Laudet-Vincent; Gachelin-Gabriel
SO: Molecular-Biology-and-Evolution. April, 2000; 17 (4): 519-529..
AB: There are two competing theories about the interrelationships of
craniates: the cyclostome theory assumes that lampreys and hagfishes
are a clade, the cyclostomes, whose sister group is the jawed
vertebrates (gnathostomes); the vertebrate theory assumes that
lampreys and gnathostomes are a clade, the vertebrates, whose sister
group is hagfishes. The vertebrate theory is best supported by a number
of unique anatomical and physiological characters. Molecular sequence
data from 18S and 28S rRNA genes rather support the cyclostome theory,
but mtDNA sequence of Myxine glutinosa rather supports the vertebrate
theory. Additional molecular data are thus needed to elucidate this
three-taxon problem. We determined the complete nucleotide sequence of
the mtDNA of the lamprey Lampetra fluviatilis. The mtDNA of L.
fluviatilis possesses the same genomic organization as Petromyzon
marinus, which validates this gene order as a synapomorphy of lampreys.
The mtDNA sequence of L. fluviatilis was used in combination with
relevant mtDNA sequences for an approach to the hagfish/lamprey
relationships using the maximum-parsimony, neighbor-joining, and
maximum-likelihood methods. Although trees compatible with our present
knowledge of the phylogeny of craniates can be reconstructed by using
the three methods, the data collected do not support the vertebrate or
the cyclostome hypothesis. The present data set does not allow the
resolution of this three-taxon problem, and new kinds of data, such
as nuclear DNA sequences, need to be collected.
TI: The mitochondrial DNA molecule of the hagfish (Myxine glutinosa)
and vertebrate phylogeny.
AU: Rasmussen-Ann-Sofie; Janke-Axel; Arnason-Ulfur {a}
SO: Journal-of-Molecular-Evolution. April, 1998; 46 (4) 382-388..
AB: The vertebrates are traditionally classified into two distinct
groups, Agnatha (jawless vertebrates) and Gnathostomata (jawed
vertebrates). Extant agnathans are represented by hagfishes
(Myxiniformes) and lampreys (Petromyzontiformes), frequently -grouped
together within the Cyclostomata. Whereas the recognition of the
Gnathostomata as a clade is commonly acknowledged, a consensus has not
been reached regarding whether or not Cyclostomata represents a clade.
In the present study we have used newly established sequences of the
protein-coding genes of the mitochondrial DNA molecule of the hagfish
to explore agnathan and gnathostome relationships. The phylogenetic
analysis of Pisces, using echinoderms as outgroup, placed the hagfish
as a sister group of Vertebrata sensu stricto, i.e., the lamprey and
the gnathostomes. The phylogenetic analysis of the Gnathostomata i
dentified a basal divergence between gnathostome fishes and a branch
leading to birds and mammals, i.e., between "Anamnia" and Amniota. The
lungfish has a basal position among gnathostome fishes with the
teleosts as the most recently evolving lineage. The findings portray a
hitherto unrecognized polarity in the evolution of bony fishes. The
presently established relationships are incompatible with previous
molecular studies.
So it seems there is more to learn about their molecular
systematics.
cheers
Peter Nyikos
>On 12 Jun 2001, Peter Nyikos wrote:
>> Gnathostomata is, I believe, a paraphyletic taxon like
>> Agnatha. This simply means that it doesn't include
>> all its descendants. For reasons only known to them,
>> this makes the two groups anathema to what I call "cladophiles":
>> people who insist that all groups be clades. A clade
>> is a single species and all creatures descended from it.
>_Gnathostomata_ is a clade, not a paraphyletic group.
I'd like to hear from Kinman about that. He's just
posted a nice article on classification including
Gnathostomata, on:
Class Agnathea (classification)
to which I've replied in t.o. and s.b.p. just now.
>> Yes, but not everyone deals with the Superclass concept. There
>> is even a movement underfoot to do away with ALL Linnean
>> categories above the Genus level--sort of like abolishing
>> all divisions of history into eras like Ancient, Medieval,
>> Modern.
>Actually, some of us would also like to do away with genera someday,
>although that would be a difficult operation...
You would almost have to do away with binomial nomenclature
for that, wouldn't you?
(It would most likely
>involve converting genera to clades, so that there would only be two types
>of biological taxa -- clades and species. See
>http://www.ohiou.edu/phylocode/)
The introduction does not say how to overcome the difficulty
of figuring out whether, say, Ambulocetus natans should
be renamed "Cetacea natans". It puts an enormous burden
on deciding just what is the last common ancestor of
a given clade--and that is just about the most ephemeral
sort of decision one could make, given the imperfectness
of fossililzation (no complete genome to sequence, etc.)
>A cladistic classification of _Vertebrata_:
>http://dinosauricon.com/taxa/vertebrata.html
>> And lampreys are, by several standards, the only living things that
>> are about as far from humans as lampreys are from eels.
>Difficult to quantify that....
There is one (not necessarily the best) quantification readily at hand:
when the divergence from the last common ancestor took place.
The answer is the same in both cases.
This quantification is closely related to the usual concept cladists use,
whereby we get such things as "We are more closely
related to Ambulocetus natans than we are to Didelphis,
even though Didelphis looks a whole lot more like
one of our remote ancestors than Ambulocetus does."
[Didelphis is the common opossum.]
Peter Nyikos
>In article <991ea4ae.01061...@posting.google.com>,
>gro...@cco.caltech.edu [Andy Groves] wrote...
>>Peter Nyikos <nyi...@math.sc.edu> wrote in message
>news:<2001061212...@kappa.math.sc.edu>...
>>> mtu...@snipthis.acpub.duke.edu (mel turner) writes:
>>>>Hagfishes [also sometimes called "eels"] evidently aren't
>>>>close to lampreys.
>
>>> Yes, they are a mystery. They may even have arisen
>>> independently from the lower chordates from not only
>>> lampreys
>Right, that was my impression from the literature & such sites as
>http://phylogeny.arizona.edu/tree/eukaryotes/animals/chordata/craniata.html
>http://phylogeny.arizona.edu/tree/eukaryotes/animals/chordata/vertebrata.html
>http://www.geocities.com/CapeCanaveral/Hall/1636/craniata.html
>http://www.geocities.com/CapeCanaveral/Hall/1636/clades.html
>>> but from ALL known fossil vertebrates (craniates).
>[Although IIRC there are one or more probable fossil hagfish
>relatives known]
>>The implication fom the two studies below is that hagfish and lampreys
>>are monophyletic,
>>and that hagfish (Myxinoidea) have lost certain morphological
>>characteristics secondarily.
>Very interesting!
But also very tentative.
>>Some limited data suggest that hagfish may have some craniofacial
>>placodes; I don't know if anyone has
>>looked to see if they have a rudimentary neural crest.
>>Science 1992 Aug 7;257(5071):787-9
>>Evidence from 18S ribosomal RNA sequences that lampreys and hagfishes
>>form a natural group.
>>Stock DW, Whitt GS.
>>Lampreys and hagfishes (cyclostomes) traditionally were considered to
>>be a natural (monophyletic) group. Recently, the consensus of
>>opinion, based largely on morphological analyses, has shifted to a
>>view that lampreys are more closely related to jawed vertebrates
>>(gnathostomes) than to hagfishes. Phylogenetic comparisons of 18S
>>ribosomal RNA sequences from two hagfishes, two lampreys, a
>>tunicate, a lancelet, and a number of gnathostomes support the
>>monophyly of the cyclostomes. These data force a reassessment of
>>several features of early vertebrate evolution.
Ribosomal RNA is only one yardstick; I'd be more comfortable
if a wide variety of DNA were sampled and uniformly
confirmed this reassessment; it does not--see below.
I'm reminded of the time Laurence A. Moran proudly
displayed a reference which he claimed showed that
alpha globins showed birds are more closely related
to "reptiles" than to mammals.
Fushitani K, Higashiyama K, Moriyama EN, Imai K, Hosokawa K,
Evolution of Amniote Hb alpha Globin Sequences
Mol Biol Evol 1996 Sep;13(7):1039-1043
He was parroting the foolishly worded abstract
of the article, which should have said,
"reptiles other than lizards". But this flies
in the face of the consensus of paleontologists
that lizards are NOT an exception, that they
too are more closely related to birds than mammals are.
The authors seem blissfully unaware of this, and
also of the still more startling fact that alpha
globins show birds to be more closely related
to turtles than to crocodilians!
>>Mol Biol Evol 1998 Dec;15(12):1706-18
>>28S and 18S rDNA sequences support the monophyly of lampreys and
>>hagfishes.
>>Mallatt J, Sullivan J.
>[snip]
>>All these analyses provide moderate to very strong support
>>for the monophyly of the cyclostomes. Furthermore, the currently
>>accepted hypothesis of a lamprey-gnathostome clade is moderately
>>rejected by the Kishino-Hasegawa test (P = 0.099) and resoundingly
>>rejected by parametric bootstrap tests (P < 0.01) in favor of
>>monophyly of living cyclostomes.
I am unfamiliar with this notation. I am used
to bootstrap numbers running from 0 to 100; does this
mean a bootstrap number of 99+?
Also, what system was used? NJ? parsimony("cladistics") ?
For comparison, bootstrap values for putting birds closer to turtles
than to crocodilians were 58 for NJ and 27 for cladistics in
the study by Fushitani et. al. Here is part of the tree,
which strongly supports the heterodox view that Sphenodon
is more closely related to Archosaurs (and even, less
strongly, to mammals!!) than to lizards:
______________Caiman
|
|
|100/98
________|
| |_____________Alligator
|
|
----------| 96/68
| ___________Turtle
| |
| | _______Ostrich
|________| |
|58/27 |
| _________|90/92
| | |
| | |________Chicken
|_____|
|74/32
|
|
|_____________Sphenodon
The first number is for NJ, the latter for maximum parsimony.
The sister group for the above was the pair of mammals,
rather than the lizards. With the viper left out of the analysis,
the NJ bootstrap value for this "sister grouping" was 80, but
maximum parsimony was below 50.
>> Another significant finding is that
>>the hagfish E. stouti has the longest 28S rDNA gene known in
>>any organism (> 5,200 nt).
And what are the figures for the lamprey and for gnathostomes?
>A search finds the above as well as
>TI: The complete nucleotide sequence of the mitochondrial DNA of the
>agnathan Lampetra fluviatilis: Bearings on the phylogeny of
>cyclostomes.
>AU: Delarbre-Christiane; Escriva-Hector; Gallut-Cyril;
>Barriel-Veronique; Kourilsky-Philippe; Janvier-Philippe;
>Laudet-Vincent; Gachelin-Gabriel
[...]
Molecular sequence
>data from 18S and 28S rRNA genes rather support the cyclostome theory,
>but mtDNA sequence of Myxine glutinosa rather supports the vertebrate
>theory. Additional molecular data are thus needed to elucidate this
>three-taxon problem.
And so on in the same vein. I concur.
We determined the complete nucleotide sequence of
>the mtDNA of the lamprey Lampetra fluviatilis. The mtDNA of L.
>fluviatilis possesses the same genomic organization as Petromyzon
>marinus, which validates this gene order as a synapomorphy of lampreys.
>The mtDNA sequence of L. fluviatilis was used in combination with
>relevant mtDNA sequences for an approach to the hagfish/lamprey
>relationships using the maximum-parsimony, neighbor-joining, and
>maximum-likelihood methods. Although trees compatible with our present
>knowledge of the phylogeny of craniates can be reconstructed by using
>the three methods, the data collected do not support the vertebrate or
>the cyclostome hypothesis. The present data set does not allow the
>resolution of this three-taxon problem, and new kinds of data, such
>as nuclear DNA sequences, need to be collected.
>TI: The mitochondrial DNA molecule of the hagfish (Myxine glutinosa)
>and vertebrate phylogeny.
>AU: Rasmussen-Ann-Sofie; Janke-Axel; Arnason-Ulfur {a}
>SO: Journal-of-Molecular-Evolution. April, 1998; 46 (4) 382-388..
[...]
>In the present study we have used newly established sequences of the
>protein-coding genes of the mitochondrial DNA molecule of the hagfish
>to explore agnathan and gnathostome relationships. The phylogenetic
>analysis of Pisces, using echinoderms as outgroup, placed the hagfish
>as a sister group of Vertebrata sensu stricto, i.e., the lamprey and
>the gnathostomes. The phylogenetic analysis of the Gnathostomata i
>dentified a basal divergence between gnathostome fishes and a branch
>leading to birds and mammals, i.e., between "Anamnia" and Amniota. The
>lungfish has a basal position among gnathostome fishes with the
>teleosts as the most recently evolving lineage.
As one would expect from paleontology. What I would
love to see is a study that includes *Latimeria*,
generally (though not unanimously) believed to be
closer to tetrapods than lungfishes are.
> The findings portray a
>hitherto unrecognized polarity in the evolution of bony fishes.
I can't see that from the rest of the abstract.
Do you have a clue as to what this is all about, Mel?
T. Mike Keesey
> >_Gnathostomata_ is a clade, not a paraphyletic group.
>
> I'd like to hear from Kinman about that. He's just
> posted a nice article on classification including
> Gnathostomata, on:
>
> Class Agnathea (classification)
>
> to which I've replied in t.o. and s.b.p. just now.
I've never heard anyone propose _Gnathostomata_ (jawed vertebrates) as
paraphyletic. What would it have given rise to?
> >Actually, some of us would also like to do away with genera someday,
> >although that would be a difficult operation...
>
> You would almost have to do away with binomial nomenclature
> for that, wouldn't you?
That's the idea, actually. Currently, if a species is moved, its name
changes, causing instability in the literature. The ultimate idea would be
to have species names be independent and robust. Of course, it is very
difficult to come up with a workable method for doing this! However,
several have been proposed.
> (It would most likely
> >involve converting genera to clades, so that there would only be two types
> >of biological taxa -- clades and species. See
> >http://www.ohiou.edu/phylocode/)
>
> The introduction does not say how to overcome the difficulty
> of figuring out whether, say, Ambulocetus natans should
> be renamed "Cetacea natans".
Under one scheme, it could be called either one, assuming _Ambulocetus_
had been given a cladistic definition.
Another scheme has current binomina being translated into single names,
e.g., the species _ambulocetus-natans_.
Under another scheme, _natans_ would be listed alone, but with its
citation, at least the first time it's printed. (Or every time, if another
species named _natans_ is being mentioned.)
Or, if _Ambulocetus_ is currently a montotypic genus, it could become a
species: _ambulocetus_.
There are many other proposed methods, but all have some flaws.
> It puts an enormous burden
> on deciding just what is the last common ancestor of
> a given clade--and that is just about the most ephemeral
> sort of decision one could make, given the imperfectness
> of fossililzation (no complete genome to sequence, etc.)
Since when do you need to know that? Oh, you mean if _natans_ is the
ancestral cetacean? Is _Cetacea_ defined as something like
Clade(_Ambulocetus_ + _Balaena_)? If not, I'd tend to doubt it. If so, I
guess it is (remotely) possible and your point is valid. (We had a similar
discussion about _Archaeopteryx_ and _Aves_ on the PhyloCode Mailing
List.) As I said, nobody's come up with a perfect system yet.
> >> And lampreys are, by several standards, the only living things that
> >> are about as far from humans as lampreys are from eels.
>
> >Difficult to quantify that....
>
> There is one (not necessarily the best) quantification readily at hand:
> when the divergence from the last common ancestor took place.
>
> The answer is the same in both cases.
Indeed, members of the lamprey stem-clade are the only things that fit
that criterion. Seems like a rather unremarkable claim. Given...
--+--A
`--+--B
`--C
... where A, B, and C are contemporaneous, of course A is the only thing
that has as much divergent history between itself and C as between A and
B.
> This quantification is closely related to the usual concept cladists use,
> whereby we get such things as "We are more closely
> related to Ambulocetus natans than we are to Didelphis,
> even though Didelphis looks a whole lot more like
> one of our remote ancestors than Ambulocetus does."
I never liked that terminology, and prefer the less ambiguous "we share
more recent ancestry with _Ambulocetus_ than with _Didelphis_".
Andy Groves
<snip>
To be fair to the authors, it was a fair amount of work to get the
conclusions that they did.
Isolating new sequences from new species was not exactly a cakewalk
back in 1992, and for a referee to
have demanded they look at a cohort of "molecular clock" genes would
have been seen as a tad churlish.
Andy
mel turner
Nyikos] wrote...
>mtu...@snipthis.acpub.duke.edu (mel turner) writes:
>>In article <991ea4ae.01061...@posting.google.com>,
>>gro...@cco.caltech.edu [Andy Groves] wrote...
>>>The implication fom the two studies below is that hagfish and lampreys
>>>are monophyletic, and that hagfish (Myxinoidea) have lost certain
>>>morphological characteristics secondarily.
>
>>Very interesting!
>
>But also very tentative.
Undoubtedly.
[snip]
>>TI: The mitochondrial DNA molecule of the hagfish (Myxine glutinosa)
>>and vertebrate phylogeny.
>>AU: Rasmussen-Ann-Sofie; Janke-Axel; Arnason-Ulfur {a}
>>SO: Journal-of-Molecular-Evolution. April, 1998; 46 (4) 382-388..
>
>[...]
>>In the present study we have used newly established sequences of the
>>protein-coding genes of the mitochondrial DNA molecule of the hagfish
>>to explore agnathan and gnathostome relationships. The phylogenetic
>>analysis of Pisces, using echinoderms as outgroup, placed the hagfish
>>as a sister group of Vertebrata sensu stricto, i.e., the lamprey and
>>the gnathostomes. The phylogenetic analysis of the Gnathostomata
>>identified a basal divergence between gnathostome fishes and a branch
>>leading to birds and mammals, i.e., between "Anamnia" and Amniota. The
>>lungfish has a basal position among gnathostome fishes with the
>>teleosts as the most recently evolving lineage.
>
>As one would expect from paleontology.
Certainly not that last bit about Amniota coming out
as sister to all the non-amniote Gnathostomata.
>What I would
>love to see is a study that includes *Latimeria*,
>generally (though not unanimously) believed to be
>closer to tetrapods than lungfishes are.
I thought the consensus [based on molecular and morphological
data] had clearly shifted toward the Dipnoi being closer relatives
to tetrapods than coelacanths are [or some studies suggesting a
Dipnoi/Latimeria sister group relationship, with neither lungfish
nor coelacanths bding more closely related to tetrapods than the
other].
See below for some refs/abstracts..
>> The findings portray a
>>hitherto unrecognized polarity in the evolution of bony fishes.
>
>I can't see that from the rest of the abstract.
>Do you have a clue as to what this is all about, Mel?
Basically? Sure, although it's clearly not my field of expertise.
According to the abstract, their analysis supported a basal branching
of the jawed vertebrates with Amniota [reptiles, birds and mammals] on
one branch, and all the fishlike jawed vertebrates [presumably such as
sharks, lungfish and ray-finned bony fishes (and non-amniote
tetrapods?)] on the other. Sounds like there must be some problems
with the data or its analysis, since of course the amniotes and other
tetrapods should be nested deeply within a bony fish/sarcopterygian
clade, not sister to all other jawed vertebrates.
You'd asked about comparative molecular studies including
_Latimeria_. A BioAbstracts search turns up a few such:
TI: Gene structure and amino acid sequence of Latimeria chalumnae
(coelacanth) myelin DM20: Phylogenetic relation of the fish.
AU: Tohyama-Yoko; Kasama-Yoshida-Hiromi; Sakuma-Mitsuhiro;
Kobayashi-Yoko; Cao-Ying; Hasegawa-Masami; Kojima-Hisako;
Tamai-Yoichi; Tanokura-Masaru; Kurihara-Tadashi {a}
SO: Neurochemical-Research. July, 1999; 24 (7): 867-873..
AB: The structure of Latimeria chalumnae (coelacanth) proteolipid
protein/DM20 gene excluding exon 1 was determined, and the amino acid
sequence of Latimeria DM20 corresponding to exons 2-7 was deduced. The
nucleotide sequence of exon 3 suggests that only DM20 isoform is
expressed in Latimeria. The structure of proteolipid protein/DM20 gene
is well preserved among human, dog, mouse, and Latimeria.Southern blot
analysis indicates that Latimeria DM20 gene is a single-copy gene. When
the amino acid sequences of DM20 were compared among various species,
Latimeria was more similar to tetrapods than other fishes including
lungfish, confirming the previous finding by immunoreactivity
(Waehneldt and Malotka 1989 J. Neurochem. 52:1941-1943). However, when
phylogenetic trees were constructed from the DM20 sequences, lungfish
was clearly the closest to tetrapods. Latimeria was situated outside of
lungfish by the maximum likelihood method. The apparent similarity of
Latimeria DM20 to tetrapod proteolipid protein/DM20 is explained by the
slow amino acid substitution rate of Latimeria DM20.
TI: Searching for the closet living relative(s) of tetrapods through
evolutionary analyses of mitochondrial and nuclear data.
AU: Zardoya-Rafael {a}; Cao-Ying; Hasegawa-Masami; Meyer-Axel
SO: Molecular-Biology-and-Evolution. May, 1998; 15 (5) 506-517..
