Hemoglobin Genes and the Fossil Record
Laurence A. Moran
Last week (January 12, 1998) Peter Nyikos was responding to a statement made
by Matt Silberstein. Here's the relevant quotations,
Peter Nyikos said,
>Matt Silberstein said,
>>The fossils are the icing on the cake. The
>>definitive "proof", if you will, was discovering that the nested
>>hierarchy of DNA similarity matches the nested hierarchy of
>>morphology.
>This "discovery" is still many years in the future. In the
>meantime, we have anomalies like the various kinds of hemoglobin
>all agreeing that mammals are more closely related to birds
>than birds are to lizards, snakes, or turtles, which is
>falsified by the fossil evidence.
I pointed out that Peter's statement was not correct. The various kinds of
hemoglobin do not all agree that mammals are more closely related to birds
than birds are to reptiles. I gave Peter a recent reference to the scientific
literature that supports my claim. In a subsequent posting I pointed out that
recent work with hemoglobin genes indicates that birds are related to reptiles
and there are many papers that show this.
This is the paper we are discussing,
Fushitani et al. (1996) The Amino Acid Sequences of Two alpha
Chains of Hemoglobin from Komodo Dragon _Varanus komodoensis_
and Phylogenetic Relationships of Amniotes.
Mol. Biol. Evol. 13, 1039-1043.
For some reason Peter choose not to read the paper that I referenced. I assume
that he hasn't had time to get to the library or perhaps his library does not
have the important journals on molecular evolution. In this posting I will
respond to some of the scientific points that Peter brings up.
Peter said,
>Moran found a source more
>recent than the ones I was using, apparently gathering data from ONE
>species of reptile. Why would they be using a rare creature
>like the Komodo Dragon lizard for a study, unless Moran
>had to scrape the bottom of the barrel for a study which
>AGREES with the fossil record?
The new *data* was from the Komodo dragon. They then compared these sequences
with all those in the current databases. I chose this particular paper because
the abstract clearly stated that "birds form a sister group with other
reptiles but not with mammals". Since the authors were studying hemoglobin
genes this seemed particularly relevant to your previous statement. There are
plenty of other recent studies that also show agreement between hemoglobin
dendrograms and the fossil record. I'd be happy to supply you with the
references if you think they will help you to understand the current state of
knowledge in the field.
Peter says,
>Isn't it interesting how Dr. Moran chose to go on the offensive
>and STILL hasn't indicated that he's read the paper, as opposed
>to pulling down an abstract from a website and making it seem
>like it presented ALL "the real data" on this issue?
I read the paper two years ago when it was first published and I re-read it
last week. I posted the abstract from the NCBI Entrez site so that I wouldn't
have to type it myself. The particular paper that I choose does not represent
ALL of the real data. We agree that there are several older studies that
seemed to show a bird/mammal relationship. However, most of the _modern_ work
conflicts directly with what you said to Matt Silberstein.
In responding to Matt you specifically said that the "discovery" of congruence
between molecular and fossil data was many years in the future and that the
hemoglobin data was an example of anomaly. I wanted to correct you on this
because you run the risk of misleading others who may not be familiar with the
scientific literature.
Peter says,
>Gee, with so many other lizards available, why did they choose
>such a rare lizard? And as long as they were sampling endangered
>species, why didn't they pick the tuatara (Sphenodon) which would
>have given more diversity than another squamate?
I suspect that they chose the Komodo dragon because they were interested in
knowing whether it had paraologous alpha-globin genes, particularly an
embryonic alpha globin gene (alpha-D). The other squamate sequences are adult
alpha-globins (alpha-A). As you probably know, there was some speculation that
only birds and turtles contained this particular form of alpha-globin gene and
some of the confusion in the older literature is due to comparisons that do
not invlove orthologous genes.
They didn't need to sequence Sphenodon genes because sequences of both alpha-D
and alpha-A genes from this species have been available since 1988. Why would
you expect them to sequence something that had already been sequenced?
Peter said,
>Larry Moran said,
>>After they added their own sequence data to the
>>dataset they go on to compare the sequence with what's already been
>>published. This is how science is done in this field and Peter Myikos
>>would know this if he actually read the primary literature.)
>Peter knows such elementary stuff, as well as a lot of things
>Moran seems to be unaware of.
My apologies. From what you have been posting I assumed that you were not
familiar with the field. Your questions seemed to indicate that you didn't
understand how these experiments are done.
>>Here's a paper that deals with the issue. Note that
>>the authors seem to think that bird globins are closest to reptile
>>globins, as expected from the fossil evidence, and not to mammalian
>>globins as Nyikos claims.
>
>That's one set of authors. I see your one set and raise you four
>primary sources and one secondary source.
I think you misunderstood my point. I believe that your older references have
been superseded by recent, more careful work, with additional data. That's why
the statement you made to Matt is incorrect. Are you suggesting that the older
papers have the same standing as the newest work? Besides, I am not relying
on just one paper as you seem to suggest.
>My point is that Moran was either blissfully unaware of these
>earlier studies or deliberately ignored them because they
>didn't support his claims.
I have been teaching this stuff for twenty years. In the 1980's I used to
point out to my students that the globin trees were hard to interpret. At
that time there were several possible explanations and we used to discuss
the possibilities. By 1990 the problems had been largely resolved and now
I don't even use globin genes as examples because they're boring.
>>Not only that but Nyikos said that *ALL* the work with globins showed
>>birds related to mammals and not reptiles.
>I didn't say "all," nor did I mean to imply that there were no
>anomalous data sets. But the general trend in the literature
>with which I was familiar was as I indicated.
Here's what you said,
"In the meantime, we have anomalies like the various kinds of
hemoglobin all agreeing that mammals are more closely related
to birds ... "
When you said "all agreeing ..." I interpreted that differently than you
meant. I thought you were saying that _all_ of the various kinds of hemoglobin
showed a bird/mammal cluster. I now know that you didn't mean to say this.
I'm still not exactly sure what you _did_ mean though.
In any case, my primary objection is that you misrepresented the "general
trend in the literature". Since we are agreed that this is what you intended
to communicate then all that remains is to decide whether you were correct
or whether you were simply unfamiliar with the recent literature in the
field. You won't be able to come to a conclusion until you read the
papers.
[snip]
>> Peter's response is to
>>mention older references from the 1980's. We have a pretty good idea why
>>some of the initial work from fifteen years ago was misinterpreted.
>Was it? Moran gives no indication why, and perhaps he can't--perhaps
>he just pulled down the abstract from a website and hasn't a clue
>as to whether the article even mentions these earliler studies.
The paper discusses some of the older work - you really should read it.
I do have some idea why there was controversy in the 1980's and how it was
resolved. I'd be happy to explain it to you after you have read the recent
papers. What is it that you don't understand? Do you know about gene families
and the importance of examining orthologous genes? Do you understand the
methodology of sequence alignment, similarity scores, and tree construction?
If you could identify those areas that you are having trouble with it would
make it easier for me to enlighten you. But first you have to read the
papers, I can't help you if you won't put in some effort.
>The issue was whether *HEMOGLOBIN* agreed with the fossil
>evidence. Moran retreats to glittering generalities:
Yes, this was the issue. I say that the hemoglobin dendrograms agree with
the fossil record and you say they do not.
>>But the main point is that most of the recent work, involving more careful
>>analysis and more data, all shows birds related to reptiles. Peter's
>>original statement is unequivocally wrong. There are lots of other papers
>>that show the same thing.
>Which, of course, Moran doesn't mention. Might these be papers
>that compare morphology? or genes other than the ones for
>hemoglobin and myoglobin?
I'm talking about papers that examine hemoglobin genes - those are the ones
that you claim are anomalous. Myoglobin genes are not hemoglobin genes. If
you want to discuss the myoglobin genes then let's start another thread.
>>Now, the appropriate thing for Peter to do is to read the papers and think
>>about what he said. Then he should post a correction to talk.origins and
>>apologize for his factual error. This is the honorable thing to do, and we
>>all know that Peter Nyikos is an honorable man.
>Indeed, but I will only read the papers if Moran explicitly
>assures me that HE has read them.
Of course I have read them. Why on earth would you think otherwise?
I'm having trouble following your logic here. What difference would it really
make if I hadn't read the papers? Wouldn't you want to know the truth about
hemoglobin genes anyway? Why would you refuse to go and look up a paper that
clearly conflicted with your understanding of the issue? Am I missing
something?
When can we expect an apology? Do you agree that it is the honorable thing
to do under the circumstances?
>>Peter made a statement about the state of knowledge in the literature. I'm
>>simply pointing out that Peter's summary of the current data is wrong.
>You are blatantly asserting it, having quoted an abstract of an article
>you show no sign of having read yourself.
>> They have known this for about seven or eight
>>years. Furthermore, these workers understand why older studies were
>>misleading.
>Why? Moran won't tell you here, folks. Does he even know why?
>Because they used the specific globins above instead of all globins?
>Because they used non-cladistic methods instead of cladistic ones?
>Moran doesn't give a blessed clue anywhere?
After you've read the papers and realize that the earlier studies were
misleading I'll be happy to help you out. Please tell me what parts you don't
understand. The important thing right now is to get you to understand that
you made a mistake. Only then can we discuss why you were fooled by
relying on old papers.
In their abstract Fushitani et al. (1996) said,
"4) squamates first split off from the ancestor of other reptiles and
birds."
Peter asked,
>Including turtles???? this should be interesting.
Yes, they included both the turtle alpha-D and alpha-A genes in their
analysis. If you are particularly interested in turtles then you should
check out the following paper,
Caspers, G-J., Reinders, G-J., Leunissen, J.A.M., Wattel, J.,
and de Jong, W.W. (1996) Protein Sequences Indicate That Turtles
Branched Off from the Amniote Tree After Mammals.
J.Mol.Evol. 42, 580-586
These workers examined the phylogenetic relationship of birds (B), mammals (M)
and turtles (T). They looked at 12 different genes and compared three
different methods of constructing trees. Seven out of twelve genes strongly
supported a (M(B,T)) relationship by all three methods. In the case of the
other five genes the three different methods did not all support the same
phylogeny. Note that the best tree was the one that clustered birds and
reptiles as suggested by the fossil record.
Caspers et al. (1996) looked at both the alpha- and beta-hemoglobins. In both
cases the analysis by maximum parsimony, neighbor-joining, and maximum
likelihood all agreed on a (M(B,T)) tree. This is another recent example of
the analysis of hemoglobin genes agreeing with the fossil record. You should
read this paper as well. It has lots of references to the literature from the
past ten years. Note that I have now given you two papers that refute your
summary of the literature. There are more.
Larry Moran
bull.net Cal King
In article <6a32sg$s5m$1...@bioinfo.med.utoronto.ca>,
lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) wrote...
>Last week (January 12, 1998) Peter Nyikos was responding to a statement made
>by Matt Silberstein. Here's the relevant quotations,
>
>Peter Nyikos said,
>>Matt Silberstein said,
>>>The fossils are the icing on the cake. The
>>>definitive "proof", if you will, was discovering that the nested
>>>hierarchy of DNA similarity matches the nested hierarchy of
>>>morphology.
>
>>This "discovery" is still many years in the future. In the
>>meantime, we have anomalies like the various kinds of hemoglobin
>>all agreeing that mammals are more closely related to birds
>>than birds are to lizards, snakes, or turtles, which is
>>falsified by the fossil evidence.
>
>I pointed out that Peter's statement was not correct. The various kinds of
>hemoglobin do not all agree that mammals are more closely related to birds
>than birds are to reptiles. I gave Peter a recent reference to the scientific
>literature that supports my claim. In a subsequent posting I pointed out that
>recent work with hemoglobin genes indicates that birds are related to
>reptiles and there are many papers that show this.
Pardon me for jumping in, I skimmed through part of the paper by Caspers et
al. (1996) that you cited below. They wrote in the discussion section
(p.583) that "Previous studies of protein and nucleic acid sequences failed to
give conclusive evidence about the position of turtles among the amniotes."
They went on to show how several molecular studies done in the early 90's
were either inconclusive or contradicted one another. Then Caspers et al.
continued, amusingly, that "...28S rRNA sequences, which had earlier been
inconclusive (Hedges et al. 1990), did group turtles within a bird-reptile
clade, but as sister group to crocodiles, while salamanders were also included
in the bird-reptile clade in this analysis (Eernisse and Kluge 1993)."
If different sets of DNA data do not agree with one another, how can we then
claim that DNA data coincide with morphology data as a general trend?
>In responding to Matt you specifically said that the "discovery" of
>congruence between molecular and fossil data was many years in the future and
>that the hemoglobin data was an example of anomaly. I wanted to correct you
>on this because you run the risk of misleading others who may not be familiar
>with the scientific literature.
I would agree with Nyikos on this point because molecular methodology is still
evolving. There is no consensus on the best method for data analysis or which
molecules are the most informative. As Eernisse and Kluge's (1993) paper
shows, some amusing (and demonstrably erroneous) results such as salamanders
being part of the bird-reptile clade are possible.
>Peter says,
>>Gee, with so many other lizards available, why did they choose
>>such a rare lizard? And as long as they were sampling endangered
>>species, why didn't they pick the tuatara (Sphenodon) which would
>>have given more diversity than another squamate?
One can ask a different but similar question of Caspers et al., "With so many
turtles available, why did they choose one that has long been part of the pet
trade --the red-eared slider?" I don't know if the choice of a different
species would have changed the results but the red-eared slider may have been
subjected to abnormal selection pressures because of its history as a pet
animal and captive breeding.
>>>Here's a paper that deals with the issue. Note that
>>>the authors seem to think that bird globins are closest to reptile
>>>globins, as expected from the fossil evidence, and not to mammalian
>>>globins as Nyikos claims.
>>
>>That's one set of authors. I see your one set and raise you four
>>primary sources and one secondary source.
>
>I think you misunderstood my point. I believe that your older references have
>been superseded by recent, more careful work, with additional data. That's
>why the statement you made to Matt is incorrect. Are you suggesting that the
>older papers have the same standing as the newest work? Besides, I am not
>relying on just one paper as you seem to suggest.
Newer papers are not always better. Gardiner's (1982) hypothesis of a mammal
and bird clade was definitely not any better than previous hypotheses of a
closer bird-reptile link. Some other "new" cladistic studies by Cracraft
shows a owl-hawk clade according to Feduccia (1996). Is Cracraft's analysis
more accurate than previous conclusions that these two groups are only
convergently similar because it is newer?
>In any case, my primary objection is that you misrepresented the "general
>trend in the literature". Since we are agreed that this is what you intended
>to communicate then all that remains is to decide whether you were correct
>or whether you were simply unfamiliar with the recent literature in the
>field. You won't be able to come to a conclusion until you read the
>papers.
The general trend in the literature do support Nyikos' claim that congruence
between data sets are an ideal that may only be met many years in the future,
IMO.
>Caspers et al. (1996) looked at both the alpha- and beta-hemoglobins. In both
>cases the analysis by maximum parsimony, neighbor-joining, and maximum
>likelihood all agreed on a (M(B,T)) tree. This is another recent example of
>the analysis of hemoglobin genes agreeing with the fossil record. You should
>read this paper as well. It has lots of references to the literature from the
>past ten years. Note that I have now given you two papers that refute your
>summary of the literature. There are more.
>Larry Moran
I think what is written in this paper pretty much debunks any belief that
agreement among data sets are a general trend.
Regards.
Laurence A. Moran
In article <6a65pv$s...@bgtnsc01.worldnet.att.net> get...@worldnet.att.net
writes:
The question we are discussing is whether analysis of hemoglobin genes
show that birds cluster with reptiles or with mammals. There are lots of
other interesting questions that we could talk about later but let's try
and deal with one question at a time.
>>In responding to Matt you specifically said that the "discovery" of
>>congruence between molecular and fossil data was many years in the future and
>>that the hemoglobin data was an example of anomaly. I wanted to correct you
>>on this because you run the risk of misleading others who may not be familiar
>>with the scientific literature.
>
>I would agree with Nyikos on this point because molecular methodology is still
>evolving. There is no consensus on the best method for data analysis or which
>molecules are the most informative. As Eernisse and Kluge's (1993) paper
>shows, some amusing (and demonstrably erroneous) results such as salamanders
>being part of the bird-reptile clade are possible.
I'm not sure that I understand your point. Do you claim that no molecular
evolution studies are valid because there are some anomalies?
>>Peter says,
>>>Gee, with so many other lizards available, why did they choose
>>>such a rare lizard? And as long as they were sampling endangered
>>>species, why didn't they pick the tuatara (Sphenodon) which would
>>>have given more diversity than another squamate?
>
>One can ask a different but similar question of Caspers et al., "With so many
>turtles available, why did they choose one that has long been part of the pet
>trade --the red-eared slider?" I don't know if the choice of a different
>species would have changed the results but the red-eared slider may have been
>subjected to abnormal selection pressures because of its history as a pet
>animal and captive breeding.
Isn't this a bit picky? Do you have any reason to doubt the results of
their experiments?
>>>>Here's a paper that deals with the issue. Note that
>>>>the authors seem to think that bird globins are closest to reptile
>>>>globins, as expected from the fossil evidence, and not to mammalian
>>>>globins as Nyikos claims.
>>>
>>>That's one set of authors. I see your one set and raise you four
>>>primary sources and one secondary source.
>>
>>I think you misunderstood my point. I believe that your older references have
>>been superseded by recent, more careful work, with additional data. That's
>>why the statement you made to Matt is incorrect. Are you suggesting that the
>>older papers have the same standing as the newest work? Besides, I am not
>>relying on just one paper as you seem to suggest.
>
>Newer papers are not always better. Gardiner's (1982) hypothesis of a mammal
>and bird clade was definitely not any better than previous hypotheses of a
>closer bird-reptile link. Some other "new" cladistic studies by Cracraft
>shows a owl-hawk clade according to Feduccia (1996). Is Cracraft's analysis
>more accurate than previous conclusions that these two groups are only
>convergently similar because it is newer?
What is your point? We can't trust the earliest work when the field was
just being developed but we can't trust the latest work either because you
know of at least one apparent anomaly? Is their any paper that you feel is
reliable?
>>In any case, my primary objection is that you misrepresented the "general
>>trend in the literature". Since we are agreed that this is what you intended
>>to communicate then all that remains is to decide whether you were correct
>>or whether you were simply unfamiliar with the recent literature in the
>>field. You won't be able to come to a conclusion until you read the
>>papers.
>
>The general trend in the literature do support Nyikos' claim that congruence
>between data sets are an ideal that may only be met many years in the future,
>IMO.
I do not agree.
>>Caspers et al. (1996) looked at both the alpha- and beta-hemoglobins. In both
>>cases the analysis by maximum parsimony, neighbor-joining, and maximum
>>likelihood all agreed on a (M(B,T)) tree. This is another recent example of
>>the analysis of hemoglobin genes agreeing with the fossil record. You should
>>read this paper as well. It has lots of references to the literature from the
>>past ten years. Note that I have now given you two papers that refute your
>>summary of the literature. There are more.
>I think what is written in this paper pretty much debunks any belief that
>agreement among data sets are a general trend.
I disagree. On a topic where there has been much disagreement the authors
show that seven out of twelve genes give the same result by three
different methods of analysis. There are some good reasons to suspect that
some of the five others may be prone to artifacts.
You have to realize that we are focusing on some special cases where there
have been disagreements in the past. In general, molecular data strongly
supports the fossil evidence and the phylogenies deduced by comparative
morphology. If you really think that there is no trend to agreement among
data sets then you must be very skeptical of all molecular studies.
Larry Moran
bull.net Cal King
In article <6a6iuo$mah$1...@bioinfo.med.utoronto.ca>,
>>If different sets of DNA data do not agree with one another, how can we then
>>claim that DNA data coincide with morphology data as a general trend?
>
>The question we are discussing is whether analysis of hemoglobin genes
>show that birds cluster with reptiles or with mammals. There are lots of
>other interesting questions that we could talk about later but let's try
>and deal with one question at a time.
Let's go back to the beginning of your original post. Matt Silberstein made
the point that "The fossils are the icing on the cake. The definitive "proof",
if you will, was discovering that the nested hierarchy of DNA similarity
matches the nested hierarchy of morphology." Hence Matt is claiming that DNA
trees coincide with the morphology tree. To which Peter Nyikos responded with
a definitive no.
P. Nyikos:
>>>>This "discovery" is still many years in the future. In the
>>>>meantime, we have anomalies like the various kinds of hemoglobin
>>>>all agreeing that mammals are more closely related to birds
>>>>than birds are to lizards, snakes, or turtles, which is
>>>>falsified by the fossil evidence.
Then you responded to Nyikos thusly:
>>>In responding to Matt you specifically said that the "discovery" of
>>>congruence between molecular and fossil data was many years in the future
>>>and that the hemoglobin data was an example of anomaly. I wanted to correct
>>>you on this because you run the risk of misleading others who may not be
>>>familiar with the scientific literature.
I pointed out the articles of Caspers et al., which you cited, in which they
pointed out the incongruences between many DNA data sets and morphology data
sets in the early 1990's. Hence Nyikos is correct that data congruence is an
ideal that has not been realized.
Cal King:
>>I would agree with Nyikos on this point because molecular methodology is
>>still evolving. There is no consensus on the best method for data analysis
>>or which molecules are the most informative. As Eernisse and Kluge's (1993)
>>paper shows, some amusing (and demonstrably erroneous) results such as
>>salamanders being part of the bird-reptile clade are possible.
Larry Moran:
>I'm not sure that I understand your point. Do you claim that no molecular
>evolution studies are valid because there are some anomalies?
No, absolutely not, I am just pointing out that there is no congruence
between data sets and that the choice of characters can have a profound effect
on the results. Eernisse and Kluge's choice of characters and methodology
have resulted in an amusingly false result.
>>>Peter says,
>>>>Gee, with so many other lizards available, why did they choose
>>>>such a rare lizard? And as long as they were sampling endangered
>>>>species, why didn't they pick the tuatara (Sphenodon) which would
>>>>have given more diversity than another squamate?
>>One can ask a different but similar question of Caspers et al., "With so
>>many turtles available, why did they choose one that has long been part of
>>the pet trade --the red-eared slider?" I don't know if the choice of a
>>different species would have changed the results but the red-eared slider
>>may have been subjected to abnormal selection pressures because of its
>>history as a pet animal and captive breeding.
>
>Isn't this a bit picky? Do you have any reason to doubt the results of
>their experiments?
My question is legit. After all, captive breeding and artificial selection
can have a profound effect on morphology and perhaps on the distribution of
certain alleles. May be the red-eared slider has not been subjected to the
same degree of selective breeding as the domestic dog, but why use this
particular species ot turtle if there are so many others available?
>>> Are you suggesting that the
>>>older papers have the same standing as the newest work? Besides, I am not
>>>relying on just one paper as you seem to suggest.
>>Newer papers are not always better. Gardiner's (1982) hypothesis of a
>>mammal
>>and bird clade was definitely not any better than previous hypotheses of a
>>closer bird-reptile link. Some other "new" cladistic studies by Cracraft
>>shows a owl-hawk clade according to Feduccia (1996). Is Cracraft's analysis
>>more accurate than previous conclusions that these two groups are only
>>convergently similar because it is newer?
>What is your point? We can't trust the earliest work when the field was
>just being developed but we can't trust the latest work either because you
>know of at least one apparent anomaly?
The field is still very much in a state of flux. So there is little reason to
suggest that newer papers are necessarily more reliable.
>Is their any paper that you feel is reliable?
They would be more reliable if they don't show such obvious falsehoods as
salamanders being part of the bird-reptile clade.
>>The general trend in the literature do support Nyikos' claim that congruence
>>between data sets are an ideal that may only be met many years in the
>>future, IMO.
>
>I do not agree.
You are entitled to.
>You have to realize that we are focusing on some special cases where there
>have been disagreements in the past. In general, molecular data strongly
>supports the fossil evidence and the phylogenies deduced by comparative
>morphology. If you really think that there is no trend to agreement among
>data sets then you must be very skeptical of all molecular studies.
>
>Larry Moran
I am skeptical of cladistic analysis of morphological data because they are
easily fooled by convergent similarities. You idea of "data sets" do not seem
to include cladistic analyses of morphological characters. If these data sets
are included, then there is no trend at all for agreement among data sets
because there are many differences among the many morphology cladograms of
amniote relationship and morphlogy data sets often conflict DNA data sets.
bull.net Cal King
In article <6a89d7$339$1...@bioinfo.med.utoronto.ca>,
>Peter disagreed with Matt and gave an example that I dispute.
He in turn disputed your example.
>I certainly don't claim that there are no problems in the field. In most
>cases there is remarkable congruence between data sets
Is there any statistical survey that could back up your claim of "in most
cases there is remarkable congruence" or is it your subjective impression?
>The
>problem we are discussing in this thread is whether the analysis of
>hemoglobin genes supports a bird/reptile cluster. It does. Do you dispute
>this?
One study does, Nyikos gave many examples that don't. The larger question is
whether there is general consensus among morphology, fossil and DNA data sets.
>Your point is valid but hardly seems to apply to these turtles. You should
>direct your criticism to those who use E. coli, B. subtilis, C. elegans,
>D. melanogaster, yeast (especially), rice, corn, wheat, rats, cows, and
>mice as examples. The problem you raise is much, much more likely to cause
>difficulties with these species than with some turtles that have been
>kept as pets for a few generations.
>
>It sounds to me as though you are stretching pretty hard in order to come
>up with excuses.
Excuses for what? I am not saying that the use of the red-eared slider
or Komodo dragons invalidated their studies. Never said that. I just thought
that it was peculiar for them to have chosen these particular species.
>This is a strange attitude as far as I am concerned. When there have been
>unusual results that need to be addressed I will continue to have more
>confidence in recent work, thank-you very much. You may choose to behave
>differently.
Absolutely, I look at the methods, results and conclusions, and I would not
put too much weight on the date of the paper for guidance. Otherwise I would
have bought Cracraft's hypothesis of an owl-hawk clade in stead of the older
and more likely hypothesis of these two groups being convergent.
>"there is no trend at all for agreement among data sets"! Is this really a
>statement that you think you can defend?
Yes, I have chosen this as a stand. I welcome any objective data that would
falsify my claim.
>Don't you think you might be exaggerating a tiny bit?
Not according to my experiences based on the somewhat arbitrary set of papers
that I have sampled.
>Do you think that the relationship between
>mammals, birds and reptiles is completely unresolved?
The details are far from resolved. We don't know, for example, when and from
what group the birds are derived.
>Is (birds,(mammals, reptiles)) just as likely to be correct as ((birds,
>mammals),reptiles)?
>
>
>Larry Moran
I would agree that birds are probably closer to reptiles than mammals.