AB:The phylogenetic relationships of the African lungfish (Protopterus
dolloi) and the coelacanth (Latimeria chalumnae) with respect to
tetrapods were analyzed using complete mitochondrial genome DNA
sequences. A lungfish + coelacanth clade was favored by maximum
parsimony (although this result is dependent on which transition:
transversion weights are applied), and a lungfish + tetrapod clade was
supported by neighbor-joining and maximum-likelihood analyses. These
two hypotheses received the strongest statistical and bootstrap support
to the exclusion of the third alternative, the coelacanth + tetrapod
sister group relationship. All mitochondrial protein coding genes
combined favor a lungfish + tetrapod grouping. We can confidently
reject the hypothesis that the coelacanth is the closest living
relative of tetrapods. When the complete mitochondrial sequence data
were combined with nuclear 28S rRNA gene data, a lungfish + coelacanth
clade was supported by maximum parsimony and maximum likelihood, but
a lungfish + tetrapod clade was favored by neighbor-joining. The
seemingly conflicting results based on different data sets and
phylogenetic methods were typically not statistically strongly
supported based on Kishino-Hasegawa and Templeton tests, although they
were often supported by strong bootstrap values. Differences in rate
of evolution of the different mitochondrial genes (slowly evolving
genes such as the cytochrome oxidase and tRNA genes favored a lungfish
+ coelacanth clade, whereas genes of relatively faster substitution
rate, such as several NADH dehydrogenase genes, supported a lungfish
+ tetrapod grouping), as well as the rapid radiation of the lineages
back in the Devonian, rather than base compositional biases among taxa
seem to be directly responsible for the remaining uncertainty in
accepting one of the two alternate hypotheses.
TI: The complete DNA sequence of the mitochondrial genome of a "living
fossil", the coelacanth (Latimeria chalumnae).
AU: Zardoya-Rafael {a}; Meyer-Axel
SO: Genetics-. 1997; 146 (3) 995-1010..
AB: The complete nucleotide sequence of the 16,407-bp mitochondrial
genome of the coelacanth (Latimeria chalumnae) was determined. The
coelacanth mitochondrial genome order is identical to the consensus
vertebrate gene order which is also found in all ray-finned fishes,
the lungfish, and most tetrapods. Base composition and codon usage
also conform to typical vertebrate patterns. The entire mitochondrial
genome was PCR-amplified with 24 sets of primers that are expected to
amplify homologous regions in other related vertebrate species.
Analyses of the control region of the coelacanth mitochondrial
genome revealed the existence of four 22-bp tandem repeats close to
its 3' end. The phylogenetic analyses of a large data set combining
genes coding for rRNAs, tRNAs, and proteins (16,140 characters)
confirmed the phylogenetic position of the coelacanth as a lobe-finned
fish; it is more closely related to tetrapods than to ray-finned fishes.
However, different phylogenetic methods applied to this largest
available molecular data set were unable to resolve unambiguously the
relationship of the coelacanth to the two other groups of extant
lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony
favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup
relationship depending on which transversion:transition weighting is
assumed. Neighbor-joining and maximum likelihood supported a lungfish/
tetrapod sistergroup relationship.
TI: Evolutionary relationships of the coelacanth, lungfishes, and
tetrapods based on the 28S ribosomal RNA gene.
AU: Zardoya-Rafael {a}; Meyer-Axel
SO: Proceedings-of-the-National-Academy-of-Sciences-of-the-United-
States-of-America. 1996; 93 (11) 5449-5454..
AB: The origin of land vertebrates was one of the major transitions
in the history of vertebrates. Yet, despite many studies that are
based on either morphology or molecules, the phylogenetic
relationships among tetrapods and the other two living groups of
lobe-finned fishes, the coelacanth and the lungfishes, are still
unresolved and debated. Knowledge of the relationships among these
lineages, which originated back in the Devonian, has profound
implications for the reconstruction of the evolutionary scenario of
the conquest of land. We collected the largest molecular data set on
this issue so far, about 3,500 base pairs from seven species of the
large 28S nuclear ribosomal gene. All phylogenetic analyses (maximum
parsimony, neighbor-joining, and maximum likelihood) point toward the
hypothesis that lungfishes and coelacanths form a monophyletic group
and are equally closely related to land vertebrates. This evolutionary
hypothesis complicates the identification of morphological or
physiological preadaptations that might have permitted the common
ancestor of tetrapods to colonize land. This is because the
reconstruction of its ancestral conditions would be hindered by the
difficulty to separate uniquely derived characters from shared derived
characters in the coelacanth/lungfish and tetrapod lineages. This
molecular phylogeny aids in the reconstruction of morphological
evolutionary steps by providing a framework; however, only
paleontological evidence can determine the sequence of morphological
acquisitions that allowed lobe-finned fishes to colonize land.
TI: Relationship among coelacanths, lungfishes and tetrapods: A
phylogenetic analysis based on mitochondrial cytochrome oxidase I
gene sequences.
AU: Yokobori-Shin-Ichi; Hasegawa-Masami; Ueda-Takuya; Okada-Norihiro;
Nishikawa-Kazuya; Watanabe-Kimitsuna {a}
SO: Journal-of-Molecular-Evolution. 1994; 38 (6) 602-609..
AB: To clarify the relationship among coelacanths, lungfishes, and
tetrapods, the amino acid sequences deduced from the nucleotide
sequences of mitochondrial cytochrome oxidase subunit I (COI) genes
were compared. The phylogenetic tree of these animals, including the
coelacanth Latimeria chalumnae and the lungfish Lepidosiren paradoxa,
was inferred by several methods. These analyses consistently indicate
a coelacanth/lungfish clade, to which little attention has been paid
by previous authors with the exception of some morphologists. Overall
evidence of other mitochondrial genes reported previously and the
results of this study equally support the coelacanth/lungfish and
lungfish/tetrapod clades, ruling out the coelacanth/tetrapod clade.
TI: Molecules, fossils, and the origin of tetrapods.
AU: MEYER-A; DOLVEN-S-I
SO: JOURNAL OF MOLECULAR EVOLUTION 35(2): 102-113.
PY: 1992
AB: Since the discovery of the coelacanth, Latimeria chalumnae, more
than 50 years ago, paleontologists and comparative morphologies have
debated whether coelacanths or lungfishes, two groups of lobe-finned
fishes, are the closest living relatives of land vertebrates
(Tetrapoda). Previously, Meyer and Wilson (1990) determined partial
DNA sequences from two conservative mitochondrial genes and found
support for a close relationship of lungfishes to tetrapods. We
present additional DNA sequences from the 12S rRNA mitochondrial gene
for three species of the two lineages of lungfishes that were not
represented in the first study: Protopterus annectens and Protopterus
aethiopicus from Africa and Neoceratodus forsteri (kindly provided
by B. Hedges and L. Maxson) from Australia. This extended data set
trends to group the two lepidosirenid lungfish lineages (Lepidosiren
and Protopterus) with Neoceratodus as their sister group. All
lungfishes seem to be more closely related to tetrapods than the
coelacanth is. This result appears to rule out the possibility that
the coelacanth lineage gave rise to land vertebrates. The common
ancestor of lungfishes and tetrapods might have possessed multiple
morphological traits that are shared by lungfishes and tetrapods
(Meyer and Wilson (1990) listed 14 such traits). Those traits that
seem to link Latimeria and tetrapods are arguably due to convergent
evolution or reversals and not to common descent. In this way, the
molecular tree facilitates an evolutionary interpetation of the
morphological differences among the living forms. We recommended that
the extinct group of lobe-finned fishes be placed onto the molecular
tree that has lungfishes and not the coelacanth more closely related
to tetrapods. The placement of fossils would help to further interpret
the sequence of morphological events and innovations associated with
the orgin of tetrapods but appears to be problematic because the
quality of fossils is not always high enough, and differences among
paleontologists in the interpretation of the fossils have stood in the
way of a consensus opinion for the branching order among lobe-finned
fishes. Marshall and Schultze (1992) criticized the morphological
analysis presented by Meyer and Wilson (1990) and suggest that 13 of
the 14 morphological traits that support the sister group relationship
of lungfishes and tetrapods are not shared derived characaters. Here
we present further alternative viewpoints to the ones of Marshall and
Schultze (1992) from the paleotological literature. We argue that
all available information (paleontological, neontological, and
molecular data) and rigorous cladistic methodology should be used
when relating fossils and extant taxa in a phylogenetic framework.
TI: The relationships of the coelacanth Latimeria chalumnae: Evidence
from sequences of vertebrate 28S ribosomal RNA genes.
AU: HILLIS-D-M; DIXON-M-T; AMMERMAN-L-K
SO: ENVIRONMENTAL BIOLOGY OF FISHES 32(1-4): 119-130.
PY: 1991
AB: A subgenomic library created from genomic DNA of Latimeria
chalumnae was screened for 28S ribosomal RNA (rRNA) clones. The
resulting clone was subcloned into a plasmid vector, and over 2kb of
the 28S rRNA region was sequenced. Sequences of 28S rRNA genes were
also obtained for Rhineura floridana (Squamata), Cyprinella lutrensis
(Actinopterygii), and Lampetra aepyptera (Petromyzontiformes) by
cloning and/or amplification by the polymerase chain reaction. The 28S
rDNA sequences were aligned for all the above species as well as for
the previously published 28S rDNA sequences of the genera Mus, Rattus,
and Homo (Mammalia), Xenopus (Amphibia), and Drosophila(Insecta).
Phylogenetic analysis of these species (using both the insect and
lamprey sequences for outgroup comparison, or using only the lamprey
sequence in the outgroup) produced a single optimal solution:
(Outgroup(Cyprinella(Latimeria(Xenopus(Rhineura(Homo(Rattus(Mus)))))))).
Bootstrap analysis indicated that the placement of L. chalumnae on this
tree was significant at p lt 0.01. Previously published alternative
hypotheses of relationships of Latimeria require at least 19 additional
steps compared to the optimal solution; the rDNA data are sufficient to
reject the hypotheses that place Latimeria in groups other than the
sarcopterygians.
cheers
Peter Nyikos
>Peter Nyikos <nyi...@math.sc.edu> wrote in message news:<2001061415...@kappa.math.sc.edu>...
>> mtu...@snipthis.acpub.duke.edu (mel turner) writes:
>>
>> >In article <991ea4ae.01061...@posting.google.com>,
>> >gro...@cco.caltech.edu [Andy Groves] wrote...
>> >>Some limited data suggest that hagfish may have some craniofacial
><snip>
Who said anything about "molecular clock" genes? Simply,
I was asking for a wide variety of genes.
Don't be misled by the fact that the only other study
anyone cited had to do with mitochondrial DNA. We
need more samples, period.
Andy Groves
I know. Clock genes would be useful, as would genes now known to play
a role in the development of craniofacial
structures which might provide an insight into craniate evolution. If
you're going to look at the problem, you might as well pick genes
known not to diverge too drastically,
or genes that are expressed in structures that appear in the
evolutionary sequence you are examining.
For example, the Dlx gene family has been studied quite a bit in this
context:
Proc Natl Acad Sci U S A 2001 Feb 13;98(4):1665-70
Lamprey Dlx genes and early vertebrate evolution.
Neidert AH, Virupannavar V, Hooker GW, Langeland JA.
Gnathostome vertebrates have multiple members of the Dlx family of
transcription factors that are expressed during the development of
several tissues considered to be vertebrate synapomorphies, including
the forebrain, cranial neural crest, placodes, and pharyngeal
arches. The Dlx gene family thus presents an ideal system in which to
examine the relationship between gene duplication and
morphological innovation during vertebrate evolution. Toward this end,
we have cloned Dlx genes from the lamprey Petromyzon
marinus, an agnathan vertebrate that occupies a critical phylogenetic
position between cephalochordates and gnathostomes. We have
identified four Dlx genes in P. marinus, whose orthology with
gnathostome Dlx genes provides a model for how this gene family
evolved in the vertebrate lineage. Differential expression of these
lamprey Dlx genes in the forebrain, cranial neural crest, pharyngeal
arches, and sensory placodes of lamprey embryos provides insight into
the developmental evolution of these structures as well as a
model of regulatory evolution after Dlx gene duplication events.
J Exp Zool 2001 Apr 15;291(1):68-84
Isolation of Dlx and Emx gene cognates in an agnathan species,
Lampetra japonica, and their expression
patterns during embryonic and larval development: conserved and
diversified regulatory patterns of
homeobox genes in vertebrate head evolution.
Myojin M, Ueki T, Sugahara F, Murakami Y, Shigetani Y, Aizawa S,
Hirano S, Kuratani S.
Agnathan cognates of vertebrate homeobox genes, Emx and Dlx, were
isolated from embryonic cDNA of a Japanese marine lamprey,
Lampetra japonica. Analyses of amino acid sequences indicated that the
Dlx cognate was closely related to the common ancestor of
gnathostome Dlx1 and Dlx6 groups and termed LjDlx1/6. Southern blot
analyses could not rule out the possibility that L. japonica
possesses more than one paralog for both LjDlx1/6 and LjEmx, the
lamprey cognate of Emx. Expression of LjDlx1/6 was regulated
spatially as well as developmentally, and its transcripts were mainly
found in the craniofacial and pharyngeal mesenchyme and in the
forebrain. The expression pattern of LjEmx changed dramatically during
embryogenesis; expression was seen initially in the entire
neural tube and mesoderm, which were secondarily downregulated, and
secondarily in cranial nerve ganglia and in the craniofacial
mesenchyme. No specific expression of LjEmx was seen in the
telencephalon. Comparisons of Dlx and Otx gene expression patterns
suggested a shared neuromeric pattern of the vertebrate brain. Absence
of Emx expression implied that the patterning of the lamprey
telencephalon is not based on the tripartite plan that has been
presumed in gnathostomes. Expression domains of LjDlx1/6 in the upper
lip and of LjEmx in the craniofacial mesenchyme were peculiar features
that have not been known in gnathostomes. Such differences in
expression pattern may underlie distinct morphogenetic pathway of the
mandibular arch between the agnathans and gnathostomes.
Proc Natl Acad Sci U S A 1996 Oct 1;93(20):10858-63
The evolution of the vertebrate Dlx gene family.
Stock DW, Ellies DL, Zhao Z, Ekker M, Ruddle FH, Weiss KM.
The vertebrate Dlx gene family consists of homeobox-containing
transcription factors distributed in pairs on the same chromosomes as
the Hox genes. To investigate the evolutionary history of Dlx genes,
we have cloned five new zebrafish family members and have
provided additional sequence information for two mouse genes.
Phylogenetic analyses of Dlx gene sequences considered in the context
of their chromosomal arrangements suggest that an initial tandem
duplication produced a linked pair of Dlx genes after the divergence
of chordates and arthropods but prior to the divergence of tunicates
and vertebrates. This pair of Dlx genes was then duplicated in the
chromosomal events that led to the four clusters of Hox genes
characteristic of bony fish and tetrapods. It is possible that a pair
of Dlx
genes linked to the Hoxc cluster has been lost from mammals. We were
unable to distinguish between independent duplication and
retention of the ancestral state of bony vertebrates to explain the
presence of a greater number of Dlx genes in zebrafish than mammals.
Determination of the linkage relationship of these additional
zebrafish Dlx genes to Hox clusters should help resolve this issue.
The two PNAS papers can be downloaded from the Web for free.
Andy
John Harshman
<nyi...@math.sc.edu> wrote:
> mtu...@snipthis.acpub.duke.edu (mel turner) writes:
>
> >In article <991ea4ae.01061...@posting.google.com>,
> >gro...@cco.caltech.edu [Andy Groves] wrote...
> >>Peter Nyikos <nyi...@math.sc.edu> wrote in message
> >news:<2001061212...@kappa.math.sc.edu>...
> >>> mtu...@snipthis.acpub.duke.edu (mel turner) writes:
> >>Mol Biol Evol 1998 Dec;15(12):1706-18
> >>28S and 18S rDNA sequences support the monophyly of lampreys and
> >>hagfishes.
> >>Mallatt J, Sullivan J.
> >[snip]
> >>All these analyses provide moderate to very strong support
> >>for the monophyly of the cyclostomes. Furthermore, the currently
> >>accepted hypothesis of a lamprey-gnathostome clade is moderately
> >>rejected by the Kishino-Hasegawa test (P = 0.099) and resoundingly
> >>rejected by parametric bootstrap tests (P < 0.01) in favor of
> >>monophyly of living cyclostomes.
>
> I am unfamiliar with this notation. I am used
> to bootstrap numbers running from 0 to 100; does this
> mean a bootstrap number of 99+?
Nobody seems to be answering this question, so I'll try.
The parametric bootstrap is different from the more common non-parametric
bootstrap (usually just called "bootstrap". These notations are P values.
The Kishino-Hasegawa test determines whether one tree is supported by the
data significantly better than a second tree, both trees being specified a
priori. It's unclear from the abstract exactly what sort of parametric
bootstrap test was performed here, but parametric bootstrap means
simulation of data using parameters taken from real data, rather than
resampling actual characters from the real data. Whatever they did with
this simulated data, and whatever tree they simulated it on, the result
was that (I suspect) the lamprey-gnathostome tree never appeared in a run
of 100 simulations.
> Also, what system was used? NJ? parsimony("cladistics") ?
Since they've gone to the trouble of simulating the data using a model, I
bet they used maximum likelihood for the analysis itself.
> For comparison, bootstrap values for putting birds closer to turtles
> than to crocodilians were 58 for NJ and 27 for cladistics in
> the study by Fushitani et. al.
That's non-parametric bootstrap. Don't confuse the two.
--
*Note the obvious spam-defeating modification
to my address if you reply by email.
Peter Nyikos
"tiglath" at the end. Andy comes off a lot better but still not very
favorably, while Howard Hershey occupies some unknown ground, perhaps
coincident with "tiglath" but not with Andy.
gro...@cco.caltech.edu (Andy Groves) writes:
>Peter Nyikos <nyi...@math.sc.edu> wrote in message news:<2001061512...@kappa.math.sc.edu>...
>> gro...@cco.caltech.edu (Andy Groves) writes:
>>
>> >Peter Nyikos <nyi...@math.sc.edu> wrote in message news:<2001061415...@kappa.math.sc.edu>...
[about a very tentative reassessment of the relationships
of hagfishes to other chordates:]
>> >> Ribosomal RNA is only one yardstick; I'd be more comfortable
>> >> if a wide variety of DNA were sampled and uniformly
>> >> confirmed this reassessment; it does not--see below.
>>
>> ><snip>
>>
>> >To be fair to the authors, it was a fair amount of work to get the
>> >conclusions that they did.
>> >Isolating new sequences from new species was not exactly a cakewalk
>> >back in 1992, and for a referee to
>> >have demanded they look at a cohort of "molecular clock" genes would
>> >have been seen as a tad churlish.
>>
>> Who said anything about "molecular clock" genes? Simply,
>> I was asking for a wide variety of genes.
>I know. Clock genes would be useful, as would genes now known to play
>a role in the development of craniofacial
>structures which might provide an insight into craniate evolution.
I'm still puzzled as to why you wrote what you did.
Molecular sequencing wasn't new in 1992; in fact,
already in 1980 it was familiar enough so that the book
_Primates_, Volume 1 of the Time-Life series _Illustrated
Library of Nature_, showed the results of a sequencing
analysis done by one Dr. Vincent Sarich at U. of California
[campus not specified] of over twenty primates [including
*Homo sapiens*, referred to as "man"] and tree shrews
and the "flying lemur" [the colugo, a dermopteran].
It did not say which molecules were used in the test,
but the outcome was startling, to say the least:
{tarsier, tree shrew, flying lemur} were in a clade
by themselves, nested in Primates, which had a trichotomy
at the base: this clade, prosimians besides the tarsier,
and all others.
Later molecular studies evicted the tree shrews
and flying lemurs--but did they also evict the tarsier
along with them?
>If you're going to look at the problem, you might as well pick genes
>known not to diverge too drastically,
>or genes that are expressed in structures that appear in the
>evolutionary sequence you are examining.
>For example, the Dlx gene family has been studied quite a bit in this
>context:
>Proc Natl Acad Sci U S A 2001 Feb 13;98(4):1665-70
>Lamprey Dlx genes and early vertebrate evolution.
>Neidert AH, Virupannavar V, Hooker GW, Langeland JA.
[...]
>position between cephalochordates and gnathostomes. We have
>identified four Dlx genes in P. marinus, whose orthology with
>gnathostome Dlx genes provides a model for how this gene family
>evolved in the vertebrate lineage. Differential expression of these
>lamprey Dlx genes in the forebrain, cranial neural crest, pharyngeal
>arches, and sensory placodes of lamprey embryos provides insight into
>the developmental evolution of these structures as well as a
>model of regulatory evolution after Dlx gene duplication events.
Hell, don't they have any phylogenetic conclusions to relate,
however tentative?
>J Exp Zool 2001 Apr 15;291(1):68-84
>Isolation of Dlx and Emx gene cognates in an agnathan species,
>Lampetra japonica, and their expression
>patterns during embryonic and larval development: conserved and
>diversified regulatory patterns of
>homeobox genes in vertebrate head evolution.
> Myojin M, Ueki T, Sugahara F, Murakami Y, Shigetani Y, Aizawa S,
>Hirano S, Kuratani S.
>Agnathan cognates of vertebrate homeobox genes, Emx and Dlx, were
>isolated from embryonic cDNA of a Japanese marine lamprey,
Andy, you would be doing us all a service if you didn't
just blindly pull these down from the website where you
got them, but zeroed in on relevant matters. I
could find NOTHING about hagfish placement in the
LONG abstract you copied.
[...]
>Proc Natl Acad Sci U S A 1996 Oct 1;93(20):10858-63
>The evolution of the vertebrate Dlx gene family.
>Stock DW, Ellies DL, Zhao Z, Ekker M, Ruddle FH, Weiss KM.
The same old story--nothing about hagfish, or even lampreys
this time around.
>The two PNAS papers can be downloaded from the Web for free.
No url given, even. You are like Jose "tiglath" Suriol,
copying big swatches of information with no attempt
to correlate them to the basic issues we have been
interested in.
Howard Hershey was also fond of posting big swatches
only superficially related to the issues under discussion.
I sometimes suspect he was just pulling down information
from websites without giving credit to the sources.
John Harshman
<nyi...@math.sc.edu> wrote:
> I've restored soc.history.medieval because of the comparison with
> "tiglath" at the end. Andy comes off a lot better but still not very
> favorably, while Howard Hershey occupies some unknown ground, perhaps
> coincident with "tiglath" but not with Andy.
I'm probably not alone in finding this constant scorekeeping unpleasant.
Does it really serve a useful purpose?
No, that wasn't sequencing. It was immunological distances. DNA sequencing
was still very difficult and tedious in 1980, and there wasn't much of it
being done.
> done by one Dr. Vincent Sarich at U. of California
> [campus not specified]
Berkeley
> of over twenty primates [including
> *Homo sapiens*, referred to as "man"] and tree shrews
> and the "flying lemur" [the colugo, a dermopteran].
>
> It did not say which molecules were used in the test,
That would be serum proteins and antibodies to them.
> but the outcome was startling, to say the least:
> {tarsier, tree shrew, flying lemur} were in a clade
> by themselves, nested in Primates, which had a trichotomy
> at the base: this clade, prosimians besides the tarsier,
> and all others.
>
> Later molecular studies evicted the tree shrews
> and flying lemurs--but did they also evict the tarsier
> along with them?
No.
[snips]
John Harshman
> I've restored soc.history.medieval because of the comparison with
> "tiglath" at the end. Andy comes off a lot better but still not very
> favorably, while Howard Hershey occupies some unknown ground, perhaps
> coincident with "tiglath" but not with Andy.
I'm probably not alone in finding this constant scorekeeping unpleasant.
Does it really serve a useful purpose?
> gro...@cco.caltech.edu (Andy Groves) writes:
No, that wasn't sequencing. It was immunological distances. DNA sequencing
was still very difficult and tedious in 1980, and there wasn't much of it
being done.
> done by one Dr. Vincent Sarich at U. of California
> [campus not specified]
Berkeley
> of over twenty primates [including
> *Homo sapiens*, referred to as "man"] and tree shrews
> and the "flying lemur" [the colugo, a dermopteran].
>
> It did not say which molecules were used in the test,
That would be serum proteins and antibodies to them.
> but the outcome was startling, to say the least:
> {tarsier, tree shrew, flying lemur} were in a clade
> by themselves, nested in Primates, which had a trichotomy
> at the base: this clade, prosimians besides the tarsier,
> and all others.
>
> Later molecular studies evicted the tree shrews
> and flying lemurs--but did they also evict the tarsier
> along with them?
No.
John Harshman
> I've restored soc.history.medieval because of the comparison with
> "tiglath" at the end. Andy comes off a lot better but still not very
> favorably, while Howard Hershey occupies some unknown ground, perhaps
> coincident with "tiglath" but not with Andy.
I'm probably not alone in finding this constant scorekeeping unpleasant.
Does it really serve a useful purpose?
> gro...@cco.caltech.edu (Andy Groves) writes:
No, that wasn't sequencing. It was immunological distances. DNA sequencing
was still very difficult and tedious in 1980, and there wasn't much of it
being done.
> done by one Dr. Vincent Sarich at U. of California
> [campus not specified]
Berkeley
> of over twenty primates [including
> *Homo sapiens*, referred to as "man"] and tree shrews
> and the "flying lemur" [the colugo, a dermopteran].
>
> It did not say which molecules were used in the test,
That would be serum proteins and antibodies to them.
> but the outcome was startling, to say the least:
> {tarsier, tree shrew, flying lemur} were in a clade
> by themselves, nested in Primates, which had a trichotomy
> at the base: this clade, prosimians besides the tarsier,
> and all others.
>
> Later molecular studies evicted the tree shrews
> and flying lemurs--but did they also evict the tarsier
> along with them?
No.
Wade Hines
> >> ><snip>
Who said it was new. He said it was a fair amount of work.
You've shown continued ignorance on issues related to how hard
it is to generate sequence data. With modern instrumentation and
reagents, the cost in human labor and materials is way way down.
Blindly is an adverb to describe someone but it isn't Andy.
Andy does work to help the deaf but as they say, there is
none so deaf as those who will not hear, none so blind as
those who will not see.
Brett K. Heath
> I've restored soc.history.medieval because of the comparison with
> "tiglath" at the end.
Sounds like an excuse to me.
Why didn't you just eliminate the comparison with tiglath. It
certainly doesn't seem to be crucial to your argument.
Brett K. Heath
Andy Groves
(s.h.m. removed).
<snip>
> gro...@cco.caltech.edu (Andy Groves) writes:
> I'm still puzzled as to why you wrote what you did.
> Molecular sequencing wasn't new in 1992; in fact,
> already in 1980 it was familiar enough so that the book
> _Primates_, Volume 1 of the Time-Life series _Illustrated
> Library of Nature_, showed the results of a sequencing
> analysis done by one Dr. Vincent Sarich at U. of California
> [campus not specified] of over twenty primates [including
> *Homo sapiens*, referred to as "man"] and tree shrews
> and the "flying lemur" [the colugo, a dermopteran].
Well, all I can say, Peter, is that it represents a large amount of
time and effort now, and this was even more true in 1992. I have a
summer student who is doing some work like this right now. If you
would like to come and help out, I'd be very happy.
<snip>
I cited them to illustrate my point about how looking at the
regulatory genes implicated in the evolution of novel structures can
help address some phyolgeny issues. I'm sorry if you feel this is a
little too off-topic for you.
<snip>
>
> >The two PNAS papers can be downloaded from the Web for free.
>
> No url given, even.
http://www.pnas.org/cgi/content/full/98/4/1665
http://www.pnas.org/cgi/reprint/93/20/10858
<ad hominems snipped>
Paul J. Gans
> In article <2001061611...@kappa.math.sc.edu>, Peter Nyikos
> <nyi...@math.sc.edu> wrote:
>> I've restored soc.history.medieval because of the comparison with
>> "tiglath" at the end. Andy comes off a lot better but still not very
>> favorably, while Howard Hershey occupies some unknown ground, perhaps
>> coincident with "tiglath" but not with Andy.
> I'm probably not alone in finding this constant scorekeeping unpleasant.
> Does it really serve a useful purpose?
So remove soc.history.medieval from the headers. You don't
have to follow the loon just because he's a loon.
---- Paul J. Gans, who also wonders what molecular
biology has to do with soc.history.medieval
Peter Nyikos
Paul Gans and his cohorts have on that newsgroup, and chemist Gans's
fraud about a standard chemistry experiment is recalled below.
Wade Hines <wade....@rcn.com> writes:
>Peter Nyikos wrote:
>> gro...@cco.caltech.edu (Andy Groves) writes:
>> >Peter Nyikos <nyi...@math.sc.edu> wrote in message news:<2001061512...@kappa.math.sc.edu>...
>> >> gro...@cco.caltech.edu (Andy Groves) writes:
>> >> >Peter Nyikos <nyi...@math.sc.edu> wrote in message news:<2001061415...@kappa.math.sc.edu>...
>>
>> [about a very tentative reassessment of the relationships
>> of hagfishes to other chordates:]
>> >> >> Ribosomal RNA is only one yardstick; I'd be more comfortable
>> >> >> if a wide variety of DNA were sampled and uniformly
>> >> >> confirmed this reassessment; it does not--see below.
>> >> ><snip>
>> >> >To be fair to the authors, it was a fair amount of work to get the
>> >> >conclusions that they did.
>> >> >Isolating new sequences from new species was not exactly a cakewalk
>> >> >back in 1992, and for a referee to
>> >> >have demanded they look at a cohort of "molecular clock" genes would
>> >> >have been seen as a tad churlish.
Note the specificity. Looking at three genes instead of just
one would surely not strain their resources. Look at how
Doolittle was sequencing dozens of serine proteases already
back in 1987. I responded to Andy's red herring as follows:
>> >> Who said anything about "molecular clock" genes? Simply,
>> >> I was asking for a wide variety of genes.
>> >I know. Clock genes would be useful, as would genes now known to play
>> >a role in the development of craniofacial
>> >structures which might provide an insight into craniate evolution.
>> I'm still puzzled as to why you wrote what you did.
>> Molecular sequencing wasn't new in 1992; in fact,
>> already in 1980 it was familiar enough so that the book
>> _Primates_, Volume 1 of the Time-Life series _Illustrated
>> Library of Nature_, showed the results of a sequencing
>> analysis done by one Dr. Vincent Sarich at U. of California
>> [campus not specified] of over twenty primates [including
>> *Homo sapiens*, referred to as "man"] and tree shrews
>> and the "flying lemur" [the colugo, a dermopteran].
>Who said it was new. He said it was a fair amount of work.
Nice to know you don't keep up with the news or even
the thread--or was Harshman WRONG about Sarich not using
sequencing?
>You've shown continued ignorance on issues related to how hard
>it is to generate sequence data.
So I don't keep up with shop talk any better than
you do. At least that's
better than pretending there are regulations from OSHA about
the standard hydrogen high school lab experiment being
banned as being too dangerous.
You're still too deeply devoted to the CHEMIST Paul Gans
and his accomplice Ken Cox to breathe a word about the
chicanery they indulged in about that, I see.
> With modern instrumentation and
>reagents, the cost in human labor and materials is way way down.
Keep blasting away at trivial bits of "ignorance" on my
part while overlooking professional fraud on the part of
Paul Gans and Ken Cox. It will be SO easy to keep on
pigeonholing you, and letting people like Julie Thomas
know what manner of man you really are.
You fooled her because you were too shrewd to tangle
with her on biochemistry, but your tacit approval
of professional fraud by Gans and Cox should convince anyone
not to praise you the way she naively did when she said
good-bye to us.
>> It did not say which molecules were used in the test,
>> but the outcome was startling, to say the least:
>> {tarsier, tree shrew, flying lemur} were in a clade
>> by themselves, nested in Primates, which had a trichotomy
>> at the base: this clade, prosimians besides the tarsier,
>> and all others.
>>
>> Later molecular studies evicted the tree shrews
>> and flying lemurs--but did they also evict the tarsier
>> along with them?
Nice to know about your ignorance as to the answer.
[...]
>> Andy, you would be doing us all a service if you didn't
>> just blindly pull these down from the website where you
>> got them, but zeroed in on relevant matters. I
>> could find NOTHING about hagfish placement in the
>> LONG abstract you copied.
>Blindly is an adverb to describe someone but it isn't Andy.
Yes, it is you and Andrew MacRae,
both of whom have deliberately decided to blind yourselves
to wholesale dishonesty by Gans, Cox, and Myers.
>Andy does work to help the deaf but as they say, there is
>none so deaf as those who will not hear, none so blind as
>those who will not see.
And YOU had the gall to start a thread about irony-o-meters!
You did it because if people knew the way to REALLY
shut Giwer up, you and Myers and Gans would be exposed as giving
bum steers to people for years on end as to how to do it.
Just look at how badly William Black got suckered into
thinking that the way to get rid of Matt Giwer is to
hit him with mindless insults!
Peter Nyikos -- standard disclaimer --
University of South Carolina
John Harshman
<harshman.diespamdi...@user-2ivek2v.dialup.mindspring.com>,
harshman....@sjm.infi.net (John Harshman) wrote:
[the same thing three times]
Excuse the extra posts, but my news server keeps telling me there's been
an error and my post may not have been sent. Apparently the emphasis is on
the "may".
Peter Nyikos
>In article
><harshman.diespamdi...@user-2ivek2v.dialup.mindspring.com>,
>harshman....@sjm.infi.net (John Harshman) wrote:
>[the same thing three times]
>Excuse the extra posts, but my news server keeps telling me there's been
>an error and my post may not have been sent. Apparently the emphasis is on
>the "may".
Fine with me. I can use all three posts to respond to
in different ways on different newsgroups.
Here, for instance, is the one you are actually following
up to yourself:
References: <jfbV6.1878$rS4....@eagle.america.net> <9g3j4o$scm$1...@news.duke.edu> <2001061212...@kappa.math.sc.edu> <991ea4ae.01061...@posting.google.com> <9g6m4a$42b$1...@news.duke.edu> <2001061415...@kappa.math.sc.edu> <991ea4ae.0106...@posting.google.com> <2001061512...@kappa.math.sc.edu> <991ea4ae.01061...@posting.google.com> <2001061611...@kappa.math.sc.edu> <harshman.diespamdi...@user-2ivek2v.dialup.mindspring.com>
harshman....@sjm.infi.net (John Harshman) writes:
>In article <2001061611...@kappa.math.sc.edu>, Peter Nyikos
><nyi...@math.sc.edu> wrote:
>> I've restored soc.history.medieval because of the comparison with
>> "tiglath" at the end. Andy comes off a lot better but still not very
>> favorably, while Howard Hershey occupies some unknown ground, perhaps
>> coincident with "tiglath" but not with Andy.
>I'm probably not alone in finding this constant scorekeeping unpleasant.
>Does it really serve a useful purpose?
Yes. The situation is symptomatic of a deep malaise affecting
soc.history.medieval and talk.origins. Since the other
two newsgroups seem to be blessedly free of it at the present
time, I'll omit them when I do the other two followups and
explain in detail later this week.
>> gro...@cco.caltech.edu (Andy Groves) writes:
>>
>> >Peter Nyikos <nyi...@math.sc.edu> wrote in message
>news:<2001061512...@kappa.math.sc.edu>...
>> >> gro...@cco.caltech.edu (Andy Groves) writes:
[...]
>> >> >To be fair to the authors, it was a fair amount of work to get the
>> >> >conclusions that they did.
>> >> >Isolating new sequences from new species was not exactly a cakewalk
>> >> >back in 1992, and for a referee to
>> >> >have demanded they look at a cohort of "molecular clock" genes would
>> >> >have been seen as a tad churlish.
>> >> Who said anything about "molecular clock" genes? Simply,
>> >> I was asking for a wide variety of genes.
>> >I know. Clock genes would be useful, as would genes now known to play
>> >a role in the development of craniofacial
>> >structures which might provide an insight into craniate evolution.
Groves included references to homeobox genes, which are
notorious for being highly conserved. Why would
these be expected to shed much light on chordate
phylogeny?
>> I'm still puzzled as to why you wrote what you did.
>> Molecular sequencing wasn't new in 1992; in fact,
>> already in 1980 it was familiar enough so that the book
>> _Primates_, Volume 1 of the Time-Life series _Illustrated
>> Library of Nature_, showed the results of a sequencing
>> analysis
>No, that wasn't sequencing. It was immunological distances. DNA sequencing
>was still very difficult and tedious in 1980, and there wasn't much of it
>being done.
Could you explain immunological distances, and how
the molecules were used to establish them?
>> done by one Dr. Vincent Sarich at U. of California
>> [campus not specified]
>Berkeley
Thanks.
>> of over twenty primates [including
>> *Homo sapiens*, referred to as "man"] and tree shrews
>> and the "flying lemur" [the colugo, a dermopteran].
>>
>> It did not say which molecules were used in the test,
>That would be serum proteins and antibodies to them.
Any idea what kinds of tests were
run on them?
>> but the outcome was startling, to say the least:
>> {tarsier, tree shrew, flying lemur} were in a clade
>> by themselves, nested in Primates, which had a trichotomy
>> at the base: this clade, prosimians besides the tarsier,
>> and all others.
>>
>> Later molecular studies evicted the tree shrews
>> and flying lemurs--but did they also evict the tarsier
>> along with them?
>No.
Were the tarsiers subjected to the same tests as
the other two? Do you have a reference?
Peter Nyikos -- standard disclaimer --
Professor, Dept. of Mathematics
University of South Carolina
Columbia, SC 29208
Andy Groves
<snip>
> >> >I know. Clock genes would be useful, as would genes now known to play
> >> >a role in the development of craniofacial
> >> >structures which might provide an insight into craniate evolution.
>
> Groves included references to homeobox genes, which are
> notorious for being highly conserved. Why would
> these be expected to shed much light on chordate
> phylogeny?
Because the evidence suggests that homeobox-containing genes exist in
clusters. The clusters arose as a result of two kinds of duplication -
duplication *in cis*, in which extra genes were duplicated on a given
chromosome, and duplication *in trans*, in which whole clusters were
duplicated onto other chromosomes. The Dlx gene family is an excellent
example of this. Primitive chordates have a small number of Dlx genes;
more derived chordates have larger numbers (sometimes 6 or even 8).
This point was made clearly in the two PNAS papers I cited, and for
which I provided URLs.
Figure 6 of the Neidert et al. paper shows this quite nicely.
<snip>
Andy
John Harshman
<nyi...@math.sc.edu> wrote:
> harshman....@sjm.infi.net (John Harshman) writes:
>
> >In article
> ><harshman.diespamdi...@user-2ivek2v.dialup.mindspring.com>,
> >harshman....@sjm.infi.net (John Harshman) wrote:
[snip]
> >> gro...@cco.caltech.edu (Andy Groves) writes:
> >>
> >> >Peter Nyikos <nyi...@math.sc.edu> wrote in message
> >news:<2001061512...@kappa.math.sc.edu>...
> >> >> gro...@cco.caltech.edu (Andy Groves) writes:
>
> [...]
>
> >> >> >To be fair to the authors, it was a fair amount of work to get the
> >> >> >conclusions that they did.
> >> >> >Isolating new sequences from new species was not exactly a cakewalk
> >> >> >back in 1992, and for a referee to
> >> >> >have demanded they look at a cohort of "molecular clock" genes would
> >> >> >have been seen as a tad churlish.
>
> >> >> Who said anything about "molecular clock" genes? Simply,
> >> >> I was asking for a wide variety of genes.
>
> >> >I know. Clock genes would be useful, as would genes now known to play
> >> >a role in the development of craniofacial
> >> >structures which might provide an insight into craniate evolution.
>
> Groves included references to homeobox genes, which are
> notorious for being highly conserved. Why would
> these be expected to shed much light on chordate
> phylogeny?
Possibly it's not the sequence he's talking about, but the pattern of
duplications/losses within clusters, and origins of new clusters. Also,
silent sites and the occasional replacement should still have information
content, even in a highly conserved gene.
> >> I'm still puzzled as to why you wrote what you did.
> >> Molecular sequencing wasn't new in 1992; in fact,
> >> already in 1980 it was familiar enough so that the book
> >> _Primates_, Volume 1 of the Time-Life series _Illustrated
> >> Library of Nature_, showed the results of a sequencing
> >> analysis
>
> >No, that wasn't sequencing. It was immunological distances. DNA sequencing
> >was still very difficult and tedious in 1980, and there wasn't much of it
> >being done.
>
> Could you explain immunological distances, and how
> the molecules were used to establish them?
Roughly. It's quite a complicated set of methods, and there are indeed
many methods. But you inject blood serum from species A into species X.
Then you collect serum from the injected individual of X, which now has
antibodies to A's blood proteins. You mix this serum with some serum from
species B. The degree to which the antibodies to A recognize (react with)
B give an index of the similarity of B to A: the more reaction, the more
similar. These can be turned into distances, and then into trees. I've
oversimplified grossly, but that's the general idea.
> >> done by one Dr. Vincent Sarich at U. of California
> >> [campus not specified]
>
> >Berkeley
>
> Thanks.
>
>
> >> of over twenty primates [including
> >> *Homo sapiens*, referred to as "man"] and tree shrews
> >> and the "flying lemur" [the colugo, a dermopteran].
> >>
> >> It did not say which molecules were used in the test,
>
> >That would be serum proteins and antibodies to them.
>
> Any idea what kinds of tests were
> run on them?
No, beyond what I've told you. There are all sorts of different assays on
the same general theme. One would have to look up the paper. Perhaps you
would like to.
> >> but the outcome was startling, to say the least:
> >> {tarsier, tree shrew, flying lemur} were in a clade
> >> by themselves, nested in Primates, which had a trichotomy
> >> at the base: this clade, prosimians besides the tarsier,
> >> and all others.
> >>
> >> Later molecular studies evicted the tree shrews
> >> and flying lemurs--but did they also evict the tarsier
> >> along with them?
>
> >No.
>
> Were the tarsiers subjected to the same tests as
> the other two? Do you have a reference?
No. But if Sarich had ever suggested that tarsiers weren't primates, I
would have remembered that.
Cal King
<nyi...@math.sc.edu> wrote:
>>> I'm still puzzled as to why you wrote what you did.
>>> Molecular sequencing wasn't new in 1992; in fact,
>>> already in 1980 it was familiar enough so that the book
>>> _Primates_, Volume 1 of the Time-Life series _Illustrated
>>> Library of Nature_, showed the results of a sequencing
>>> analysis
>
>>No, that wasn't sequencing. It was immunological distances. DNA sequencing
>>was still very difficult and tedious in 1980, and there wasn't much of it
>>being done.
>
>Could you explain immunological distances, and how
>the molecules were used to establish them?
>
>
>>> done by one Dr. Vincent Sarich at U. of California
>>> [campus not specified]
>
>>Berkeley
>
>Thanks.
I think I can help here. The technique was pioneered by the late
biochemist Allan Wilson and physical anthropologist Vincent Sarich of the
University of California in the 1970's. Basically serum albumin is
purified from blood drawn from a "reference" species, and the albumin is
then injected into a host species (a rabbit I believe). Antibodies to the
foreign albumin will form in the host and the blood containing these
antibodies are then extracted from the host. The production of antivenin
to snake venom is a similar process, although the horse is usually used in
the production of snake antivenin.
The immunological distance between two species is estimated by measuring
how strongly the serum of one species react with the antiserum of the
reference species. The immunological distance of one species' serum
against its own antiserum should be zero, and it is also a test of whether
the test samples are pure. Since serum albumin appeared to have no known
function, amino acid substitutions were thought to occur randomly through
pure chance and in a clock-like manner. According to Linda Maxson, who
published a number of systematics papers based on the use of this
technique, "The albumin immunological distance (ID) is a quantitative
estimate of the sequence difference between the albumin of the reference
species for which antiserum has been prepared and the albumin of the
species with which it is compared. Each unit of ID corresponds
approximately to a single amino acid difference between the two albumins
compared (Maxson and Wilson 1974). It is estimated that 1.7 ID units
accumulate for every million years that the 2 species have been separated
(Maxson, Sarich et al., 1975; Wilson, Carson et al. 1977)" (Dowling et al.