But then gain, the exact details of the origins of these groups and many taxa
therein remain largely unresolved. That is why we need more data.
howard hershey
Cal King wrote:
>
> In article <6a6iuo$mah$1...@bioinfo.med.utoronto.ca>,
> lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) wrote...
> >
> >In article <6a65pv$s...@bgtnsc01.worldnet.att.net> get...@worldnet.att.net
> >writes:
>
> >>If different sets of DNA data do not agree with one another, how can we then
> >>claim that DNA data coincide with morphology data as a general trend?
Perhaps because *as a general trend* different sets of DNA data *do*
agree with one another, although one can certainly find anomalous cases
where they do not.
[snip]
>
> Let's go back to the beginning of your original post. Matt Silberstein made
> the point that "The fossils are the icing on the cake. The definitive "proof",
> if you will, was discovering that the nested hierarchy of DNA similarity
> matches the nested hierarchy of morphology." Hence Matt is claiming that DNA
> trees coincide with the morphology tree. To which Peter Nyikos responded with
> a definitive no.
No. To which Peter pointed out an anomalous case where the nested
hierarchies do not (or, more acurately, did not a decade ago) coincide.
One does not discredit an entire set of hierarchies by pointing out a
few cases where there is a lack of congruence. One uses those
necessarily rare (if they are indeed anomalous) cases to determine what
kinds of things can lead to a 'false' conclusion (such as might occur by
choosing the wrong member of a multigene family or in cases of
convergence) or one gathers more data to try to resolve the lack of
congruence.
*If*, OTOH, you are saying that there is no or very little congruence
between the nested hierarchies of DNA similarity and the nested
hierarchies of morphology in living organisms and the nested hierachies
of fossil evidence, I think you would be quite mistaken, but you could
convince me by pointing out the studies that show that the *mass* of DNA
similarity data produces a nested hierachy so different from the
standard one as to be utterly different. But only use the most modern
data, not decade old stuff, which, as Larry points out, has been added
to, a process that sometimes removes anomalies.
>
> P. Nyikos:
> >>>>This "discovery" is still many years in the future. In the
> >>>>meantime, we have anomalies like the various kinds of hemoglobin
> >>>>all agreeing that mammals are more closely related to birds
> >>>>than birds are to lizards, snakes, or turtles, which is
> >>>>falsified by the fossil evidence.
>
> Then you responded to Nyikos thusly:
>
> >>>In responding to Matt you specifically said that the "discovery" of
> >>>congruence between molecular and fossil data was many years in the future
> >>>and that the hemoglobin data was an example of anomaly. I wanted to correct
> >>>you on this because you run the risk of misleading others who may not be
> >>>familiar with the scientific literature.
>
> I pointed out the articles of Caspers et al., which you cited, in which they
> pointed out the incongruences between many DNA data sets and morphology data
> sets in the early 1990's. Hence Nyikos is correct that data congruence is an
> ideal that has not been realized.
In the early 1990's. How many of these anomalies have been resolved
since then?
>
> Cal King:
> >>I would agree with Nyikos on this point because molecular methodology is
> >>still evolving. There is no consensus on the best method for data analysis
> >>or which molecules are the most informative. As Eernisse and Kluge's (1993)
> >>paper shows, some amusing (and demonstrably erroneous) results such as
> >>salamanders being part of the bird-reptile clade are possible.
>
> Larry Moran:
> >I'm not sure that I understand your point. Do you claim that no molecular
> >evolution studies are valid because there are some anomalies?
>
> No, absolutely not, I am just pointing out that there is no congruence
> between data sets
Is this a general claim? Are you saying that, in general, sequence
analysis for gene A gives *entirely* different results from sequence
analysis for gene B? That method A for generating trees gives
*entirely* different results from method B? Or are you saying that
there can be some disagreements and incongruities (mostly minor) when
using different molecules and/or different methods and that mindless
application of method or poor choice of molecule or feature
occassionally can, under certain circumstances, produce silly results?
I certainly agree with the latter sentence. The former is quite
problematical and you need more evidence than a single paper showing the
latter effect to support it.
> and that the choice of characters can have a profound effect
> on the results. Eernisse and Kluge's choice of characters and methodology
> have resulted in an amusingly false result.
>
[snip]
>
> My question is legit. After all, captive breeding and artificial selection
> can have a profound effect on morphology and perhaps on the distribution of
> certain alleles. May be the red-eared slider has not been subjected to the
> same degree of selective breeding as the domestic dog, but why use this
> particular species ot turtle if there are so many others available?
And you really think that you can change hemoglobin sequence
dramatically in a few years of breeding (when there is regular input
from wild specimens into the pet trade and you have no idea whether the
authors got their specimen from pet store or the wild)? I call this
grasping at will-o-the-wisps.
>
> >>> Are you suggesting that the
> >>>older papers have the same standing as the newest work? Besides, I am not
> >>>relying on just one paper as you seem to suggest.
>
> >>Newer papers are not always better.
No. But newer papers that add new sequences or other information do
increase the amount of evidence for or against alternatives and can, as
in this case, result in a change in interpretation. Similar events
occur all the time in the field of human genetics as more data is added
to family trees. Sometimes the combined and expanded data confirm a
prior paper. Sometimes they reduce the likelihood of the former paper's
conclusion that, say, a gene important in bipolar disorder is on
chromosome n.
[snip]
>
> The field is still very much in a state of flux. So there is little reason to
> suggest that newer papers are necessarily more reliable.
When the *reason* for the flux is that earlier papers are making
conclusions from analysis of more limited data sets, new papers that add
to the data set and/or improve the methodology for analysing data sets
certainly should be given added weight. It is not that the earlier
papers are more or less reliable, but they are limited to analysis at
the more limited level of knowledge imposed by the available evidence.
>
> >Is their any paper that you feel is reliable?
>
> They would be more reliable if they don't show such obvious falsehoods as
> salamanders being part of the bird-reptile clade.
See my comments about the nature of anomalies.
>
> >>The general trend in the literature do support Nyikos' claim that congruence
> >>between data sets are an ideal that may only be met many years in the
> >>future, IMO.
> >
> >I do not agree.
>
> You are entitled to.
If you mean by 'congruence' *perfect* congruence between all data sets
at every point in every data set, that ideal state will probably never
come. If you mean *general* congruence between sequence analysis
phylogenies and phylogenies determined by other means (with a certain
permitted number of anomalies when looking at minor points or places
with limited information or the occassional special case, like places
where there are gene families, that might confuse a lineage analysis),
that time has already come and passed you by.
> >You have to realize that we are focusing on some special cases where there
> >have been disagreements in the past. In general, molecular data strongly
> >supports the fossil evidence and the phylogenies deduced by comparative
> >morphology. If you really think that there is no trend to agreement among
> >data sets then you must be very skeptical of all molecular studies.
> >
> >Larry Moran
>
> I am skeptical of cladistic analysis of morphological data because they are
> easily fooled by convergent similarities. You idea of "data sets" do not seem
> to include cladistic analyses of morphological characters. If these data sets
> are included, then there is no trend at all for agreement among data sets
> because there are many differences among the many morphology cladograms of
> amniote relationship and morphlogy data sets often conflict DNA data sets.
And these independent DNA data sets present the opportunity for
resolving some of the conflicts that arise from purely morphological
analysis that result from the difficulty in distinguishing between
convergence and homology by descent. If, for example, the morphological
data is unable to distinguish (note that this is not a case of
*disagreement* between the morphological data and DNA data, it is a case
where one set of data is genuinely ambiguous and uninformative to the
question) between common recent divergence between hawks and owls and
convergence to common features from a separate lineage, but the majority
of DNA evidence from several different genes all point to convergence,
then I would preliminarily opt for the convergence argument and expect
that when fossils capable of resolving the morphological questions are
found that they will be congruent with the DNA data and show an
independent derivation of owls. That is how the process works.
Alternatively, if the DNA data you currently have are ambiguous about
descent relationships or show a relationship that makes no sense,
morphological evidence can help you find out what new information you
need to resolve the ambiguity or what assumption in the method was being
violated to produce the incongruity. That is how the process works.
But you seem to be trying to make a much stronger statement. You seem
to be implying that there is so little congruence between the DNA data
sets of the morphological and fossil data sets that they are regularly
and usually producing totally ingongruent and incompatible phylogenies.
If that is the statement you are making, I think you need better support
for that thesis than picking out a few cases (no matter how deviant from
expectation) in a 1993 paper that presents anomalous findings.
Bruce Salem
In article writes:
>MATCH!ediacara.org!there.is.no.cabal
>From: getulus@no bull.net (Cal King)
>Newsgroups: talk.origins
>Subject: Re: Hemoglobin Genes and the Fossil Record
>Date: 22 Jan 1998 13:53:50 -0500
>Message-ID: <6a84n6$f...@bgtnsc03.worldnet.att.net>
>References: <6a32sg$s5m$1...@bioinfo.med.utoronto.ca> <6a65pv$s...@bgtnsc01.worldnet.att.net> <6a6iuo$mah$1...@bioinfo.med.utoronto.ca>
>Reply-To: get...@worldnet.att.net
>
[...]
>I am skeptical of cladistic analysis of morphological data because they are
>easily fooled by convergent similarities. You idea of "data sets" do not seem
>to include cladistic analyses of morphological characters. If these data sets
>are included, then there is no trend at all for agreement among data sets
>because there are many differences among the many morphology cladograms of
>amniote relationship and morphlogy data sets often conflict DNA data sets.
I wonder that prehaps it is easier to find convergant traits within
morphologic typologies than you would admit. Noone is going to confuse the
phylogeny of a bat and a ptersaur because of the convergant anatomy of
the limbs. Why? Taxinomy and phylogeny, no matter how they are approached,
have a logic that is based on emperical facts. That different methods of
arriving at phylogeny give conflicting results is to be expected. This
spurs research, so people don't really champion one or other approach
in bad faith.
Bruce Salem
--
========================================================================
______
/_____/\
bull.net Cal King
In article <34C866...@indiana.edu>, hers...@indiana.edu (howard hershey)
wrote...
>
>Cal King wrote:
>>
>> In article <6a6iuo$mah$1...@bioinfo.med.utoronto.ca>,
>> lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) wrote...
>> >
>> >In article <6a65pv$s...@bgtnsc01.worldnet.att.net> get...@worldnet.att.net
>> >writes:
>>
>> >>If different sets of DNA data do not agree with one another, how can we
>> >>then claim that DNA data coincide with morphology data as a general >>
>>trend?
>
>Perhaps because *as a general trend* different sets of DNA data *do*
>agree with one another, although one can certainly find anomalous cases
>where they do not.
I would welcome the citation of an objective survey that would support such a
general trend.
>No. To which Peter pointed out an anomalous case where the nested
>hierarchies do not (or, more acurately, did not a decade ago) coincide.
Caspers et al. (1996) pointed out cases in the early 1990's, just a few short
years ago, that show no trend of agreement.
>One does not discredit an entire set of hierarchies by pointing out a
>few cases where there is a lack of congruence.
Actually if one study shows non-congruence, it should be investigated fully
rather than being brushed aside.
>One uses those
>necessarily rare (if they are indeed anomalous) cases
Again, please cite your statistics before labelling them as rare.
>*If*, OTOH, you are saying that there is no or very little congruence
>between the nested hierarchies of DNA similarity and the nested
>hierarchies of morphology in living organisms and the nested hierachies
>of fossil evidence, I think you would be quite mistaken
No only is there no congruence between types of data sets, there is often no
consensus, say, in the morphology data set. Sometimes different data sets
conflict strongly within the same paper. For example the allozyme data set
conflicted strongly with the DNA data in de Queiroz and Lawson's (1994 Biol.
J. Linn. Soc.) analysis of the garter snakes (Thamnophis). Shaffer et al.
(1991, Systematics Zool. 40:284-303) similarly find no congruence between data
sets in the Ambystomatid salamanders.
> but you could
>convince me by pointing out the studies that show that the *mass* of DNA
>similarity data produces a nested hierachy so different from the
>standard one as to be utterly different.
Then there is Lopez and Maxson's (1995, Biochem System. Ecol.) DNA tree of the
Lampropeltini, which conflicts strongly Keogh's (1996 Herpetologica) tree
based on morphology.
>But only use the most modern
>data, not decade old stuff, which, as Larry points out, has been added
>to, a process that sometimes removes anomalies.
These are all studies done within the last few years. Besides, what is wrong
with old data? Many immunological studies done in the 80's are still well
supported by new data. It is not date, it is the method and character that
may be the problem. There is no gurarantee that the newest techniques and the
newest characters will be more reliable.
>In the early 1990's. How many of these anomalies have been resolved
>since then?
None that I know of.
>Is this a general claim? Are you saying that, in general, sequence
>analysis for gene A gives *entirely* different results from sequence
>analysis for gene B?
Not my claim. My claim is that different data sets from morphology, fossil
and DNA often conflict with one another. If there are a few branches that are
the same, the results still conflict because a reptile as descendant of bird
cladogram and a bird as reptile descendant cladogram may differ by only one
branch, they are strongly conflicting nevertheless.
>If you mean by 'congruence' *perfect* congruence between all data sets
>at every point in every data set, that ideal state will probably never
>come.
Since there is only one historical tree, if the methods are good, then the day
should come. Heck, Hennig predicted that HIS method would do just that, but
flaws in his methodology of course have made it a hope rather than a reality.
>And these independent DNA data sets present the opportunity for
>resolving some of the conflicts that arise from purely morphological
>analysis that result from the difficulty in distinguishing between
>convergence and homology by descent.
Agreed.
>But you seem to be trying to make a much stronger statement. You seem
>to be implying that there is so little congruence between the DNA data
>sets of the morphological and fossil data sets that they are regularly
>and usually producing totally ingongruent and incompatible phylogenies.
That is not what I am implying. I don't imply total incongruence, just that
there is strong conflict among data sets.
Laurence A. Moran
In article <6aaomh$l...@bgtnsc03.worldnet.att.net> get...@worldnet.att.net
writes:
>>>
>>> In article <6a6iuo$mah$1...@bioinfo.med.utoronto.ca>,
>>> lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) wrote...
>>> >
>>> >In article <6a65pv$s...@bgtnsc01.worldnet.att.net> get...@worldnet.att.net
>>> >writes:
>>>
>>> >>If different sets of DNA data do not agree with one another, how can we
>>> >>then claim that DNA data coincide with morphology data as a general >>
>>>trend?
>>
>>Perhaps because *as a general trend* different sets of DNA data *do*
>>agree with one another, although one can certainly find anomalous cases
>>where they do not.
>
>general trend.
I took a quick look in my pile of papers and came up with a few that
survey many genes and some that discuss the integration of molecular and
morphological data. Here's a few to start you off.
Nikoh, N. et al. (1994) Phylogenetic Relationships of the Kingdoms
Animalia, Plantae, and Fungi, Inferred from 23 Different Protein
Sequences. Mol. Biol. Evol. 1, 762-768.
Novacek, M.J. (1992) Mammalian Phylogeny: shaking the tree.
Nature 356, 121-125.
Benton, M.J. (1990) Phylogeny of the Major Tetrapod Groups:
Morphological Data and Divergence Dates. J. Mol. Evol. 30, 409-424.
Doolittle, R.F. et al. (1996) Determining Divergence Times of the
Major Kingdoms of Living Organisms with a Protein Clock.
Science 271, 470-477.
Wray, G.A. et al. (1996) Molecular Evidence for Deep Precambrian
Divergences Among Metazoan Phyla. Science 274, 568-573.
Happy reading.
Larry Moran
Peter Nyikos
Hang on to your seats, folks, and prepare for a big
surprise.
lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) writes:
A CC goes to him.
>Last week (January 12, 1998) Peter Nyikos was responding to a statement made
>by Matt Silberstein. Here's the relevant quotations,
>Peter Nyikos said,
>>Matt Silberstein said,
>>>The fossils are the icing on the cake. The
>>>definitive "proof", if you will, was discovering that the nested
>>>hierarchy of DNA similarity matches the nested hierarchy of
>>>morphology.
>>This "discovery" is still many years in the future. In the
>>meantime, we have anomalies like the various kinds of hemoglobin
>>all agreeing
I should have restricted myself to alpha and beta hemoglobin,
and myoglobin.
that mammals are more closely related to birds
>>than birds are to lizards, snakes, or turtles, which is
>>falsified by the fossil evidence.
>I pointed out that Peter's statement was not correct.
The "lizards" part looks better than ever. Yes, some
studies disagree, but the last word is far from in.
BTW, I even pulled my punches somewhat in what I said up there. I
could have related how alpha hemoglobin and myoglobin both agreed
in the earlier study
that birds are more closely related to mammals than they
(birds) are to CROCODILIANS. Even beta hemoglobin agreed with this
in one study, but not in two others. One of those two others, though,
still showed birds closer to mammals than to snakes. [Lizards
weren't tested, apparently.]
Also, I misremembered about the lizards, snakes, and turtles
where alpha hemoglobin is concerned. The studies cited
only used it to compare birds, mammals, and crocodilians,
with the anomalous result just described.
However, your study came to my rescue as far as lizards are
concerned.
Reference:
Michael J. Benton, "Amniote Phylogeny", in:
_Origins of the Higher Groups of Tetrapods: Controversy and Consensus_,
ed. by Hans-Peter Schultze and Linda Trueb, co. 1991, Cornell
University Press, pp. 317-330, at p. 323.
He cites four papers, two of which are cited by Moran's source as
well (see below).
The various kinds of
>hemoglobin do not all agree that mammals are more closely related to birds
>than birds are to reptiles. I gave Peter a recent reference to the scientific
>literature that supports my claim. In a subsequent posting I pointed out that
>recent work with hemoglobin genes indicates that birds are related to reptiles
>and there are many papers that show this.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
"pointed out" is too self-serving. The only "pointing out" was
a bald assertion such as the highlighted words do here too.
But more to the point is that you left out some all important
quantifiers. NOBODY was denying that birds are related to
reptiles. The question you seem shaky on is WHICH reptiles
are they MORE closely related to than they are to MAMMALS.
>This is the paper we are discussing,
> Fushitani et al. (1996) The Amino Acid Sequences of Two alpha
> Chains of Hemoglobin from Komodo Dragon _Varanus komodoensis_
> and Phylogenetic Relationships of Amniotes.
> Mol. Biol. Evol. 13, 1039-1043.
>For some reason Peter choose not to read the paper that I referenced. I assume
>that he hasn't had time to get to the library
...until this afternoon. And two of the things it "shows" are
<drum roll>
Birds are more closely related to turtles than to crocodilians and
<drum roll>
<****FIREWORKS****>
Birds are more closely related to humans and horses than they
are to lizards.
One of those lizards was the one they were sampling, the
Komodo Dragon.
>Peter said,
>>Moran found a source more
>>recent than the ones I was using, apparently gathering data from ONE
>>species of reptile. Why would they be using a rare creature
>>like the Komodo Dragon lizard for a study, unless Moran
>>had to scrape the bottom of the barrel for a study which
>>AGREES with the fossil record?
>The new *data* was from the Komodo dragon.
WHY? Why not a less endangered monitor lizard, for crying out loud?
> They then compared these sequences
Two *alpha* globin sequences. Do these people have some sort
of problem with heme sequences, by the way?
>with all those in the current databases. I chose this particular paper because
>the abstract clearly stated that "birds form a sister group with other
>reptiles but not with mammals".
HIGHLY misleading. Birds form a sister group with 4 of the 8
reptiles tested, but one of them, a viper, was "shown" to
be more closely related to mammals than it was even to
these four.
But that's kid stuff compared to the fact that the remaining
three reptiles, all lizards, formed an outgroup; the four
"birdlike" (according to alpha) reptiles had as a sister
group the cluster {horse, human, viper}
By the way, the four "birdlike" reptiles were the turtle,
Sphenodon, an alligator and a caiman. The latter two
lost out to Sphenodon and the turtle for the honor
of "most birdlike" again in defiance of paleontological
theory.
Didn't any of this SURPRISE you?
Since the authors were studying hemoglobin
>genes
Correction: they were studying only ALPHA hemoglobin genes;
no analysis of beta. Also, only ONE of the alpha hemoglobin genes
is found in mammals and crocodilians; the other, embryonic one, has only been
found in the other reptiles--except for *Viper viper*.
Instead of clearing up the discrepancy between molecular and
paleontological data, this deepens it. The authors, who trust
the paleontological data to a limited extent, hypothesize that
either the gene will be found in crocodilians as well, or else
they've lost it; ditto for *Viper viper*.
>this seemed particularly relevant to your previous statement. There are
>plenty of other recent studies that also show agreement between hemoglobin
>dendrograms and the fossil record. I'd be happy to supply you with the
>references if you think they will help you to understand the current state of
>knowledge in the field.
Please do.
>Peter says,
>>Isn't it interesting how Dr. Moran chose to go on the offensive
>>and STILL hasn't indicated that he's read the paper, as opposed
>>to pulling down an abstract from a website and making it seem
>>like it presented ALL "the real data" on this issue?
>I read the paper two years ago when it was first published and I re-read it
>last week.
Did you? Why didn't you notice that Table 3 contradicts the
abstract?
TO BE CONTINUED
Peter Nyikos -- standard disclaimer --
Professor, Dept. of Mathematics
University of South Carolina
Columbia, SC 29208
Peter Nyikos
Hang on to your seats, folks, and prepare for a big
surprise.
lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) writes:
A CC goes to him.
>Last week (January 12, 1998) Peter Nyikos was responding to a statement made
>by Matt Silberstein. Here's the relevant quotations,
>Peter Nyikos said,
>>Matt Silberstein said,
>>>The fossils are the icing on the cake. The
>>>definitive "proof", if you will, was discovering that the nested
>>>hierarchy of DNA similarity matches the nested hierarchy of
>>>morphology.
>>This "discovery" is still many years in the future. In the
>>meantime, we have anomalies like the various kinds of hemoglobin
>>all agreeing
I should have restricted myself to alpha and beta hemoglobin,
and myoglobin.
that mammals are more closely related to birds
>>than birds are to lizards, snakes, or turtles, which is
>>falsified by the fossil evidence.
>I pointed out that Peter's statement was not correct.
The "lizards" part looks better than ever. Yes, some
studies disagree, but the last word is far from in.
BTW, I even pulled my punches somewhat in what I said up there. I
could have related how alpha hemoglobin and myoglobin both agreed
in the earlier study
that birds are more closely related to mammals than they
(birds) are to CROCODILIANS. Even beta hemoglobin agreed with this
in one study, but not in two others. One of those two others, though,
still showed birds closer to mammals than to snakes. [Lizards
weren't tested, apparently.]
Also, I misremembered about the lizards, snakes, and turtles
where alpha hemoglobin is concerned. The studies cited
only used it to compare birds, mammals, and crocodilians,
with the anomalous result just described.
However, your study came to my rescue as far as lizards are
concerned.
Reference:
Michael J. Benton, "Amniote Phylogeny", in:
_Origins of the Higher Groups of Tetrapods: Controversy and Consensus_,
ed. by Hans-Peter Schultze and Linda Trueb, co. 1991, Cornell
University Press, pp. 317-330, at p. 323.
He cites four papers, two of which are cited by Moran's source as
well (see below).
The various kinds of
>hemoglobin do not all agree that mammals are more closely related to birds
>than birds are to reptiles. I gave Peter a recent reference to the scientific
>literature that supports my claim. In a subsequent posting I pointed out that
>recent work with hemoglobin genes indicates that birds are related to reptiles
>and there are many papers that show this.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
"pointed out" is too self-serving. The only "pointing out" was
a bald assertion such as the highlighted words do here too.
But more to the point is that you left out some all important
quantifiers. NOBODY was denying that birds are related to
reptiles. The question you seem shaky on is WHICH reptiles
are they MORE closely related to than they are to MAMMALS.
>This is the paper we are discussing,
> Fushitani et al. (1996) The Amino Acid Sequences of Two alpha
> Chains of Hemoglobin from Komodo Dragon _Varanus komodoensis_
> and Phylogenetic Relationships of Amniotes.
> Mol. Biol. Evol. 13, 1039-1043.
>For some reason Peter choose not to read the paper that I referenced. I assume
>that he hasn't had time to get to the library
...until this afternoon. And two of the things it "shows" are
<drum roll>
Birds are more closely related to turtles than to crocodilians and
<drum roll>
<****FIREWORKS****>
Birds are more closely related to humans and horses than they
are to lizards.
One of those lizards was the one they were sampling, the
Komodo Dragon.
>Peter said,
>>Moran found a source more
>>recent than the ones I was using, apparently gathering data from ONE
>>species of reptile. Why would they be using a rare creature
>>like the Komodo Dragon lizard for a study, unless Moran
>>had to scrape the bottom of the barrel for a study which
>>AGREES with the fossil record?
>The new *data* was from the Komodo dragon.
WHY? Why not a less endangered monitor lizard, for crying out loud?
> They then compared these sequences
Two *alpha* globin sequences. Do these people have some sort
of problem with heme sequences, by the way?
>with all those in the current databases. I chose this particular paper because
>the abstract clearly stated that "birds form a sister group with other
>reptiles but not with mammals".
HIGHLY misleading. Birds form a sister group with 4 of the 8
reptiles tested, but one of them, a viper, was "shown" to
be more closely related to mammals than it was even to
these four.
But that's kid stuff compared to the fact that the remaining
three reptiles, all lizards, formed an outgroup; the four
"birdlike" (according to alpha) reptiles had as a sister
group the cluster {horse, human, viper}
By the way, the four "birdlike" reptiles were the turtle,
Sphenodon, an alligator and a caiman. The latter two
lost out to Sphenodon and the turtle for the honor
of "most birdlike" again in defiance of paleontological
theory.
Didn't any of this SURPRISE you?
Since the authors were studying hemoglobin
>genes
Correction: they were studying only ALPHA hemoglobin genes;
no analysis of beta. Also, only ONE of the alpha hemoglobin genes
is found in mammals and crocodilians; the other, embryonic one, has only been
found in the other reptiles--except for *Viper viper*.
Instead of clearing up the discrepancy between molecular and
paleontological data, this deepens it. The authors, who trust
the paleontological data to a limited extent, hypothesize that
either the gene will be found in crocodilians as well, or else
they've lost it; ditto for *Viper viper*.
>this seemed particularly relevant to your previous statement. There are
>plenty of other recent studies that also show agreement between hemoglobin
>dendrograms and the fossil record. I'd be happy to supply you with the
>references if you think they will help you to understand the current state of
>knowledge in the field.
Please do.
>Peter says,
>>Isn't it interesting how Dr. Moran chose to go on the offensive
>>and STILL hasn't indicated that he's read the paper, as opposed
>>to pulling down an abstract from a website and making it seem
>>like it presented ALL "the real data" on this issue?