1983, J. Zool.).
While not strictly a sequencing technique, immunological distance is a
quantitative measure of the differences in the amino acid sequences of the
serum albumin of the tested species.
Cal King
<2001061415...@kappa.math.sc.edu>:
>mtu...@snipthis.acpub.duke.edu (mel turner) writes:
>>>Mol Biol Evol 1998 Dec;15(12):1706-18
>>>28S and 18S rDNA sequences support the monophyly of lampreys and
>>>hagfishes.
>>>Mallatt J, Sullivan J.
>>[snip]
>>>All these analyses provide moderate to very strong support
>>>for the monophyly of the cyclostomes. Furthermore, the currently
>>>accepted hypothesis of a lamprey-gnathostome clade is moderately
>>>rejected by the Kishino-Hasegawa test (P = 0.099) and resoundingly
>>>rejected by parametric bootstrap tests (P < 0.01) in favor of
>>>monophyly of living cyclostomes.
>
[...]
>Also, what system was used? NJ? parsimony("cladistics") ?
They "primarily focused on maximum likelihood" but they also used maximum
parsimony.
>>> Another significant finding is that
>>>the hagfish E. stouti has the longest 28S rDNA gene known in
>>>any organism (> 5,200 nt).
>
>And what are the figures for the lamprey and for gnathostomes?
Homo sapiens 5025, Mus musculus 4712, Xenopus laevis 4115, lamprey
3924+54 est.
One problem I have with this particular study is that there is no
analysis based strictly on distance data.
The hagfish lineage is depicted at the end of a very long branch (branch
length = number of substitutions/site), the longest one in the cladogram,
indicating that its genes had the most nucleotide substitutions. The
lamprey, on the other hand, has a much shorter branch, quite similar in
length to those of the sturgeon and chimaera. The authors suggest that
the hagfish had a fast evolutionary rate but I am not convinced. It
should not be that much faster than the lamprey's! The tunicate and the
lancelet also had a great number of nucleotide substitutions in their
genes, so the large number of substitutions in the hagfish's genes may be
due at least in part to the probability that the hagfish branched off
from the ancestral stock really early.
Another potential problem is that the outgroup chosen in this study is a
tunicate, an urochordate. The authors criticize an earlier study uniting
lampreys with gnathostomes for having chosen a snail as an outgroup,
claiming that it is too distant. But the authors may have erred in the
oppoiste direction, by choosing a chordate, a member of the ingroup, as
an outgroup. If the hagfish actually diverged early from the ancestral
stock, then the lamprey and the hagfish, if they are not convergently
similar, at the very most form a paraphyletic group, not a holophyletic
group. The lamprey, on the basis of molecular distance, is much closer
to the gnathostomes than the hagfish is.
My 2 cents.
Cal King
<Pine.BSF.4.33.010612...@dinosaur.umbc.edu>:
>On 12 Jun 2001, Peter Nyikos wrote:
>
>> Gnathostomata is, I believe, a paraphyletic taxon like
>> Agnatha. This simply means that it doesn't include
>> all its descendants. For reasons only known to them,
>> this makes the two groups anathema to what I call "cladophiles":
>> people who insist that all groups be clades. A clade
>> is a single species and all creatures descended from it.
>
>_Gnathostomata_ is a clade, not a paraphyletic group.
clade = monophyletic group
paraphyletic group = monophyletic group
paraphyletic group = clade
Keep in mind that the terms clade and monophyletic were coined during the
period of time when systematists did not distinguish the difference between
monophyletic groups and holophyletic groups. The cladists want to give new
meaning to an old term, as is their usual practice. In order to prevent any
confusion, Ernst Mayr (1998, This is Biology) has suggested that the term
"cladon" be used to denote what Peter Ashlock calls "holophyletic" groups.
Cal King
>Actually, some of us would also like to do away with genera someday,
>although that would be a difficult operation... (It would most likely
>involve converting genera to clades, so that there would only be two
>types of biological taxa -- clades and species. See
Why do away with genera, are they not clades? If species are by implication
not "clades," then why not go ahead and eliminate the species category as
well? In the brave new (cladistic) world, there will be no biomials, no
species, just "clades" of organisms, perhaps each with a unique numerical id.
This kind of stuff sounds like good material for a science fiction and/or
horror story.
Cal King
>On 14 Jun 2001, Peter Nyikos wrote:
>
>> >_Gnathostomata_ is a clade, not a paraphyletic group.
>>
>> I'd like to hear from Kinman about that. He's just
>> posted a nice article on classification including
>> Gnathostomata, on:
>>
>> Class Agnathea (classification)
>>
>> to which I've replied in t.o. and s.b.p. just now.
>
>I've never heard anyone propose _Gnathostomata_ (jawed vertebrates) as
>paraphyletic. What would it have given rise to?
It can certainly be defined as a paraphyletic taxon by excluding the
Tetrapoda. Gnathostomata can be defined as the jawed fishes
(Chondrichthyes + Osteichthyes - Tetrapoda), since definitions are
arbitrary.
>> >Actually, some of us would also like to do away with genera someday,
>> >although that would be a difficult operation...
>>
>> You would almost have to do away with binomial nomenclature
>> for that, wouldn't you?
>
>That's the idea, actually. Currently, if a species is moved, its name
>changes, causing instability in the literature.
Some instability is tolerable as long as it is absolutely necessary, e.g.
to eliminate polyphyly. Taxonomic changes are actually a good thing because
it reminds us that scientific knowledge is not absolute. What most
biologists oppose to are wholesale and/or unnecessarily name changes that
are due to changes in the winds of fashion.
>The ultimate idea would
>be to have species names be independent and robust.
The only way to do that would be to assign each a unique number, kind of
like the social security number that we have. That way, no two species can
have the same number, and hundreds of millions of species can be
accomodated without problem. Such a system would obscure relationships
though because we have no way of knowing whether two numbers adjacent to
each other are closely related (for example the number adjacent to mine may
be a total stranger whereas my own siblings may have very different
numbers). Under the Linnaean system, it is implicit that Pan troglodytes
and Pan paniscus are more closely related to each other than they are to
any other organism because they are the only two members of Pan, and Pan
is a unique name that no other genus may possess. Pan is also a clade, so
the cladists do not even have a reason to abolish it.
>Of course, it is
>very difficult to come up with a workable method for doing this!
Absolutely. Linnaeus' system is ingenious, and no one has come up with a
better system for naming organisms. No one.
>However, several have been proposed.
>
>> (It would most likely
>> >involve converting genera to clades, so that there would only be two
>> >types of biological taxa -- clades and species. See
>> >http://www.ohiou.edu/phylocode/)
>>
>> The introduction does not say how to overcome the difficulty
>> of figuring out whether, say, Ambulocetus natans should
>> be renamed "Cetacea natans".
>
>Under one scheme, it could be called either one, assuming _Ambulocetus_
>had been given a cladistic definition.
>
>Another scheme has current binomina being translated into single names,
>e.g., the species _ambulocetus-natans_.
That is nothing more than the emperor's new clothes since the "single name"
is nothing more than a hyphenated binomial. It is not any more stable than
the binomial it purportedly replaces. For example, if hypothetico-primus
is later found to be more closely related to nonesuchio-elegans than it is
to hypothetico-inornatus, then do we leave the names alone and continue to
mislead the biological community about relationships? Do we sacrifice
phylogenetic correctness at the altar of taxonomic stability?
>Under another scheme, _natans_ would be listed alone, but with its
>citation, at least the first time it's printed. (Or every time, if
>another species named _natans_ is being mentioned.)
>
>Or, if _Ambulocetus_ is currently a montotypic genus, it could become a
>species: _ambulocetus_.
What if someone unearths the sister species of Ambulocetus tomorrow?
>There are many other proposed methods, but all have some flaws.
Certainly they do. The young turks think they have a better idea than
Linnaeus but they don't. Their "remedy" would only make a healthy patient
sick.
>> It puts an enormous burden
>> on deciding just what is the last common ancestor of
>> a given clade--and that is just about the most ephemeral
>> sort of decision one could make, given the imperfectness
>> of fossililzation (no complete genome to sequence, etc.)
>
>Since when do you need to know that?
That is the goal of evolutionary biology. Evolutionary biologists want to
find the ancestors of all higher taxa, even though the cladists do not.
>Oh, you mean if _natans_ is the
>ancestral cetacean? Is _Cetacea_ defined as something like
>Clade(_Ambulocetus_ + _Balaena_)? If not, I'd tend to doubt it. If so, I
>guess it is (remotely) possible and your point is valid. (We had a
>similar discussion about _Archaeopteryx_ and _Aves_ on the PhyloCode
>Mailing List.) As I said, nobody's come up with a perfect system yet.
And I bet no one will be able to better Linnaeus in the foreseeable future.
>> >> And lampreys are, by several standards, the only living things that
>> >> are about as far from humans as lampreys are from eels.
>>
>> >Difficult to quantify that....
>>
>> There is one (not necessarily the best) quantification readily at
>> hand: when the divergence from the last common ancestor took place.
>>
>> The answer is the same in both cases.
>
>Indeed, members of the lamprey stem-clade are the only things that fit
>that criterion. Seems like a rather unremarkable claim. Given...
>
>--+--A
> `--+--B
> `--C
>
>... where A, B, and C are contemporaneous, of course A is the only thing
>that has as much divergent history between itself and C as between A and
>B.
>
>> This quantification is closely related to the usual concept cladists
>> use, whereby we get such things as "We are more closely
>> related to Ambulocetus natans than we are to Didelphis,
>> even though Didelphis looks a whole lot more like
>> one of our remote ancestors than Ambulocetus does."
>
>I never liked that terminology, and prefer the less ambiguous "we share
>more recent ancestry with _Ambulocetus_ than with _Didelphis_".
>
>_________________________________________________________________________
>____ T. MICHAEL KEESEY
I do like that terminology. Relationship implies more than just branching
order. It takes into account levels of biological organization, e.g.
unicellular vs. multicellular, fins vs. limbs, and scales vs. feathers,
ectothermy vs. endothermy. Branching events which produce no evolutionary
novelty, only neutral DNA substitutions, are uninteresting biologically.
But branching events that produced such novelties as wings, feathers,
epidermal scales and jaws are vastly more interesting to biologists who are
not obsessed with branching order to the exclusion of all other biological
phenomena.
Peter Nyikos
>t...@dinosauricon.com (T. Mike Keesey) wrote in
><Pine.BSF.4.33.010614...@dinosaur.umbc.edu>:
>>On 14 Jun 2001, Peter Nyikos wrote:
[Keesey? wrote:]
>>> > (It would most likely
>>> >involve converting genera to clades, so that there would only be two
>>> >types of biological taxa -- clades and species. See
>>> >http://www.ohiou.edu/phylocode/)
>>> The introduction does not say how to overcome the difficulty
>>> of figuring out whether, say, Ambulocetus natans should
>>> be renamed "Cetacea natans".
>>Under one scheme, it could be called either one, assuming _Ambulocetus_
>>had been given a cladistic definition.
>>
>>Another scheme has current binomina being translated into single names,
>>e.g., the species _ambulocetus-natans_.
>That is nothing more than the emperor's new clothes since the "single name"
>is nothing more than a hyphenated binomial.
[...]
>>Under another scheme, _natans_ would be listed alone, but with its
>>citation, at least the first time it's printed. (Or every time, if
>>another species named _natans_ is being mentioned.)
>>
>>Or, if _Ambulocetus_ is currently a montotypic genus, it could become a
>>species: _ambulocetus_.
>What if someone unearths the sister species of Ambulocetus tomorrow?
>>There are many other proposed methods, but all have some flaws.
>Certainly they do. The young turks think they have a better idea than
>Linnaeus but they don't. Their "remedy" would only make a healthy patient
>sick.
>>> It puts an enormous burden
>>> on deciding just what is the last common ancestor of
>>> a given clade--and that is just about the most ephemeral
>>> sort of decision one could make, given the imperfectness
>>> of fossililzation (no complete genome to sequence, etc.)
>>
>>Since when do you need to know that?
Since the idea was wafted about naming whole clades after
the genera of the common ancestor. Looks like Keesey didn't think
all the implications through.
>That is the goal of evolutionary biology. Evolutionary biologists want to
>find the ancestors of all higher taxa, even though the cladists do not.
Many cladists ban the last common ancestors they give lip
service to from their trees, and move everything up to
the tips. They claim one can ALWAYS make a better case
for, say, Archie being the sister species of Aves than the
last common ancestor, so their trees make Archie just as much
a descendant of the hypothetical and never-to-be-identified
common ancestor as the Ruby-throated humming bird.
And unless they include characters in their enormous trees
of Aves [the bigger the tree, the less likely you are to
see them] you get no clue that Archie looks MORE like
a common ancestor than the Ruby-throated hummingbird does.
>>Oh, you mean if _natans_ is the
>>ancestral cetacean? Is _Cetacea_ defined as something like
>>Clade(_Ambulocetus_ + _Balaena_)?
The problem, besides deciding whether Ambulocetus is an
actual ancestor, is that some people might want to take
Cetacea back to Pakicetus or forward to Rodhocetus or
maybe to a yet-to-be-discovered mesonychid/artiodactyl.
>> If not, I'd tend to doubt it. If so, I
>>guess it is (remotely) possible and your point is valid. (We had a
>>similar discussion about _Archaeopteryx_ and _Aves_ on the PhyloCode
>>Mailing List.) As I said, nobody's come up with a perfect system yet.
Renaming "Aves" and calling it "Archaeopteryx"???
[...]
>>> This quantification is closely related to the usual concept cladists
>>> use, whereby we get such things as "We are more closely
>>> related to Ambulocetus natans than we are to Didelphis,
>>> even though Didelphis looks a whole lot more like
>>> one of our remote ancestors than Ambulocetus does."
>>
>>I never liked that terminology, and prefer the less ambiguous "we share
>>more recent ancestry with _Ambulocetus_ than with _Didelphis_".
>>
>>_________________________________________________________________________
>>____ T. MICHAEL KEESEY
>I do like that terminology. Relationship implies more than just branching
>order. It takes into account levels of biological organization, e.g.
>unicellular vs. multicellular, fins vs. limbs, and scales vs. feathers,
>ectothermy vs. endothermy. Branching events which produce no evolutionary
>novelty, only neutral DNA substitutions, are uninteresting biologically.
>But branching events that produced such novelties as wings, feathers,
>epidermal scales and jaws are vastly more interesting to biologists who are
>not obsessed with branching order to the exclusion of all other biological
>phenomena.
Hear, hear!
Cal King
>get...@nobull.net (Cal King) writes:
>
>>t...@dinosauricon.com (T. Mike Keesey) wrote in
>><Pine.BSF.4.33.010614...@dinosaur.umbc.edu>:
>>>Since when do you need to know that?
>Since the idea was wafted about naming whole clades after
>the genera of the common ancestor. Looks like Keesey didn't think
>all the implications through.
Keesey is only questioning whether we need to know the common ancestor's
identity because cladistics cannot, in theory, identify that ancestor.
>>That is the goal of evolutionary biology. Evolutionary biologists want
>>to find the ancestors of all higher taxa, even though the cladists do
>>not.
>
>Many cladists ban the last common ancestors they give lip
>service to from their trees,
Amazing isn't it? All that talk about the common ancestor of this and that
and all of its descendants, and then they claim that they can never
identify any ancestor of any higher taxon, even if this animal is inside
one of their museum drawers.
>and move everything up to
>the tips. They claim one can ALWAYS make a better case
>for, say, Archie being the sister species of Aves than the
>last common ancestor, so their trees make Archie just as much
>a descendant of the hypothetical and never-to-be-identified
>common ancestor as the Ruby-throated humming bird.
Indeed. Archaeopteryx is the oldest known bird. It became extinct in the
Jurassic. It is the "urvogel" and accordingly possesses many characters
that are primitive for birds, such as a long tail. It cannot possibly
appear at the crown of the avian tree, at the same level as a living
species such as the hummer. Well said!
>And unless they include characters in their enormous trees
>of Aves [the bigger the tree, the less likely you are to
>see them] you get no clue that Archie looks MORE like
>a common ancestor than the Ruby-throated hummingbird does.
That is true again. Archaeopteryx is, according to Larry Martin and Alan
Feduccia, a side branch of the avian tree. It is a member of the Sauriurae,
which lacks many of the morphological and physiological innovations seen in
ornithurine birds, such as abdominal air sacs, endothermy and a more
different and more efficient flight apparatus. It is even more distant
from the neornithine birds than it is from the common ancestor of all
birds, but as you say one cannot see this from the cladogram.
Ken Cox
> Amazing isn't it? All that talk about the common ancestor of this and that
> and all of its descendants, and then they claim that they can never
> identify any ancestor of any higher taxon, even if this animal is inside
> one of their museum drawers.
Yes, sadly, very few dinosaurs were buried with little
tombstones saying "Beloved Father of William and Martha".
Heck, without the tombstones -- or equivalent written
evidence -- we can't even tell if a *human* skeleton was
an ancestor of anyone living today.
--
Ken Cox k...@research.bell-labs.com
John Harshman
<k...@lucent.com> wrote:
Ask yourself: Do I really want to start an argument with Cal King?
Cal King
<harshman.diespamdi...@user-2iveljt.dialup.mindspring.
><k...@lucent.com> wrote:
>
>> Cal King wrote:
>> > Amazing isn't it? All that talk about the common ancestor of this and that
>> > and all of its descendants, and then they claim that they can never
>> > identify any ancestor of any higher taxon, even if this animal is inside
>> > one of their museum drawers.
>>
>> Yes, sadly, very few dinosaurs were buried with little
>> tombstones saying "Beloved Father of William and Martha".
>>
>> Heck, without the tombstones -- or equivalent written
>> evidence -- we can't even tell if a *human* skeleton was
>> an ancestor of anyone living today.
>Ask yourself: Do I really want to start an argument with Cal King?
Better questions: Can one actually defend the absurdities of cladism?
If not, then which of the following familiar cladistic responses should
one use when the cladistic emperor's clothelessness is revealed?
1. engage in ad hominem
2. openly ignore criticism
3. use dishonest tactics
4. Any combination of the above
Cal King
Scientists obviously cannot rely on any written evidence when attempting
to identify the ancestor of a higher taxon, since many organisms have
appeared and disappeared tens or hundreds of millions, even billions, of
years before the appearance of the first hominids a scant few million
years ago.
Owing to the incomplete fossil record, identifying ancestors is
extremely difficult but not impossible to the Darwinian systematist.
But to the cladists, identifying the ancestor is theoretically
impossible even if the fossil record is complete, because their
methodology is designed in such a way that it is absolutely incapable of
identifying the ancestor. This is a very important distinction between
cladistics and evolutionary, or Darwinian, systematics.
Ken Cox
> Owing to the incomplete fossil record, identifying ancestors is
> extremely difficult but not impossible to the Darwinian systematist.
> But to the cladists, identifying the ancestor is theoretically
> impossible even if the fossil record is complete, because their
> methodology is designed in such a way that it is absolutely incapable of
> identifying the ancestor.
Let's say I give you a collection of a dozen housecat
skeletons, all DNA material carefully removed. I tell
you that, possibly, one or more of the specimens were
the parents of one or more of the others. How would
you determine the relatedness of the skeletons?
Is a theory that acknowledges that this is impossible
*really* such a bad thing?
--
Ken Cox k...@research.bell-labs.com
Cal King
All house cats belong to the same species, so their skeletons should
fall within the variation found within a single species.
Paleontologists do not search for relationships among individuals of the
same species; they search instead for relationships among different
species. The best that the cladistic paleontologist can do, even when
given a complete fossil record, is to say that two species are closely
related to each other. They are not allowed, by cladistic dogma, to say
that one species is ancestral to another. They are not allowed to say,
for example, that Homo erectus is ancestral to Homo sapiens, even though
the available evidence suggests that it is most likely the case.
It is not impossible for one species to be ancestral to another, unless
one is a creationist. Cladists are not creationists, so they know that
ancestral species exist. It is just that their methodology say that the
ancestor can never be identified. Therefore an ideology that insists
that ancestors can never be identified, even though they must have
existed, is scientifically untenable, or "bad".
Ken Cox
> Ken Cox <k...@lucent.com> wrote:
> >Let's say I give you a collection of a dozen housecat
> >skeletons, all DNA material carefully removed. I tell
> >you that, possibly, one or more of the specimens were
> >the parents of one or more of the others. How would
> >you determine the relatedness of the skeletons?
> All house cats belong to the same species, so their skeletons should
> fall within the variation found within a single species.
That's not the question. What are the relationships
between the skeletons? Which cat is the parent of
which other cat?
Let me try a different example. I presume you've
heard of Pompeii, and the casts of people found in
the ash deposits. Some of these are interpreted
as family groupings, e.g. an adult woman found with
two children. How would you show that the woman
was indeed the mother of the children, and not the
nanny, or just some random person who died in the
same place as the two children?
--
Ken Cox k...@research.bell-labs.com
Maximiliano Corredor
"Cal King" <getulus@no bull.net > escribió en el mensaje
news:D5I47.46742$J91.2...@bgtnsc06-news.ops.worldnet.att.net...