>I read the paper two years ago when it was first published and I re-read it
>last week.
Did you? Why didn't you notice that Table 3 contradicts the
Laurence A. Moran
In article <1998012400...@milo.math.sc.edu>
Peter Nyikos <nyi...@math.sc.edu> writes:
>lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) writes:
>>Last week (January 12, 1998) Peter Nyikos was responding to a statement made
>>by Matt Silberstein. Here's the relevant quotations,
>
>>Peter Nyikos said,
>>>Matt Silberstein said,
>>>>The fossils are the icing on the cake. The
>>>>definitive "proof", if you will, was discovering that the nested
>>>>hierarchy of DNA similarity matches the nested hierarchy of
>>>>morphology.
>
>>>This "discovery" is still many years in the future. In the
>>>meantime, we have anomalies like the various kinds of hemoglobin
>>>all agreeing
>
>I should have restricted myself to alpha and beta hemoglobin,
>and myoglobin.
I interpreted your statement to mean alpha and beta-globin genes. Did you
mean to include myoglobin? Myoglobin is not hemoglobin but maybe you
didn't know that.
>>> that mammals are more closely related to birds
>>>than birds are to lizards, snakes, or turtles, which is
>>>falsified by the fossil evidence.
>
>>I pointed out that Peter's statement was not correct.
>
>The "lizards" part looks better than ever. Yes, some
>studies disagree, but the last word is far from in.
I interpreted your statement to mean that the data shows birds are more
closely related to mammals than to reptiles. Is there some nuance that
escaped me?
>BTW, I even pulled my punches somewhat in what I said up there. I
>could have related how alpha hemoglobin and myoglobin both agreed
>in the earlier study
No problem. I agree that there are earlier studies where both alph-globin
and myoglobin genes show birds closer to mammals than to reptiles. You
don't have to worry about pulling punches with me, Peter.
Would "indicate" or "casually mention" suit you better? I'm not wedded to
the term "pointed out" if it offends you so much.
>But more to the point is that you left out some all important
>quantifiers. NOBODY was denying that birds are related to
>reptiles. The question you seem shaky on is WHICH reptiles
>are they MORE closely related to than they are to MAMMALS.
This isn't what I understood from your comment to Matt Silberstein. I
agree that you were not arguing against a bird/retile relationship. What
you did do was state that the *hemoglobin* data showed a bird/mammal
relationship. It is that statement that I am challenging. I haven't
mentioned anything about which reptiles are closest to birds and, quite
frankly, I'm not that interested in discussing it.
You seem to be moving the goalposts here but since we all know that you
are an honorable man I guess that can't be true. I assume that I must have
somehow conveyed the false impression that I was interested in which
reptiles were closest to birds. Sorry.
>>This is the paper we are discussing,
>
>> Fushitani et al. (1996) The Amino Acid Sequences of Two alpha
>> Chains of Hemoglobin from Komodo Dragon _Varanus komodoensis_
>> and Phylogenetic Relationships of Amniotes.
>> Mol. Biol. Evol. 13, 1039-1043.
>
>>For some reason Peter choose not to read the paper that I referenced. I assume
>>that he hasn't had time to get to the library
>
>...until this afternoon. And two of the things it "shows" are
Good. I'm glad you were finally able to look it up. I can understand how
busy you must have been in the past week and I appreciate the effort you
made. Now, let's discuss the paper. Have you answered most of the
questions you had last week?
>Birds are more closely related to turtles than to crocodilians and
This is correct for the alpha-A genes. Did you notice that birds fall
within the reptiles and are not clustered with mammals? That is the data
that seems to disagree with what you said when you told Matt that "we
have anomalies like the various kinds of hemoglobin all agreeing that
mammals are more closely related to birds than birds are to lizards,
snakes, or turtles".
>Birds are more closely related to humans and horses than they
>are to lizards.
This is correct, the three lizard alpha-globins branch off before the
divergence of the human/horse cluster from the turtle/alligator/
Sphenodon/chicken/ostrich cluster. The point, of course, is that birds are
more closely related to reptiles than they are to mammals.
>One of those lizards was the one they were sampling, the
>Komodo Dragon.
>
>>Peter said,
>>>Moran found a source more
>>>recent than the ones I was using, apparently gathering data from ONE
>>>species of reptile. Why would they be using a rare creature
>>>like the Komodo Dragon lizard for a study, unless Moran
>>>had to scrape the bottom of the barrel for a study which
>>>AGREES with the fossil record?
>
>>The new *data* was from the Komodo dragon.
>
>WHY? Why not a less endangered monitor lizard, for crying out loud?
Don't cry, Peter. I'm sure the authors would be happy to explain it to you
if you give them a call. Is it important or are you just expressing your
concern for Komodo dragons? The authors do say that their blood sample was
legally collected from an animal in Indonesia.
>> They then compared these sequences
>
>Two *alpha* globin sequences. Do these people have some sort
>of problem with heme sequences, by the way?
I don't understand what you mean by "heme sequences". It doesn't parse.
This must be because I'm misunderstanding you. Could you ask your question
in another way for those of us who are stupid?
>>with all those in the current databases. I chose this particular paper because
>>the abstract clearly stated that "birds form a sister group with other
>>reptiles but not with mammals".
>
>HIGHLY misleading. Birds form a sister group with 4 of the 8
>reptiles tested, but one of them, a viper, was "shown" to
>be more closely related to mammals than it was even to
>these four.
The two bird sequences (chicken and ostrich) cluster *within* the group
that includes turtle, Sphenodon, caiman, and alligator. I don't find their
abstract misleading. Could you explain, please? Do you think there is
still support here for your claim that hemoglobin sequences show birds
grouped with mammals?
>But that's kid stuff compared to the fact that the remaining
>three reptiles, all lizards, formed an outgroup; the four
>"birdlike" (according to alpha) reptiles had as a sister
>group the cluster {horse, human, viper}
These are interesting issues but not related to your claim that hemoglobin
sequences show birds clustered with mammals in conflict with the fossil
evidence. Perhaps we could settle that point before moving on?
>By the way, the four "birdlike" reptiles were the turtle,
>Sphenodon, an alligator and a caiman. The latter two
>lost out to Sphenodon and the turtle for the honor
>of "most birdlike" again in defiance of paleontological
>theory.
>
>Didn't any of this SURPRISE you?
Actually no. It didn't surprise me because I'm not terribly interested in
such things. I *was* interested in earlier work that showed birds and
mammals to be more closely related than birds and reptiles but now that
that issue seems to be resolved I have pretty much stopped paying
attention to the details. You do agree, don't you, that this paper shows
birds more closely related to reptiles than to mammals?
> Since the authors were studying hemoglobin
>>genes
>
>Correction: they were studying only ALPHA hemoglobin genes;
>no analysis of beta. Also, only ONE of the alpha hemoglobin genes
>is found in mammals and crocodilians; the other, embryonic one, has only been
>found in the other reptiles--except for *Viper viper*.
Yes, *alpha* globin genes, just like it says in the title that I gave you.
Remember that you said all hemoglobin studies showed birds related to
mammals. I thought that one paper would be a good beginning. Are you
criticizing these authors for not using more sequences? Have you also been
critical of the earlier work that use even fewer sequences?
>Instead of clearing up the discrepancy between molecular and
>paleontological data, this deepens it.
I don't understand why you say that. It seems to me that the biggest
problem was whether molecular data supported a bird/mammal cluster or a
bird/reptile cluster. Surely the earlier work that suggested birds were
related to mammals was a bigger discrepancy than what we have now? Do you
think that these other problems are more serious than a possible bird/
mammal relationship?
In any case, I'm not very interested in these other discrepancies now that
we've settled the issue that I raised in the first place.
> The authors, who trust
>the paleontological data to a limited extent, hypothesize that
>either the gene will be found in crocodilians as well, or else
>they've lost it; ditto for *Viper viper*.
>
>>this seemed particularly relevant to your previous statement. There are
>>plenty of other recent studies that also show agreement between hemoglobin
>>dendrograms and the fossil record. I'd be happy to supply you with the
>>references if you think they will help you to understand the current state of
>>knowledge in the field.
>
>Please do.
Did you read the other reference that I gave you? Have you tracked down
the references to post-1990 papers in Fushitani et al.? Let me know when
you read those papers if you still think that hemoglobin genes supprt a
bird/mammal relationship.
>>Peter says,
>>>Isn't it interesting how Dr. Moran chose to go on the offensive
>>>and STILL hasn't indicated that he's read the paper, as opposed
>>>to pulling down an abstract from a website and making it seem
>>>like it presented ALL "the real data" on this issue?
>
>>I read the paper two years ago when it was first published and I re-read it
>>last week.
>
>Did you? Why didn't you notice that Table 3 contradicts the
>abstract?
I assume you mean Figure 3? There doesn't seem to be a contradiction to
me. Could you explain?
Larry Moran
PZ Myers
In article <1998012400...@milo.math.sc.edu>, Peter Nyikos
<nyi...@math.sc.edu> wrote:
[snip]
>
> Two *alpha* globin sequences. Do these people have some sort
> of problem with heme sequences, by the way?
This has already been pointed out to you, but it is such a silly
point you are making that I have to mention it again.
Heme is *not* a protein. It does not have a sequence. It rather
seriously undercuts your claim of competence in this matter to
persist in this kind of muddled argument.
So, yeah, those people do have a sort of problem with heme
sequences.
[snip]
--
PZ Myers
Wade Hines
>>>This is the paper we are discussing,
>>> Fushitani et al. (1996) The Amino Acid Sequences of Two alpha
>>> Chains of Hemoglobin from Komodo Dragon _Varanus komodoensis_
>>> and Phylogenetic Relationships of Amniotes.
>>> Mol. Biol. Evol. 13, 1039-1043.
>>>For some reason Peter choose not to read the paper that I referenced. I assume
>>>that he hasn't had time to get to the library
>>...until this afternoon. And two of the things it "shows" are
<<< snip >>>
>>>The new *data* was from the Komodo dragon.
>>WHY? Why not a less endangered monitor lizard, for crying out loud?
>Don't cry, Peter. I'm sure the authors would be happy to explain it to you
>if you give them a call. Is it important or are you just expressing your
>concern for Komodo dragons? The authors do say that their blood sample was
>legally collected from an animal in Indonesia.
Point of marginal interest. The komodo dragon has a rather long generational
time which I pressume matters in such studies.
I don't know how the sequencing was done as I haven't been to the library.
If by DNA techniques, we all know that it doesn't take much of a sample
to go at it by PCR.
If at the protein level, hemoglobin is a cake walk.
A small sample, say 10 ul, has about 150 ug of hemoglobin which is about
5 x 10^9 moles of each chain. If you are a really sloppy protein chemist
and suffer 90% losses in separating out the Hb, digesting the samples
and collecting fractions for Edman sequencing, you still have enough material
to get your sequences. 10% losses are more likely. Hemoglobin sequencing
used to be quite common in the 70s but people would do quality LC and only
sequences peptides that were different from known peptides.
While the concern for the komodo dragon is touching, an understanding of
how data is collected should eliminate fears that any dragons were harmed
in the making of the paper.
Wade Hines
my...@netaxs.com (PZ Myers) writes:
><nyi...@math.sc.edu> wrote:
>> Two *alpha* globin sequences. Do these people have some sort
>> of problem with heme sequences, by the way?
>This has already been pointed out to you, but it is such a silly
>point you are making that I have to mention it again.
>Heme is *not* a protein. It does not have a sequence. It rather
>seriously undercuts your claim of competence in this matter to
>persist in this kind of muddled argument.
>So, yeah, those people do have a sort of problem with heme
>sequences.
My problem with heme is in the things like cytochrome C where it
is covalently attached and therefore gives me a mass for the
modified peptide which isn't trivially or even non trivially
deducable from reading a database entry.
That and they aren't all the same heme across heme associated
proteins. But we shouldn't let details get in the way of
pseudoerudition.
Heme associated globin genes are easy 'cause its non covalent
(whoops, there we go again) unless you go for some of the rare
cross links you can find in smokers blood but the money from
RJR has dried up.
bull.net Cal King
In article <6aar7d$lvj$1...@bioinfo.med.utoronto.ca>,
>>>> >In article <6a65pv$s...@bgtnsc01.worldnet.att.net>
get...@worldnet.att.ne
>t
>>>> >writes:
>>>>
>>>> >>If different sets of DNA data do not agree with one another, how can we
>>>> >>then claim that DNA data coincide with morphology data as a general >>
>>>>trend?
>>>
>>>Perhaps because *as a general trend* different sets of DNA data *do*
>>>agree with one another, although one can certainly find anomalous cases
>>>where they do not.
>>
>>I would welcome the citation of an objective survey that would support such
>>a general trend.
>
>
>I took a quick look in my pile of papers and came up with a few that
>survey many genes and some that discuss the integration of molecular and
>morphological data. Here's a few to start you off.
>
> Nikoh, N. et al. (1994) Phylogenetic Relationships of the Kingdoms
> Animalia, Plantae, and Fungi, Inferred from 23 Different Protein
> Sequences. Mol. Biol. Evol. 1, 762-768.
>
> Novacek, M.J. (1992) Mammalian Phylogeny: shaking the tree.
> Nature 356, 121-125.
>
> Benton, M.J. (1990) Phylogeny of the Major Tetrapod Groups:
> Morphological Data and Divergence Dates. J. Mol. Evol. 30, 409-424.
>
> Doolittle, R.F. et al. (1996) Determining Divergence Times of the
> Major Kingdoms of Living Organisms with a Protein Clock.
> Science 271, 470-477.
>
> Wray, G.A. et al. (1996) Molecular Evidence for Deep Precambrian
> Divergences Among Metazoan Phyla. Science 274, 568-573.
>
>
>Happy reading.
>
>
>Larry Moran
Well, it doesn't look like any statistical survey of congruence in general but
only specific cases where such congruence has been observed. Besides, most of
these cited works deal with taxa at the highest taxonomic ranks: kingdoms,
phyla, orders and classes. At the species level there is often very little
congruence. I have reposted an excerpt from a response I gave to Howard
Hershey below to illustrate my point:
=================================================================
H. Hershey:
>*If*, OTOH, you are saying that there is no or very little congruence
>between the nested hierarchies of DNA similarity and the nested
>hierarchies of morphology in living organisms and the nested hierachies
>of fossil evidence, I think you would be quite mistaken
C. King:
No only is there no congruence between types of data sets, there is often no
consensus, say, in the morphology data set. Sometimes different data sets
conflict strongly within the same paper. For example the allozyme data set
conflicted strongly with the DNA data in de Queiroz and Lawson's (1994 Biol.
J. Linn. Soc.) analysis of the garter snakes (Thamnophis). Shaffer et al.
(1991, Systematics Zool. 40:284-303) similarly find no congruence between data
sets in the Ambystomatid salamanders.
> but you could
>convince me by pointing out the studies that show that the *mass* of DNA
>similarity data produces a nested hierachy so different from the
>standard one as to be utterly different.
Then there is Lopez and Maxson's (1995, Biochem System. Ecol.) DNA tree of the
Lampropeltini, which conflicts strongly Keogh's (1996 Herpetologica) tree
based on morphology.
>But only use the most modern
>data, not decade old stuff, which, as Larry points out, has been added
>to, a process that sometimes removes anomalies.
These are all studies done within the last few years. Besides, what is wrong
with old data? Many immunological studies done in the 80's are still well
supported by new data. It is not date, it is the method and character that
may be the problem. There is no gurarantee that the newest techniques and the
newest characters will be more reliable.
>In the early 1990's. How many of these anomalies have been resolved
>since then?
None that I know of.
>Is this a general claim? Are you saying that, in general, sequence
>analysis for gene A gives *entirely* different results from sequence
>analysis for gene B?
Not my claim. My claim is that different data sets from morphology, fossil
and DNA often conflict with one another. If there are a few branches that are
the same, the results still conflict because a reptile as descendant of bird
cladogram and a bird as reptile descendant cladogram may differ by only one
branch, they are strongly conflicting nevertheless.
>If you mean by 'congruence' *perfect* congruence between all data sets
>at every point in every data set, that ideal state will probably never
>come.
Since there is only one historical tree, if the methods are good, then the day
should come. Heck, Hennig predicted that HIS method would do just that, but
flaws in his methodology of course have made it a hope rather than a reality.
=============================================================================
End of excerpt.
I may add that, in another thread, the extremely well resolved relationships
among human, chimp and gorilla was said to be an unresolved trichotomy because
the morphology tree ostensibly conflicted with the molecular tree. From this
example, it is quite evident that the morphology tree is based on the
assumption of equal rates of evolution and that morphological similarity is
used to group organisms in cladistics. But since rates of morphological
evolution are highly variable within and between lineages, such assumption
virtually guarantees that the morphology tree will most likely conflict with
the DNA tree, especially if the DNA tree is constructed using molecular
distance or molecular clock.
bull.net Cal King
In article <6abgpr$qqu$1...@bioinfo.med.utoronto.ca>,
In article <6abgpr$qqu$1...@bioinfo.med.utoronto.ca>,
>>>This is the paper we are discussing,
>>
>>> Fushitani et al. (1996) The Amino Acid Sequences of Two alpha
>>> Chains of Hemoglobin from Komodo Dragon _Varanus komodoensis_
>>> and Phylogenetic Relationships of Amniotes.
>>> Mol. Biol. Evol. 13, 1039-1043.
P. Nyikos:
>>Birds are more closely related to turtles than to crocodilians and
L. Moran:
>This is correct for the alpha-A genes. Did you notice that birds fall
>within the reptiles and are not clustered with mammals? That is the data
>that seems to disagree with what you said when you told Matt that "we
>have anomalies like the various kinds of hemoglobin all agreeing that
>mammals are more closely related to birds than birds are to lizards,
>snakes, or turtles".
As Nyikos said before, this is one study, albeit the most recent, but that
doesn't necessarily mean that this is the most correct tree, even if I think
that birds are probably more closely related to reptiles than to the mammals.
The fact remains that there are conflicts among different past and present
DNA data sets.
[deleted]
>>HIGHLY misleading. Birds form a sister group with 4 of the 8
>>reptiles tested, but one of them, a viper, was "shown" to
>>be more closely related to mammals than it was even to
>>these four.
>The two bird sequences (chicken and ostrich) cluster *within* the group
>that includes turtle, Sphenodon, caiman, and alligator. I don't find their
>abstract misleading. Could you explain, please? Do you think there is
>still support here for your claim that hemoglobin sequences show birds
>grouped with mammals?
I have a problem with the type of tree chosen by the authors. It is very
confusing and difficult to read. The same species occurs more than once
within a tree so that there is no single hypothesis of relationships based on
the available evidence. They should either show several different trees based
on the different sequences and/or show a consensus tree with each species
appearing only once instead of the type of hybrid tree that they showed. Also
I would have liked more amino acid sequences shown than the short one
presented, in which not all species are included. Consequently, we are
getting the results of their analysis but unless we have access to the
database, we cannot re-analyze their data or do a transversion count only
analysis ourselves. Some other authors have taken the trouble and time to
list complete amino acid sequences that may take up a few pages.
Unfortunately these authors have not chosen to do more than they did.
The issue of bird, mammal and reptile relationships is far from settled and
the above paper is far from being the last word, even if we confine ourselves
to DNA data only.
Laurence A. Moran
In article <6ad806$d...@bgtnsc03.worldnet.att.net>
>Well, it doesn't look like any statistical survey of congruence in general but
>only specific cases where such congruence has been observed. Besides, most of
>these cited works deal with taxa at the highest taxonomic ranks: kingdoms,
>phyla, orders and classes. At the species level there is often very little
>congruence.
Yes, the molecular data on higher taxa show excellent congruence with
the morphological data (and the fossil record). There are some anomalies
at the level of species and genera but this are relatively unimportant
compared to the mass of molecular data that is out there. (Don't get me
wrong, there are some very interesting problems at the higher levels as
well, including the biggest one of all.)
Note that the morlecular data consistently shows mammals grouped together
and separate from other groups such as marsupials, amphibians, fish or
reptiles. Look at the insects, fungi, flowering plants, various orders of
bacteria, anelids, nematodes, bryophytes, etc. etc. - all of these groups
are confirmed by molecular data.
We have a glass that is 90% full (to use a popular analogy) but you are
making a big fuss about the 10% that is empty. That's fine, the 10%
contains some really exciting areas of investigation, but don't make the
mistake of discrediting all molecular data just because there are a few
problems.
Larry Moran
Laurence A. Moran
In article <6add2a$o...@bgtnsc03.worldnet.att.net>
get...@worldnet.att.net writes:
>In article <6abgpr$qqu$1...@bioinfo.med.utoronto.ca>,
>In article <6abgpr$qqu$1...@bioinfo.med.utoronto.ca>,
>>>
>>>> Fushitani et al. (1996) The Amino Acid Sequences of Two alpha
>>>> Chains of Hemoglobin from Komodo Dragon _Varanus komodoensis_
>>>> and Phylogenetic Relationships of Amniotes.
>>>> Mol. Biol. Evol. 13, 1039-1043.
>
>>>Birds are more closely related to turtles than to crocodilians and
>
>>This is correct for the alpha-A genes. Did you notice that birds fall
>>within the reptiles and are not clustered with mammals? That is the data
>>that seems to disagree with what you said when you told Matt that "we
>>have anomalies like the various kinds of hemoglobin all agreeing that
>>mammals are more closely related to birds than birds are to lizards,
>>snakes, or turtles".
>
>doesn't necessarily mean that this is the most correct tree, even if I think
>that birds are probably more closely related to reptiles than to the mammals.
> The fact remains that there are conflicts among different past and present
>DNA data sets.
Could you please indicate whether you agree with the exact statement that
Peter made to Matt? If not, would you mind stating your position more
clearly. I seem to be arguing with a phantom .....
>I have a problem with the type of tree chosen by the authors. It is very
>confusing and difficult to read. The same species occurs more than once
>within a tree so that there is no single hypothesis of relationships based on
>the available evidence. They should either show several different trees based
>on the different sequences and/or show a consensus tree with each species
>appearing only once instead of the type of hybrid tree that they showed.
I fear that you lack understanding of gene families. The two main branches
are the alpha-A and alpha-D genes. Two different genes in the same genome
(species). The reason for analyzing them together is to find out which
gnes belong to which family.
> Also
>I would have liked more amino acid sequences shown than the short one
>presented, in which not all species are included. Consequently, we are
>getting the results of their analysis but unless we have access to the
>database, we cannot re-analyze their data or do a transversion count only
>analysis ourselves.
This is a problem with all scientific papers today. There is never enough
data to be able to analyze the results in detail. However, we all have
free access to the database of sequences so if you want you could repeat
the experiment.
>Some other authors have taken the trouble and time to
>list complete amino acid sequences that may take up a few pages.
>Unfortunately these authors have not chosen to do more than they did.
You can't usually publish your complete amino acid alignments. It won't be
accepted by the editors.
>The issue of bird, mammal and reptile relationships is far from settled and
>the above paper is far from being the last word, even if we confine ourselves
>to DNA data only.
No problem. You are more than welcome to question these relationships if
you want. As far as I am, concerned it has been settled to my satisfaction
and I have moved on to more interesting problems. My intention was merely
to show that Peter Nyikos was misrepresenting the state of knowledge with
respect to hemoglobin genes.
Larry Moran
bull.net Cal King
In article <6ae3ev$bru$1...@bioinfo.med.utoronto.ca>,
>Yes, the molecular data on higher taxa show excellent congruence with
>the morphological data (and the fossil record). There are some anomalies
>at the level of species and genera but this are relatively unimportant
>compared to the mass of molecular data that is out there. (Don't get me
>wrong, there are some very interesting problems at the higher levels as
>well, including the biggest one of all.)
>
>Note that the morlecular data consistently shows mammals grouped together
>and separate from other groups such as marsupials, amphibians, fish or
>reptiles. Look at the insects, fungi, flowering plants, various orders of
>bacteria, anelids, nematodes, bryophytes, etc. etc. - all of these groups
>are confirmed by molecular data.
>
>We have a glass that is 90% full (to use a popular analogy) but you are
>making a big fuss about the 10% that is empty. That's fine, the 10%
>contains some really exciting areas of investigation, but don't make the
>mistake of discrediting all molecular data just because there are a few
>problems.
>Larry Moran
Did I come across as discrediting DNA research? That is amusing especially
because I have been accused of being enamored with molecular data in the past!
I would not dismiss the incongruence at the species and genus level as
anomalies, because evolution occurs at the species level. Higher taxa do not
evolve. The incongruence at these levels shows that evolutionary rates are
vastly different between molecular and morphological evolution. This is a
fundamental fact and the sooner we realize it, the less taxonomic chaos we
will generate at the species, genus and family levels. As to your claim that
there is 90% congruence, that is quite plausibly a grossly inflated subjective
estimate because you still haven't cited any objective survey to back up your
claim.
bull.net Cal King
In article <6ae48j$c0s$1...@bioinfo.med.utoronto.ca>,
>>As Nyikos said before, this is one study, albeit the most recent, but that
>>doesn't necessarily mean that this is the most correct tree, even if I think
>>that birds are probably more closely related to reptiles than to the
>>mammals.
>
>> The fact remains that there are conflicts among different past and present
>>DNA data sets.
>
>Could you please indicate whether you agree with the exact statement that
>Peter made to Matt?
Did I not make it clear that I agree with Nyikos in my very first post in this
thread?
>>I have a problem with the type of tree chosen by the authors. It is very
>>confusing and difficult to read. The same species occurs more than once
>>within a tree so that there is no single hypothesis of relationships based
>>on the available evidence. They should either show several different trees
>>based on the different sequences and/or show a consensus tree with each
>>species appearing only once instead of the type of hybrid tree that they
>>showed.
>I fear that you lack understanding of gene families. The two main branches
>are the alpha-A and alpha-D genes. Two different genes in the same genome
>(species). The reason for analyzing them together is to find out which
>gnes belong to which family.
You are barking up the wrong tree. My objection is the type of trees they
show, not the type of genes they used. They can analyze 1500 genes for all I
care. But if all 1500 genes produced different cladograms, then they should
show all 1500 different trees. As such, they lumped 4 different sets of trees
into one, with some species showing up more than once in some clusters and
some not showing up at all in some of the clusters. It is highly confusing
and difficult to read. They should have shown the 4 different clusters as
separate trees and, if they so choose, then show one single consensus
cladogram generated from the 4 trees. Instead the way they show all 4
clusters in one diagram is extremely confusing.
>>Some other authors have taken the trouble and time to
>>list complete amino acid sequences that may take up a few pages.
>>Unfortunately these authors have not chosen to do more than they did.
>
>You can't usually publish your complete amino acid alignments. It won't be
>accepted by the editors.
I have seen quite a few papers that do that. Besides, these authors could
definitely do much better than they did in Fig. 2
>>The issue of bird, mammal and reptile relationships is far from settled and
>>the above paper is far from being the last word, even if we confine
>>ourselves to DNA data only.
>
>No problem. You are more than welcome to question these relationships if
>you want. As far as I am, concerned it has been settled to my satisfaction
>and I have moved on to more interesting problems. My intention was merely
>to show that Peter Nyikos was misrepresenting the state of knowledge with
>respect to hemoglobin genes.
>Larry Moran
There is no misrepresentation on his part. He did say that there were more
papers showing a different result than the present one. That is an undisputed
fact. Your point is that Fusitani et al.'s paper make all the earlier ones
irrelevant because it is newer. But that is not the case. If someone
publishes a paper corroborating the earlier results, then what? Are you going
to ignore it even though it is, according to you, newer and thus supersedes an
earlier one like Fusitani et al.'s paper? Aren't you interested in the source
of the anomalies in the earlier paper if they are indeed anomalous?
Laurence A. Moran
In article <6aevb5$2...@bgtnsc02.worldnet.att.net>
get...@worldnet.att.net writes:
>In article <6ae3ev$bru$1...@bioinfo.med.utoronto.ca>,
>>the morphological data (and the fossil record). There are some anomalies
>>at the level of species and genera but this are relatively unimportant
>>compared to the mass of molecular data that is out there. (Don't get me
>>wrong, there are some very interesting problems at the higher levels as
>>well, including the biggest one of all.)
>>
>>Note that the morlecular data consistently shows mammals grouped together
>>and separate from other groups such as marsupials, amphibians, fish or
>>reptiles. Look at the insects, fungi, flowering plants, various orders of
>>bacteria, anelids, nematodes, bryophytes, etc. etc. - all of these groups
>>are confirmed by molecular data.
>>
>>We have a glass that is 90% full (to use a popular analogy) but you are
>>making a big fuss about the 10% that is empty. That's fine, the 10%
>>contains some really exciting areas of investigation, but don't make the
>>mistake of discrediting all molecular data just because there are a few
>>problems.
>Did I come across as discrediting DNA research?
Yes.
>That is amusing especially
>because I have been accused of being enamored with molecular data in the past!
I didn't know that. In this thread you seem to be emphasizing the fact
that there are "anomalies" in some of the molecular phylogenies. Thus it
seems like you are attacking the entire field of molecular evolution.
> I would not dismiss the incongruence at the species and genus level as
>anomalies, because evolution occurs at the species level. Higher taxa do not
>evolve. The incongruence at these levels shows that evolutionary rates are
>vastly different between molecular and morphological evolution. This is a
>fundamental fact and the sooner we realize it, the less taxonomic chaos we
>will generate at the species, genus and family levels.
Do you agree with me that the vast majority of molecular phylogenies are
congruent with the fossil evidence and the morphological data? This
includes most of the results at the species level.
You seem to be trying to make a case for *frequent* ingongruency at the
species level. You seem to think, for some unexplained reason, that the
classification of organisms into a tree-like structure depends on the rate
of evolution. Because the molecular rates and the morphological rates are
different, according to your theory, then it follows that the resulting
trees should not be congruent. Is this a fair summary of what you are
trying to say?
>As to your claim that
>there is 90% congruence, that is quite plausibly a grossly inflated subjective
>estimate because you still haven't cited any objective survey to back up your
>claim.
I gave you some papers with lots of data that is congruent with the fossil
record and the morphological classification. I am not aware of any papers
that specifically answer your question about the frequency of anomalies in
the molecular data.
The 90% figure is my subjective impression of the data. (Actually I think
it is an underestimeate.) You believe that the estimate is "grossly
inflated" but, to be fair, you can't come up with an objective survey to
back *your* impression either. So let's just leave it at that. We have
both spent some time reading this literature and constructung and
analyzing phylogenetic trees. You have come away with the impression that
there are many "anomalies" and and I have come away with the impression
that the molecular data agrees with other studies. I'm not very interested
in continuing this discussion because I suspect we have run out of
arguments.
Larry Moran
howard hershey
So your point is that there *is* largely congruence between DNA
phylogenies and morphological phylogenies at the higher taxonomic ranks
where the *morphological* phylogenies are most secure (where all the
experts concur on a standard or consensus phylogeny on the basis of
fossil/morphological evidence), but that there is often discordancies at
lower taxonomic levels where the *morphological* phylogenies are least
secure (often where different groups within the field argue for
*different* phylogenies on the basis of morphology alone) because of
problems with convergence and non-uniform rates of evolutionary change.
I would agree. In fact, knowing the way that scientists work, I would
suspect that they would gravitate toward performing tests in these areas
that are problematic for morphological analysis alone in the hope that
the new data will help to differentiate between alternative theories of
phylogeny. That, of course, would cause a lot of tests that will
disagree with *some* of these phylogenies. I also suspect that there
will be occassional surprises in the tests (more rarely done) on groups
where people had agreed on a consensus phylogeny before the DNA/sequence
test was performed.
No one is saying that the old data was unreliable. It is still being
used and is being included. But when you add *new information* that
leads to a change in interpretation, the new *interpretation* is more
likely to be true because it is based on a larger data set that includes
the old data *and* the new information.
Sometimes, of course, conflicts exist between data sets *because* of
factors that led to an initial misinterpretation because some of the
underlying assumptions of the method were not met. For sequencing
analysis, these underlying assumptions of the method include:
a) Most of the changes observed are neutral in effect. This is
expecially important in using the molecular clock, but can also be
important in the assumption that one is not seeing convergence to a
particular part of a sequence because of selection. For example, if
there is a particular sequence site in globin genes that are important
for efficient O2 transfer at the elevated temperatures of homeothermic
organisms, one might see convergence in these sites in birds and
mammals.
b) The sequence has the same protein function and the product you are
examining is related by descent. For example, if a gene which is part
of a two gene family you are examining in one group as being, say, the
adult form is actually derived from a duplication that serves an
embryonic function in the other lineage (and vice versa), that means you
are not going to get exactly correct results by comparing adult forms in
the two groups, because, although related to each other through the
initial duplication, they are not directly related from the same gene.
c) The assumption that all sequence changes are equally likely is
clearly erroneous at points, leading to particular sites being more
prone to re-ratting. If you are examining closely related species,
these non-random features are more important than if you are examining
the longer picture.
I am sure Larry, who is more expert than I, can come up with half a
dozen more ways in which the assumptions of the method can be violated
in particular cases with particular proteins and particular sets of
organisms. That is why it is normal to do more than one type of
analysis, and try to reach a 'consensus'.
Sometimes
>
> >In the early 1990's. How many of these anomalies have been resolved
> >since then?
>
> None that I know of.
>
> >Is this a general claim? Are you saying that, in general, sequence
> >analysis for gene A gives *entirely* different results from sequence
> >analysis for gene B?
>
> Not my claim. My claim is that different data sets from morphology, fossil
> and DNA often conflict with one another. If there are a few branches that are
> the same, the results still conflict because a reptile as descendant of bird
> cladogram and a bird as reptile descendant cladogram may differ by only one
> branch, they are strongly conflicting nevertheless.
>
> >If you mean by 'congruence' *perfect* congruence between all data sets
> >at every point in every data set, that ideal state will probably never
> >come.
>
> Since there is only one historical tree, if the methods are good, then the day
> should come. Heck, Hennig predicted that HIS method would do just that, but
> flaws in his methodology of course have made it a hope rather than a reality.
But even though there is only one historical tree, why would one expect
that every method of devining that tree will come up with the exact same
tree if the branch points are close together and the distances small?
> =============================================================================
> End of excerpt.
>
> I may add that, in another thread, the extremely well resolved relationships
> among human, chimp and gorilla was said to be an unresolved trichotomy because
> the morphology tree ostensibly conflicted with the molecular tree. From this
> example, it is quite evident that the morphology tree is based on the
> assumption of equal rates of evolution and that morphological similarity is
> used to group organisms in cladistics. But since rates of morphological
> evolution are highly variable within and between lineages, such assumption
> virtually guarantees that the morphology tree will most likely conflict with
> the DNA tree, especially if the DNA tree is constructed using molecular
> distance or molecular clock.
But please note that DNA trees also have many of the same assumptions.
One cannot say that this represents a case of disagreement as much as a
case rendered difficult because it violates some of the assumptions of
the methods used. Which is not to say that an eventual consensus cannot
be built *as more and different independent data sets accumulate*. We
just ain't there yet.
Laurence A. Moran
In article <6af0k8$m...@bgtnsc03.worldnet.att.net>
get...@worldnet.att.net writes:
>In article <6ae48j$c0s$1...@bioinfo.med.utoronto.ca>,
>>get...@worldnet.att.net writes:
>
>>>As Nyikos said before, this is one study, albeit the most recent, but that
>>>doesn't necessarily mean that this is the most correct tree, even if I think
>>>that birds are probably more closely related to reptiles than to the
>>>mammals.
>>
>>> The fact remains that there are conflicts among different past and present
>>>DNA data sets.
>>
>>Could you please indicate whether you agree with the exact statement that
>>Peter made to Matt?
>
>Did I not make it clear that I agree with Nyikos in my very first post in this
>thread?
You made it very clear that you wanted to support Peter Nyikos and that
you don't think that there is congruence between molecular and
morphological data. But that's not the question I asked. This thread began
when I challenged Peter's specific statement aabout hemoglobins genes and
whether birds were closer to mammals or reptiles. I want to know whether
you agree with Peter on this specific point.
>>>I have a problem with the type of tree chosen by the authors. It is very
>>>confusing and difficult to read. The same species occurs more than once
>>>within a tree so that there is no single hypothesis of relationships based
>>>on the available evidence. They should either show several different trees
>>>based on the different sequences and/or show a consensus tree with each
>>>species appearing only once instead of the type of hybrid tree that they
>>>showed.
>
>>I fear that you lack understanding of gene families. The two main branches
>>are the alpha-A and alpha-D genes. Two different genes in the same genome
>>(species). The reason for analyzing them together is to find out which
>>gnes belong to which family.
>
>You are barking up the wrong tree. My objection is the type of trees they
>show, not the type of genes they used. They can analyze 1500 genes for all I
>care. But if all 1500 genes produced different cladograms, then they should
>show all 1500 different trees. As such, they lumped 4 different sets of trees
>into one, with some species showing up more than once in some clusters and
>some not showing up at all in some of the clusters. It is highly confusing
>and difficult to read. They should have shown the 4 different clusters as
>separate trees and, if they so choose, then show one single consensus
>cladogram generated from the 4 trees. Instead the way they show all 4
>clusters in one diagram is extremely confusing.
There is only one dendrogram in the Fushitani et al. paper. They analyzed
19 different alpha-globin genes by the neighbor-joining method. Figure 3
shows the result they obtained. Each of the branches represents one of the
genes they examined. In some cases there were two different genes from the
same species ("Turtle D" and "Turtle A"). Please note that these trees
show the relationship of genes and not necessarily species. In the case of
gene families we have to be confident that the genes we compare will trace
the history of the species in order to make conclusions about the
evolution of organisms. In the jargon of the trade this means that the
genes have to be orthologous. When dealing with gene families you can
easily run into problems by comparing the wrong genes and that's why some
of the earlier globin data was misleading.
I have no idea what your complaint is all about. What do you mean when you
say "four different sets of trees"? Are you referring to the fact that
they label the various clusters that they obtained when they did the
analysis? The two main branches of the tree separate all of the globin-A
genes from the globin-D genes. Each half of the tree is now a valid
representation of the evolution of the species. Note that the two halves
agree except for a minor shift in the positon of Sphenodon. It is
particularly noteworthy that birds cluster *within* reptiles in both
halves of the tree. (Some readers might recall that this was the original
point we were discussing.)
[snip]
>>No problem. You are more than welcome to question these relationships if
>>you want. As far as I am, concerned it has been settled to my satisfaction
>>and I have moved on to more interesting problems. My intention was merely
>>to show that Peter Nyikos was misrepresenting the state of knowledge with
>>respect to hemoglobin genes.
>There is no misrepresentation on his part. He did say that there were more
>papers showing a different result than the present one. That is an undisputed
>fact.
Actually he said that *all* of the work with alpha- and beta-globins
showed a bird/mammal relationship. That is certainly not an "undisputed
fact".
>Your point is that Fusitani et al.'s paper make all the earlier ones
>irrelevant because it is newer.
Yes, although I'm not necessarly wedded to the idea that all new papers
are better than the older ones.
> But that is not the case. If someone
>publishes a paper corroborating the earlier results, then what?
Then I'll have to reconsider. Meanwhile Peter's statement will still be
wrong.
>Are you going
>to ignore it even though it is, according to you, newer and thus supersedes an
>earlier one like Fusitani et al.'s paper? Aren't you interested in the source
>of the anomalies in the earlier paper if they are indeed anomalous?
One of the reasons why the latest papers are better that the older ones,
in this particular case, is because the newer ones extend the results and
help explain the anomalies. That's why it is so misleading of Peter (and
you) to refer to the older work in your criticisms of hemoglobin genes and
bird phylogeny. Please don't try and divert this into a philosophical
discussion about whether *all* new papers are better than *all* old
papers. Of course they're not. Nobody in their right mind would make such
a silly claim.
Larry Moran
bull.net Cal King
In article <6afkt0$lq9$1...@bioinfo.med.utoronto.ca>,
>In article <6aevb5$2...@bgtnsc02.worldnet.att.net>
>get...@worldnet.att.net writes:
>Yes.
Then you may be unnecessarily orthodox.
>>That is amusing especially
>>because I have been accused of being enamored with molecular data in the
>>past!
>
>I didn't know that. In this thread you seem to be emphasizing the fact
>that there are "anomalies" in some of the molecular phylogenies. Thus it
>seems like you are attacking the entire field of molecular evolution.
I did not use the term "anomaly." I used the term "strongly conflict." I
claimed and continue to claim that DNA studies often strongly conflict those
from morphological studies and made clear that I have little confidence in the
cladistic analysis of morphological characters. I have no idea how such a
position can be misconstrued as being anti-DNA studies.
>Do you agree with me that the vast majority of molecular phylogenies are
>congruent with the fossil evidence and the morphological data? This
>includes most of the results at the species level.
No I don't and let me reiterate that I have more confidence in the DNA data
than the morphology data in most (but not all) cases. I also have more
confidence in pure DNA analysis than I do in those that blends morphological
and DNA characters in the same analysis.
>You seem to be trying to make a case for *frequent* ingongruency at the
>species level. You seem to think, for some unexplained reason, that the
>classification of organisms into a tree-like structure depends on the rate
>of evolution.
In the cases that I have examined, there is little congruence between
morphology and DNA data sets. Morphology trees group organisms with similar
morphological characters, but DNA data group organisms temporally. The two
sets of trees thus often conflict because of highly different rates of
morphological evolution.
>The 90% figure is my subjective impression of the data. (Actually I think
>it is an underestimeate.) You believe that the estimate is "grossly
>inflated" but, to be fair, you can't come up with an objective survey to
>back *your* impression either.
So we have a tie. My subjective estimate is different from yours. BTW, does
the hemoglobin fall within your 90% figure or outside it? To me it is an
exammple of non-congruence.
> I'm not very interested
>in continuing this discussion because I suspect we have run out of
>arguments.
That is entirely your prerogative.
Regards.
bull.net Cal King
In article <6afn3h$m7q$1...@bioinfo.med.utoronto.ca>,
>You made it very clear that you wanted to support Peter Nyikos
If you ask him personally he can cite the many different times that we
disagree.
>and that
>you don't think that there is congruence between molecular and
>morphological data.
I did agree with him this time that there is no congruence in the DNA data and
fossil data in the case of amniote relationships. That was HIS point and I
think he was right that there are no agreements between the earlier DNA data
sets and the fossil data.
>But that's not the question I asked. This thread began
>when I challenged Peter's specific statement about hemoglobins genes and
>whether birds were closer to mammals or reptiles.
His specific statement was that he disagreed with Silberstein's claim that
"that the nested hierarchy of DNA similarity matches the nested hierarchy of
morphology." Nyikos claimed that there is no such match and cited the
hemoglobin data to support his claim.
Excerpt from your original post:
==================================
Last week (January 12, 1998) Peter Nyikos was responding to a statement made
by Matt Silberstein. Here's the relevant quotations,
Peter Nyikos said,
>Matt Silberstein said,
>>The fossils are the icing on the cake. The
>>definitive "proof", if you will, was discovering that the nested
>>hierarchy of DNA similarity matches the nested hierarchy of
>>morphology.
>This "discovery" is still many years in the future. In the
>meantime, we have anomalies like the various kinds of hemoglobin
>all agreeing that mammals are more closely related to birds
>than birds are to lizards, snakes, or turtles, which is
>falsified by the fossil evidence.
=================================
End of Excerpt
>There is only one dendrogram in the Fushitani et al. paper. They analyzed
>19 different alpha-globin genes by the neighbor-joining method. Figure 3
>shows the result they obtained.
And it is a highly confusing dendrogram.
> Each of the branches represents one of the
>genes they examined. In some cases there were two different genes from the
>same species ("Turtle D" and "Turtle A"). Please note that these trees
>show the relationship of genes and not necessarily species.
Then they should have at least tried to come up with a dendrogram of the
species, not just the genes, if their goal is to generate a hypothesis of the
relationships of these taxa.
>I have no idea what your complaint is all about.
My complaint is that the dendrogram they presented is extremely difficult to
read for the general biologist.
>What do you mean when you say "four different sets of trees"?
They should have used separate trees to depict the 4 different "species
clusters." For example, the other paper you cited, Caspers et al. (1996 J.
Mol. Evol.), did not use the same type of confusing tree that Fusitani did.
Fig. 2 of their paper show the hypothetical relationships of the species they
studied and it is easily understood by most biologists. Like Fusitani et al.,
Caspers et al. used a large number of genes, but unlike Fusitani et al.,
Caspers et al.'s tree is much more readable because each species is
represented only once.
> The two main branches of the tree separate all of the globin-A
>genes from the globin-D genes. Each half of the tree is now a valid
>representation of the evolution of the species.
See what I mean? It takes an expert like you to know that the 2 main branches
represent separate genes. Would it not be easier if they had split the tree
in two, and labeled the first tree globin-A and the second one globin-D? And
if they so choose, construct a consensus cladogram combining the two trees?
>Note that the two halves
>agree except for a minor shift in the positon of Sphenodon.
Since there are only 6 species in the first half and 12 in the second half and
only 5 of the species are common to both halves, that is difficult to say.
>It is
>particularly noteworthy that birds cluster *within* reptiles in both
>halves of the tree. (Some readers might recall that this was the original
>point we were discussing.)
Not quite, Vipera is definitely a reptile but it is clustered with the
mammals, not the birds.
>Actually he said that *all* of the work with alpha- and beta-globins
>showed a bird/mammal relationship. That is certainly not an "undisputed
>fact".
There is still no misrepresentation because he was unaware of the new studies
that you subsequently cited and he made that very clear.
>One of the reasons why the latest papers are better that the older ones,
>in this particular case, is because the newer ones extend the results and
>help explain the anomalies. That's why it is so misleading of Peter (and
>you) to refer to the older work in your criticisms of hemoglobin genes and
>bird phylogeny. Please don't try and divert this into a philosophical
>discussion about whether *all* new papers are better than *all* old
>papers. Of course they're not. Nobody in their right mind would make such
>a silly claim.
>Larry Moran
As I pointed out, the newest paper is not without its problem, specifically
the placements of Vipera (Viperidae) and Liophis miliaris (Colubridae).
Fusitani et al.'s cladogram (taken literally) means that the snakes may have
had a polyphyletic origin. While possible and certainly interesting if true,
this view is certainly not held by most biologists, and definitely not
supported by Knight and Mindell (1994, Copeia p.1-9) in which the vipers and
colubrids are found to share a more recent common ancestor than they do with
the boid snakes.
Laurence A. Moran
In article <6ag64h$g...@bgtnsc03.worldnet.att.net>
>In article <6afn3h$m7q$1...@bioinfo.med.utoronto.ca>,
>lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) wrote...
>
>>You made it very clear that you wanted to support Peter Nyikos
>
>If you ask him personally he can cite the many different times that we
>disagree.
>
>>and that
>>you don't think that there is congruence between molecular and
>>morphological data.
>
>I did agree with him this time that there is no congruence in the DNA data and
>fossil data in the case of amniote relationships. That was HIS point and I
>think he was right that there are no agreements between the earlier DNA data
>sets and the fossil data.
There is plenty of congruence between the DNA data and the fossil/
morphological data in the case of amniote relationships. Peter's point was
that there are some genes that show birds closer to mammals and he
specifically mentioned alpha- and beta-globin genes. I casually mentioned
that this was not true - recent work with those two specific genes show
that birds are closer to reptiles than to mammals.
>>But that's not the question I asked. This thread began
>>when I challenged Peter's specific statement about hemoglobins genes and
>>whether birds were closer to mammals or reptiles.
>
>His specific statement was that he disagreed with Silberstein's claim that
>"that the nested hierarchy of DNA similarity matches the nested hierarchy of
>morphology." Nyikos claimed that there is no such match and cited the
>hemoglobin data to support his claim.
I am questioning his example.
>Excerpt from your original post:
>==================================
>Last week (January 12, 1998) Peter Nyikos was responding to a statement made
>by Matt Silberstein. Here's the relevant quotations,
>
>Peter Nyikos said,
>>Matt Silberstein said,
>>>The fossils are the icing on the cake. The
>>>definitive "proof", if you will, was discovering that the nested
>>>hierarchy of DNA similarity matches the nested hierarchy of
>>>morphology.
>
>>This "discovery" is still many years in the future. In the
>>meantime, we have anomalies like the various kinds of hemoglobin
>>all agreeing that mammals are more closely related to birds
>>than birds are to lizards, snakes, or turtles, which is
>>falsified by the fossil evidence.
>=================================
>End of Excerpt
>
>>There is only one dendrogram in the Fushitani et al. paper. They analyzed
>>19 different alpha-globin genes by the neighbor-joining method. Figure 3
>>shows the result they obtained.
>
>And it is a highly confusing dendrogram.
I don't find it confusing. The whole point of the paper was to discover
the relationships of the two different alpha-globin genes in the Komodo
dragon. Their dendrogram shows that relationship.
>> Each of the branches represents one of the
>>genes they examined. In some cases there were two different genes from the
>>same species ("Turtle D" and "Turtle A"). Please note that these trees
>>show the relationship of genes and not necessarily species.
>
>Then they should have at least tried to come up with a dendrogram of the
>species, not just the genes, if their goal is to generate a hypothesis of the
>relationships of these taxa.
The point is that some species have only a single alpha-globin gene that
has been sequenced. It is important to know whether these genes are
alpha-D or alpha-A orthologs. You can only do this by generating a tree
that includes both types.
>>I have no idea what your complaint is all about.
>
>My complaint is that the dendrogram they presented is extremely difficult to
>read for the general biologist.
We are dealing with a gene family. I'm sorry if this makes the analysis
too confusing for you. Since, by your own admission, you don't understand
the work how can you be sure that Nyikos is right?
>>What do you mean when you say "four different sets of trees"?
>
>They should have used separate trees to depict the 4 different "species
>clusters." For example, the other paper you cited, Caspers et al. (1996 J.
>Mol. Evol.), did not use the same type of confusing tree that Fusitani did.
>Fig. 2 of their paper show the hypothetical relationships of the species they
>studied and it is easily understood by most biologists.
Caspers et al. were looking at "amniote relationships inferred from
alpha-A crystallin amino acid sequences". They don't have the complication
of multiple members of a gene family that confuse the issue as in the
hemoglobin genes. That's why it's easier to understand. You did note,
didn't you, that all the placental mammals form a monophyletic cluster
and their closest relatives are the marsupials? I assume you also noted
that the reptiles and birds cluster together and that this group diverged
before the marsupial/placental clade? More importantly, the bird sequence
falls within the reptile group. Is this one of those rare cases where the
DNA data agree with mophological evidence?
> Like Fusitani et al.,
>Caspers et al. used a large number of genes, but unlike Fusitani et al.,
>Caspers et al.'s tree is much more readable because each species is
>represented only once.
These are gene trees, not species trees.
>> The two main branches of the tree separate all of the globin-A
>>genes from the globin-D genes. Each half of the tree is now a valid
>>representation of the evolution of the species.
>
>See what I mean? It takes an expert like you to know that the 2 main branches
>represent separate genes. Would it not be easier if they had split the tree
>in two, and labeled the first tree globin-A and the second one globin-D? And
>if they so choose, construct a consensus cladogram combining the two trees?
I'm sorry if the analysis of gene families confuses you. They did label
each gene that was duplicated as "Turtle D" or "Turtle A" etc. If you
don't feel that you are expert enough to understand the molecular data
then how can you make the claims that you make?
>>Note that the two halves
>>agree except for a minor shift in the positon of Sphenodon.
>
>Since there are only 6 species in the first half and 12 in the second half and
>only 5 of the species are common to both halves, that is difficult to say.
Not difficult at all, in fact I already said it! (-:
>>It is
>>particularly noteworthy that birds cluster *within* reptiles in both
>>halves of the tree. (Some readers might recall that this was the original
>>point we were discussing.)
>
>Not quite, Vipera is definitely a reptile but it is clustered with the
>mammals, not the birds.
Yes quite. The point was whether birds cluster with mammals or with
reptiles and that point is resolved in their analysis. You are bringing up
a different point, namely whether the snake sequence is anomalous or not.
It looks to me like there is a problem with the viper sequence and the
authors discuss this problem in their paper. They point out that the
position of viper (closest to mammals) is not well supported by their
data. On the other hand, the position of birds clustering with reptiles
and not mammals is extremely well supported. Are you deliberately trying
to obscure the main point of this thread or are your questions related to
your lack of understanding of molecular phylogenies?
>>Actually he said that *all* of the work with alpha- and beta-globins
>>showed a bird/mammal relationship. That is certainly not an "undisputed
>>fact".
>
>There is still no misrepresentation because he was unaware of the new studies
>that you subsequently cited and he made that very clear.
That is exactly my point. He misrepresented the evidence because he was
unaware of more recent studies and relied on older work.
>>One of the reasons why the latest papers are better that the older ones,
>>in this particular case, is because the newer ones extend the results and
>>help explain the anomalies. That's why it is so misleading of Peter (and
>>you) to refer to the older work in your criticisms of hemoglobin genes and
>>bird phylogeny. Please don't try and divert this into a philosophical
>>discussion about whether *all* new papers are better than *all* old
>>papers. Of course they're not. Nobody in their right mind would make such
>>a silly claim.