Well, what I know about cladistics is that you can with this methodology say
what was the common ancestor of two species like. And if you have a fossil
one, and the theoretical ancestor is identical to it, why can't you think
about a speciation event in the fossil species? Thus, part of the fossil
species is a "new" species, the last common ancestor of the rest of the
fossil (that has to be another "new" species) one and the other more close
related. Of course that kind of assumption is always a hypotesis that can
*never* be tested if we don't have the complete fossil record. And assuming
that our critery to make the phylogeny really represents the real one, so
even then, it would be a hypothesis.
Regards
Cal King
>Cal King wrote:
>> Ken Cox <k...@lucent.com> wrote:
>> >Let's say I give you a collection of a dozen housecat
>> >skeletons, all DNA material carefully removed. I tell
>> >you that, possibly, one or more of the specimens were
>> >the parents of one or more of the others. How would
>> >you determine the relatedness of the skeletons?
>
>> All house cats belong to the same species, so their skeletons should
>> fall within the variation found within a single species.
>
>That's not the question. What are the relationships
>between the skeletons? Which cat is the parent of
>which other cat?
That may be an interesting question, but it is one that paleontologists
do not normally ask. They, as (hopefully) evolutionary biologists, are
more interested in the relationship between species, not between
individuals.
>Let me try a different example. I presume you've
>heard of Pompeii, and the casts of people found in
>the ash deposits. Some of these are interpreted
>as family groupings, e.g. an adult woman found with
>two children. How would you show that the woman
>was indeed the mother of the children, and not the
>nanny, or just some random person who died in the
>same place as the two children?
They are interpreted as families because human families, throughout
history, often live in the same house. Assuming that your stipulation
that all DNA evidence is unavailable still holds, the relationships
among the individuals would be unclear. Paleontologists are not usually
the ones who study sites such as Pompeii, which usually fall within the
expertise of archaeologists.
It seems that you are talking about quite different things than
evolutionary relationships. Hence your comments are not really relevant
to cladistic ideology, which is indeed scientifically untenable since it
cannot ascertain ancestor-descendant relationships even if the fossil
record were complete, and thus both ancestor and descendant SPECIES are
present.
Mike
> >> Ken Cox <k...@lucent.com> wrote:
> >> >Let's say I give you a collection of a dozen housecat
> >> >skeletons, all DNA material carefully removed. I tell
> >> >you that, possibly, one or more of the specimens were
> >> >the parents of one or more of the others. How would
> >> >you determine the relatedness of the skeletons?
>
> >> All house cats belong to the same species, so their skeletons should
> >> fall within the variation found within a single species.
> >
> >That's not the question. What are the relationships
> >between the skeletons? Which cat is the parent of
> >which other cat?
>
> That may be an interesting question, but it is one that paleontologists
> do not normally ask. They, as (hopefully) evolutionary biologists, are
> more interested in the relationship between species, not between
> individuals.
HAHAHAHAHA!
I really must remove you from my killfile, alias Cal!
You talk such wonderful rubbish!
If you don't wish to answer Cox's question, please detail, using DNA
or fossils, just how you'd prove that fossil species A was directly
ancestral to fossil species B.
I know that it can't be done. Ken Cox knows it can't be done. All the
paleontologists here knows it can't be done.
What do you know that no-one else does?
And if you want to talk SPECIES you're actually no better off with DNA
than with just bones for inferring that one species is directly
ancestral to another (ie up the creek = 1, paddle = 0).
> It seems that you are talking about quite different things than
> evolutionary relationships. Hence your comments are not really relevant
> to cladistic ideology, which is indeed scientifically untenable since it
> cannot ascertain ancestor-descendant relationships even if the fossil
> record were complete, and thus both ancestor and descendant SPECIES are
> present.
1) If the fossil record was complete, and, and this is important, we
KNEW that it was complete, then we could say that speices A is
ancestral to species B.
2) The fossil record ISN'T complete, and even where it may be, we
don't KNOW that it is, and hence we can't say that species A is
ancestral to species B.
3) NO stringent methodology can, given the incompleteness of the
fossil record, say that species A is ancestral to species B. Any such
claim is merely the personal opinion of the person making it.
Mike
> > It is not impossible for one species to be ancestral to another, unless
> > one is a creationist. Cladists are not creationists, so they know that
> > ancestral species exist. It is just that their methodology say that the
> > ancestor can never be identified. Therefore an ideology that insists
> > that ancestors can never be identified, even though they must have
> > existed, is scientifically untenable, or "bad".
>
> Well, what I know about cladistics is that you can with this methodology say
> what was the common ancestor of two species like. And if you have a fossil
> one, and the theoretical ancestor is identical to it, why can't you think
> about a speciation event in the fossil species?
No. Inferring an ancestor from a tree is not proof of how the ancestor
actually looked.
Consider a tree with Human, Kiwi, and Kangaroo. From this tree we'd
infer that the ancestor of birds, mammals and marsupials was a hairy
warm-blooded long-nosed creature which walked on two legs...
The approach works reasonably well for "short" evolutionary distances
(ie the ancestor of Gorilla, chimp, and humans probably really was a
hairy warm-blooded creature which at least occasionally walked on two
legs), but it's best seen as a very rough approximation.
Even if your reconstruction happens to be similar to a real fossil
species, you can't know that that particular fossil species is the
ancestor, mostly because there may be any number of unknown similar
species, but also since your reconstruction may be plain wrong...
> related. Of course that kind of assumption is always a hypotesis that can
> *never* be tested if we don't have the complete fossil record.
Just having it isn't sufficient - we must also KNOW that the fossil
record is complete.
Cal King
>If you don't wish to answer Cox's question, please detail, using DNA
>or fossils, just how you'd prove that fossil species A was directly
>ancestral to fossil species B.
>
>I know that it can't be done. Ken Cox knows it can't be done. All the
>paleontologists here knows it can't be done.
>What do you know that no-one else does?
All the paleontologists here knows that fossil species A cannot be
directly ancestral to fossil species B? How do they "know" that?
How do they know, for example, that Homo erectus cannot be directly
ancstral to Homo sapiens? AFAIk, this is virtually consential among
physical anthropologists. If the "paleontologists here" deny this
scientific fact, then it is because the "paleontologists here" are
mostly cladists, thus proving my point that cladists deny that
ancestor-descendant relationships is knowable.
Ken Cox was not talking about relationships among species. He was
talking about relationships between different individuals within a
single species, for example, whether one house cat was the parent of
another, and whether one individual human in Pompeii was the parent of
another individual human. You are simply barking up the wrong tree.
Don Cates
>In article <98f4a681.01071...@posting.google.com>, mikemi...@my-dejanews.com (Mike) wrote:
>
>>If you don't wish to answer Cox's question, please detail, using DNA
>>or fossils, just how you'd prove that fossil species A was directly
>>ancestral to fossil species B.
>>
>>I know that it can't be done. Ken Cox knows it can't be done. All the
>>paleontologists here knows it can't be done.
>>What do you know that no-one else does?
>
>All the paleontologists here knows that fossil species A cannot be
>directly ancestral to fossil species B? How do they "know" that?
That's not what he said.
He said they cannot *know* that A is directly ancestral to B. The
information required to come to such a conclusion is simply not
available.
>How do they know, for example, that Homo erectus cannot be directly
>ancstral to Homo sapiens?
They don't know that it is not. They also *can't* know that it is. They
may suspect it is, but it could well be a close sister species to the
'real' ancestor which we do not have a sample fossil of.
AFAIk, this is virtually consential among
>physical anthropologists. If the "paleontologists here" deny this
>scientific fact,
What "scientific fact" is that? That most physical anthropologists
believe it *may* be a fact, but it isn't scientific. It would be a
speculation/hypothesis/conjecture, not a fact.
then it is because the "paleontologists here" are
>mostly cladists, thus proving my point that cladists deny that
>ancestor-descendant relationships is knowable.
Yes, no one is denying "that cladists deny that ancestor-descendant
relationships is knowable", but that is not the same as saying that
ancestor-descendant relationships do not exist.
>
>Ken Cox was not talking about relationships among species. He was
>talking about relationships between different individuals within a
>single species, for example, whether one house cat was the parent of
>another, and whether one individual human in Pompeii was the parent of
>another individual human. You are simply barking up the wrong tree.
>
Ummm... it's an analogy. You are saying that it is possible to prove
that species A is the 'parent' of species B from
skeletal/temporal/positional information alone. What makes this possible
between species but not between individuals?
Don Cates
ca...@cc.umanitoba.ca
Ken Cox
> In article <3B5367E8...@research.bell-labs.com>, Ken Cox <k...@lucent.com> wrote:
> >That's not the question. What are the relationships
> >between the skeletons? Which cat is the parent of
> >which other cat?
> That may be an interesting question, but it is one that paleontologists
> do not normally ask. They, as (hopefully) evolutionary biologists, are
> more interested in the relationship between species, not between
> individuals.
Ah. And can you think of a way to say, with assurance,
"species A is ancestral to species B" when you cannot
say, with assurance, that any individual member of
species A was ancestral to any individual member of
species B?
--
Ken Cox k...@research.bell-labs.com
Maximiliano Corredor
"Ken Cox" <k...@lucent.com> escribió en el mensaje
news:3B544BB5...@research.bell-labs.com...
Let me defend Cal by arguing that the *usual* cladistic methodology uses
characters unvariable among a single species, so it's variation is a proof
of a speciation event. So, yo can with a polarized transformation series
make a hypothesis about ancestor-descendant relations. But this characters
for all the members of a species are plesiotypic, so useless to cladificate.
You have to use other kind of characters that denote individual heritable
variation. And of course, if you can find these characters and polarize
them, you will have hypothesis about the relatedness of the individuals, as
for the species.
Maximiliano Corredor
Ken Cox
> mikemi...@my-dejanews.com (Mike) wrote:
> >If you don't wish to answer Cox's question, please detail, using DNA
> >or fossils, just how you'd prove that fossil species A was directly
> >ancestral to fossil species B.
> >I know that it can't be done. Ken Cox knows it can't be done. All the
> >paleontologists here knows it can't be done.
> >What do you know that no-one else does?
> All the paleontologists here knows that fossil species A cannot be
> directly ancestral to fossil species B?
That's not what he said. Read it again.
There *is* a difference between "it is impossible to know X"
and "I am certain that not-X".
--
Ken Cox k...@research.bell-labs.com
Cal King
>Let me defend Cal
I appreciate the thought but I am perfectly capable of defending my
viewpoint. What you may say is entirely your own opinion and it has
nothing to do with mine.
Regards.
Mike
> In article <98f4a681.01071...@posting.google.com>, mikemi...@my-dejanews.com (Mike) wrote:
>
> >If you don't wish to answer Cox's question, please detail, using DNA
> >or fossils, just how you'd prove that fossil species A was directly
> >ancestral to fossil species B.
> >
> >I know that it can't be done. Ken Cox knows it can't be done. All the
> >paleontologists here knows it can't be done.
> >What do you know that no-one else does?
>
> All the paleontologists here knows that fossil species A cannot be
> directly ancestral to fossil species B? How do they "know" that?
Evasion, thy name is alias Cal...
Are you really saying that you have not grasped that our position is
that we cannot know EITHER WAY?
And I'm still waiting for you to:
"detail, using DNA or fossils, just how you'd prove that fossil
species A was directly ancestral to fossil species B".
In your own time.
> How do they know, for example, that Homo erectus cannot be directly
> ancstral to Homo sapiens? AFAIk, this is virtually consential among
> physical anthropologists.
I take it you are not familiar with the terms chronospecies and
cladospecies.
Please look them up. They're central to your argument.
Not that you can prove that any given H. erectus fossil or even the
population to which they belonged actually is ancestral to any H.
sapiens* either.
> If the "paleontologists here" deny this
> scientific fact, then it is because the "paleontologists here" are
> mostly cladists, thus proving my point that cladists deny that
> ancestor-descendant relationships is knowable.
Whatever. Now please detail, using DNA or fossils, just how you'd
prove that fossil species A was directly ancestral to fossil species
B.
> Ken Cox was not talking about relationships among species. He was
> talking about relationships between different individuals within a
> single species
In other words much like your H. erectus example.
Cal King
>Cal King wrote:
>> In article <3B5367E8...@research.bell-labs.com>, Ken Cox
> <k...@lucent.com> wrote:
>> >That's not the question. What are the relationships
>> >between the skeletons? Which cat is the parent of
>> >which other cat?
>
>> That may be an interesting question, but it is one that paleontologists
>> do not normally ask. They, as (hopefully) evolutionary biologists, are
>> more interested in the relationship between species, not between
>> individuals.
>
>Ah. And can you think of a way to say, with assurance,
>"species A is ancestral to species B" when you cannot
>say, with assurance, that any individual member of
>species A was ancestral to any individual member of
>species B?
Nothing in science is an absolute certainty. Keeping that in mind, then
yes, it is possible to say, for example, that Homo erectus is most
likely ancestral to Homo sapiens. And, no, scientists cannot say that
individual X of species A is ancestral to individual Y of species B
because that would imply that individual X is the founding member of
species B. There simply is no known scientific method that would be
capable of making that determination in most cases. What the cladists
deny is the ability to determine whether one particular species, say
Homo erectus, is the ancestor of another species, say Homo sapiens.
Science is fully capable of making that particular determination,
despite the cladists' insistence that it cannot be done theoretically.
There is thus a deficiency in cladistic methodology, but not in science,
if cladists cannot say that Homo erectus is probably ancestral to Homo
sapiens.
Cal King
mikemi...@my-dejanews.com (Mike) wrote:
>getulus@no?bull.net? (Cal King) wrote in message
> news:<ZrT47.39623$C81.3...@bgtnsc04-news.ops.worldnet.att.net>...
>> In article <98f4a681.01071...@posting.google.com>,
> mikemi...@my-dejanews.com (Mike) wrote:
>>
>> >If you don't wish to answer Cox's question, please detail, using DNA
>> >or fossils, just how you'd prove that fossil species A was directly
>> >ancestral to fossil species B.
>> >
>> >I know that it can't be done. Ken Cox knows it can't be done. All the
>> >paleontologists here knows it can't be done.
>> >What do you know that no-one else does?
>>
>> All the paleontologists here knows that fossil species A cannot be
>> directly ancestral to fossil species B? How do they "know" that?
>
>Evasion, thy name is alias Cal...
Thanks for proving my point. I said that one way cladists defend the
absurdities of cladism is by engaging in ad hominem. There is it! Ad
hominem!
>Are you really saying that you have not grasped that our position is
>that we cannot know EITHER WAY?
No. I am saying that cladism is absurd because it claims that
ancestor-descendant relationships cannot be determined. But yet,
practically all physical anthropologists will agree that Homo erectus is
most likely to be ancestral to Homo sapiens. The cladists will deny
that possibility because they claim that it is not knowable.
>And I'm still waiting for you to:
>"detail, using DNA or fossils, just how you'd prove that fossil
>species A was directly ancestral to fossil species B".
That could be done without using even DNA evidence. Paleontologists use
morphological similarities and stratigraphy to determine if one fossil
species is most likely to be ancestral to another. Cladists of course
rely almost entirely on morphology, and they ignore stratigraphy. Hence
it is not surprising that they come up with such temporal paradoxes as
the dromaeosaurid origin of birds.
>In your own time.
>
>> How do they know, for example, that Homo erectus cannot be directly
>> ancstral to Homo sapiens? AFAIk, this is virtually consential among
>> physical anthropologists.
>
>I take it you are not familiar with the terms chronospecies and
>cladospecies.
>Please look them up. They're central to your argument.
Are you Mike Noren, now claiming to be "Mikemikemike" or just "Mike"?
These terms you refer to are entirely irrelevant to my argument, but
they are Noren's favorite terms.
>Not that you can prove that any given H. erectus fossil or even the
>population to which they belonged actually is ancestral to any H.
>sapiens* either.
>
>> If the "paleontologists here" deny this
>> scientific fact, then it is because the "paleontologists here" are
>> mostly cladists, thus proving my point that cladists deny that
>> ancestor-descendant relationships is knowable.
>
>Whatever. Now please detail, using DNA or fossils, just how you'd
>prove that fossil species A was directly ancestral to fossil species
>B.
To give you a real world example. Homo erectus is intermediate
morphologically between the small brained bipedal hominids called
Australopithecus and the large brained bipedal hominid called Homo
sapiens. Stratigraphically, H. erectus also occupies an intermediate
position. Hence it is most likely to be the ancestral species to Homo
sapiens. This is a virtual consensus among physical anthropologists.
Of course the cladists will deny this theory because to them,
ancestor-descendant relationships can never be determined. Hence there
must be something wrong with cladistic methodology if they cannot infer
what physical anthropology can infer.
>> Ken Cox was not talking about relationships among species. He was
>> talking about relationships between different individuals within a
>> single species
>
>In other words much like your H. erectus example.
Absolutely not. He was talking about how one house cat can be
shown to be ancestral to another house cat. That is not evolution.
That is not the kind of questions paleontologists are normally
interested in. That kind of question is also unanswerable for most
fossils because DNA deteriorates quickly and because DNA is rarely
preserved in the fossilization process, not to mention the fact that
DNA sequencing is a technique that is unavailable until quite recently.
So you are dishonest (another favorite claditic tactic when defending
the absurdity of cladism) if you claim that what Ken Cox was asking has
any relevance as to whether one species can be shown to be ancestral to
another species. He was asking an entirely different question.
Ken Cox
> >"species A is ancestral to species B" when you cannot
> >say, with assurance, that any individual member of
> >species A was ancestral to any individual member of
> >species B?
> Nothing in science is an absolute certainty.
Then why does it bother you that cladistics acknowledges
this, and refuses to say given two fossils that one was
ancestral to the other?
--
Ken Cox k...@research.bell-labs.com
Cal King
Au contraire, cladists treat the outcomes of their cladograms as some
sort of absolute truth. One cladist proclaims that "Birds ARE
dinosaurs" (emphasis mine). Another well known cladist proclaims that
the dinosaurian ancestry of birds is "a done deal." Yet another cladist
says that "The earth is round, the sun does not go around it, the
continents move and birds evolved from dinosaurs." That is certainly
not how scientists ought to behave since nothing in science is an
absolute certainty. So, cladists have a propensity to act in a manner
that is contrary to established scientific principles.
Ken Cox
> Ken Cox <k...@lucent.com> wrote:
> >Cal King wrote:
> >> Ken Cox <k...@lucent.com> wrote:
> >> >Ah. And can you think of a way to say, with assurance,
> >> >"species A is ancestral to species B" when you cannot
> >> >say, with assurance, that any individual member of
> >> >species A was ancestral to any individual member of
> >> >species B?
> >
> >> Nothing in science is an absolute certainty.
> >
> >Then why does it bother you that cladistics acknowledges
> >this, and refuses to say given two fossils that one was
> >ancestral to the other?
>
> Au contraire, cladists treat the outcomes of their cladograms as some
> sort of absolute truth. One cladist proclaims that "Birds ARE
> dinosaurs" (emphasis mine).
Again, that's an entirely different claim. "Dinosaur"
is not a species, and no cladist would even try to
identify a particular fossil dinosaur as ancestral to
birds. On the other hand, they have no problem with
saying "If you define a 'dinosaur' as having these
characteristics, then birds are also included in that
group".
--
Ken Cox k...@research.bell-labs.com
Cal King
>Cal King wrote:
>> Ken Cox <k...@lucent.com> wrote:
>> >Cal King wrote:
>> >> Ken Cox <k...@lucent.com> wrote:
>> >> >Ah. And can you think of a way to say, with assurance,
>> >> >"species A is ancestral to species B" when you cannot
>> >> >say, with assurance, that any individual member of
>> >> >species A was ancestral to any individual member of
>> >> >species B?
>> >
>> >> Nothing in science is an absolute certainty.
>> >
>> >Then why does it bother you that cladistics acknowledges
>> >this, and refuses to say given two fossils that one was
>> >ancestral to the other?
>>
>> Au contraire, cladists treat the outcomes of their cladograms as some
>> sort of absolute truth. One cladist proclaims that "Birds ARE
>> dinosaurs" (emphasis mine).
>
>Again, that's an entirely different claim. "Dinosaur"
>is not a species, and no cladist would even try to
>identify a particular fossil dinosaur as ancestral to
>birds.
Correct, their ideology forbids them from doing so. It similarly
forbids them from claiming or even agreeing that Homo erectus is most
likely to be ancestral to Homo sapiens.
> On the other hand, they have no problem with
>saying "If you define a 'dinosaur' as having these
>characteristics, then birds are also included in that
>group".
And because the outcome of their cladograms say that birds are part of
the group they call dinosaurs, they call birds dinosaurs, as though it
were absolute truth. In both practices (denying that
ancestor-descendant relationship is knowable and asserting that birds
are dinosaurs), the cladists deviate strongly from established
scientific practice. In the first case, they deny what is knowable and
in the second case, they assert with certainty what they don't actually
know.
syvanen
"Mike" <mikemi...@my-dejanews.com> wrote in message
news:98f4a681.01071...@posting.google.com...
> getulus@no?bull.net? (Cal King) wrote in message
news:<ZrT47.39623$C81.3...@bgtnsc04-news.ops.worldnet.att.net>...
> > In article <98f4a681.01071...@posting.google.com>,
mikemi...@my-dejanews.com (Mike) wrote:
> >
> > >If you don't wish to answer Cox's question, please detail, using DNA
> > >or fossils, just how you'd prove that fossil species A was directly
> > >ancestral to fossil species B.
> > >
> > >I know that it can't be done. Ken Cox knows it can't be done. All the
> > >paleontologists here knows it can't be done.
> > >What do you know that no-one else does?
> >
> > All the paleontologists here knows that fossil species A cannot be
> > directly ancestral to fossil species B? How do they "know" that?
>
> Evasion, thy name is alias Cal...
>
> Are you really saying that you have not grasped that our position is
> that we cannot know EITHER WAY?