>As I pointed out, the newest paper is not without its problem, specifically
>the placements of Vipera (Viperidae) and Liophis miliaris (Colubridae).
>Fusitani et al.'s cladogram (taken literally) means that the snakes may have
>had a polyphyletic origin. While possible and certainly interesting if true,
>this view is certainly not held by most biologists, and definitely not
>supported by Knight and Mindell (1994, Copeia p.1-9) in which the vipers and
>colubrids are found to share a more recent common ancestor than they do with
>the boid snakes.
There are still some problems with alpha-globin genes but they don't have
anything to do with the bird/mammal controversy from the 1980's. The
most recent work shows that bird genes cluster with reptiles and not with
mammals. This contradicts the statement that Peter Nyikos made to Matt
Silberstein. Let's not forget that we are dealing with a particularly
difficult set of genes here. The other hemoglobin genes (beta) are better
in spite of what Nyikos said.
Larry Moran
bull.net Cal King
In article <6agcf7$qok$1...@bioinfo.med.utoronto.ca>,
>There is plenty of congruence between the DNA data and the fossil/
>morphological data in the case of amniote relationships.
In fact, Nyikos pointed out the number of incongruences outnumber of the
number of congruences. Only by ignoring the earlier papers can you say that
there is congruence.
>Peter's point was
>that there are some genes that show birds closer to mammals and he
>specifically mentioned alpha- and beta-globin genes. I casually mentioned
>that this was not true - recent work with those two specific genes show
>that birds are closer to reptiles than to mammals.
It is true what Nyikos said. Recent work does not equal the only work or even
the most credible work. We have gone through that many times.
>>>There is only one dendrogram in the Fushitani et al. paper. They analyzed
>>>19 different alpha-globin genes by the neighbor-joining method. Figure 3
>>>shows the result they obtained.
>>
>>And it is a highly confusing dendrogram.
>
>I don't find it confusing.
That is because you are an expert in the field. Most general biologists would
have found that tree confusing.
>We are dealing with a gene family. I'm sorry if this makes the analysis
>too confusing for you. Since, by your own admission, you don't understand
>the work how can you be sure that Nyikos is right?
I am not surprised that you jump all over this point. :) If you want
to appeal to authority, be my guest. Nyikos is right because he said that
there is not always congruence between DNA data sets and morphology/fossil
data sets, and he is right because the number of studies showing such
incongruence outnumber those that do as far as the hemoglobin genes are
concerned.
>Caspers et al. were looking at "amniote relationships inferred from
>alpha-A crystallin amino acid sequences". They don't have the complication
>of multiple members of a gene family that confuse the issue as in the
>hemoglobin genes. That's why it's easier to understand. You did note,
>didn't you, that all the placental mammals form a monophyletic cluster
>and their closest relatives are the marsupials?
No I didn't. I never mentioned the correctness of Caspers et al.'s results.
I only made the point that their tree was a lot easier to read than Fusitani
et al.'s tree.
>More importantly, the bird sequence
>falls within the reptile group. Is this one of those rare cases where the
>DNA data agree with mophological evidence?
As I said before, the cases in which I have found incongruence are mostly
those done at the species level.
>I'm sorry if the analysis of gene families confuses you. They did label
>each gene that was duplicated as "Turtle D" or "Turtle A" etc. If you
>don't feel that you are expert enough to understand the molecular data
>then how can you make the claims that you make?
What claim are you referring to? I admit I was stumped by Fusitani's diagram
but I won't be the last one. The fault lies in Fusitani's presentation of the
data. They make no concession to the general biologist. BTW, I forgot to
mention that the amino acid sequences in fig. 1 of Caspers et al. is a lot
more comprehensive than Fusitani et al.'s in fig. 2.
>>>It is
>>>particularly noteworthy that birds cluster *within* reptiles in both
>>>halves of the tree. (Some readers might recall that this was the original
>>>point we were discussing.)
>>
>>Not quite, Vipera is definitely a reptile but it is clustered with the
>>mammals, not the birds.
>
>Yes quite. The point was whether birds cluster with mammals or with
>reptiles and that point is resolved in their analysis. You are bringing up
>a different point, namely whether the snake sequence is anomalous or not.
The snake sequence does cast doubt on the correctness of their data and the
earlier studies do cast doubt on the suitability of the hemoglobin gene in the
study of amniote relationships. Beside, since this is a consensus tree, there
may have been some computer outputs that show birds clustering with the
mammals but such output may have been dumped by the authors. Can you say with
certainty that this is not the case? That other tree may have showed the
Vipers clustering with Liophis but birds with mammals.
>It looks to me like there is a problem with the viper sequence and the
>authors discuss this problem in their paper. They point out that the
>position of viper (closest to mammals) is not well supported by their
>data. On the other hand, the position of birds clustering with reptiles
>and not mammals is extremely well supported.
There are other problems with their tree now that you have mentioned it. The
birds are shown more closely related to Sphenodon and turtles than they are to
their traditional sister group the crocs. Hence there are incongruences
between this tree and the morphology/fossil tree.
>Are you deliberately trying
>to obscure the main point of this thread or are your questions related to
>your lack of understanding of molecular phylogenies?
Yes, keep up your appeal to authority. OTOH, if you want to discuss the
evidence objectively, the main point of this thread is whether the hemoglobin
gene is congruent with the fossil record and even this particular tree show
several incongruences, not only with the fossil record, but also with another
DNA study, that of Caspers et al.
>Let's not forget that we are dealing with a particularly
>difficult set of genes here. The other hemoglobin genes (beta) are better
>in spite of what Nyikos said.
>Larry Moran
Hence it is not unusual that it sometimes shows "anomalous" results. Not all
genes are useful for phylogenetic analysis. That is a fact and it is not a
knock on molecular systematics, just a fact of life. Sweeping the earlier
hemoglobin studies and the anomalies in the present one under the rug will not
help improve DNA techniques.
Wade Hines
Someone called Cal King wrote:
> lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) wrote...
>>And the king snake again ...
> >>And it is a highly confusing dendrogram.
> >I don't find it confusing.
> That is because you are an expert in the field. Most general biologists would
> have found that tree confusing.
<<<snip>>>
> >Are you deliberately trying
> >to obscure the main point of this thread or are your questions related to
> >your lack of understanding of molecular phylogenies?
> Yes, keep up your appeal to authority. OTOH, if you want to discuss the
> evidence objectively, the main point of this thread is whether the hemoglobin
> gene is congruent with the fossil record and even this particular tree show
> several incongruences, not only with the fossil record, but also with another
> DNA study, that of Caspers et al.
I'm confused by the attempt to sound authoritative and knowledgeable
intermingled with gross mistakes such that "the hemoglobin gene" and the
earlier questions about what people have against heme. It does indeed require
more than a grasp of English to read scientific papers. If this is an appeal to
authority, then I make such an appeal. Get more background and then come
back and play journal club. It could be fun if you didn't get sidetracked by
trivialities and could instead work on some actual problems, of which there
are plenty for your needs.
> >Let's not forget that we are dealing with a particularly
> >difficult set of genes here. The other hemoglobin genes (beta) are better
> >in spite of what Nyikos said.
> >Larry Moran
> Hence it is not unusual that it sometimes shows "anomalous" results. Not all
> genes are useful for phylogenetic analysis. That is a fact and it is not a
> knock on molecular systematics, just a fact of life. Sweeping the earlier
> hemoglobin studies and the anomalies in the present one under the rug will not
> help improve DNA techniques.
Ignoring the less than trivial aspects of comparisons indeed reveals apparent
conflicts. Interpreting sequences as nothing more than letters indeed could
lead to apparent conflicts. Using nearest neighbor pairing methods with small or
unrepresentative data sets could indeed lead to apparent conflicts. If one knows
how such methods are invented and is cautious in their use, such conflicts
or anomolies are understood to be in the expected level of noise and thus are
not in any honest way actual conflicts.
As ever, one needs to understand the error bars associated with ones methods.
Some people who post to talk.origins have shown a rather poor grasp of
that concept.
Wade Hines
Cal King wrote:
> Another post with nothing but ad hominem attacks. I am sorry to inform you
> that I have put you in my killfile.
>
> Goodbye.
Let me repost some of those ad hominem attacks for you to ignore.
|>Ignoring the less than trivial aspects of comparisons indeed reveals apparent
|>conflicts. Interpreting sequences as nothing more than letters indeed could
|>lead to apparent conflicts. Using nearest neighbor pairing methods with small or
|>unrepresentative data sets could indeed lead to apparent conflicts. If one knows
|>how such methods are invented and is cautious in their use, such conflicts
|>or anomolies are understood to be in the expected level of noise and thus are
|>not in any honest way actual conflicts.
|
|>As ever, one needs to understand the error bars associated with ones methods.
I lost which part of that was "nothing but ad hominem attacks".
Here's the really nasty part.
|>I'm confused by the attempt to sound authoritative and knowledgeable
|>intermingled with gross mistakes such that "the hemoglobin gene" and the
|>earlier questions about what people have against heme. It does indeed require
|>more than a grasp of English to read scientific papers. If this is an appeal
to
|>authority, then I make such an appeal. Get more background and then come
|>back and play journal club. It could be fun if you didn't get sidetracked by
|>trivialities and could instead work on some actual problems, of which there
|>are plenty for your needs.
I did add a nasty party shot in the original but I've seen much worse from
somebody
that Cal King seems to admire greatly.
Peter Nyikos
Moran manages not to bat an eye over two major discrepancies between
what is all but certainly known from fossils, and what is "shown"
by comparisons of alpha hemoglobin:
1. Birds, which fossil evidence overwhelmingly shows to have crocodilians
as a sister group among extant organisms, are "shown" to
be more closely related to turtles than to crocodilians.
2. Birds, which fossil evidence overwhelmingly shows to be
more closely related to lizards than to mammals, are "shown"
to be more closely related to mammals than to lizards.
A cc goes to two specialists in reptile paleontology, Thomas
Holtz and Chris Brochu, who participate in t.o. from time to
time and are s.b.p. and s.b.s regulars, because I am very curious to see
how they react to these discrepancies.
lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) writes:
>In article <1998012400...@milo.math.sc.edu>
>Peter Nyikos <nyi...@math.sc.edu> writes:
>>lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) writes:
>>>Last week (January 12, 1998) Peter Nyikos was responding to a statement made
>>>by Matt Silberstein. Here's the relevant quotations,
>>
>>>Peter Nyikos said,
>>>>Matt Silberstein said,
>>>>>The fossils are the icing on the cake. The
>>>>>definitive "proof", if you will, was discovering that the nested
>>>>>hierarchy of DNA similarity matches the nested hierarchy of
>>>>>morphology.
Note the unequivocal word "matches", which Moran has not
corrected in all his followups stemming from this exchange
between me and Matt.
>>>>This "discovery" is still many years in the future. In the
>>>>meantime, we have anomalies like the various kinds of hemoglobin
>>>>all agreeing
>>
>>I should have restricted myself to alpha and beta hemoglobin,
>>and myoglobin.
To be precise: "and also included myoglobin".
>I interpreted your statement to mean alpha and beta-globin genes.
Well, I seem to recall something about human embryos having
another kind of globin gene. But since that hasn't been
talked about here or in the source you gave earlier, let's
stick to alphas and betas.
By the way, do you have any idea the ONE article you
cited up to now didn't do any beta comparisons, when they DID isolate
the beta chains in the Komodo dragon?
>>>> that mammals are more closely related to birds
>>>>than birds are to lizards, snakes, or turtles, which is
>>>>falsified by the fossil evidence.
>>
>>>I pointed out that Peter's statement was not correct.
>>
>>The "lizards" part looks better than ever. Yes, some
>>studies disagree, but the last word is far from in.
>I interpreted your statement to mean that the data shows birds are more
>closely related to mammals than to reptiles. Is there some nuance that
>escaped me?
Yes, the elementary fact that crocodilians are reptiles, and
my failure to mention them, a failure I rectified in my last
post:
>>BTW, I even pulled my punches somewhat in what I said up there. I
>>could have related how alpha hemoglobin and myoglobin both agreed
>>in the earlier study
>>that birds are more closely related to mammals than they
>>(birds) are to CROCODILIANS. Even beta hemoglobin agreed with this
>>in one study, but not in two others. One of those two others, though,
>>still showed birds closer to mammals than to snakes. [Lizards
>>weren't tested, apparently.]
>>
>>Also, I misremembered about the lizards, snakes, and turtles
>>where alpha hemoglobin is concerned. The studies cited
>>only used it to compare birds, mammals, and crocodilians,
>>with the anomalous result just described.
>>
>>However, your study came to my rescue as far as lizards are
>>concerned.
The following was my secondary reference to the hemoglobin
and myoglobin studies:
>>Reference:
>>
>> Michael J. Benton, "Amniote Phylogeny", in:
>> _Origins of the Higher Groups of Tetrapods: Controversy and Consensus_,
>> ed. by Hans-Peter Schultze and Linda Trueb, co. 1991, Cornell
>> University Press, pp. 317-330, at p. 323.
[...]
>>But more to the point is that you left out some all important
>>quantifiers. NOBODY was denying that birds are related to
>>reptiles. The question you seem shaky on is WHICH reptiles
>>are they MORE closely related to than they are to MAMMALS.
>This isn't what I understood from your comment to Matt Silberstein. I
>agree that you were not arguing against a bird/retile relationship. What
>you did do was state that the *hemoglobin* data showed a bird/mammal
>relationship.
Only that birds are more closely related to mammals than they are to
SOME reptiles. I just got the reptiles wrong from relying on
my imperfect memory, together with my failure to even suspect
that a study involving alpha hemoglobin would put birds
closer to turtles than to crocodilians.
It is that statement that I am challenging. I haven't
>mentioned anything about which reptiles are closest to birds and, quite
>frankly, I'm not that interested in discussing it.
"closest" isn't the `fireworks' issue; "closer than mammals" is.
>You seem to be moving the goalposts here but since we all know that you
>are an honorable man I guess that can't be true.
You are absolutely correct, although I believe this comment of
yours was meant in sarcasm. I did have to correct my imperfect
memory, and I should have originally refreshed my memory from
my source instead of relying on it.
I assume that I must have
>somehow conveyed the false impression that I was interested in which
>reptiles were closest to birds. Sorry.
No, I never assumed you were interested in that, only
in the `fireworks' issue.
>>>This is the paper we are discussing,
>>
>>> Fushitani et al. (1996) The Amino Acid Sequences of Two alpha
>>> Chains of Hemoglobin from Komodo Dragon _Varanus komodoensis_
>>> and Phylogenetic Relationships of Amniotes.
>>> Mol. Biol. Evol. 13, 1039-1043.
>>
>>>For some reason Peter choose not to read the paper that I referenced. I assume
>>>that he hasn't had time to get to the library
>>
>>...until this afternoon. And two of the things it "shows" are
>Good. I'm glad you were finally able to look it up. I can understand how
>busy you must have been in the past week and I appreciate the effort you
>made. Now, let's discuss the paper. Have you answered most of the
>questions you had last week?
Yes.
>>Birds are more closely related to turtles than to crocodilians and
>This is correct for the alpha-A genes. Did you notice that birds fall
>within the reptiles and are not clustered with mammals?
Birds AND mammals fell within the reptiles, and birds are
clustered with Sphenodon, turtles, crocodilians, MAMMALS,
and even *Viper viper* and away from lizards.
>>Birds are more closely related to humans and horses than they
>>are to lizards.
>This is correct, the three lizard alpha-globins branch off before the
>divergence of the human/horse cluster from the turtle/alligator/
>Sphenodon/chicken/ostrich cluster. The point, of course, is that birds are
>more closely related to reptiles than they are to mammals.
You sure have a strange way of talking, as though lizards
weren't reptiles.
[...]
>>>Peter said,
>>>>Moran found a source more
>>>>recent than the ones I was using, apparently gathering data from ONE
>>>>species of reptile. Why would they be using a rare creature
>>>>like the Komodo Dragon lizard for a study, unless Moran
>>>>had to scrape the bottom of the barrel for a study which
>>>>AGREES with the fossil record?
Of course, the study you scraped up does NOT agree with the
fossil record, but you didn't mention that, perhaps out
of ignorance of the fact that it is all but certain from
the fossil record that birds are more closely
related to lizards than to mammals. No surprise: the
authors of his article also seem to be blissfully
ignorant of that fact.
[deletia of things to be dealt with in separate followup]
>>>with all those in the current databases. I chose this particular paper because
>>>the abstract clearly stated that "birds form a sister group with other
>>>reptiles but not with mammals".
>>
>>HIGHLY misleading. Birds form a sister group with 4 of the 8
>>reptiles tested, but one of them, a viper, was "shown" to
>>be more closely related to mammals than it was even to
>>these four.
>The two bird sequences (chicken and ostrich) cluster *within* the group
>that includes turtle, Sphenodon, caiman, and alligator. I don't find their
>abstract misleading.
"a number of other reptiles" should have been used instead of "reptiles".
>>But that's kid stuff compared to the fact that the remaining
>>three reptiles, all lizards, formed an outgroup; the four
>>"birdlike" (according to alpha) reptiles had as a sister
>>group the cluster {horse, human, viper}
[confusion by Moran over the issues deleted here.]
>>By the way, the four "birdlike" reptiles were the turtle,
>>Sphenodon, an alligator and a caiman. The latter two
>>lost out to Sphenodon and the turtle for the honor
>>of "most birdlike" again in defiance of paleontological
>>theory.
>>
>>Didn't any of this SURPRISE you?
>Actually no. It didn't surprise me because I'm not terribly interested in
>such things. I *was* interested in earlier work that showed birds and
>mammals to be more closely related than birds and reptiles
You really seem to have a terrible time with quantifiers like
"some".
[quantifier-free question by Moran deleted]
[deletia of things to be dealt with in separate followup]
>>Instead of clearing up the discrepancy between molecular and
>>paleontological data, this deepens it.
>I don't understand why you say that. It seems to me that the biggest
>problem was whether molecular data supported a bird/mammal cluster or a
>bird/reptile cluster.
No, that wasn't the biggest problem, although the authors of
that article may have misled you into thinking that it was.
The only problem they acknowledged in their paper was whether
mammals or CROCODILIANS were the sister group of birds; having
seemingly resolved the question in favor of "neither, but
crocodilians are more closely related to birds than mammals
are" they dropped the whole issue.
Surely the earlier work that suggested birds were
>related to mammals was a bigger discrepancy than what we have now?
No, because the earlier alpha work I was citing used only
birds, mammals, and crocodilians. With turtles and Sphenodon
and lizards and sharks (!!) added into the mix, mammals got
displaced to outside the crocodilians. But such rearrangements
are not unusual: the authors themselves cite how deleting
*Viper viper* from the data shifted the relationships of
the REMAINING groups around from what it was before.
Sharks were, I suppose, put in so that they could properly
root the amniote tree, but they would have done better to
include frogs or some other amphibian. Should I explain why?
>In any case, I'm not very interested in these other discrepancies now that
>we've settled the issue that I raised in the first place.
...an issue of yours that was ambiguously worded and not the same as
the issue that divided me and Matt.
[about a duplicate alpha gene found in birds, turtles, lizards,
and Sphenodon:]
>> The authors, who trust
>>the paleontological data to a limited extent, hypothesize that
>>either the gene will be found in crocodilians as well, or else
>>they've lost it; ditto for *Viper viper*.
And, bizarrely enough, they make NO mention of mammals at this
point.
>>>this seemed particularly relevant to your previous statement. There are
>>>plenty of other recent studies that also show agreement between hemoglobin
>>>dendrograms and the fossil record. I'd be happy to supply you with the
>>>references if you think they will help you to understand the current state of
>>>knowledge in the field.
>>
>>Please do.
>Did you read the other reference that I gave you?
WHAT other reference? I recall none.
Have you tracked down
>the references to post-1990 papers in Fushitani et al.?
No, because they give NO clue as to which ones compare alpha
chains of birds, mammals, and various reptiles besides crocodilians.
They do NOT cite Bishop and Friday when they talk about the
bird-mammal-crocodilian issue, so I would guess that the
alpha study alluded to by Benton in my reference was done in:
Goodman, M., M. M. Miyamoto, and J. Czelusniak. 1987.
Pattern and process in vertebrate phylogeny revealed
by coevolution of molecules and morphologies.
PP. 141-176 in....
...in the same Patterson, ed. volume that one of the Bishop and
Friday papers was found in!! Fushitani et. al. mysteriously fail to
cite this even though they reference a 1975 paper co-authored by Goodman.
[about the Fushitani et. al. paper:]
>>>I read the paper two years ago when it was first published and I re-read it
>>>last week.
>>
>>Did you? Why didn't you notice that Table 3 contradicts the
>>abstract?
>I assume you mean Figure 3?
Yes. There I went again relying on my memory instead of reading.
There doesn't seem to be a contradiction to
>me. Could you explain?
Perhaps a grade school teacher could explain to you the meaning
of quantifiers like "some" and what the default assumptions
are when they are lacking.
Peter Nyikos
Thanks for setting my mind at ease about the Komodo dragon, Wade.
I think the real reason the authors used it is that it is the
first squamate in which BOTH alpha chains have been sequenced.
Since other squamates (lizards and snakes) have been found in
which both genes have been DETECTED, I'm still a bit surprised
that the KD is the first one for which both have been sequenced,
given the ease with which this is done according to you.
I'm also a bit surprised to find an unequiviocal prediction
from this one datum.
Figure 3 shows clearly that the [adult alpha] is clustered
with another adult type of alpha chain from the living
squamates and forms the SQ group, whereas [embryonic alpha]
chain of V. komodoensis is in the EM group. Therefore,
when both of the two alpha chains from other squamates
are sequenced, they will be clustered in the way that the
two alpha chains from *V. komodoensis* are grouped into
the separate groups EM and SQ. [pp. 1041-2]
This is a far more unequivocal prediction than I've EVER seen
in talk.origins as far as "evolutionary predictions" go,
and it will be interesting to see whether:
1. it is ever falsified and
2. whether Wesley Elsberry and others here will take a single successful
instance of the prediction as "confirim"ing the prediction.
Peter Nyikos
hi...@cgl.ucsf.EDU (Wade Hines) writes:
>my...@netaxs.com (PZ Myers) writes:
>><nyi...@math.sc.edu> wrote:
>>> Two *alpha* globin sequences. Do these people have some sort
>>> of problem with heme sequences, by the way?
>>This has already been pointed out to you,
I don't think anyone ever pointed it out to me before Myers
did just now. Even Moran played coy earlier in this thread.
but it is such a silly
>>point you are making that I have to mention it again.
>>Heme is *not* a protein. It does not have a sequence. It rather
>>seriously undercuts your claim of competence in this matter to
>>persist in this kind of muddled argument.
What is undercut, IMO, is Myers's credibility when he
claims things have been told people before.
Of course, Myers undercut that lots of times last year
when he kept saying things had been pointed out to me
by biologists repeatedly, and repeatedly refused to name
a single one of the alleged biologists.
He also undercut it this year when he claimed it had
been repeatedly pointed out to me that Moore's embryology
text is out of date, when in fact the first to do that
was Myers himself in the very post where he made this
false claim about him and Hershey having both pointed
this out to me many times.
>>So, yeah, those people do have a sort of problem with heme
>>sequences.
>My problem with heme is in the things like cytochrome C where it
>is covalently attached and therefore gives me a mass for the
>modified peptide which isn't trivially or even non trivially
>deducable from reading a database entry.
>That and they aren't all the same heme across heme associated
>proteins. But we shouldn't let details get in the way of
>pseudoerudition.
>Heme associated globin genes are easy 'cause its non covalent
>(whoops, there we go again) unless you go for some of the rare
>cross links you can find in smokers blood but the money from
>RJR has dried up.
Thanks for the neat little details, Wade.
Peter Nyikos -- standard disclaimer --
University of South Carolina
bull.net Cal King
Peter Nyikos
CC: get...@worldnet.att.net, asking him to please remove the
"backslash 240" from his anti-spam `address' because I have
to keep removing it to get my netserver to handle replies to him.
Also, I'd like to urge you, Cal, to slow down a bit in your
replies to Moran. Several rounds in one day can really
clog up a thread, especially one where Moran keeps missing
the boat as to what the issues are.
get...@nobull.net (Cal King) writes:
>In article <6ae3ev$bru$1...@bioinfo.med.utoronto.ca>,
>lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) wrote...
>>Yes, the molecular data on higher taxa show excellent congruence
Obviously, Moran is not using "congruence" the way a mathematician
would, to denote a perfect match with no anomalies.
with
>>the morphological data (and the fossil record). There are some anomalies
>>at the level of species and genera
...and ORDERS and even SUBCLASSES, as in the relevant study.
We even have the *wrong* relationship between:
1. Family Lacertilia of order Squamata
2. CLASS Aves
3. CLASS Mammalia
right in the study which Moran says he read twice and which
he proudly posted the abstract from, to try and refute me.
>> but this are relatively unimportant
>>compared to the mass of molecular data that is out there.
Moran is whistling Dixie, as they say.
(Don't get me
>>wrong, there are some very interesting problems at the higher levels as
>>well, including the biggest one of all.)
Moran is changing the subject. We have nothing from the fossil
record which sheds light on how the kingdoms should be grouped.
On the other hand, the fossil evidence is overwhelming that
the correct grouping is:
[{Lizards [Birds]} Mammals]
And not [{[Birds] Mammals} Lizards] as claimed by the article.
>>Note that the morlecular data consistently shows mammals grouped together
>>and separate from other groups such as marsupials,
Marsupials ARE mammals.
amphibians, fish or
>>reptiles. Look at the insects, fungi, flowering plants, various orders of
>>bacteria, anelids, nematodes, bryophytes, etc. etc. - all of these groups
>>are confirmed by molecular data.
Reptiles are NOT confirmed by molecular data involving either
alpha hemoglobin or myoglobin, and only one beta hemoglobin
study out of three I (or Moran, apparently) knows about confirms
Reptilia--the other two do not.
I wonder whether Moran is leveling with us about the rest. For sure,
any "confirmation" obtained up to now would involve only small samples
of genomes and hence would have to be provisional.
>>We have a glass that is 90% full (to use a popular analogy)
No, a glass which is maybe .01% full...
but you are
>>making a big fuss about the 10% that is empty.
No, about the .001% that is full of baloney. See comments about
genomes above.
That's fine, the 10%
>>contains some really exciting areas of investigation,
Yup, it's exciting to see how the baloney will be eliminated by
sampling a larger fraction of the whole genome--or will it?
Stay tuned, folks, for the rest of your lives maybe. ;-)
>>Larry Moran
>Did I come across as discrediting DNA research? That is amusing especially
>because I have been accused of being enamored with molecular data in the
>past!
Yes, even I think you go overboard in that direction, Cal.
> I would not dismiss the incongruence at the species and genus level as
>anomalies, because evolution occurs at the species level. Higher taxa do not
>evolve.
They do evolve as collectives. You don't see people laughing
themselves silly over book titles like Colbert's
_Evolution of the Vertebrates_, do you? In it you can see
him explicitly talking about shark evolution, bird evolution, etc.
The incongruence at these levels shows that evolutionary rates are
>vastly different between molecular and morphological evolution.
And that applies to the higher levels, in spades.
This is a
>fundamental fact and the sooner we realize it, the less taxonomic chaos we
>will generate at the species, genus and family levels. As to your claim that
>there is 90% congruence, that is quite plausibly a grossly inflated subjective
>estimate because you still haven't cited any objective survey to back up your
>claim.
You are right on target here, Cal, and Larry will not be able to
cite an objective survey for the next decade, IMO.
Peter Nyikos -- standard disclaimer --
bull.net Cal King
In article <1998012617...@milo.math.sc.edu>, nyi...@math.sc.edu (Peter
Nyikos) wrote...
>Obviously, Moran is not using "congruence" the way a mathematician
>would, to denote a perfect match with no anomalies.
I agree. He kept pointing to the bird-reptile relationship in the Fusitaini
paper as evidence of congruence, but totally ignored all the other anomalies
in that study.
>On the other hand, the fossil evidence is overwhelming that
>the correct grouping is:
>
> [{Lizards [Birds]} Mammals]
Is it really? If the squamata is the first group to branch off from the
amniotes, and the mammalian ancestors were next, followed by the archosaurs,
then the correct grouping should be
___ Squamates
| __ birds
Basal amniotes----| _______ |
| |__ crocs
|
|___________ mammals
>And not [{[Birds] Mammals} Lizards] as claimed by the article.
Mammals should then cluster more closely to birds than to the Squamates.
>Stay tuned, folks, for the rest of your lives maybe. ;-)
We live and we learn. :)
>>Did I come across as discrediting DNA research? That is amusing especially
>>because I have been accused of being enamored with molecular data in the
>>past!
>
>Yes, even I think you go overboard in that direction, Cal.
Actually many morphologists cum cladists are turning in that direction as
well. I liken the revolution in systematics to the electronics revolution.
That are still some who claim that the vacuum tube is superior just as those
who claim that morphology is better at resolving phylogenies, but the main
stream of phylogenetic analysis is turning to molecular techniques and to
transistors. That does not mean that we should abandon morphological analysis
altogether. We still need to group organisms preliminarily by morphology
before we can test for monophyly using molecular techniques. I read that
Norell and Benton made a survey of the congruence between fossil and
morphological analysis and not surprisingly found some very good congruences.
That is partly because many morphological analyses were done by the
paleontologists who would probably reject computer output that shows an
obvious temporal paradox. Incongruences do occur though and we have one study
pointed by Gould (1991 Paleobiology), in which the trilobites were said to be
the most derived and the crustaceans the most primitive arthropod.
>> I would not dismiss the incongruence at the species and genus level as
>>anomalies, because evolution occurs at the species level. Higher taxa do
>>not evolve.
>
>They do evolve as collectives.
I do agree that parallelism is rampant. Species with very similar genetic
makeups do respond in similar ways to the same environmental pressures. For
example, tortoises do become gigantic on island habitats that are devoid of
grazing mammals (Galapagos and Aldabra). Otherwise, each species pretty much
evolves on its own and at its own rate. That is why we have all sorts of
living fossils ranging from bacteria all the way to the chimpanzees.
>You don't see people laughing
>themselves silly over book titles like Colbert's
>_Evolution of the Vertebrates_, do you? In it you can see
>him explicitly talking about shark evolution, bird evolution, etc.
Birds are highly constrained in their evolution by the requirements of flight
(Feduccia 1996 Origin and Evolution of Birds) and sharks haven't changed much
since their origin. There may be trends in the evolution of some groups, but
there definitely is no trend in the bony fishes, some of which invaded the
land and radiated to an amazing variety of body forms and niches.
>> As to your claim that there is 90% congruence, that is quite plausibly a
>> grossly inflated subjective estimate because you still haven't cited any >>
objective survey to back up your
>
>>claim.
>
>You are right on target here, Cal, and Larry will not be able to
>cite an objective survey for the next decade, IMO.
>
>Peter Nyikos
Actually the cases of incongruences are the most interesting as they may have
something to tell us. That is why we should never sweep them under the rug.
Every incongruent branch is a potential hot spot that requires further
research. Better techniques and/or better understanding of nature can only
come when we pay attention to the incongruences rather than trivialize them.
Laurence A. Moran
In article <1998012617...@milo.math.sc.edu> Peter Nyikos
<nyi...@math.sc.edu> writes:
>Moran is whistling Dixie, as they say.
Peter, I can appreciate why you want to divert attention away from the
original statement that you made to Matt Silberstein. As far as I am
concerned you were wrong when you said that the molecular data from
hemoglobin genes showed birds more closely related to mammals than to
reptiles.
I'm not the least bit interested in quibbling with you about subtle
nuances in your original statement. You are now trying to claim that you
were correct because in the study I quoted lizards are closer to mammals
than they are to other reptiles. If it makes you happy to note that
the paper I referenced has some other anomalies then I'm happy for you
as well. It doesn't change the fact that what you said was wrong.
Furthermore, if you want to believe that most of the molecular data is
flawed then be my guest. If this is really your position then why are we
bothering to discuss molecular data at all?
I've said all I need to say on this topic - the thread is rapidly
degenerating into something that nobody is interested in (except
you). I prefer to end this discussion rather than lower myself to the
level of responding to your obfuscations and insinuations. Quite frankly,
I doubt very much that you know what you are talking about.
Goodbye Peter.
Larry Moran
PZ Myers
In article <1998012615...@milo.math.sc.edu>, Peter Nyikos
<nyi...@math.sc.edu> wrote:
> hi...@cgl.ucsf.EDU (Wade Hines) writes:
>
> >my...@netaxs.com (PZ Myers) writes:
>
> >><nyi...@math.sc.edu> wrote:
>
> >>> Two *alpha* globin sequences. Do these people have some sort
> >>> of problem with heme sequences, by the way?
>
> >>This has already been pointed out to you,
>
> I don't think anyone ever pointed it out to me before Myers
> did just now. Even Moran played coy earlier in this thread.
>
> but it is such a silly
> >>point you are making that I have to mention it again.
>
> >>Heme is *not* a protein. It does not have a sequence. It rather
> >>seriously undercuts your claim of competence in this matter to
> >>persist in this kind of muddled argument.
>
> What is undercut, IMO, is Myers's credibility when he
> claims things have been told people before.
>
My apologies. Here's where it was posted before:
--- begin quote ---
Subject: Re: Aw, Peter, have a heart! was Re: rat to bat
From: howard hershey <hers...@indiana.edu>
Date: 1998/01/22
Message-ID: <34C737...@indiana.edu>
Newsgroups: talk.origins
Peter Nyikos wrote:
>
> howard hershey <hers...@indiana.edu> writes:
>
[snip]
> By the way, why this exclusive reliance on "globins"? What do you
> and Moran have against the heme groups?
Huh? You might want to actually read that 1970s biochem book you have
and find out why heme groups are not prime candidates for sequence
analysis. Hint: Proteins are encoded in DNA. Heme groups are not.
--- end quote ---
I will presume that the mysteries of usenet propagation let me see
it before it got to you.
Of course, the gist of the complaint is *not* that you hadn't noticed
the correction before, but that you were surprised that heme had not
been sequenced.
However, there too I must offer my apologies. You are 100% correct.
I made a quick scan of the literature through PubMed, and to my immense
surprise, discovered that you are right: NO ONE has sequenced heme! I
double-checked on GenBank -- no sequence there, either.
Then I noticed something else. A great many very significant, biologically
active molecules of immense importance in development and throughout
evolution have not been sequenced either. Steroidal hormones, retinoids,
alkaloids, terpenoids...there is a long, long list of critical elements
of the cellular and organismal machinery that have not been sequenced. I
looked through various reviews, and discovered something even more shocking:
the lack of these critical data is rather pointedly ignored.
It gets worse. It's not as if biologists have failed to recognize the
importance of these molecules, or have simply been too busy to sequence
them. There are a great many articles on them, they all just ignore the
missing sequence data. Additionally, in many cases, they may have sequenced
other critical elements of the pathway. There are quite a few articles that
discuss the sequence of retinoid *receptors*, for instance, but they all
fail to mention or cite the sequence of the ligand!
I repeat, Peter, that you may be right. There were a few tantalizing hints
in the literature that these molecules may be virtually identical in different
species, even in different phyla. Perhaps the reason that these molecules
are never mentioned is that their sequences are so similar that any phylogenetic
trees derived from them deviate radically from the conventional taxonomy?
It galls me to have to say it again, but I am sorry. You could be right,
here. With this little throwaway line:
> >><nyi...@math.sc.edu> wrote:
>
> >>> Do these people have some sort
> >>> of problem with heme sequences, by the way?
you may have offered us a hugely significant insight into a tremendous
problem in molecular biology.
May I suggest that you start a new thread, "Evolutionary mysteries
in molecular biology", and that you put this major question right at
the top of your list?
[snip]
--
PZ Myers
PZ Myers
In article <6ah68o$c...@bgtnsc02.worldnet.att.net>, get...@worldnet.att.net
wrote:
> Another post with nothing but ad hominem attacks. I am sorry to inform you
> that I have put you in my killfile.
>
> Goodbye.
"you"??? Who is "you"? Is it me? Gosh, whatever did I do to you to deserve
this most heinous fate?
As a matter of netiquette, whenever you killfile someone you are supposed
to announce it portentiously, with full listing of the anathematic's name.
You are also supposed to punctuate it with the incantation, "** PLONK **".
There is also the important ritual of putting thumb to nose, waggling
your fingers at the monitor, and saying "neener, neener, neener", but
since that is a private and personal part of the act, I will presume that
you carried it out faithfully. (hey, it's the fun part! Sometimes I do it
to people's posts without killfiling them, and I don't even tell them, so
there.)
--
PZ Myers
howard hershey
Peter Nyikos wrote:
>
> CC: get...@worldnet.att.net, asking him to please remove the
> "backslash 240" from his anti-spam `address' because I have
> to keep removing it to get my netserver to handle replies to him.
>
> Also, I'd like to urge you, Cal, to slow down a bit in your
> replies to Moran. Several rounds in one day can really
> clog up a thread, especially one where Moran keeps missing
> the boat as to what the issues are.
>
> get...@nobull.net (Cal King) writes:
>
> On the other hand, the fossil evidence is overwhelming that
> the correct grouping is:
>
> [{Lizards [Birds]} Mammals]
>
> And not [{[Birds] Mammals} Lizards] as claimed by the article.
>
The lineage that eventually led to birds (archosaurs) and the lineages
that led to sphenedon, turtles, lizards, and mammals (pelycosaurs) all
appeared as separate lineages quite early and at and around the same
time from more primitive reptiles and it is an open question (given the
necessary ambiguity in determining when the 'first' of any fossil
lineage started, since new finds can easily change a 'first') as to
where and when the pelycosaur/therapsid/mammal lineage should link into
any phylogeny based on the points of divergence from primitive reptile
stock. As Cal King points out, it is, in fact, quite possible that the
ancestors to present day 'lizards' diverged from this stock *before* a
later divergence led to separate evolution of the archosaurs (and later
birds) and the pelycosaur -> therapsid -> mammal divergence.
One would expect the mass of molecular evidence (but not necessarily any
*single* bit of data) to reflect the timing of these probable
evolutionary divergences, but it may not support the one you want (with
all the group we now call 'reptiles' staying together as a unified
primitive grouping until after the pelycosaurs diverged from them) and
may not clearly and unequivocably support any particular branching
pathway if the lineages all diverged approximately simultaneously. It
may well produce results at least as ambiguous as the morphological and
fossil evidence.
But all mammals should cluster together in the DNA/protein sequencing.
All birds should cluster together. These are the end flowerings on
branches long separated from the others. They do, of course, cluster.
Where the fossil/morphological evidence is unambiguous, the sequence
information is equally unambiguous *and congruent* with that evidence.
Whether any of the other features of the globin analysis is a reflection
of errors in the 'common-sense' idea of 'reptiles' as a single group
(just as the idea of 'fishes' as a common single group is an erroneous
'common sense' idea) or errors due to the choice of hemoglobin can only
be resolved (if it is possible to resolve it) by adding more sequences.
When more sequences are added, the conclusions reached may change from
their current status, just as the idea that birds are closer to mammals
and not within the reptile group changed.
David Iain Greig
PZ Myers <my...@netaxs.com> wrote:
>In article <6ah68o$c...@bgtnsc02.worldnet.att.net>, get...@worldnet.att.net
>wrote:
>
>> Another post with nothing but ad hominem attacks. I am sorry to inform you
>> that I have put you in my killfile.
>>
>> Goodbye.
>
>"you"??? Who is "you"? Is it me? Gosh, whatever did I do to you to deserve
>this most heinous fate?
>
>As a matter of netiquette, whenever you killfile someone you are supposed
>to announce it portentiously, with full listing of the anathematic's name.
>You are also supposed to punctuate it with the incantation, "** PLONK **".
And then send Richard Sexton (ric...@vrx.net) a dollar for using his
'plonk' method.
--D.
Peter Nyikos
lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) writes:
>In article <1998012617...@milo.math.sc.edu> Peter Nyikos
><nyi...@math.sc.edu> writes:
>>Moran is whistling Dixie, as they say.
>Peter, I can appreciate why you want to divert attention away from the
>original statement that you made to Matt Silberstein.
On the contrary. I've corrected it to the extent it needs to
be corrected. I was guilty of a faulty memory, but one
which, when corrected, was every bit as devastating to
what Matt claimed as my original inaccurate statement.
Why did you even bother to mention Matt? Could it be that
he is such a valuable mainstay of the anti-creationist
ideologues here that you want to make him look good by hook or
by crook?
As far as I am
>concerned you were wrong when you said that the molecular data from
>hemoglobin genes showed birds more closely related to mammals than to
>reptiles.
You are knocking down a strawman. I never said that.
>I'm not the least bit interested in quibbling with you about subtle
>nuances in your original statement. You are now trying to claim that you
>were correct because in the study I quoted lizards are closer to mammals
>than they are to other reptiles.
You are lying. I admitted that what I wrote was inaccurate.
If it makes you happy to note that
>the paper I referenced has some other anomalies then I'm happy for you
>as well. It doesn't change the fact that what you said was wrong.
Come off your high horse, Moran. You were more wrong than I,
and you badly misled Howard Hershey on the original thread.
>Furthermore, if you want to believe that most of the molecular data is
>flawed then be my guest.
Whatever made you think I might want to believe that?
>I've said all I need to say on this topic - the thread is rapidly
>degenerating into something that nobody is interested in (except
>you).
On the contrary, it is what you made it from the very beginning:
a Nyikos-bashing exercise built on misrepresenting what I wrote
as "birds are more closely related to mammals than to reptiles"--
something you kept doing over and over again, in EVERY post
to this thread and the parent thread that I recall reading.
I prefer to end this discussion rather than lower myself to the
>level of responding to your obfuscations and insinuations.
It is your misrepresentation of what I wrote that
Quite frankly,
>I doubt very much that you know what you are talking about.
Quite frankly, if you want to know what I am talking about,
you can read the discussion in sci.bio.systematics where
we are taking your beloved Fushitani article apart with
tweezers.
But you weren't really frank just now, were you?
>Goodbye Peter.
Well, I'm glad you disinterred your head from the sand long
enough to show me just how little you know about tetrapod
phylogeny.
Peter Nyikos -- standard disclaimer --
University of South Carolina
Peter Nyikos
my...@netaxs.com (PZ Myers) writes:
>[snip]
>--- end quote ---
It got to me only after I posted the above. I don't read posts
in the order in which they are posted: instead, I read some
threads one day, another set another day, etc. Usually
I only get to read a thread once or twice a week, because
I am involved in so many threads.
>Of course, the gist of the complaint is *not* that you hadn't noticed
>the correction before, but that you were surprised that heme had not
>been sequenced.
I didn't know heme was NOT a polypeptide. End of story.
[umpteen lines of sarcasm based on this simple little
fact, deleted. Amazing what some people will do instead
of seriously discussing embryology texts by Moore, Arey,
Phillips, and Larsen. Myers keeps using himself as
an authority on all major matters of embryological dispute
and citing chapter and verse on matters that were not in
dispute.]
howard hershey
Peter Nyikos wrote:
>
[snip]
>
> I didn't know heme was NOT a polypeptide. End of story.
[snip]
No comment. But this does answer *one* of the questions I asked in
another thread. I will accordingly drop my search for the protein
sequence of heme. :-)
PZ Myers
In article <1998013100...@milo.math.sc.edu>, Peter Nyikos
<nyi...@math.sc.edu> wrote:
> I didn't know heme was NOT a polypeptide. End of story.
>
"Well, I'm glad you disinterred your head from the sand long
enough to show me just how little you know about molecular
biology."
How does somebody who doesn't comprehend this kind of critical
little fact expect to be able to take on article on molecular
systematics apart with tweezers?
Have you ever noticed how appropriate your own words are in
reference to yourself?
--
PZ Myers
PZ Myers
[snip]
> I didn't know heme was NOT a polypeptide. End of story.
>
> [umpteen lines of sarcasm based on this simple little
> fact, deleted. Amazing what some people will do instead
> of seriously discussing embryology texts by Moore, Arey,
> Phillips, and Larsen. Myers keeps using himself as
> an authority on all major matters of embryological dispute
> and citing chapter and verse on matters that were not in
> dispute.]
Interesting that you accuse me of avoiding serious discussion
of embryological matters. I've replied to your "evolutionary
mysteries of embryology" thread, and have shown that your
"mysteries" are nothing but a result of some substantial
miscomprehensions on your part. The one reply you made to those
comments revealed even deeper errors of fact. I have posted
references that discuss the substantial homologies between all
vertebrates in early development, which is the matter that *you*
claim is in dispute. It is not. I have even posted a couple of
figures on my web site to clarify these homologies and expose
your confusion -- I notice you've taken a look at them (at least,
"milo.math.sc.edu" is on the logs).
I don't expect much serious discussion from you, Peter. There isn't
much you can offer. But I would at least expect that somebody with
as much integrity as you claim to have would make a short statement,
along the lines of:
> I didn't understand the relationship of the basic germ layers of the
> embryo to one another. End of story.
--
PZ Myers
howard hershey
PZ Myers wrote:
>
> In article <1998013100...@milo.math.sc.edu>, Peter Nyikos
> <nyi...@math.sc.edu> wrote:
>
> [snip]
> > I didn't know heme was NOT a polypeptide. End of story.
> >
confused about the number and nature of globin genes involved in the
various hemoglobins in different organisms. [He had apparently heard a
rumor of a different globin gene being used in embryonic humans.] This
is even more relevant to discussions of the evolutionary relationships
among the proteins, so I would suggest that Peter do a little more
reading on these basics before expounding on the defects of certain
papers.
[snip]
> But I would at least expect that somebody with
> as much integrity as you claim to have would make a short statement,
> along the lines of:
>
> > I didn't understand the relationship of the basic germ layers of the
> > embryo to one another. End of story.
>
That whole sorry thread came about when I corrected Peter on his misuse
of 'endoderm' wrt to the amnion in ways that were *even less sarcastic*
than my mentioning that he might want to look up heme in his biochem
book; I honestly thought Peter had simply printed a typo - 'endo' for
'ecto'. I was wrong. The things you find out when you correct a simple
little mistake, especially about how some people respond to being
corrected.
But a statement along the lines that Paul suggested would be acceptable.
Peter Nyikos
get...@nobull.net (Cal King) writes:
>In article <1998012617...@milo.math.sc.edu>, nyi...@math.sc.edu (Peter
>Nyikos) wrote...
>>Obviously, Moran is not using "congruence" the way a mathematician
>>would, to denote a perfect match with no anomalies.
>I agree. He kept pointing to the bird-reptile relationship in the Fusitaini
>paper as evidence of congruence, but totally ignored all the other anomalies
>in that study.
>>On the other hand, the fossil evidence is overwhelming that
>>the correct grouping is:
>>
>> [{Lizards [Birds]} Mammals]
>Is it really? If the squamata is the first group to branch off from the
>amniotes,
There is no good reason to think that. The consensus among
paleontologists is that mammals branched off earlier.
and the mammalian ancestors were next, followed by the archosaurs,
>then the correct grouping should be
> ___ Squamates
> | __ birds
>Basal amniotes----| _______ |
> | |__ crocs
> |
> |___________ mammals
>>And not [{[Birds] Mammals} Lizards] as claimed by the article.
>Mammals should then cluster more closely to birds than to the Squamates.
Well, sure. That's what the article CLAIMED. Garbage in,
garbage out.
>Actually many morphologists cum cladists are turning in that direction as
>well. I liken the revolution in systematics to the electronics revolution.
>That are still some who claim that the vacuum tube is superior just as those
>who claim that morphology is better at resolving phylogenies, but the main
>stream of phylogenetic analysis is turning to molecular techniques and to
>transistors. That does not mean that we should abandon morphological analysis
>altogether. We still need to group organisms preliminarily by morphology
>before we can test for monophyly using molecular techniques.
And we need to use anatomical insight and fossil evidence too.
The fact remains that traditional systematists, vertebrate
paleontologists AND cladists have agreed,
all through this century (with a few minor exceptions of course)
that mammals branched off before squamates.
>>> I would not dismiss the incongruence at the species and genus level as
>>>anomalies, because evolution occurs at the species level. Higher taxa do
>>>not evolve.
>>
>>They do evolve as collectives.
>I do agree that parallelism is rampant.
That's not what I was referring to. I was referring to the fact
that trees of major taxa like those above can get just as screwed
up as trees on the species and genus level. I was referring to
things like the language used by Colbert:
[...]
>>You don't see people laughing
>>themselves silly over book titles like Colbert's
>>_Evolution of the Vertebrates_, do you? In it you can see
>>him explicitly talking about shark evolution, bird evolution, etc.
Simply put, the collective evolution of the vertebrates and
those subgroups is what Colbert was talking about.
Peter Nyikos -- standard disclaimer --
Peter Nyikos
my...@netaxs.com (PZ Myers) writes:
>In article <6ah68o$c...@bgtnsc02.worldnet.att.net>, get...@worldnet.att.net
>wrote:
>> Another post with nothing but ad hominem attacks. I am sorry to inform you
>> that I have put you in my killfile.
>>
>> Goodbye.
>"you"??? Who is "you"? Is it me? Gosh, whatever did I do to you to deserve
>this most heinous fate?
>As a matter of netiquette, whenever you killfile someone you are supposed
>to announce it portentiously, with full listing of the anathematic's name.
>You are also supposed to punctuate it with the incantation, "** PLONK **".
>There is also the important ritual of putting thumb to nose, waggling
>your fingers at the monitor, and saying "neener, neener, neener", but
>since that is a private and personal part of the act, I will presume that
>you carried it out faithfully. (hey, it's the fun part! Sometimes I do it
>to people's posts without killfiling them, and I don't even tell them, so
>there.)
Don't let Myers get your goat with such relatively harmless
kidding around, Cal. Just keep in mind that he did NOT post
ANYTHING like that in response to Moran when Moran said "goodbye"
to me, because he has no standards to speak of, and is a
polemical opportunist, choosing what he says to people because
of WHOM he is talking to rather than because of any standards
he consistently adheres to.
Peter Nyikos
howard hershey <hers...@indiana.edu> writes:
>Peter Nyikos wrote:
>> get...@nobull.net (Cal King) writes:
>>
>> >In article <6ae3ev$bru$1...@bioinfo.med.utoronto.ca>,
>> >lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) wrote...
>>
>[SNIP]
>> On the other hand, the fossil evidence is overwhelming that
>> the correct grouping is:
>>
>> [{Lizards [Birds]} Mammals]
>>
>> And not [{[Birds] Mammals} Lizards] as claimed by the article.
>The lineage that eventually led to birds (archosaurs) and the lineages
>that led to sphenedon, turtles, lizards, and mammals (pelycosaurs) all
>appeared as separate lineages quite early and at and around the same
>time from more primitive reptiles
This is not necessarily the case. Estimates as to how long ago
mammals diverged from other reptiles range up to 350mya; estimates
as to how long ago sphenodon diverged from lizards can be as
recently as 220mya.
[routine talk about molecular anomalies deleted]
>But all mammals should cluster together in the DNA/protein sequencing.
Not if monotremes diverged more than 150 mya, as some estimates
put it.
>All birds should cluster together. These are the end flowerings on
>branches long separated from the others. They do, of course, cluster.
>Where the fossil/morphological evidence is unambiguous, the sequence
>information is equally unambiguous *and congruent* with that evidence.
False. Fossil/morphological evidence ins unambiguous that birds
branched off from crocodilians after they branched off from turtles.
The one study that Moran has proudly trumpeted shows the opposite.
>When more sequences are added, the conclusions reached may change from
>their current status, just as the idea that birds are closer to mammals
>and not within the reptile group changed.
This is all part of a game Moran was playing. By not putting in
the quantifier "some" (as in: Birds are closer to mammals than
they are to SOME reptiles, e.g. lizards") he kept eating his cake
and having it too.
Bottom line: the globins overwhelmingly AND FALSELY show that birds are closer
to mammals than they are to SOME reptiles. Only the actual identity
of that "some" has been in dispute, but the consensus seems to
be that "some" includes lizards.
Peter Nyikos -- standard disclaimer --
University of South Carolina
Peter Nyikos
my...@netaxs.com (PZ Myers) writes:
>In article <1998013100...@milo.math.sc.edu>, Peter Nyikos
><nyi...@math.sc.edu> wrote:
>> I didn't know heme was NOT a polypeptide. End of story.
>>
>"Well, I'm glad you disinterred your head from the sand long
>enough to show me just how little you know about molecular
>biology."
I did not make one false statement after another about hemes,
and did not indulge in massive word games like Moran did
about hemes. I asked a question. Two or three times
before I finally saw an answer. End of story.
>How does somebody who doesn't comprehend this kind of critical
>little fact expect to be able to take on article on molecular
>systematics apart with tweezers?
By knowing all he needs to know about globins, and about
phylogeny, that's how.
>Have you ever noticed how appropriate your own words are in
>reference to yourself?
No, because I don't subject things to a One Shade of Gray
Meltdown like you did here.