>
> And I'm still waiting for you to:
> "detail, using DNA or fossils, just how you'd prove that fossil
> species A was directly ancestral to fossil species B".
Actually it can be done using DNA, as I have done so. Of course, it is not
direct proof, but polarity can be ascertained using parsimony. (And since
when is a parsimony argument direct proof of anything.) The argument comes
down to A > B is a change that uses well known mutationaly mechanisms, but
the change B > A is mechanistically improbable. This situation arises
occassionally when attempting to order changes giving rise to indels.
Mike Syvanen
Ken Cox
> Ken Cox <k...@lucent.com> wrote:
> >> >Cal King wrote:
> >> >> Ken Cox <k...@lucent.com> wrote:
> >> >> >Ah. And can you think of a way to say, with assurance,
> >> >> >"species A is ancestral to species B" when you cannot
> >> >> >say, with assurance, that any individual member of
> >> >> >species A was ancestral to any individual member of
> >> >> >species B?
> >> >> Nothing in science is an absolute certainty.
> >Again, that's an entirely different claim. "Dinosaur"
> >is not a species, and no cladist would even try to
> >identify a particular fossil dinosaur as ancestral to
> >birds.
> Correct, their ideology forbids them from doing so.
This is the same "ideology" that you express above, when
you say "nothing in science is an absolute certainty".
Why is it good when you do it and bad when they do it?
--
Ken Cox k...@research.bell-labs.com
syvanen
"Ken Cox" <k...@lucent.com> wrote in message
news:3B5499EB...@research.bell-labs.com...
Because we are willing to talk about ancestral-descendent relationships and
they refuse to do so, even though we both know that formal proof is lacking.
Imagine Simpson writing about the evolution of the horse without making
allusions to ancestral-descendent relationships. Now have Patterson talk
about pattern cladistics and horse fossils. Who has the more interesting
story?
Mike Syvanen
John Harshman
<syv...@ucdavis.edu> wrote:
Same story. The interesting part of the story is character evolution, not
ancestry and descent. You can have strong hypotheses of character
evolution (in cheek teeth and toes, for example) without making particular
known species ancestral to other particular known species.
It seems to me that inferring ancestry makes sense if you make two
assumptions: 1) we have sampled most of the relevant species that ever
lived and 2) closely related species are almost always distinguishable in
the fossil record. Sometimes these assumptions may be warranted. But I
think they are rarely warranted. They may be warranted in the case of
Homo, but I'm not sure.
--
*Note the obvious spam-defeating modification
to my address if you reply by email.
Cal King
No sir, you are quite mistaken. Science would never say that
ancestor-descendant relationships can never be knowable; cladism does.
Scientists would never say that "birds are dinosaurs"; cladists would.
Science suggests that ancestor-descendant relationships are knowable,
but such relationships cannot be determined with absolute certainty.
Hence scientists can indeed say that Homo erectus is most likely
ancestral to Homo sapiens with a good degree of certainty but not
absolute certainty. OTOH, cladists claim that Homo erectus cannot be
ancestral to Homo sapiens since ancestor-descendant relationships are
unknowable.
Steven J.
the term _H. erectus_ to the Asian specimens, then in fact most
physical anthropologists think they are *not* our ancestors. Our
ancestors, at that time, were erectus-grade hominins living in Africa.
We can't say for certain if any of the known African species is our
ancestor (as opposed to a closely related but distinct species, as
Neanderthals seem to have been to us), because, among other problems,
we don't have a complete fossil record. No matter how similar a
fossil species is to us, and how plausible an ancestor it might be, we
cannot know that somewhere, buried in East Africa, the bones of some
even more plausible ancestor might be hiding. Two species as
morphologically similar as, say, lions and tigers, might have been
living in slightly different areas; if one species was our ancestor,
but we only have bones of the other, how would we know?
>
> >And I'm still waiting for you to:
> >"detail, using DNA or fossils, just how you'd prove that fossil
> >species A was directly ancestral to fossil species B".
>
> That could be done without using even DNA evidence. Paleontologists use
> morphological similarities and stratigraphy to determine if one fossil
> species is most likely to be ancestral to another. Cladists of course
> rely almost entirely on morphology, and they ignore stratigraphy. Hence
> it is not surprising that they come up with such temporal paradoxes as
> the dromaeosaurid origin of birds.
>
imperfection both of the fossil record and our excavation and study of
it. The fact that we find a genus existing at 80 million years ago is
no proof that species of the same genus didn't exist 120 million years
ago, or 50 million years ago. For a lot of lineages, the fossil
record is simply to sketchy to say, with any great confidence "this
form didn't exist before this time, or after this time." Now, it
seems quite possible that dromeosaurids are the descendants, not the
ancestors, of archaeopterigids. In certain respects they seem more
advanced. Still, the absence of fossils of Jurassic dromeosaurs falls
short of proof that no Jurassic dromeosaurs existed. After all, once
we had no fossils of any dinosaur species whatsoever.
several others by noting that the Galapagos held three similar but
separate species of mockingbirds. This tendency for a species
fragmented into isolated populations to speciate, without enormous
changes or major new adaptions, is very typical of evolution. It is
perfectly reasonable to suspect that as early hominins gave rise to
successful new species, those species would in turn spread out, form
isolated populations, and give rise to multiple similar new species,
retaining the derived traits intermediate between australopiths and
us. One of them would be our ancestor -- but again, it might not be
the one whose fossils we've recovered.
>
> >> Ken Cox was not talking about relationships among species. He was
> >> talking about relationships between different individuals within a
> >> single species
> >
> >In other words much like your H. erectus example.
>
> Absolutely not. He was talking about how one house cat can be
> shown to be ancestral to another house cat. That is not evolution.
> That is not the kind of questions paleontologists are normally
> interested in. That kind of question is also unanswerable for most
> fossils because DNA deteriorates quickly and because DNA is rarely
> preserved in the fossilization process, not to mention the fact that
> DNA sequencing is a technique that is unavailable until quite recently.
> So you are dishonest (another favorite claditic tactic when defending
> the absurdity of cladism) if you claim that what Ken Cox was asking has
> any relevance as to whether one species can be shown to be ancestral to
> another species. He was asking an entirely different question.
-- Steven J.
Mike
: > And I'm still waiting for you to:
: > "detail, using DNA or fossils, just how you'd prove that fossil
: > species A was directly ancestral to fossil species B".
:
: Actually it can be done using DNA, as I have done so.
Really? How did you eliminate the possibility that A is really the
sister species of the (as yet unknown) ancestor of B? Or that the (as
yet unknown) sister species of A is the true direct ancestor of B?
I maintain that those, and other, possibilities *cannot* be
eliminated, and hence that a fossils status as direct ancestor
*cannot* be demonstrated. If you maintain you have, I would appreciate
a reference, as I'd really, really, like to read that paper.
: Of course, it is not
: direct proof, but polarity can be ascertained using parsimony.
If I read you right that's a completely different issue (whether A is
more basal than B or the other way around). Alias Cals claim is that
it is possible to identify a direct ancestor if found in the fossil
record - the guys which normally only show up as unnamed internodes.
: (And since
: when is a parsimony argument direct proof of anything.)
Which is why I don't claim to be able to show much anything.
: The argument comes
: down to A > B is a change that uses well known mutationaly
mechanisms, but
: the change B > A is mechanistically improbable. This situation
arises
: occassionally when attempting to order changes giving rise to
indels.
This is still just indications. One can never be certain - mutations,
even complex ones like rearrangement of genes or karyotype, CAN be
duplicated purely by chance. Then there's always those 'ghost' species
we have not yet found and perhaps never will, and on top of that we
can add the possibility of species complexes where morphology may be
identical between reproductively isolated species (a contemporary
example would be many warblers, for instance).
: Mike Syvanen
Mike
: >> >If you don't wish to answer Cox's question, please detail, using
DNA
: >> >or fossils, just how you'd prove that fossil species A was
directly
: >> >ancestral to fossil species B.
: >> >
: >> >I know that it can't be done. Ken Cox knows it can't be done.
All the
: >> >paleontologists here knows it can't be done.
: >> >What do you know that no-one else does?
: >>
: >> All the paleontologists here knows that fossil species A cannot
be
: >> directly ancestral to fossil species B? How do they "know" that?
: >
: >Evasion, thy name is alias Cal...
:
: Thanks for proving my point. I said that one way cladists defend
the
: absurdities of cladism is by engaging in ad hominem. There is it!
Ad
: hominem!
It isn't ad hominem if it's true.
As is shown by the three quoted paragraphs at the top of this post,
you are either engaging in evasion or have not understood that our
position is that one cannot know if fossil species A is directly
ancestral to fossil species B OR NOT.
You have indicated that you understand that that is our position.
: I am saying that cladism is absurd because it claims that
: ancestor-descendant relationships cannot be determined.
I've asked you, what, five? times in three posts to detail _how_ you'd
determine a direct ancestor-descendant relationship between two fossil
species. Just asserting it doesn't fly.
: But yet,
: practically all physical anthropologists will agree that Homo
erectus is
: most likely to be ancestral to Homo sapiens. The cladists will deny
: that possibility because they claim that it is not knowable.
OK, I see that I've overshot your knowledge base: it is hypothesized
that no speciation event separates african H. erectus and H. sapiens -
they're the same one (clado)species. If this is the case, then H.
erectus is a chronospecies, an arbitrary snippet of the history of H.
sapiens defined by preservational bias; an artefact.
If H.erectus is a chronospecies, then if the fossil record had been
complete, H. erectus would never have been described.
Not that one can _prove_ that H. erectus is a chronospecies, mind you
- precisely because direct ancestry cannot be proven.
: >And I'm still waiting for you to:
: >"detail, using DNA or fossils, just how you'd prove that fossil
: >species A was directly ancestral to fossil species B".
:
: That could be done without using even DNA evidence. Paleontologists
use
: morphological similarities and stratigraphy to determine if one
fossil
: species is most likely to be ancestral to another.
Like - how? What method of analysis do they use to analyse those
morphological similarities and stratigraphy? Surely they're not just
GUESSING, are they?
: Cladists of course
: rely almost entirely on morphology,
Utter nonsense.
: and they ignore stratigraphy.
Huh?
: >> How do they know, for example, that Homo erectus cannot be
directly
: >> ancstral to Homo sapiens? AFAIk, this is virtually consential
among
: >> physical anthropologists.
: >
: >I take it you are not familiar with the terms chronospecies and
: >cladospecies.
: >Please look them up. They're central to your argument.
:
: Are you Mike Noren, now claiming to be "Mikemikemike" or just
"Mike"?
: These terms you refer to are entirely irrelevant to my argument, but
: they are Noren's favorite terms.
I am indeed Mike Noren now claiming to be Mikemikemike or just Mike.
Your argument is that fossil species A can be shown to be ancestral to
fossil species B, whereas the same is not the case for fossilized
individuals of one single species.
Surely you must see that it then is relevant to your argument whether
two named taxa are indeed separate species?
(However, as it happens, it doesn't matter, since it's no more
possible to prove direct ancestry between species than between
individuals. I think Cox has been trying to impress that fact on you.)
: Stratigraphically, H. erectus also occupies an intermediate
: position. Hence it is most likely to be the ancestral species to
Homo
: sapiens. This is a virtual consensus among physical
anthropologists.
When you say 'most likely', how did you come to that conclusion?
Exactly HOW likely is it - 100%? 76%?
Or is it just an educated guess which is not actually based on any
kind of reproducible analysis at all?
I repeat:
please detail, using DNA or fossils, just how you'd prove that fossil
species A was directly ancestral to fossil species B.
And please note that you have so far just ASSERTED that H. erectus is
directly ancestral to H. sapiens. I want to know how you _support_ an
assertion like that.
I'll happily accept hypothetical arguments - if it makes things easier
for you we can assume that DNA has been recovered from fossil species
A and fossil species B.
Maximiliano Corredor
"Cal King" <getulus@no bull.net > escribió en el mensaje
news:ejZ47.40219$C81.3...@bgtnsc04-news.ops.worldnet.att.net...
Sorry, never wanted to mean that you aren't capable of defending yourself.
It was only a way to align my own opinion with yours in some aspects.
PS. I sent this yesterday, but it hasn't appeared, so it's the second time i
send it, so excuse me if it at last appears twice. In fact, I'm having to do
the same with every response I sent yesterday, I don't know why
Maximiliano Corredor
news:9j284b$nnh$1...@woodrow.ucdavis.edu...
> Imagine Simpson writing about the evolution of the horse without making
> allusions to ancestral-descendent relationships. Now have Patterson talk
> about pattern cladistics and horse fossils. Who has the more interesting
> story?
>
>
Paterson's? :)
I've taken lessons in cladistics from two different teachers, one taught me
that ancestors were mere reconstructions, that is, we can't stablish the
ancestor-descendant relationship between two species, but the other taught
me that once you got the tree, you can reconstruct the ancestors, and
comparing their characteristics, assimilate them to any real species (living
or fossil) included in the study. That is, if the LCA between A and B was
A-like, why can't we say that A is the ancestor of B? I know it isn't
*orthodox*, but I propose a *middle way*, I mean, split A in two new
species, A' and A'', and let A' be the ancestor of A'' and B. In fact,
that's the impression I have about H. ergaster and H. erectus, but perhaps
its a lack of knowlegdge from my part.
Maximiliano Corredor
Maximiliano Corredor
"Mike" <mikemi...@my-dejanews.com> escribió en el mensaje
news:98f4a681.01071...@posting.google.com...
What I was trying to say is that if we could reconstruct the complete
phylogeny of life, including all the fossil species we know, then we woul be
able to make hypothesis on the characteristics of a theoretical ancestor.
With this information, we could make some hypothesis about a species (fossil
or not) to be the ancestor of another species. This hypothesis would be more
realistic the better fossil record we have. And never, of course, can this
hypothesis became a certainty, because we can't know not only if the fossil
record is complete, but also the *living record*. And the question about
the method used to make the hypothesis for the phylogeny.
Best regards,
Ken Cox
> Because we are willing to talk about ancestral-descendent relationships and
> they refuse to do so, even though we both know that formal proof is lacking.
> Imagine Simpson writing about the evolution of the horse without making
> allusions to ancestral-descendent relationships. Now have Patterson talk
> about pattern cladistics and horse fossils. Who has the more interesting
> story?
I'm not sure I would have chosen that example. After all,
aren't many or most of the ancestor-descendant relationships
that Simpson posited now viewed as wrong?
It almost sounds like you are saying that you prefer a method
that tells good but possibly-wrong stories to a method that
refuses to go beyond what is supported by the data.
--
Ken Cox k...@research.bell-labs.com
Ken Cox
> No sir, you are quite mistaken. Science would never say that
> ancestor-descendant relationships can never be knowable; cladism does.
Apparently cladism is not part of science. Do tell me, where
is this information about what science would and would not do
set out? Are there stone tablets somewhere?
What cladism claims is that, without a perfect fossil record,
science can never distinguish between these two relationships
of species A and B:
A X
| / \
| A Y
| |
B B
In the left-hand case, species A is directly ancestral to B.
In the right-hand case, species A is a sister species to an
(undiscovered, and perhaps not even preserved) species Y,
which is the actual ancestor of B. Since we cannot know if
Y existed or not, we cannot know which tree is correct.
Now, how does "science" manage to say that we can *know*
which of these trees is correct?
> Science suggests that ancestor-descendant relationships are knowable,
> but such relationships cannot be determined with absolute certainty.
And you see some important distinction between science's "we
cannot know the relationship with absolute certainty" and
cladistics "we can never be sure that A is ancestral to B"?
> Hence scientists can indeed say that Homo erectus is most likely
> ancestral to Homo sapiens with a good degree of certainty but not
> absolute certainty. OTOH, cladists claim that Homo erectus cannot be
> ancestral to Homo sapiens since ancestor-descendant relationships are
> unknowable.
Ah, I see the problem. "We cannot know erectus is ancestral to
sapiens" is *not* the same thing as "erectus cannot be ancestral
to sapiens".
--
Ken Cox k...@research.bell-labs.com
Cal King
>
>: >> >If you don't wish to answer Cox's question, please detail, using
>DNA
>: >> >or fossils, just how you'd prove that fossil species A was
>directly
>: >> >ancestral to fossil species B.
>: >> >
>: >> >I know that it can't be done. Ken Cox knows it can't be done.
>All the
>: >> >paleontologists here knows it can't be done.
>: >> >What do you know that no-one else does?
>: >>
>: >> All the paleontologists here knows that fossil species A cannot
>be
>: >> directly ancestral to fossil species B? How do they "know" that?
>: >
>: >Evasion, thy name is alias Cal...
>:
>: Thanks for proving my point. I said that one way cladists defend
>the
>: absurdities of cladism is by engaging in ad hominem. There is it!
>Ad
>: hominem!
>
>It isn't ad hominem if it's true.
Precisely. It is not true. I did not in anyway "evade" Ken Cox's
question. You are therefore guilty of engaging in ad hominem.
>As is shown by the three quoted paragraphs at the top of this post,
>you are either engaging in evasion or have not understood that our
>position is that one cannot know if fossil species A is directly
>ancestral to fossil species B OR NOT.
Once again, Ken Cox asked if one individual can be shown to be the
ancestor of another individual of the same species. I have pointed out
to him several times that this type of question is not what
paleontologists usually ask and it is not germane to the cladists' claim
that the ancestor-descendant relationships cannot be knowable. You are
being dishonest if you claim that what Ken Cox asked pertains to
evolutionary relationships.
>You have indicated that you understand that that is our position.
I have indicated that you are dishonest.
>: I am saying that cladism is absurd because it claims that
>: ancestor-descendant relationships cannot be determined.
>
>I've asked you, what, five? times in three posts to detail _how_ you'd
>determine a direct ancestor-descendant relationship between two fossil
>species. Just asserting it doesn't fly.
>
>: But yet,
>: practically all physical anthropologists will agree that Homo
>erectus is
>: most likely to be ancestral to Homo sapiens. The cladists will deny
>: that possibility because they claim that it is not knowable.
>
>OK, I see that I've overshot your knowledge base: it is hypothesized
>that no speciation event separates african H. erectus and H. sapiens -
>they're the same one (clado)species.
If this is your "knowledge" then you know more than most physical
anthropologists. Most of them treat H. erectus and H. sapiens as
different species.
> If this is the case,
Prove that it is.!
> then H.
>erectus is a chronospecies, an arbitrary snippet of the history of H.
>sapiens defined by preservational bias; an artefact.
You are reaching a lot of weird conclusions that is based on a weird,
unproven assumption. And you do all that in order to deny what most
physical anthropologists agree: that Homo erectus is most likely to be
ancestral to H. sapiens. Again, you prove my point that cladists insist
that ancestor-descendant relationships are knowable. BTW, if H. sapiens
is a "chronospecies" then when did the change from H. erectus to H.
sapiens take place?
>If H.erectus is a chronospecies, then if the fossil record had been
>complete, H. erectus would never have been described.
>
>Not that one can _prove_ that H. erectus is a chronospecies, mind you
>- precisely because direct ancestry cannot be proven.
So you are assuming something that you admit can never be proven, and
then you reach all sorts of weird conclusions based on that unproven
assumption. Very scientific!
>: >And I'm still waiting for you to:
>: >"detail, using DNA or fossils, just how you'd prove that fossil
>: >species A was directly ancestral to fossil species B".
>:
>: That could be done without using even DNA evidence. Paleontologists
>use
>: morphological similarities and stratigraphy to determine if one
>fossil
>: species is most likely to be ancestral to another.
>
>Like - how? What method of analysis do they use to analyse those
>morphological similarities and stratigraphy? Surely they're not just
>GUESSING, are they?
Comparative anatomy, or something that the cladists have abandoned.
They rely instead on superficial similarities.
>: Cladists of course
>: rely almost entirely on morphology,
>
>Utter nonsense.
You are simply in denial.
>: and they ignore stratigraphy.
>
>Huh?
More denial.
>: >> How do they know, for example, that Homo erectus cannot be
>directly
>: >> ancstral to Homo sapiens? AFAIk, this is virtually consential
>among
>: >> physical anthropologists.
>: >
>: >I take it you are not familiar with the terms chronospecies and
>: >cladospecies.
>: >Please look them up. They're central to your argument.
>:
>: Are you Mike Noren, now claiming to be "Mikemikemike" or just
>"Mike"?
>: These terms you refer to are entirely irrelevant to my argument, but
>: they are Noren's favorite terms.
>
>I am indeed Mike Noren now claiming to be Mikemikemike or just Mike.
So you have abandoned the older name. Is Mike Noren/Mikemikemike/Mike a
chronospecies? I doubt that. There has not been any change at all.
Mike Noren was dishonest and a practitioner of ad hominem. So is
"Mikemikemike" aka "Mike."
>Your argument is that fossil species A can be shown to be ancestral to
>fossil species B
Yes, with as much certainty as the available scientific information may
allow.
>, whereas the same is not the case for fossilized
>individuals of one single species.
That can be done too, but not in the absence of DNA data. There have
been some genealogical work performed on King Tut to ascertain his
ancestry using DNA data. But in most cases, DNA is absent or too
deteoriorated from fossil remains for this type of work to be performed.
>Surely you must see that it then is relevant to your argument whether
>two named taxa are indeed separate species?
Fortunately, different species do differ, in most cases, morphologically
since they are often adapted to different niches. That is how
paleontologists can recognize different species even in the absence of
DNA data or evidence of reproductive isolation.
>(However, as it happens, it doesn't matter, since it's no more
>possible to prove direct ancestry between species than between
>individuals. I think Cox has been trying to impress that fact on you.)
You are ascribing something that is not there to Ken Cox's simplistic
questions in order to justify your ad hominem.