Peter Nyikos
my...@netaxs.com (PZ Myers) writes:
>In article <1998013100...@milo.math.sc.edu>, Peter Nyikos
><nyi...@math.sc.edu> wrote:
>[snip]
>> I didn't know heme was NOT a polypeptide. End of story.
>>
>> [umpteen lines of sarcasm based on this simple little
>> fact, deleted. Amazing what some people will do instead
>> of seriously discussing embryology texts by Moore, Arey,
>> Phillips, and Larsen. Myers keeps using himself as
>> an authority on all major matters of embryological dispute
>> and citing chapter and verse on matters that were not in
>> dispute.]
>Interesting that you accuse me of avoiding serious discussion
>of embryological matters.
That's not what I said. You are once more indulging in
a One Shade of Gray Meltdown.
I've replied to your "evolutionary
>mysteries of embryology" thread, and have shown that your
>"mysteries" are nothing but a result of some substantial
>miscomprehensions on your part.
On your part, because you confused an elementary description
of something that takes place at four weeks with a description
of gastrulation, and an obvious reference to phylogeny
with a concept of phylogeny.
The only real question is whether you were making an
honest misreading or indulging in a pair of scams, and
I lean towards the latter because you have been misrepresenting
the bejesus out of me on that other "Peter, have a heart..."
thread on embryology.
The one reply you made to those
>comments revealed even deeper errors of fact. I have posted
>references that discuss the substantial homologies between all
>vertebrates in early development, which is the matter that *you*
>claim is in dispute.
One of which you repudiated when I revealed that it claimed
the yolk sac is homologous to the archenteron. Is there
ANY reference you will stick to when I start citing things
from it?
It is not. I have even posted a couple of
>figures on my web site to clarify these homologies and expose
>your confusion -- I notice you've taken a look at them (at least,
>"milo.math.sc.edu" is on the logs).
Yes, and the key figure was mislabeled and not sufficiently
relevant to what we were discussing.
>I don't expect much serious discussion from you, Peter. There isn't
>much you can offer. But I would at least expect that somebody with
>as much integrity as you claim to have would make a short statement,
>along the lines of:
>> I didn't understand the relationship of the basic germ layers of the
>> embryo to one another. End of story.
That remains to be seen.
Peter Nyikos -- standard disclaimer --
University of South Carolina
PZ Myers
In article <1998020318...@milo.math.sc.edu>, Peter Nyikos
<nyi...@math.sc.edu> wrote:
>my...@netaxs.com (PZ Myers) writes:
>
>>In article <6ah68o$c...@bgtnsc02.worldnet.att.net>, get...@worldnet.att.net
>>wrote:
>
>>> Another post with nothing but ad hominem attacks. I am sorry to inform you
>>> that I have put you in my killfile.
>>>
>>> Goodbye.
>
>>"you"??? Who is "you"? Is it me? Gosh, whatever did I do to you to deserve
>>this most heinous fate?
>
>>As a matter of netiquette, whenever you killfile someone you are supposed
>>to announce it portentiously, with full listing of the anathematic's name.
>>You are also supposed to punctuate it with the incantation, "** PLONK **".
>
>>There is also the important ritual of putting thumb to nose, waggling
>>your fingers at the monitor, and saying "neener, neener, neener", but
>>since that is a private and personal part of the act, I will presume that
>>you carried it out faithfully. (hey, it's the fun part! Sometimes I do it
>>to people's posts without killfiling them, and I don't even tell them, so
>>there.)
>
>Don't let Myers get your goat with such relatively harmless
>kidding around, Cal. Just keep in mind that he did NOT post
>ANYTHING like that in response to Moran when Moran said "goodbye"
Right. And there was absolutely no ambiguity in the target of
Moran's goodbye, now was there?
He also didn't say he was killfiling anyone. As a long-standing
and dignified member of the Cabal/Pack/Conspiracy, I'm sure we could
trust Moran to execute the ritual completely and thoroughly. For all
we know, he may practice the secret rites of the "Raspberry", the
"Two-Handed Waggle", and the dreaded "Mooning of the Monitor" as
well.
>to me, because he has no standards to speak of, and is a
>polemical opportunist, choosing what he says to people because
>of WHOM he is talking to rather than because of any standards
>he consistently adheres to.
That's true. Sometimes I say "neener, neener, neener" to the screen
when I'm reading *your* posts, and I'm inconsistent and don't follow
through with the traditional "** PLONK **". I admit it. I'm very liberal
in my practice of the liturgy.
And, my, Peter, aren't we portentious and pontifical and judgemental and
humorless in response to a light-hearted post directed at someone else!
I guess you are just trying to be consistent.
--
PZ Myers
PZ Myers
>my...@netaxs.com (PZ Myers) writes:
>
>>In article <1998013100...@milo.math.sc.edu>, Peter Nyikos
>><nyi...@math.sc.edu> wrote:
>
>
>
>>> I didn't know heme was NOT a polypeptide. End of story.
>>>
>
>>"Well, I'm glad you disinterred your head from the sand long
>>enough to show me just how little you know about molecular
>>biology."
>
>I did not make one false statement after another about hemes,
>and did not indulge in massive word games like Moran did
>about hemes. I asked a question. Two or three times
>before I finally saw an answer. End of story.
>
>>How does somebody who doesn't comprehend this kind of critical
>>little fact expect to be able to take on article on molecular
>>systematics apart with tweezers?
>
>By knowing all he needs to know about globins, and about
>phylogeny, that's how.
Figured out what fetal hemoglobin is, yet?
>
>>Have you ever noticed how appropriate your own words are in
>>reference to yourself?
>
>No, because I don't subject things to a One Shade of Gray
>Meltdown like you did here.
>
>Peter Nyikos -- standard disclaimer --
--
PZ Myers
Wade Hines
Peter Nyikos <nyi...@math.sc.edu> writes:
>get...@nobull.net (Cal King) writes:
>>nyi...@math.sc.edu (Peter Nyikos) wrote...
Bwaahaahaa.
I love it, I really do.
howard hershey
Peter Nyikos wrote:
>
> my...@netaxs.com (PZ Myers) writes:
>
> >In article <1998013100...@milo.math.sc.edu>, Peter Nyikos
> ><nyi...@math.sc.edu> wrote:
>
> >> I didn't know heme was NOT a polypeptide. End of story.
> >>
>
> >> I didn't understand the relationship of the basic germ layers of the
> >> embryo to one another. End of story.
>
> That remains to be seen.
>
relationship of the basic germ layers are, and it ain't me and Paul.
Your errors in this area are just as egregious as not knowing that heme
is not a peptide when one is discussing hemoglobin.
howard hershey
Peter Nyikos wrote:
>
> howard hershey <hers...@indiana.edu> writes:
>
> >Peter Nyikos wrote:
>
> >> get...@nobull.net (Cal King) writes:
> >>
> >> >In article <6ae3ev$bru$1...@bioinfo.med.utoronto.ca>,
> >> >lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) wrote...
> >>
> >[SNIP]
>
> >> On the other hand, the fossil evidence is overwhelming that
> >> the correct grouping is:
> >>
> >> [{Lizards [Birds]} Mammals]
> >>
> >> And not [{[Birds] Mammals} Lizards] as claimed by the article.
>
> >The lineage that eventually led to birds (archosaurs) and the lineages
> >that led to sphenedon, turtles, lizards, and mammals (pelycosaurs) all
> >appeared as separate lineages quite early and at and around the same
> >time from more primitive reptiles
>
> This is not necessarily the case. Estimates as to how long ago
> mammals diverged from other reptiles range up to 350mya; estimates
> as to how long ago sphenodon diverged from lizards can be as
> recently as 220mya.
So what is the other end of the ranges? And where do other lineages fit
in? Obviously 'lizards' as a group including sphenodon as well as
modern 'lizards and snakes' diverged sometime between 350 and 220 mya
according to the chonology you just gave. Was that divergence closer to
the 350 or the 220 mya? And when was the divergence of archosaurs from
the above groups? You claimed that the fossil evidence is
*overwhelming* that the order is [{Lizards [Birds]} Mammals]. Could you
present that evidence, so we may judge how *overwhelming* it really is?
The timing is crucial, because, as I pointed out in the part you snipped
below, molecular sequencing reflects time of divergence and if the
branch points are bunched together one would not expect *every* protein
to point in the right direction wrt the order of the branching (for
purely probablistic reasons aside from protein specific reasons) and
conclusions would have to be dependent upon the weight of evidence from
many independent genes.
>
> [routine talk about molecular anomalies deleted]
>
> >But all mammals should cluster together in the DNA/protein sequencing.
>
> Not if monotremes diverged more than 150 mya, as some estimates
> put it.
Why would that lead to monotremes, as a group, clustering with some
(unnamed) group other than the placental mammals?
>
> >All birds should cluster together. These are the end flowerings on
> >branches long separated from the others. They do, of course, cluster.
> >Where the fossil/morphological evidence is unambiguous, the sequence
> >information is equally unambiguous *and congruent* with that evidence.
>
> False. Fossil/morphological evidence ins unambiguous that birds
> branched off from crocodilians after they branched off from turtles.
> The one study that Moran has proudly trumpeted shows the opposite.
That is the one 'true' potential anomaly that I see in this data. But
it has been mentioned that alpha-globin presents some protein specific
problems involving duplication and loss.
>
> >When more sequences are added, the conclusions reached may change from
> >their current status, just as the idea that birds are closer to mammals
> >and not within the reptile group changed.
>
> This is all part of a game Moran was playing. By not putting in
> the quantifier "some" (as in: Birds are closer to mammals than
> they are to SOME reptiles, e.g. lizards") he kept eating his cake
> and having it too.
>
> Bottom line: the globins overwhelmingly AND FALSELY
How did you decide the FALSELY part? I mentioned that one can
reasonably take the position that mammals may have diverged from the
lineage that led to birds *after* divergence of their joint lineage from
the lineages of *some* reptiles. But you claim to have *overwhelming*
evidence against this idea (at least wrt 'lizards'). Could you please
present it? I do not necessarily disagree with your idea that the
majority of evidence supports the idea that pelycosaurs diverged first;
I am simply saying that the alternative that they did not is not,
off-hand, ridiculous.
> show that birds are closer
> to mammals than they are to SOME reptiles. Only the actual identity
> of that "some" has been in dispute, but the consensus seems to
> be that "some" includes lizards.
And the evidence for that 'consensus' is...?
>
> Peter Nyikos -- standard disclaimer --
> University of South Carolina
howard hershey
>
> >>On the other hand, the fossil evidence is overwhelming that
> >>the correct grouping is:
> >>
> >> [{Lizards [Birds]} Mammals]
>
> >amniotes,
>
> There is no good reason to think that. The consensus among
> paleontologists is that mammals branched off earlier.
That consensus and a buck or three will get you a cup of coffee.
>
> and the mammalian ancestors were next, followed by the archosaurs,
> >then the correct grouping should be
>
> > ___ Squamates
> > | __ birds
> >Basal amniotes----| _______ |
> > | |__ crocs
> > |
> > |___________ mammals
>
> >>And not [{[Birds] Mammals} Lizards] as claimed by the article.
>
> >Mammals should then cluster more closely to birds than to the Squamates.
>
> Well, sure. That's what the article CLAIMED. Garbage in,
> garbage out.
>
[snip]
>
> And we need to use anatomical insight and fossil evidence too.
> The fact remains that traditional systematists, vertebrate
> paleontologists AND cladists have agreed,
> all through this century (with a few minor exceptions of course)
> that mammals branched off before squamates.
>
[snip]
Nor would it represent the first time that scientists have been shown to
be wrong when new evidence presented itself. That a consensus had been
reached on the basis of old data does not make the consensus immune from
change in the light of new evidence.
PZ Myers
In article <1998020318...@milo.math.sc.edu>, Peter Nyikos
<nyi...@math.sc.edu> wrote:
> my...@netaxs.com (PZ Myers) writes:
>
> >In article <1998013100...@milo.math.sc.edu>, Peter Nyikos
> ><nyi...@math.sc.edu> wrote:
>
> >[snip]
> >> I didn't know heme was NOT a polypeptide. End of story.
> >>
> >> [umpteen lines of sarcasm based on this simple little
> >> fact, deleted. Amazing what some people will do instead
> >> of seriously discussing embryology texts by Moore, Arey,
> >> Phillips, and Larsen. Myers keeps using himself as
> >> an authority on all major matters of embryological dispute
> >> and citing chapter and verse on matters that were not in
> >> dispute.]
>
> >Interesting that you accuse me of avoiding serious discussion
> >of embryological matters.
>
> That's not what I said. You are once more indulging in
> a One Shade of Gray Meltdown.
"Amazing what some people will do instead of seriously
discussing embryology". Are you redefining words again?
>
>
> I've replied to your "evolutionary
> >mysteries of embryology" thread, and have shown that your
> >"mysteries" are nothing but a result of some substantial
> >miscomprehensions on your part.
>
> On your part, because you confused an elementary description
> of something that takes place at four weeks with a description
> of gastrulation, and an obvious reference to phylogeny
> with a concept of phylogeny.
Peter, Peter, Peter. *You* were the one who posted the question
asking for an explanation of how something like invagination
at the blastopore (gastrulation) could have evolved into those
events at the fourth week of human development, which are clearly
not gastrulation.
[snip whining]
>
> >I don't expect much serious discussion from you, Peter. There isn't
> >much you can offer. But I would at least expect that somebody with
> >as much integrity as you claim to have would make a short statement,
> >along the lines of:
>
> >> I didn't understand the relationship of the basic germ layers of the
> >> embryo to one another. End of story.
>
> That remains to be seen.
It's been seen quite clearly.
--
PZ Myers
Peter Nyikos
my...@astro.ocis.temple.edu (PZ Myers) writes:
>In article <1998020318...@milo.math.sc.edu>, Peter Nyikos
><nyi...@math.sc.edu> wrote:
>>my...@netaxs.com (PZ Myers) writes:
>>
>>>In article <6ah68o$c...@bgtnsc02.worldnet.att.net>, get...@worldnet.att.net
>>>wrote:
>>
>>>> Another post with nothing but ad hominem attacks. I am sorry to inform you
>>>> that I have put you in my killfile.
>>>>
>>>> Goodbye.
>>
>>>"you"??? Who is "you"? Is it me? Gosh, whatever did I do to you to deserve
>>>this most heinous fate?
>>
>>>As a matter of netiquette, whenever you killfile someone you are supposed
>>>to announce it portentiously, with full listing of the anathematic's name.
>>>You are also supposed to punctuate it with the incantation, "** PLONK **".
>>
>>>There is also the important ritual of putting thumb to nose, waggling
>>>your fingers at the monitor, and saying "neener, neener, neener", but
>>>since that is a private and personal part of the act, I will presume that
>>>you carried it out faithfully. (hey, it's the fun part! Sometimes I do it
>>>to people's posts without killfiling them, and I don't even tell them, so
>>>there.)
>>
>>Don't let Myers get your goat with such relatively harmless
>>kidding around, Cal. Just keep in mind that he did NOT post
>>ANYTHING like that in response to Moran when Moran said "goodbye"
>Right. And there was absolutely no ambiguity in the target of
>Moran's goodbye, now was there?
Nor in Cal's, to anyone who knows how to read Reference: lines.
>He also didn't say he was killfiling anyone.
True, but the remarks about the important ritual apply perfectly,
as you yourself admit in the parenthetical remark.
[additional relatively harmless kidding by Myers deleted]
Peter Nyikos
my...@astro.ocis.temple.edu (PZ Myers) writes:
>In article <1998020318...@milo.math.sc.edu>, Peter Nyikos
><nyi...@math.sc.edu> wrote:
>>my...@netaxs.com (PZ Myers) writes:
>>
>>>In article <1998013100...@milo.math.sc.edu>, Peter Nyikos
>>><nyi...@math.sc.edu> wrote:
>>
>>
>>
>>>> I didn't know heme was NOT a polypeptide. End of story.
>>>>
>>
>>>"Well, I'm glad you disinterred your head from the sand long
>>>enough to show me just how little you know about molecular
>>>biology."
>>
>>I did not make one false statement after another about hemes,
On the other hand, Moran made a false statement about globins,
claiming that they showed agreement with the fossil record
as regards phylogeny, when they most certainly do not.
>>and did not indulge in massive word games like Moran did
>>about hemes.
The "about hemes" refers to my behavior.
On the other hand, Moran took my PARTIAL listing of reptiles
to jump to the conclusion that I was saying birds are closer
to mammals than they are to ALL reptiles, while taking
the Fushitani et. al. statement "birds form a sister
group with other reptiles but not with mammals" to mean
what the authors implicitly intended it to mean, namely
that the alpha globins showed birds form a sister group
with SOME reptiles (Sphenodon and maybe turtles
but NOT crocodilians, in contrast to the fossil record)
but not others (alpha "shows" mammals more closely related
to birds than either is to lizards).
I am reminded of the old saying about optimists and pessimists:
they look at the same cup and the pessimist says it is
half empty and the optimist says it is half full.
The Moranite takes the pessimist's statement to mean,
"the cup is empty" and the optimist's to mean, "the cup is full". ;-)
I asked a question. Two or three times
>>before I finally saw an answer. End of story.
>>>How does somebody who doesn't comprehend this kind of critical
>>>little fact
The "critical little fact" is utterly irrelevant to the
substantive issues on this thread, and specifically
irrelevant to the Fushitani et. al. article trumpeted
by Moran and copycat Hershey.
expect to be able to take on article on molecular
>>>systematics apart with tweezers?
>>
>>By knowing all he needs to know about globins, and about
>>phylogeny, that's how.
>Figured out what fetal hemoglobin is, yet?
In humans? The Fushitani et. al. study trumpeted
by Moran didn't touch it with a ten foot pole.
Curious sidelight: they did give a table showing only one
alpha (adult) and one beta (ditto) having been detected in
mammals, although in a footnote they say that the number of
Hb components should be taken as minima. On the other hand,
two pages later they say:
(1) Claimed that the results suggest embryonic and adult alpha globin genes
were "acquired by gene duplication of the ancestral gene before the
divergence of amniotes took place."
(2) Made the following remark about crocodilians, which are
no more and no less amniotes than humans are:
The embryonic alpha chanin of crocodilians may
exist, but it has not yet been found, or, alternatively,
it is possible that crocodilians have lost the
corresponding embryonic alpha globin gene.
Apparently they assumed that the reader would draw the
obvious parallel with mammals, because they made no mention
of them at this juncture.
Peter Nyikos -- standard disclaimer --
Peter Nyikos
howard hershey <hers...@indiana.edu> writes:
>Peter Nyikos wrote:
>>
>> get...@nobull.net (Cal King) writes:
>>
>> >In article <1998012617...@milo.math.sc.edu>, nyi...@math.sc.edu (Peter
>> >Nyikos) wrote...
>>
>[snip]
>>
>> >>On the other hand, the fossil evidence is overwhelming that
>> >>the correct grouping is:
>> >>
>> >> [{Lizards [Birds]} Mammals]
>>
>> >Is it really? If the squamata is the first group to branch off from the
>> >amniotes,
>>
>> There is no good reason to think that. The consensus among
>> paleontologists is that mammals branched off earlier.
>That consensus and a buck or three will get you a cup of coffee.
Whereas you and Myers take the tack that a LACK of consensus
in the standard embryology texts on how the amniotic
membrane is irrelevant and that
Moore's latest (1988) edition has been superseded by the LATEST
evidence despite an inability by either of you to present
that evidence in a coherent manner.
And you two take the tack that I am ignorant of the most
basic embryology through my failure to cave in and agree that
the LATEST texts now have the gospel truth.
>[snip]
>>
>> And we need to use anatomical insight and fossil evidence too.
>> The fact remains that traditional systematists, vertebrate
>> paleontologists AND cladists have agreed,
>> all through this century (with a few minor exceptions of course)
>> that mammals branched off before squamates.
>>
>[snip]
>Nor would it represent the first time that scientists have been shown to
>be wrong when new evidence presented itself. That a consensus had been
>reached on the basis of old data does not make the consensus immune from
>change in the light of new evidence.
Put that in your posts on embryology and smoke it.
howard hershey
Peter Nyikos wrote:
>
> howard hershey <hers...@indiana.edu> writes:
>
> >Peter Nyikos wrote:
> >>
> >> get...@nobull.net (Cal King) writes:
> >>
> >> >In article <1998012617...@milo.math.sc.edu>, nyi...@math.sc.edu (Peter
> >> >Nyikos) wrote...
> >>
> >[snip]
> >>
> >> >>On the other hand, the fossil evidence is overwhelming that
> >> >>the correct grouping is:
> >> >>
> >> >> [{Lizards [Birds]} Mammals]
> >>
> >> >Is it really? If the squamata is the first group to branch off from the
> >> >amniotes,
> >>
> >> There is no good reason to think that. The consensus among
> >> paleontologists is that mammals branched off earlier.
>
> >That consensus and a buck or three will get you a cup of coffee.
>
> Whereas you and Myers take the tack that a LACK of consensus
> in the standard embryology texts on how the amniotic
> membrane is irrelevant
The lack of evidence wrt to *human* material for some of the details of
early embryogenesis is a reflection of human ethical rules (which I have
no problem with) limiting experimentation on human material.
> and that
> Moore's latest (1988) edition has been superseded by the LATEST
> evidence despite an inability by either of you to present
> that evidence in a coherent manner.
Actually, as I have several times mentioned, the *human* evidence is not
all that recent. I also explicitly point out that it is my view that it
wouldn't make any difference which explanation eventually was shown to
be correct. Either way, your definition of endoderm and how it might
relate to the amnion reflects a failure on your part to understand even
the most minimal principles of embryology, probably because, by being
self-taught primarily from a human embryology text, you lack the
understanding of the underlying principles and developed your own based
on names on pictures.
>
> And you two take the tack that I am ignorant of the most
> basic embryology through my failure to cave in and agree that
> the LATEST texts now have the gospel truth.
>
My position is now and always has been that you would be just as
ignorant of basic embryology if the LATEST texts were wrong.
> >[snip]
> >>
> >> And we need to use anatomical insight and fossil evidence too.
> >> The fact remains that traditional systematists, vertebrate
> >> paleontologists AND cladists have agreed,
> >> all through this century (with a few minor exceptions of course)
> >> that mammals branched off before squamates.
Is this consensus based on overwhelming *evidence* (as you claim) or on
a consensus based on the *current weight* of evidence. There is a
difference.
> >>
> >[snip]
>
> >Nor would it represent the first time that scientists have been shown to
> >be wrong when new evidence presented itself. That a consensus had been
> >reached on the basis of old data does not make the consensus immune from
> >change in the light of new evidence.
>
> Put that in your posts on embryology and smoke it.
And what, pray tell, is the *new* evidence you are presenting? You seem
to be arguing for a new definition of an old term, endoderm, rather than
presenting new evidence that the standard definition of that term
applies to the human amnion as opposed to the pig amnion, the bird
amnion, the turtle amnion, the mouse amnion, etc.
howard hershey
Peter Nyikos wrote:
>
> my...@astro.ocis.temple.edu (PZ Myers) writes:
>
> >In article <1998020318...@milo.math.sc.edu>, Peter Nyikos
> ><nyi...@math.sc.edu> wrote:
>
> >>my...@netaxs.com (PZ Myers) writes:
> >>
> >>>In article <1998013100...@milo.math.sc.edu>, Peter Nyikos
> >>><nyi...@math.sc.edu> wrote:
> >>
> >>
> >>
> >>>> I didn't know heme was NOT a polypeptide. End of story.
> >>>>
> >>
> >>I did not make one false statement after another about hemes,
OTOH, you did display then, and do below, a rather embarrassing lack of
knowledge about the genes that code for the various components of the
various hemoglobins. I would suggest something rather basic, like any
major modern genetics textbook or molecular biology textbook, before you
embarrass yourself further.
>
> On the other hand, Moran made a false statement about globins,
> claiming that they showed agreement with the fossil record
> as regards phylogeny, when they most certainly do not.
>
> >>and did not indulge in massive word games like Moran did
> >>about hemes.
>
> The "about hemes" refers to my behavior.
>
> On the other hand, Moran took my PARTIAL listing of reptiles
Just by chance, I printed out a copy of one of the earlier discussions,
which shows your exact quote to read:
This "discovery" is still many years in the future. In the
meantime, we have anomalies like the various kinds of hemoglobin
^^^^^^^^^^^^^
all agreeing that mammals are more closely related to birds
^^^
than birds are to lizards, snakes, or turtles, which is
falsified by the fossil evidence.
^^^^^^^^^
> to jump to the conclusion that I was saying birds are closer
> to mammals than they are to ALL reptiles,
Larry replied:
I pointed out that Peter's statement was not correct.
The various kinds of hemoglobin do not all agree that
^^^^^^^^^^^^^ ^^^
mammals are more closely related to birds than birds
are to reptiles.
^^^^^^^^
> while taking
> the Fushitani et. al. statement "birds form a sister
> group with other reptiles but not with mammals" to mean
> what the authors implicitly intended it to mean, namely
> that the alpha globins showed birds form a sister group
> with SOME reptiles (Sphenodon and maybe turtles
Even aside from the fact that your original statement, by using the
ambiguous (in common useage) term 'lizard' which could, in context, be
read as meaning all reptiles, I do think Larry pointed out that the
quote was in error because it was based on the more limited amount of
older data.
Turtles are one of the groups you explicitly mentioned in your quote,
Peter. Sphenodon was not mentioned, but you clearly think it to be a
later divergence than 'lizards' and thus can be subsumed in that
grouping. I think, therefore, that Larry's statement would be equally
correct if you were to change "reptiles" to "lizards, snakes, and
turtles". Do you disagree?
> but NOT crocodilians, in contrast to the fossil record)
Uh? I thought the paper showed an unusual position of crocodilians vis
a vis turtles, but *not* vis a vis mammals. Am I wrong in this?
> but not others (alpha "shows" mammals more closely related
> to birds than either is to lizards).
And this is where you need now to present your evidence that this
relationship is so clearly *falsified* by the fossil record (your
words), and that the distances separating the divergence points of the
squamate, mammalian, and avian lineages are *so* large that only
something highly unusual could give a false molecular phylogeny, thereby
demonstrating that this is a significant anomaly rather than one
expected from time to time (even in the absence of anything unusual
about the protein itself) because the points of separation of the
lineages are rather close together. I haven't seen you address these
points yet.
>
[snip]
>
> >>>How does somebody who doesn't comprehend this kind of critical
> >>>little fact
[that heme is not a protein]
>
> The "critical little fact" is utterly irrelevant to the
> substantive issues on this thread, and specifically
> irrelevant to the Fushitani et. al. article trumpeted
> by Moran and copycat Hershey.
>
> expect to be able to take on article on molecular
> >>>systematics apart with tweezers?