>: Stratigraphically, H. erectus also occupies an intermediate
>: position. Hence it is most likely to be the ancestral species to
>Homo
>: sapiens. This is a virtual consensus among physical
>anthropologists.
>
>When you say 'most likely', how did you come to that conclusion?
>Exactly HOW likely is it - 100%? 76%?
I am sorry some things cannot be quantified exactly. But I would say
that it is definitely more likely than Homo erectus and Homo sapiens
being unrelated but only convergently similar.
>Or is it just an educated guess which is not actually based on any
>kind of reproducible analysis at all?
>
>I repeat:
>please detail, using DNA or fossils, just how you'd prove that fossil
>species A was directly ancestral to fossil species B.
I have already pointed out that one can use morphological similarities
and stratigraphy. You are ignoring what I pointed out and continue to
dishonestly argue that I "evade" your questions so you can engage in ad
hominem.
>And please note that you have so far just ASSERTED that H. erectus is
>directly ancestral to H. sapiens. I want to know how you _support_ an
>assertion like that.
I repeat, once again: morphological similarities and stratigraphy.
>I'll happily accept hypothetical arguments - if it makes things easier
>for you we can assume that DNA has been recovered from fossil species
>A and fossil species B.
It is no use arguing with someone who pretends not to see an answer
that his opponent has given, so that he can dishonestly claim that his
opponent "evades" his question.
Mike
> What I was trying to say is that if we could reconstruct the complete
> phylogeny of life, including all the fossil species we know, then we woul be
> able to make hypothesis on the characteristics of a theoretical ancestor.
> With this information, we could make some hypothesis about a species (fossil
> or not) to be the ancestor of another species. This hypothesis would be more
> realistic the better fossil record we have. And never, of course, can this
> hypothesis became a certainty, because we can't know not only if the fossil
> record is complete, but also the *living record*. And the question about
> the method used to make the hypothesis for the phylogeny.
I agree completely with this. It is exactly my understanding of the
subject
as well.
That we can never KNOW that species A is ancestral to species B
doesn't mean that we cannot form theories about ancestry, or
hypothesize about theoretical ancestors.
What we cannot do is KNOW. That's where Cal is mistaken.
> Best regards,
> Maximiliano Corredor
>
> PS. I sent this yesterday, but it hasn't appeared, so it's the second time i
> send it, so excuse me if it at last appears twice. In fact, I'm having to do
> the same with every response I sent yesterday, I don't know why
I think something, somewhere, has been screwed up with s.b.s. My own
posts from my ordinary adress doesn't ever show up in this newsgroup.
All other groups I attend work OK, but to post in s.b.s I must use
Google...
Cal King
>Cal King wrote:
>> No sir, you are quite mistaken. Science would never say that
>> ancestor-descendant relationships can never be knowable; cladism
does.
>
>Apparently cladism is not part of science. Do tell me, where
>is this information about what science would and would not do
>set out? Are there stone tablets somewhere?
No, as a matter of fact, science is constantly evolving, unlike some of
the teachings of Hennig, for example the Principle of Monophyly or Holophyly.
>What cladism claims is that, without a perfect fossil record,
>science can never distinguish between these two relationships
>of species A and B:
I think it is time to pause here because you have a complete
misunderstanding of what cladism claims. Cladisms claims that
ancestor-descendant relationships are not knowable, period, because
their methodology does not allow them to make that determination. That
is the case even if the fossil record is complete. OTOH, other
scientists, unencumbered by the cladistic straightjacket, claim that
ancestor-descendant relationships are knowable (although of course with
less than absolute certainty), and that it can indeed be inferred from
comparative anatomy and stratigraphy. The reason why not one single
ancestral species of a higher taxon has been identified is because of
the incomplete fossil record. Hence the claim of cladism has more to do
with a deficiency in their methdology than with reality or with the
incomplete fossil record.
Mike
> In article <98f4a681.01071...@posting.google.com>, mikemi...@my-dejanews.com (Mike) wrote:
> >Replying to getulus@no bull.net (Cal King) :
> >: >> All the paleontologists here knows that fossil species A cannot
> be
> >: >> directly ancestral to fossil species B? How do they "know" that?
> >: >
> >: >Evasion, thy name is alias Cal...
> >:
> >: Thanks for proving my point. I said that one way cladists defend
> the
> >: absurdities of cladism is by engaging in ad hominem. There is it!
> Ad
> >: hominem!
> >
> >It isn't ad hominem if it's true.
>
> Precisely. It is not true. I did not in anyway "evade" Ken Cox's
> question. You are therefore guilty of engaging in ad hominem.
If you had read the three quoted paragraphs you had seen that the
evasion
was that you erected a strawman argument: you misconstrued my argument
to be that A _cannot_ be directly ancestral to B.
My real, as opposed to this strawman, argument is that it is
impossible
to know if species A is directly ancestral to species B. It may be
or it may not, and there is no way to determine which is the case.
> >: I am saying that cladism is absurd because it claims that
> >: ancestor-descendant relationships cannot be determined.
> >
> >I've asked you, what, five? times in three posts to detail _how_ you'd
> >determine a direct ancestor-descendant relationship between two fossil
> >species. Just asserting it doesn't fly.
> >
> >: But yet,
> >: practically all physical anthropologists will agree that Homo
> erectus is
> >: most likely to be ancestral to Homo sapiens. The cladists will deny
> >: that possibility because they claim that it is not knowable.
> >
> >OK, I see that I've overshot your knowledge base: it is hypothesized
> >that no speciation event separates african H. erectus and H. sapiens -
> >they're the same one (clado)species.
>
> If this is your "knowledge" then you know more than most physical
> anthropologists. Most of them treat H. erectus and H. sapiens as
> different species.
What part of "Not that one can _prove_ that H. erectus is a
chronospecies, mind you - precisely because direct ancestry cannot be
proven" is it
you do not understand?
> > If this is the case,
>
> Prove that it is.!
HAHAHAHAHA!
Trying to reverse the burden of proof, are we?
No, Cal. I have nothing to prove. You have. It is you who claim that
it is knowable whether fossil species A is directly ancestral to
fossil species B.
> > then H.
> >erectus is a chronospecies, an arbitrary snippet of the history of H.
> >sapiens defined by preservational bias; an artefact.
>
> You are reaching a lot of weird conclusions that is based on a weird,
> unproven assumption. And you do all that in order to deny what most
> physical anthropologists agree: that Homo erectus is most likely to be
> ancestral to H. sapiens. Again, you prove my point that cladists insist
> that ancestor-descendant relationships are knowable. BTW, if H. sapiens
> is a "chronospecies" then when did the change from H. erectus to H.
> sapiens take place?
Is this a joke?
Firstly, I still haven't assumed anything. Secondly, I haven't even
drawn any "weird conclusions": a chronospecies IS an artefact, a
result of phyletic change and preservational bias, look it up
somewhere. Thirdly, what is this about me proving your "point that
cladists insist that ancestor-descendant relationships are knowable"?
That's YOUR position, not mine.
But your last sentence really takes the cake. Yes indeed, if H.
erectus is a chronospecies, when DID the change from H. erectus to H.
sapiens take place?
> >: >And I'm still waiting for you to:
> >: >"detail, using DNA or fossils, just how you'd prove that fossil
> >: >species A was directly ancestral to fossil species B".
> >:
> >: That could be done without using even DNA evidence. Paleontologists
> use
> >: morphological similarities and stratigraphy to determine if one
> fossil
> >: species is most likely to be ancestral to another.
> >
> >Like - how? What method of analysis do they use to analyse those
> >morphological similarities and stratigraphy? Surely they're not just
> >GUESSING, are they?
>
> Comparative anatomy, or something that the cladists have abandoned.
> They rely instead on superficial similarities.
Comparative anatomy, I see. Intuitive analysis. So, that's
reproducible, is it?
> >: Cladists of course
> >: rely almost entirely on morphology,
> >
> >Utter nonsense.
>
> You are simply in denial.
Tell you what: I'm a fairly hard-core cladist, right? I've published
articles in Nature and Cladistics, and a couple more are in the works.
You read any of those articles, and tell me if I "rely almost entirely
on morphology", OK?
References available on demand.
> >: and they ignore stratigraphy.
> >
> >Huh?
>
> More denial.
I really don't understand your argument. What is it?
> >: >> How do they know, for example, that Homo erectus cannot be
> directly
> >: >> ancstral to Homo sapiens? AFAIk, this is virtually consential
> among
> >: >> physical anthropologists.
> >: >
> >: >I take it you are not familiar with the terms chronospecies and
> >: >cladospecies.
> >: >Please look them up. They're central to your argument.
> >:
> >: Are you Mike Noren, now claiming to be "Mikemikemike" or just
> "Mike"?
> >: These terms you refer to are entirely irrelevant to my argument, but
> >: they are Noren's favorite terms.
> >
> >I am indeed Mike Noren now claiming to be Mikemikemike or just Mike.
>
> So you have abandoned the older name. Is Mike Noren/Mikemikemike/Mike a
> chronospecies? I doubt that.
As it happens I cannot post in sci.bio.systematics from my original
adress anymore. I've contacted my ISP, so far to no avail.
> >Your argument is that fossil species A can be shown to be ancestral to
> >fossil species B
>
> Yes, with as much certainty as the available scientific information may
> allow.
As your intution tells you, you mean. Your inference is based on no
kind of reproducible analysis, is it.
> >: Stratigraphically, H. erectus also occupies an intermediate
> >: position. Hence it is most likely to be the ancestral species to
> Homo
> >: sapiens. This is a virtual consensus among physical
> >anthropologists.
> >
> >When you say 'most likely', how did you come to that conclusion?
> >Exactly HOW likely is it - 100%? 76%?
>
> I am sorry some things cannot be quantified exactly. But I would say
> that it is definitely more likely than Homo erectus and Homo sapiens
> being unrelated but only convergently similar.
"Unrelated but only convergently similar" isn't the flipside of the
claim that H. erectus is directly ancestral to H. sapiens, is it. The
flipside would be "H. erectus is closely related but not necessarily
the direct ancestor of H. sapiens".
> >Or is it just an educated guess which is not actually based on any
> >kind of reproducible analysis at all?
> >
> >I repeat:
> >please detail, using DNA or fossils, just how you'd prove that fossil
> >species A was directly ancestral to fossil species B.
>
> I have already pointed out that one can use morphological similarities
> and stratigraphy. You are ignoring what I pointed out and continue to
> dishonestly argue that I "evade" your questions so you can engage in ad
> hominem.
I am asking you HOW you'd use "morphological similiarities and
stratigraphy". The answer seems to be that you'd look at them, and
then intuitively decide whether A is directly ancestral to B.
In other words, you'd show NOTHING. You'd simply ASSERT ancestorship,
and I hope I'm forgiven for not being terribly impressed by that.
syvanen
>
> : > And I'm still waiting for you to:
> : > "detail, using DNA or fossils, just how you'd prove that fossil
> : > species A was directly ancestral to fossil species B".
> :
> : Actually it can be done using DNA, as I have done so.
>
> Really? How did you eliminate the possibility that A is really the
> sister species of the (as yet unknown) ancestor of B? Or that the (as
> yet unknown) sister species of A is the true direct ancestor of B?
>
> I maintain that those, and other, possibilities *cannot* be
> eliminated, and hence that a fossils status as direct ancestor
> *cannot* be demonstrated. If you maintain you have, I would appreciate
> a reference, as I'd really, really, like to read that paper.
This paper talks about the evolution of a gene, which is found in a variety
of different species. A strong parsimony argument can be made that we have
identified the ancestral state of the gene.
Lee KY; Hopkins JD; Syvanen M. Evolved neomycin phosphotransferase from
an isolate of Klebsiella
pneumoniae. Molecular Microbiology, 1991 Aug, 5(8):2039-46.
> : Of course, it is not
> : direct proof, but polarity can be ascertained using parsimony.
>
> If I read you right that's a completely different issue (whether A is
> more basal than B or the other way around). Alias Cals claim is that
> it is possible to identify a direct ancestor if found in the fossil
> record - the guys which normally only show up as unnamed internodes.
>
> : (And since
> : when is a parsimony argument direct proof of anything.)
>
> Which is why I don't claim to be able to show much anything.
>
> : The argument comes
> : down to A > B is a change that uses well known mutationaly
> mechanisms, but
> : the change B > A is mechanistically improbable. This situation
> arises
> : occassionally when attempting to order changes giving rise to
> indels.
>
> This is still just indications. One can never be certain - mutations,
> even complex ones like rearrangement of genes or karyotype, CAN be
> duplicated purely by chance.
If a deletion can be formed by a single step, but the reverse insertion
requires multiple steps that use unknown mechanisms, then the parsimony
argument is strong for the deletion.
Mike Syvanen
syvanen
I prefer to present the simplist hypothesis consistant with the data. After
that presentation, then we can discuss caveats and factors that could
falsify the hypothesis. My complaint with cladists, is that they obsess on
the caveats, 'hidden forests', ghost species etc. Of course any thinking
person is aware that new data (ie new fossils) can easily overturn a
reconstruction. I am not sure that Simpson's reconstruction is viewed as
wrong as much as it has been picked apart by those who do not approve of his
presenting the simplist explanation for the fossil series. Perhaps you are
aware of findings new fossils since his time that has overtunred his
progressions, this is not an area in which I am competent to discuss.
Mike Syvanen
>
> --
> Ken Cox k...@research.bell-labs.com
>
bonestone
>We can't say for certain if any of the known African species is our
>ancestor (as opposed to a closely related but distinct species, as
>Neanderthals seem to have been to us), because, among other problems,
>we don't have a complete fossil record.
Please define a "Complete Fossil Record". The fossil record is, by its
nature, incomplete because only a minute number of specimens of a given
species are preserved in the fossil record. That is one of the wonderful
things about the fossil record. It allows us to use our imagination and
devise theories on what must have been, with no ability to ever know
everything. It is king of like trying to identify a paint by numbers
picture of the Mona Lisa with about a dozen paint brush strokes actually
represented. No matter how hard you imagine or try to piece together the
picture, you can never get the smile right.
James Holley
Geologist
John Harshman
<syv...@ucdavis.edu> wrote:
> "Mike" <mikemi...@my-dejanews.com> wrote in message
> news:98f4a681.01071...@posting.google.com...
> > Replying to "syvanen" <syv...@ucdavis.edu> :
> >
> > : > And I'm still waiting for you to:
> > : > "detail, using DNA or fossils, just how you'd prove that fossil
> > : > species A was directly ancestral to fossil species B".
> > :
> > : Actually it can be done using DNA, as I have done so.
> >
> > Really? How did you eliminate the possibility that A is really the
> > sister species of the (as yet unknown) ancestor of B? Or that the (as
> > yet unknown) sister species of A is the true direct ancestor of B?
> >
> > I maintain that those, and other, possibilities *cannot* be
> > eliminated, and hence that a fossils status as direct ancestor
> > *cannot* be demonstrated. If you maintain you have, I would appreciate
> > a reference, as I'd really, really, like to read that paper.
>
> This paper talks about the evolution of a gene, which is found in a variety
> of different species. A strong parsimony argument can be made that we have
> identified the ancestral state of the gene.
But that's quite different from identifying an ancestral species. The same
thing is done with morphological characters, and even the most fanatical
cladists do it: the identification of ancestral character states, and even
groups of character states ("hypothetical ancestors"). What you can't do
is equate those groups of character states to any actual, known species.
Even if, for example, you find that your ancestral sequence actually
exists in some living species, would you then infer that species to be the
ancestor of all the other species? I suspect not, but if you would, then
say so.
> Lee KY; Hopkins JD; Syvanen M. Evolved neomycin phosphotransferase from
> an isolate of Klebsiella
> pneumoniae. Molecular Microbiology, 1991 Aug, 5(8):2039-46.
[snip]
> > : The argument comes
> > : down to A > B is a change that uses well known mutationaly
> > mechanisms, but
> > : the change B > A is mechanistically improbable. This situation
> > arises
> > : occassionally when attempting to order changes giving rise to
> > indels.
> >
> > This is still just indications. One can never be certain - mutations,
> > even complex ones like rearrangement of genes or karyotype, CAN be
> > duplicated purely by chance.
>
> If a deletion can be formed by a single step, but the reverse insertion
> requires multiple steps that use unknown mechanisms, then the parsimony
> argument is strong for the deletion.
Talking about SINEs and such here? So far, so good. But the night is
young. We've found homoplasy in places I wouldn't have imagined it, so
far. Including identical insertion/deletion events in the low double
digits of length.
And besides, we were talking about identification of ancestral species,
not just ancestral character states. Nobody is claiming that ancestral
character states are impossible to identify with some confidence. It's
ancestral species that are the issue.
John Brock
Cal King <getulus@no bull.net > wrote:
>In article <98f4a681.01071...@posting.google.com>,
>mikemi...@my-dejanews.com (Mike) wrote:
>>Are you really saying that you have not grasped that our position is
>>that we cannot know EITHER WAY?
>No. I am saying that cladism is absurd because it claims that
>ancestor-descendant relationships cannot be determined. But yet,
>practically all physical anthropologists will agree that Homo erectus is
>most likely to be ancestral to Homo sapiens. The cladists will deny
>that possibility because they claim that it is not knowable.
I don't think Cal is saying that it is ever possible to know for
*certain* whether species A gave rise to species B. That clearly
seems impossible to me, and I suspect Cal thinks so also. What it
sounds to me like he is saying -- in a not especially clear way --
is that the cladistic methodology does not allow us to formally
state that A is *probably* the ancestor of B, and that this is a
defect in the methodology. I don't know enough about cladism to
know whether this claim is true, or whether its truth would mean
that cladism was "absurd", but if this is what Cal is actually
saying it does strike me as different -- and more reasonable --
than what you seem to be accusing him of saying.
--
John Brock
jbr...@panix.com
John Harshman
getulus@no bull.net (Cal King) wrote:
> In article <3B55ABE6...@research.bell-labs.com>, Ken Cox
> <k...@lucent.com> wrote:
> >Cal King wrote:
> >> No sir, you are quite mistaken. Science would never say that
> >> ancestor-descendant relationships can never be knowable; cladism
> does.
> >
> >Apparently cladism is not part of science. Do tell me, where
> >is this information about what science would and would not do
> >set out? Are there stone tablets somewhere?
>
> No, as a matter of fact, science is constantly evolving, unlike some of
> the teachings of Hennig, for example the Principle of Monophyly or Holophyly.
>
> >What cladism claims is that, without a perfect fossil record,
> >science can never distinguish between these two relationships
> >of species A and B:
>
> I think it is time to pause here because you have a complete
> misunderstanding of what cladism claims. Cladisms claims that
> ancestor-descendant relationships are not knowable, period, because
> their methodology does not allow them to make that determination. That
> is the case even if the fossil record is complete.
Potentially a true assertion on your part, depending on what we mean by
"complete". I don't know about other cladists, but if by "complete" you
simply mean that we would have good fossil material of every relevant
species that ever lived, I would agree that it still might not be possible
to distinguish ancestral species. To distinguish ancestral species, we
would need the additional assurance that we were capable of telling
closely related species apart (from their fossils) in most cases. But if
both those things were true, I agree you would be able to identify
ancestral species. (There are other potential problems having to do witht
the sufficiency of character varying among species, and the confusion
resulting from reversals, but at least you could make a go of it.)
Mind you, the fossil record is nowhere near complete, and I also suspect
that we are unable to tell apart quite a few closely related fossil
species. Certainly if all the current living bird species were known only
from complete skeletons, there are plenty of species pairs we would be
unable to distinguish from each other.
> OTOH, other
> scientists, unencumbered by the cladistic straightjacket, claim that
> ancestor-descendant relationships are knowable (although of course with
> less than absolute certainty), and that it can indeed be inferred from
> comparative anatomy and stratigraphy.
Better supply details. How can we distinguish an ancestor from the
ancestor's close relative?
> The reason why not one single
> ancestral species of a higher taxon has been identified is because of
> the incomplete fossil record.
Which seems to render the entire question moot.
> Hence the claim of cladism has more to do
> with a deficiency in their methdology than with reality or with the
> incomplete fossil record.
--
Mike
: > : > And I'm still waiting for you to:
: > : > "detail, using DNA or fossils, just how you'd prove that
fossil
: > : > species A was directly ancestral to fossil species B".
: > :
: > : Actually it can be done using DNA, as I have done so.
: >
: > Really? How did you eliminate the possibility that A is really the
: > sister species of the (as yet unknown) ancestor of B? Or that the
(as
: > yet unknown) sister species of A is the true direct ancestor of B?
: >
: > I maintain that those, and other, possibilities *cannot* be
: > eliminated, and hence that a fossils status as direct ancestor
: > *cannot* be demonstrated. If you maintain you have, I would
appreciate
: > a reference, as I'd really, really, like to read that paper.
:
: This paper talks about the evolution of a gene, which is found in a
variety
: of different species. A strong parsimony argument can be made that
we have
: identified the ancestral state of the gene.
Identifying theoretical ancestral states, even inferring theoretical
ancestors, is one thing - identifying a particular fossil species as
the direct ancestor, and eliminating all other possible
interpretations of the data (e.g. that the real ancestor is a 'ghost'
species) is quite another.
But I'll have a look at your article.
: Lee KY; Hopkins JD; Syvanen M. Evolved neomycin
phosphotransferase from
: an isolate of Klebsiella
: pneumoniae. Molecular Microbiology, 1991 Aug, 5(8):2039-46.
: > : The argument comes
: > : down to A > B is a change that uses well known mutationaly
: > mechanisms, but
: > : the change B > A is mechanistically improbable. This situation
: > arises
: > : occassionally when attempting to order changes giving rise to
: > indels.
: >
: > This is still just indications. One can never be certain -
mutations,
: > even complex ones like rearrangement of genes or karyotype, CAN be
: > duplicated purely by chance.
:
: If a deletion can be formed by a single step, but the reverse
insertion
: requires multiple steps that use unknown mechanisms, then the
parsimony
: argument is strong for the deletion.
But not 100% - even complex mutations can be duplicated, unlikely
events do occur.
Furthermore unless you know when and in which population the mutation
occurred, it is difficult to tie its arisal to a particular species.
And the fundamental possibility that A is really the sister species of
the (as yet unknown) ancestor of B, or that the (as yet unknown)
sister species of A is the true direct ancestor of B, remains.
One may be able to make a decent case for ancestorship (I am
personally quite satisfied that H. erectus really is the ancestor of
H. sapiens, for instance), but never be certain - unless one has
either divine knowledge or was present to directly observe the events.
: Mike Syvanen
Mike
> "Ken Cox" <k...@lucent.com> wrote in message
> news:3B55A97E...@research.bell-labs.com...
> > syvanen wrote:
> > > Because we are willing to talk about ancestral-descendent relationships
> and
> > > they refuse to do so, even though we both know that formal proof is
> lacking.
> > > Imagine Simpson writing about the evolution of the horse without making
> > > allusions to ancestral-descendent relationships. Now have Patterson
> talk
> > > about pattern cladistics and horse fossils. Who has the more
> interesting
> > > story?
> >
> > I'm not sure I would have chosen that example. After all,
> > aren't many or most of the ancestor-descendant relationships
> > that Simpson posited now viewed as wrong?
> >
> > It almost sounds like you are saying that you prefer a method
> > that tells good but possibly-wrong stories to a method that
> > refuses to go beyond what is supported by the data.
>
> I prefer to present the simplist hypothesis consistant with the data. After
> that presentation, then we can discuss caveats and factors that could
> falsify the hypothesis. My complaint with cladists, is that they obsess on
> the caveats, 'hidden forests', ghost species etc.
I am not clear on how you manage to equate "the simplist hypothesis
consistant with the data" with some kind of storytelling or biopoetry?
To me the simplest hypothesis would be the one which makes the fewest
number of unsupported assumptions...
> Mike Syvanen
Mike
> In article <VIZ47.40309$C81.3...@bgtnsc04-news.ops.worldnet.att.net>,
> Cal King <getulus@no bull.net > wrote:
> >In article <98f4a681.01071...@posting.google.com>,
> >mikemi...@my-dejanews.com (Mike) wrote:
>
> >>Are you really saying that you have not grasped that our position is
> >>that we cannot know EITHER WAY?
>
> >No. I am saying that cladism is absurd because it claims that
> >ancestor-descendant relationships cannot be determined. But yet,
> >practically all physical anthropologists will agree that Homo erectus is
> >most likely to be ancestral to Homo sapiens. The cladists will deny
> >that possibility because they claim that it is not knowable.
>
> I don't think Cal is saying that it is ever possible to know for
> *certain* whether species A gave rise to species B. That clearly
> seems impossible to me, and I suspect Cal thinks so also. What it
> sounds to me like he is saying -- in a not especially clear way --
> is that the cladistic methodology does not allow us to formally
> state that A is *probably* the ancestor of B, and that this is a
> defect in the methodology.
Cals suggested method is to simply assert ancestorship (is that a
word?) based on intuition. The researcher looks at the evidence,
ponders the evidence, and deduces the history of events. There is no
formal analysis involved.
Cals method doesn't allow saying *how* probable it is that species A
is ancestral to species B - it is merely a statement that of the
fossil species we know, species A _feels_ more closely related to B
than does any other.
I, personally, have a hard time seeing that a scientific method of
analysis (in this case parsimony) is flawed because it doesn't allow
the researcher to assert things based on intuition.
It may be worth noting that it is perfectly OK for a cladist to say
that species A is *possibly* the direct ancestor of B, acknowledging
that this can never be substantiated.
> I don't know enough about cladism to
> know whether this claim is true, or whether its truth would mean
> that cladism was "absurd", but if this is what Cal is actually
> saying it does strike me as different -- and more reasonable --
> than what you seem to be accusing him of saying.
Cal really has said that direct ancestry is knowable. It may be that
'knowable' to Cal means 'suspectable' or 'possible', but that is not
what he's said.
In his most recent posts he's mellowed a bit, and said things like
that one cannot know with absolute certainty - and as Ken Cox has
pointed out, that makes his position difficult to separate from that
of the cladists he accuses of being absurd.
Ken Cox
> No, Cal. I have nothing to prove. You have. It is you who claim that
> it is knowable whether fossil species A is directly ancestral to
> fossil species B.
Actually, he doesn't. See message
<Oc357.41322$C81.3...@bgtnsc04-news.ops.worldnet.att.net>
He is perfectly happy when what he calls "science" (as distinct
from "cladistics") says "H. erectus is probably the ancestor of
H. sapiens, but we can't be sure." He is unhappy when cladistics
says the same thing, presumably because of the difference in the
wording between "we can never be sure" and "we can never know".
I'm not sure why the difference bugs him, though if you read the
referenced article, there may be a hint. I refer to the way that
it bothers him when cladistics says that birds are dinosaurs; he
says that "science" would never do such a thing. If this issue
is something of a hobby horse (and/or bete noir) with him, that
might explain the, um, fervor.
--
Ken Cox k...@research.bell-labs.com
Ken Cox
> > that tells good but possibly-wrong stories to a method that
> > refuses to go beyond what is supported by the data.
>
> I prefer to present the simplist hypothesis consistant with the data.
So why is "I don't know for sure how A and B are related,
but I will say that A is the ancestor of B" simpler than
"I don't know for sure how A and B are related"?
--
Ken Cox k...@research.bell-labs.com
Mike
: Mike wrote:
: > No, Cal. I have nothing to prove. You have. It is you who claim
that
: > it is knowable whether fossil species A is directly ancestral to
: > fossil species B.
:
: Actually, he doesn't. See message
: <Oc357.41322$C81.3...@bgtnsc04-news.ops.worldnet.att.net>
: He is perfectly happy when what he calls "science" (as distinct
: from "cladistics") says "H. erectus is probably the ancestor of
: H. sapiens, but we can't be sure." He is unhappy when cladistics
: says the same thing, presumably because of the difference in the
: wording between "we can never be sure" and "we can never know".
He's both claimed that it is knowable, and said things like the above.
I suspect he does not see that saying that something is knowable even
though "we can never be sure" is inconsistent.
: I'm not sure why the difference bugs him, though if you read the
: referenced article, there may be a hint. I refer to the way that
: it bothers him when cladistics says that birds are dinosaurs; he
: says that "science" would never do such a thing. If this issue
: is something of a hobby horse (and/or bete noir) with him, that
: might explain the, um, fervor.
He's been bashing cladism for years, much of the time as Nyikos'
sidekick.
syvanen
> > > that tells good but possibly-wrong stories to a method that
> > > refuses to go beyond what is supported by the data.
> >
> > I prefer to present the simplist hypothesis consistant with the data.
>
> but I will say that A is the ancestor of B" simpler than
> "I don't know for sure how A and B are related"?
If we accept stratigraphy and that fossils in lower strata appeared before
those in higher strata and if we follow a series of fossils that are
obviously related, eg rat-like mammals in the late cretaceous and
subsequently more elaborate mammals in the early tertiary then I think it is
not unreasonable to say that not only are the mammals related, but also that
the latter mammals evolved from ancestral forms that looked like those
rat-like fossils. Of course, it is formerly possible that both evolved
independently from a ghost species that we have no idea how it appeared. It
just seems to me that the simpler hypothesis is that we have an
ancestral-descendent relationship here since the insertion of a ghost
species is adding a new variable. This reasoning is sometimes referred to
Occam's razor and forms the basis of parsimony.
Mike Syvanen
Ken Cox
> If we accept stratigraphy and that fossils in lower strata appeared before
> those in higher strata and if we follow a series of fossils that are
> obviously related, eg rat-like mammals in the late cretaceous and
> subsequently more elaborate mammals in the early tertiary then I think it is
> not unreasonable to say that not only are the mammals related, but also that
> the latter mammals evolved from ancestral forms that looked like those
> rat-like fossils.
"Looked like" is no problem, even the cladists agree with
that. "Were" is the sticking point. Are you willing to
point to any particular early mammal species and say that
it *is* the ancestor of some later species, not simply
"looks like" or "is closely related to" that ancestor?
--
Ken Cox k...@research.bell-labs.com
syvanen
Now this really is a viscous ad hominen attack.
Mike Syvanen
syvanen
The simplist hypothesis is that the rat-like ancestor evolved into modern
mammals. Your introduction of ghost species (those x and y taxa you
introduced in a response to Cal) can be rejected by Occam's razor. Of
course, I cannot say that it "is". I am saying that it is not necessary to
entertain more complex explanations until there is solid reasons to do so.
Ken Cox
> "Mike" <mikemi...@my-dejanews.com> wrote:
> > He's been bashing cladism for years, much of the time as Nyikos'
> > sidekick.
> Now this really is a viscous ad hominen attack.
Slow and sticky, you mean?
--
Ken Cox k...@research.bell-labs.com
Ken Cox
> The simplist hypothesis is that the rat-like ancestor evolved into modern
> mammals. Your introduction of ghost species (those x and y taxa you
> introduced in a response to Cal) can be rejected by Occam's razor. Of
> course, I cannot say that it "is". I am saying that it is not necessary to
> entertain more complex explanations until there is solid reasons to do so.
Some people might argue that saying "A is the ancestor of B,
probably" is *also* a violation of Occam's razor -- you are
adding the hypothesis that there was *not* a sister taxon.
Just why is it so awful to say "A looks like what we think the
ancestor of B looked like, though we can't say with certainty
that A is the ancestor of B"? Or wait, I may be confused --
is that the cladist summary, or the non-cladist summary?
--
Ken Cox k...@research.bell-labs.com
John Harshman
<syv...@ucdavis.edu> wrote:
> "Ken Cox" <k...@lucent.com> wrote in message
> news:3B57094A...@research.bell-labs.com...
> > syvanen wrote:
> > > "Ken Cox" <k...@lucent.com> wrote:
> > > > It almost sounds like you are saying that you prefer a method
> > > > that tells good but possibly-wrong stories to a method that
> > > > refuses to go beyond what is supported by the data.
> > >
> > > I prefer to present the simplist hypothesis consistant with the data.
> >
> > So why is "I don't know for sure how A and B are related,
> > but I will say that A is the ancestor of B" simpler than
> > "I don't know for sure how A and B are related"?
>
> If we accept stratigraphy and that fossils in lower strata appeared before
> those in higher strata and if we follow a series of fossils that are
> obviously related, eg rat-like mammals in the late cretaceous and
> subsequently more elaborate mammals in the early tertiary then I think it is
> not unreasonable to say that not only are the mammals related, but also that
> the latter mammals evolved from ancestral forms that looked like those
> rat-like fossils.
I'd agree that stratophenetics works, sometimes, as a vague first
approximation of phylogeny. I'd agree that the later mammals evolved from
ancestral forms that looked like those rat-like fossils. But the question
is whether they evolved *from* those rat-like fossils, i.e. whether any
particular species can be identified as the ancestor of any other
particular species. And what you just said takes no position at all on
that question.
> Of course, it is formerly possible that both evolved
> independently from a ghost species that we have no idea how it appeared. It
> just seems to me that the simpler hypothesis is that we have an
> ancestral-descendent relationship here since the insertion of a ghost
> species is adding a new variable. This reasoning is sometimes referred to
> Occam's razor and forms the basis of parsimony.
And there are paleontologists who would agree with you, at least up to a
point. John Alroy used to say "ancestry is parsimonious" at frequent
intervals, and maybe still does. But the assumption inherent in this is
that you have a good enough sample of species that we are likely to have a
given ancestor in that sample. This may sometimes be true (Pete Wagner
makes a strong claim for Ordovician snails, for example), but probably not
often. Consider these in combination: 1) the number of recent species
(take a low estimate if you like), 2) the number of known fossil species
(take a high estimate if you like), 3) the mean duration of species (would
you agree somewhere between 1 and 10 million years?), and 4) the apparent
rough constancy in standing diversity since the mid-Paleozoic, at least
among fossilizable marine invertebrates, and since the early Eocene among
North American land mammals, to generate 5) an estimate of the total
number of species that have ever lived; try this within groups if you
like. Now, compare 5 with 2 and tell me what you get.
(The other assumptions are that we can tell species apart from closely
related species -- that we don't cluster multiple species as one species,
and that we can produce a reliable cladogram from the available
characters.)
Maximiliano Corredor
"John Harshman" <harshman....@sjm.infi.net> escribió en el mensaje
news:harshman.diespamdi...@user-2ivel8o.dialup.mindspring.com
....
> But that's quite different from identifying an ancestral species. The same
> thing is done with morphological characters, and even the most fanatical
> cladists do it: the identification of ancestral character states, and even
> groups of character states ("hypothetical ancestors"). What you can't do
> is equate those groups of character states to any actual, known species.
> Even if, for example, you find that your ancestral sequence actually
> exists in some living species, would you then infer that species to be the
> ancestor of all the other species? I suspect not, but if you would, then
> say so.
>
Please, explain me why can't you make such a kind of hypothesis? If you have
two sister species, and the theoretical ancestor is "identical" to one of
them, why can't we make this hypothesis: A suffered a speciation event,
resulting two species, B, and A' which remains equal to A?
syvanen
I agree with everything that you mention. These are the caveats that
any thinking person keeps in mind when offering the simplest
explanation for the known facts. It still seems to me, that rejecting
the simplest explanation because there could be something out there
that could overturn that explanation does not advance our
understanding -- it meerly bogs us down in sterile what if scenarios
without providing us with larger theoretical structures that have the
potential to lead to greater insights.
Mike Syvanen
Mike
: "Mike" <mikemi...@my-dejanews.com> wrote in message
When I first ran into Cal (his pseudonym then was lirpA1), way back in
95/96, he was already providing backing vocals for Nyikos.
Cal apparently works alone these days, which is why I said 'much of
the time', but his arguments haven't changed noticeably.
: Mike Syvanen
Cal King
mikemi...@my-dejanews.com (Mike) wrote:
>getulus@no?bull.net? (Cal King) wrote in message
> news:<42j57.43223$C81.3...@bgtnsc04-news.ops.worldnet.att.net>...
>> In article <98f4a681.01071...@posting.google.com>,
> mikemi...@my-dejanews.com (Mike) wrote:
>> >Replying to getulus@no bull.net (Cal King) :
>
>> >: >> All the paleontologists here knows that fossil species A cannot
>> be
>> >: >> directly ancestral to fossil species B? How do they "know" that?
>> >: >
>> >: >Evasion, thy name is alias Cal...
>> >:
>> >: Thanks for proving my point. I said that one way cladists defend
>> the
>> >: absurdities of cladism is by engaging in ad hominem. There is it!
>> Ad
>> >: hominem!
>> >
>> >It isn't ad hominem if it's true.
>>
>> Precisely. It is not true. I did not in anyway "evade" Ken Cox's
>> question. You are therefore guilty of engaging in ad hominem.
>
>If you had read the three quoted paragraphs you had seen that the
>evasion
>was that you erected a strawman argument: you misconstrued my argument
>to be that A _cannot_ be directly ancestral to B.
Ken Cox, with apparently little, if any, familiarity with biology, asked
an irrelevant question of whether one individual can be shown to be the
ancestor of another individual of the same species. I pointed out
repeatedly that it is irrelevant to the cladists' claim that
ancestor-descendant relationships among different species are unknowable
even if the fossil record were complete. You, Mike Noren, as a dyed in
the wool cladist and a biologist, should know that Ken Cox's question is
irrelevant. Yet you keep pretending that it is relevant so that you can
accuse me falsely of "evading" his question. Now you claim that I
"erected a strawman argument". That is nuts. It is clear that you have
complete disregard for facts and are only interested in engaging in ad
hominem, even if you have to resort to using false premises.
>My real, as opposed to this strawman, argument is that it is
>impossible
>to know if species A is directly ancestral to species B. It may be
>or it may not, and there is no way to determine which is the case.
That is indeed the cladist's claim, which is something I have been
trying to impress upon Mr. Cox, who seems to have the misunderstanding
that cladists do not deny that ancestor-descendant relationships are
knowable. And you apparently agree with this claim. Fair enough. All
that I am saying is that cladists claim that ancestor-descendant
relationships are unknowable and you agree! So what is your problem?
Other scientists, who are not intoxicated by cladism, do not make the
same claim. They claim that ancestor-descendant relationships can
indeed be determined, with as much certainty as sister group
relationships, contra cladistic dogma.
>HAHAHAHAHA!
>Trying to reverse the burden of proof, are we?
>
>No, Cal. I have nothing to prove. You have. It is you who claim that
>it is knowable whether fossil species A is directly ancestral to
>fossil species B.
That is so typical of cladists. They make assertion and then argue that
they don't have to prove their assertion.
Of course ancestor-descendant relationships are knowable, since they can
be inferred from morphology and stratigraphy. Unless there has been
massive convergence, Homo erectus is most likely to be ancestral to Homo
sapiens. This fact can be inferred from their morphological
similarities and their stratigraphic ranges.
>> Comparative anatomy, or something that the cladists have abandoned.
>> They rely instead on superficial similarities.
>
>Comparative anatomy, I see. Intuitive analysis. So, that's
>reproducible, is it?
Comparative anatomy is an observation. It is of course repeatable. Are
you really a science student? How can you not recognize this simple
fact?
>Tell you what: I'm a fairly hard-core cladist, right? I've published
>articles in Nature and Cladistics, and a couple more are in the works.
>You read any of those articles, and tell me if I "rely almost entirely
>on morphology", OK?
Yes, of course, you are a molecular systematist, but you are not a
paleontologist. Paleontologists simply cannot rely on molecular data,
since such data is rarely available from fossils. So, they must rely on
morphology. But, not all paleontologists rely exclusively on
morphology. Only the cladists do that. Those paleontologists who are
not encumbered by the cladistic straightjacket take into account
stratigraphy, biogeography, physiology etc. in formulating their
phylogenetic hypothesis. Since you are a cladist, it is very likely
that you ignore stratigraphy, biogeography, physiology, ecology,
behavior and yes, even morphology in your analysis.
>References available on demand.
I am impressed by the heights to which you have ascended, and equally
impressed by how low you have stooped in order to engage in gratuitous
ad hominem.
>> >: and they ignore stratigraphy.
>> >
>> >Huh?
>>
>> More denial.
>
>I really don't understand your argument. What is it?
I am not surprised since you are dishonest.
>> I am sorry some things cannot be quantified exactly. But I would say
>> that it is definitely more likely than Homo erectus and Homo sapiens
>> being unrelated but only convergently similar.
>
>"Unrelated but only convergently similar" isn't the flipside of the
>claim that H. erectus is directly ancestral to H. sapiens, is it. The
>flipside would be "H. erectus is closely related but not necessarily
>the direct ancestor of H. sapiens".
Of course, the cladist only recognizes sister taxa relationships. The
problem is that Homo erectus is much older stratigraphically than Homo
sapiens (though with some stratigraphic overlap), so they cannot be
sister species. Even if they are sister species, they must share a
common ancestor, correct? Given a complete fossil record, this common
ancestor should exist, shouldn't it? Unless there has been quantum
evolution, this ancestor should be quite similar to both Homo erectus
and Homo sapiens, and thus it should be recognizable as the ancestral
species of both because it would be stratigraphically older than both
Homo erectus and Homo sapiens but morphologically very similar. Hence
it is indeed possible to determine ancestor-descendant relationships, if
the fossil record is complete, even though cladistic methodology is
incapable of making that determination. You are hopelessly intoxicated
by cladism if you insist that ancestral species cannot be identified
even if the fossil record is complete. Fortunately, not all scientists
are similarly intoxicated.
>> >Or is it just an educated guess which is not actually based on any
>> >kind of reproducible analysis at all?
>> >
>> >I repeat:
>> >please detail, using DNA or fossils, just how you'd prove that fossil
>> >species A was directly ancestral to fossil species B.
>>
>> I have already pointed out that one can use morphological similarities
>> and stratigraphy. You are ignoring what I pointed out and continue to
>> dishonestly argue that I "evade" your questions so you can engage in ad
>> hominem.
>
>I am asking you HOW you'd use "morphological similiarities and
>stratigraphy".
I just told you how.
>The answer seems to be that you'd look at them, and
>then intuitively decide whether A is directly ancestral to B.
>In other words, you'd show NOTHING. You'd simply ASSERT ancestorship,
>and I hope I'm forgiven for not being terribly impressed by that.
You seem to think that "intuition" is a dirty word. FYI, some of the
greatest advances in science originated as a hunch, or intuition, in the
mind of a great scientist. But you are quite correct, intuition is
worthless unless there is data to support the "hunch." That said, the
hypothesis that H. erectus is ancestral to Homo sapiens is not a hunch,
your misrepresentation notwithstanding. It is based on morphological
similarities between these two species, and the fact that H. erectus is
the older species stratigraphically. H. erectus is intermediate in
brain size between Australopithecus and H. sapiens. H. erectus is also
much more humanlike and much less apelike in its facial anatomy than
Australopithecus. Morphological similarities and stratigraphy are the
reasons why most physical anthropologists agree that H. erectus is most
likely to be ancestral to H. sapiens. Morphological similarities and
stratigraphy are data, which you will of course ignore. If you ignore
data, then of course you see "NOTHING." Scientists who ignore data are
"no longer scientific," according to your hero Arnold Kluge. I doubt
that scientists who ignore both data and intuition will achieve any
degree of greatness.
In the absence of Pasteur's "prepared mind," chance turns away,
accidents are not converted into serendipitous discoveries, and average
scientists are sorted from great.——James Powell, 1998, "Night Comes to
the Cretaceous"