> >>
> >>By knowing all he needs to know about globins, and about
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> >>phylogeny, that's how.
^^^^^^^^^
>
> >Figured out what fetal hemoglobin is, yet?
And here we get into areas that show that Peter's idea of what is
required for "all one needs to know about globins" and my idea of the
same concept differ.
>
> In humans? The Fushitani et. al. study trumpeted
> by Moran didn't touch it with a ten foot pole.
>
> Curious sidelight: they did give a table showing only one
> alpha (adult) and one beta (ditto) having been detected in
> mammals, although in a footnote they say that the number of
> Hb components should be taken as minima. On the other hand,
> two pages later they say:
>
> (1) Claimed that the results suggest embryonic and adult alpha globin genes
> were "acquired by gene duplication of the ancestral gene before the
> divergence of amniotes took place."
>
> (2) Made the following remark about crocodilians, which are
> no more and no less amniotes than humans are:
>
> The embryonic alpha chanin of crocodilians may
> exist, but it has not yet been found, or, alternatively,
> it is possible that crocodilians have lost the
> corresponding embryonic alpha globin gene.
>
> Apparently they assumed that the reader would draw the
> obvious parallel with mammals, because they made no mention
> of them at this juncture.
No comment, except to say that Peter should really do some reading of
something other than 20 year old biochemistry textbooks. A recent
review article on comparative molecular biology of the hemoglobins
wouldn't hurt either.
Jonathan Stone
In article <1998020416...@milo.math.sc.edu>, Peter Nyikos <nyi...@math.sc.edu> writes:
|> howard hershey <hers...@indiana.edu> writes:
|> Whereas you and Myers take the tack that a LACK of consensus
|> in the standard embryology texts on how the amniotic
|> Moore's latest (1988) edition has been superseded by the LATEST
|> evidence despite an inability by either of you to present
|> that evidence in a coherent manner.
This numbskull is _still_ arguing from obsolete textbooks?
What does he think this is, mathematics or something?
Peter Nyikos
hi...@cgl.ucsf.EDU (Wade Hines) writes:
What is it that you love? The fact that I actually disagreed with
Cal for most of my reply to him? Are you the sort of person
who thinks a person must behave towards his net.allies the
way you did when you prostituted your integrity for Matt
Silberstein and Chris Carrell?
Your prostitution of your integrity is recounted below:
================ excerpt from post, names added in brackets
[Wade:]
>>>In it you fail to understand that I only read and responded
>>>to your ubiquitous preamble.
[Peter:]
>>And made some completely irrational conclusions about it,
>>whose irrationality became evident when you did NOT apply
>>the same standards to a comment by Carrell about me having
>>taken a submachine gun to his house.
[Wade:]
>Carrell doesn't routinely post preambles claiming victory.
[Peter:]
You are, once again, grasping at straws to rationalize the
irrationality of saying my preamble was full of
"insane ramblings" and "paranoid delusion"
and not making any negative comments at all about Carrell's remark.
For one thing, I was not claiming victory. One can NEVER
claim victory over someone like Silberstein. At most,
one can do what I did, which is to describe the cunning
way Silberstein managed to avoid admitting he was wrong,
while posting something that ostensibly documented his
wrong claim, but did nothing of the sort in reality.
[Wade:]
>You continue to avoid the obvious. Your ability to irritate,
>and thus failure to comminicate effectively, is in significant
>part a matter of style. Preambles and rhetoric regards "bluffing"
>and "folding" are a fair sampling of things that earn you a
>reputation of usenet kookhood. Deny it as you like.
[Peter:]
Since you and your allies outnumber me, you can stick almost
any reputation on me that you wish.
In fact, I sometimes wonder why anyone on your side bothers to
support any claim, when they have toadies like you
who have these endearing ways of making it look like
they supported their claims...
[Peter:]
>>Or do you think that people who use figures of speech
>>taken from poker have obviously lost whatever debate
>>they were participating in, while people who use metaphors
>>about submachine guns have not?
[Wade:]
>Were that things were so simple. Kookhood is an emergent property.
[Peter:]
...toadies like you, who have these endearing ways of suggesting
that people who use figures of speech taken from poker
are on the road to kookhood while people who use metaphors
about submachine guns are not.
Toadies like you, who manage to do this high-gear backpedal
after claiming that my opening lines, in and of themselves,
were "insane" and "filled with paranoid delusions".
Is there nothing you will not do in the way of licking
the net.boots of people like Silberstein and Carrell?
==================== end of excerpt from
"Caveats on and to Hines and allies (Was: rat to bat)"
You snipped out ALL OF THE ABOVE in your reply Wade. Care
to belatedly retract your claim that the following preamble
was full of "insane ramblings" and "paranoid delusions"?
===================== begin repost of preamble
I call Matt's bluff, and he folds, laying his cards face up.
He hopes, apparently, that enough will be fooled into thinking
he is claiming victory.
A CC goes to Potter, not that I think he will be fooled, but
just so he can show it to anyone who pretends to be fooled/is fooled.
===================== end of preamble
Peter Nyikos
howard hershey <hers...@indiana.edu> writes:
>PZ Myers wrote:
>>
>> In article <1998013100...@milo.math.sc.edu>, Peter Nyikos
>> <nyi...@math.sc.edu> wrote:
>>
>> [snip]
>> > I didn't know heme was NOT a polypeptide. End of story.
>> >
>There were a few other places in that post where Peter also seemed
>confused about the number and nature of globin genes involved in the
>various hemoglobins in different organisms. [He had apparently heard a
>rumor of a different globin gene being used in embryonic humans.]
In addition to the usual ones mentioned by Fushitani et.al.
This
>is even more relevant to discussions of the evolutionary relationships
>among the proteins, so I would suggest that Peter do a little more
>reading on these basics before expounding on the defects of certain
>papers.
Your suggestion is rejected inasmuch as it seems clear that
you haven't the foggiest idea whether the rumor you
mention above is true or not. If it is, Fushitani et al
were remiss in not mentioning it. If not, then you are
just blowing smoke in suggesting that my analysis of Fushitani
et al is flawed in any way at all.
You have yet to make any substantive criticism of that analysis,
except to suggest REASONS for why the molecular and fossil
evidence disagree--thereby tacitly conceding the point that
Moran is a fool to be "bored" with this fact to the point
of simply stating that the fossil record and molecular evidence
agree--after having (or so he claims) taught about these things
for years.
>[snip]
>> But I would at least expect that somebody with
>> as much integrity as you claim to have would make a short statement,
>> along the lines of:
>>
>> > I didn't understand the relationship of the basic germ layers of the
>> > embryo to one another. End of story.
Myers is being his usual dishonest, sadistic self here.
>That whole sorry thread came about when I corrected Peter on his misuse
>of 'endoderm' wrt to the amnion in ways that were *even less sarcastic*
>than my mentioning that he might want to look up heme in his biochem
>book;
Correction: not sarcastic at all, as opposed to the sadistic
repetition of sarcasm on the heme business long after the
correction was made and acknowledged.
I honestly thought Peter had simply printed a typo - 'endo' for
>'ecto'. I was wrong. The things you find out when you correct a simple
>little mistake, especially about how some people respond to being
>corrected.
Yes, I agreed I was mistaken in thinking it was the standard term.
But that was not enough for Howard. In scores of posts, despite
repeated corrections, he kept lying that I think the amnion
is ectoderm. I do believe he will continue to lie about that.
>But a statement along the lines that Paul suggested would be acceptable.
To a sadist like Hershey, nothing less would be acceptable.
Peter Nyikos -- standard disclaimer --
University of South Carolina
Peter Nyikos
howard hershey <hers...@indiana.edu> writes:
>Peter Nyikos wrote:
>>
>> my...@netaxs.com (PZ Myers) writes:
>>
>> >In article <1998013100...@milo.math.sc.edu>, Peter Nyikos
>> ><nyi...@math.sc.edu> wrote:
>>
>> >[snip]
>> >> I didn't know heme was NOT a polypeptide. End of story.
>> >>
>[snip]
>>
>> >> I didn't understand the relationship of the basic germ layers of the
>> >> embryo to one another. End of story.
>>
>> That remains to be seen.
As to my understanding back then, that is. By now I'm so
clear on it, I could describe it blindfolded. The only
question is whether I was wrong in thinking that the Moore
theory of amnion production is the correct one, before
I learned from y'all that there were alternative theories.
>Only one individual seems to be blind and dense here wrt to what the
>relationship of the basic germ layers are, and it ain't me and Paul.
None of the three of us is blind to it, period. As for the
rest of the people in this ng, none has dared open his/her
mouth on the subject, not even Wade Hines or Matt Silberstein
or Jonathan Stone, all of whom have contributed to the
threads on embyrology.
>Your errors in this area are just as egregious as not knowing that heme
>is not a peptide when one is discussing hemoglobin.
Though not as egregious as Myers calling the embryonic disk
"the mammal".
And in any event, that former lack of knowledge is
utterly irrelevant to the substantive discussion on this thread.
You'd admit that if you had an ounce of integrity in you,
but I wouldn't even credit you with a gram.
Peter Nyikos
howard hershey <hers...@indiana.edu> writes:
>Peter Nyikos wrote:
>>
>> howard hershey <hers...@indiana.edu> writes:
>>
>> >Peter Nyikos wrote:
>> >>
>> >> get...@nobull.net (Cal King) writes:
>> >>
>> >> >In article <1998012617...@milo.math.sc.edu>, nyi...@math.sc.edu (Peter
>> >> >Nyikos) wrote...
>> >>
>> >[snip]
>> >>
>> >> >>On the other hand, the fossil evidence is overwhelming that
>> >> >>the correct grouping is:
>> >> >>
>> >> >> [{Lizards [Birds]} Mammals]
>> >>
>> >> >Is it really? If the squamata is the first group to branch off from the
>> >> >amniotes,
>> >>
>> >> There is no good reason to think that. The consensus among
>> >> paleontologists is that mammals branched off earlier.
>>
>> >That consensus and a buck or three will get you a cup of coffee.
>>
>> Whereas you and Myers take the tack that a LACK of consensus
>> in the standard embryology texts on how the amniotic
>> membrane is irrelevant
>The lack of evidence wrt to *human* material for some of the details of
>early embryogenesis is a reflection of human ethical rules (which I have
>no problem with) limiting experimentation on human material.
I've already corrected Myers on this. British law allows
experimentation with human embryos up to two weeks--plenty
of time for answering these questions. There are all kinds
of ways of getting around American laws too. AFAIK none
bans experimentation on human embryos--the only ban AFAIK
is on Federal grant money being used for that purpose.
>> and that
>> Moore's latest (1988) edition has been superseded by the LATEST
>> evidence despite an inability by either of you to present
>> that evidence in a coherent manner.
>Actually, as I have several times mentioned, the *human* evidence is not
>all that recent.
Thereby correcting Myers's ignorant statements? I think not.
I'd like to see documentation of you saying these things AFTER
Myers made his gaffes about mice experiments superseding these
earlier ones.
I also explicitly point out that it is my view that it
>wouldn't make any difference which explanation eventually was shown to
>be correct. Either way, your definition of endoderm
I never posted one. I did carelessly agree to what I thought
was a carelessly worded statement by you, because I thought
your intended meaning was different, but when you seized on
it sadistically, I immediately recanted it. But you continue
to refer to it as though I hadn't recanted it, dishonest sadist
that you are.
and how it might
>relate to the amnion reflects a failure on your part to understand even
>the most minimal principles of embryology,
Who are you, a biologist who hasn't even had the guts to tell
us what his specialty is, to be drawing such sweeping
conclusions from my failure to assent to something you
have never been able to document?
How many colleagues do you have in the biology department?
How many of them did you turn to for help in supporting
your unsupported and undocumented claim that the amnion
would be called ectoderm even if it is produced by
lamination from the cytotrophoblast?
None, right? You never gave a damn about this issue, did you,
except as somenthing to bait me with, did you?
probably because, by being
>self-taught primarily from a human embryology text, you lack the
>understanding of the underlying principles and developed your own based
>on names on pictures.
You are a pathetic excuse for a faculty member. ARE you on
the I.U. faculty? Or are you just a student?
>> And you two take the tack that I am ignorant of the most
>> basic embryology through my failure to cave in and agree that
>> the LATEST texts now have the gospel truth.
>>
>My position is now and always has been that you would be just as
>ignorant of basic embryology if the LATEST texts were wrong.
That and a dollar will get you a cup of coffee.
>> >[snip]
>> >>
>> >> And we need to use anatomical insight and fossil evidence too.
>> >> The fact remains that traditional systematists, vertebrate
>> >> paleontologists AND cladists have agreed,
>> >> all through this century (with a few minor exceptions of course)
>> >> that mammals branched off before squamates.
>Is this consensus based on overwhelming *evidence* (as you claim) or on
>a consensus based on the *current weight* of evidence. There is a
>difference.
The former.
>> >Nor would it represent the first time that scientists have been shown to
>> >be wrong when new evidence presented itself. That a consensus had been
>> >reached on the basis of old data does not make the consensus immune from
>> >change in the light of new evidence.
>>
>> Put that in your posts on embryology and smoke it.
>And what, pray tell, is the *new* evidence you are presenting?
I'm talking about the new evidence Myers was presenting on
mice, which you've been going on along with.
You seem
>to be arguing for a new definition of an old term, endoderm,
I haven't done that in about two months now, and the
Peter Principles are proof of that.
Peter Nyikos
howard hershey <hers...@indiana.edu> writes:
>Peter Nyikos wrote:
>>
>> my...@astro.ocis.temple.edu (PZ Myers) writes:
>>
>> >In article <1998020318...@milo.math.sc.edu>, Peter Nyikos
>> ><nyi...@math.sc.edu> wrote:
>>
>> >>my...@netaxs.com (PZ Myers) writes:
>> >>
>> >>>In article <1998013100...@milo.math.sc.edu>, Peter Nyikos
>> >>><nyi...@math.sc.edu> wrote:
>> >>
>> >>
>> >>
>> >>>> I didn't know heme was NOT a polypeptide. End of story.
>> >>>>
>[snip]
>> >>
>> >>I did not make one false statement after another about hemes,
>OTOH, you did display then, and do below, a rather embarrassing lack of
>knowledge about the genes that code for the various components of the
>various hemoglobins.
Not where the Fushitani et. al. paper and Moran's false and
ignorant comments are concerned.
I would suggest something rather basic, like any
>major modern genetics textbook or molecular biology textbook, before you
>embarrass yourself further.
Been there, done that.
>> On the other hand, Moran made a false statement about globins,
>> claiming that they showed agreement with the fossil record
>> as regards phylogeny, when they most certainly do not.
And he claimed to have taught this stuff for years, too.
>> >>and did not indulge in massive word games like Moran did
>> >>about hemes.
>>
>> The "about hemes" refers to my behavior.
>>
>> On the other hand, Moran took my PARTIAL listing of reptiles
>Just by chance, I printed out a copy of one of the earlier discussions,
>which shows your exact quote to read:
> This "discovery" is still many years in the future. In the
> meantime, we have anomalies like the various kinds of hemoglobin
> ^^^^^^^^^^^^^
> all agreeing that mammals are more closely related to birds
> ^^^
> than birds are to lizards, snakes, or turtles, which is
> falsified by the fossil evidence.
> ^^^^^^^^^
Right. Are you under the delusion that crocodilians are listed?
Here is what I say Larry did:
>> to jump to the conclusion that I was saying birds are closer
>> to mammals than they are to ALL reptiles,
>Larry replied:
> I pointed out that Peter's statement was not correct.
> The various kinds of hemoglobin do not all agree that
> ^^^^^^^^^^^^^ ^^^
> mammals are more closely related to birds than birds
> are to reptiles.
> ^^^^^^^^
In other words, since I left crocodilians out, Larry is
either NOT disagreeing with me (if he means "all reptiles")
or saying something false (if he means "some reptiles").
>> while taking
>> the Fushitani et. al. statement "birds form a sister
>> group with other reptiles but not with mammals" to mean
>> what the authors implicitly intended it to mean, namely
>> that the alpha globins showed birds form a sister group
>> with SOME reptiles (Sphenodon and maybe turtles
>Even aside from the fact that your original statement, by using the
>ambiguous (in common useage) term 'lizard' which could, in context, be
>read as meaning all reptiles,
You are lying, shamelessly lying. When it is used with turtles
and snakes as I did, it cannot mean that. And you are confusing common
usage of "lizard" with the latin suffix "saurus" which is a different
matter altogether.
I do think Larry pointed out that the
>quote was in error because it was based on the more limited amount of
>older data.
That was one of the few correct things he did.
>Turtles are one of the groups you explicitly mentioned in your quote,
>Peter.
Indeed, and Larry is not SO stupid as to think, despite this,
that "lizards" meant "reptiles."
> Sphenodon was not mentioned,
Because the earlier studies did not mention it. Duh.
>but you clearly think it to be a
>later divergence than 'lizards' and thus can be subsumed in that
>grouping.
Wrong. I think no such thing.
I think, therefore, that Larry's statement would be equally
>correct if you were to change "reptiles" to "lizards, snakes, and
>turtles". Do you disagree?
Larry did not make that statement, and that's the point.
He was trying to accuse me of having made statements
I never made.
>> but NOT crocodilians, in contrast to the fossil record)
>Uh? I thought the paper showed an unusual position of crocodilians vis
>a vis turtles, but *not* vis a vis mammals. Am I wrong in this?
My "NOT crocodilians" refers to what went before, not what
comes after. In other words, my listing left out crocodilians.
>> but not others (alpha "shows" mammals more closely related
>> to birds than either is to lizards).
>And this is where you need now to present your evidence that this
>relationship is so clearly *falsified* by the fossil record (your
>words),
Matt's statement, and Larry's statement, that it is in
agreement with the fossil record, is wrong; you will
not find a single book or paper on vertebrate paleontology
that agrees with it.
>and that the distances separating the divergence points of the
>squamate, mammalian, and avian lineages are *so* large that only
>something highly unusual could give a false molecular phylogeny,
I never said that. I find nothing unusual in false readings
of molecular phylogeny.
>> expect to be able to take on article on molecular
>> >>>systematics apart with tweezers?
>> >>
>> >>By knowing all he needs to know about globins, and about
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>> >>phylogeny, that's how.
> ^^^^^^^^^
>>
>> >Figured out what fetal hemoglobin is, yet?
>And here we get into areas that show that Peter's idea of what is
>required for "all one needs to know about globins" and my idea of the
>same concept differ.
I was critiquing the Fushitani et. al. paper. Only a sadist
like you would expect my statement to promise to critique
all papers on the subject you could ever come up with.
>> In humans? The Fushitani et. al. study trumpeted
>> by Moran didn't touch it with a ten foot pole.
>>
>> Curious sidelight: they did give a table showing only one
>> alpha (adult) and one beta (ditto) having been detected in
>> mammals, although in a footnote they say that the number of
>> Hb components should be taken as minima. On the other hand,
>> two pages later they say:
>>
>> (1) Claimed that the results suggest embryonic and adult alpha globin genes
>> were "acquired by gene duplication of the ancestral gene before the
>> divergence of amniotes took place."
>>
>> (2) Made the following remark about crocodilians, which are
>> no more and no less amniotes than humans are:
>>
>> The embryonic alpha chanin of crocodilians may
>> exist, but it has not yet been found, or, alternatively,
>> it is possible that crocodilians have lost the
>> corresponding embryonic alpha globin gene.
>>
>> Apparently they assumed that the reader would draw the
>> obvious parallel with mammals, because they made no mention
>> of them at this juncture.
>No comment, except to say that Peter should really do some reading of
>something other than 20 year old biochemistry textbooks. A recent
>review article on comparative molecular biology of the hemoglobins
>wouldn't hurt either.
In other words, you have no substantive comment to make
and are just being your usual sadistic self.
Wade Hines
Peter Nyikos wrote:
> howard hershey <hers...@indiana.edu> writes:
> >Peter Nyikos wrote:
> >> my...@netaxs.com (PZ Myers) writes:
> >> >In article <1998013100...@milo.math.sc.edu>, Peter Nyikos
> >> >[snip]
> >> >> I didn't know heme was NOT a polypeptide. End of story.
> >> >> I didn't understand the relationship of the basic germ layers of the
> >> >> embryo to one another. End of story.
> >> That remains to be seen.
> As to my understanding back then, that is. By now I'm so
> clear on it, I could describe it blindfolded. The only
> question is whether I was wrong in thinking that the Moore
> theory of amnion production is the correct one, before
> I learned from y'all that there were alternative theories.
> >Only one individual seems to be blind and dense here wrt to what the
> >relationship of the basic germ layers are, and it ain't me and Paul.
> None of the three of us is blind to it, period. As for the
> rest of the people in this ng, none has dared open his/her
> mouth on the subject, not even Wade Hines or Matt Silberstein
> or Jonathan Stone, all of whom have contributed to the
> threads on embyrology.
On the contrary. I have professed to a grand ignorance of embryology
and even kindly asked for the significance of certain questions to be
related so that one as ignorant as I could see what the fuss was about.
In response to this, Nyikos ran off a few insults toward the questioner
and others responded that they thought there was no grand relevance
and that instead the questions were founded on ignorance.
It has later been added that the questions may be rooting around for
something to mark humans as special though this has been carefully
hidden if it is a true agenda.
> >Your errors in this area are just as egregious as not knowing that heme
> >is not a peptide when one is discussing hemoglobin.
> Though not as egregious as Myers calling the embryonic disk
> "the mammal".
Wow, then that must be a real whopper. I wonder if it is
a.) symantic
b.) sloppiness
c.) wrong
I know that heme is rather a basic aspect of hemoglobin.
I know that people who argue about molecular phylogenies ought to know
about the nature of systematic "errors" in the molecular clock. This means
knowing something about function. For instance, those residue which coordinate
the heme group are not likely to be flopping back and forth while those which
sit in a loop have somewhat greater freedom. Sequences aren't just strings
of letters. I've said this to Peter before and he got offended.
> And in any event, that former lack of knowledge is
> utterly irrelevant to the substantive discussion on this thread.
> You'd admit that if you had an ounce of integrity in you,
> but I wouldn't even credit you with a gram.
I realize that anything Peter doesn't know, is by some definition unimportant.
The function of a protein, and the amino acids which are critical to that
function are critical to a true understanding of molecular data.
You played this out before with your CytC work where we were looking
at a difference of 2 or 4 residues out of over 100. Anyone who has a real
understanding will quickly see that this is a case of high conservation and
that there are therefore strong selective forces at work which counter the
basic assumptions of molecular clocks.
You can't really begin to believe this until you understand it.
Sadly, you will first begin to partially understand it and leap forth with
yet another neophyte revalation with which to ridicule the world.
One can hardly wait.
PZ Myers
--- standard comment ---
Peter Nyikos is demonstrably ignorant of many aspects of basic
biology. He likes to pretend to have considerable authority in
the field, however, which may mislead casual readers. Do not
accept anything he says without considerable corroboration from
other participants in this newsgroup, or without evaluating his
claims on your own.
I find assertions he has made in the post below objectionable.
It is counterproductive to argue these points, however, so I
choose not to waste my time on him. If anyone else would care
to seriously discuss any of these issues, I would be happy to
continue a civil debate either on this newsgroup or in e-mail.
--- end comment ---
In article <1998020923...@milo.math.sc.edu>, Peter Nyikos
<nyi...@math.sc.edu> wrote:
--
PZ Myers
Wade Hines
Peter Nyikos <nyi...@math.sc.edu> writes:
>howard hershey <hers...@indiana.edu> writes:
>>OTOH, you did display then, and do below, a rather embarrassing lack of
>>knowledge about the genes that code for the various components of the
>>various hemoglobins.
>Not where the Fushitani et. al. paper and Moran's false and
>ignorant comments are concerned.
Would Peter dearest make himself clearer?
Does he want to tell us, and quickly now, why it makes sense that
fetal hemoglobin would be homologous to the adult forms?
It's obvious yet seems to have unaccountably slipped by him.
> I would suggest something rather basic, like any
>>major modern genetics textbook or molecular biology textbook, before you
>>embarrass yourself further.
>Been there, done that.
Looked at teh pretty pictures, what did you learn?
They may have erred and written the books for biology students
and not math professors.
PZ Myers
> Peter Nyikos wrote:
>
> > howard hershey <hers...@indiana.edu> writes:
> > >Peter Nyikos wrote:
If you feel I gave you the runaround on a question about the significance,
please do ask again and I will try to clarify.
>
> It has later been added that the questions may be rooting around for
> something to mark humans as special though this has been carefully
> hidden if it is a true agenda.
>
>
> > >Your errors in this area are just as egregious as not knowing that heme
> > >is not a peptide when one is discussing hemoglobin.
>
>
>
> > Though not as egregious as Myers calling the embryonic disk
> > "the mammal".
>
> Wow, then that must be a real whopper. I wonder if it is
> a.) symantic
Isn't that a software company?
> b.) sloppiness
> c.) wrong
d.) none of the above. Casual usage, a reference to that portion of
the embryo that will go on to form the adult mammal in a discussion
that bounced back and forth between fish, frog, avian, and mammalian
development.
I *still* do not understand what Peter's objection is. I suspect it
has something to do with his outrage at embryologists who make distinctions
between embryonic and extra-embryonic tissues; but why that should bother
him is also incomprehensible to me.
>
> I know that heme is rather a basic aspect of hemoglobin.
> I know that people who argue about molecular phylogenies ought to know
> about the nature of systematic "errors" in the molecular clock. This means
> knowing something about function. For instance, those residue which coordinate
>
> the heme group are not likely to be flopping back and forth while those which
> sit in a loop have somewhat greater freedom. Sequences aren't just strings
> of letters. I've said this to Peter before and he got offended.
>
I suspect either of us could say "Good morning!" to Peter, and he would
get offended.
>
> > And in any event, that former lack of knowledge is
> > utterly irrelevant to the substantive discussion on this thread.
> > You'd admit that if you had an ounce of integrity in you,
> > but I wouldn't even credit you with a gram.
>
> I realize that anything Peter doesn't know, is by some definition unimportant.
>
> The function of a protein, and the amino acids which are critical to that
> function are critical to a true understanding of molecular data.
>
> You played this out before with your CytC work where we were looking
> at a difference of 2 or 4 residues out of over 100. Anyone who has a real
> understanding will quickly see that this is a case of high conservation and
> that there are therefore strong selective forces at work which counter the
> basic assumptions of molecular clocks.
>
> You can't really begin to believe this until you understand it.
> Sadly, you will first begin to partially understand it and leap forth with
> yet another neophyte revalation with which to ridicule the world.
>
> One can hardly wait.
You forgot the <sarcasm> tags.
--
PZ Myers
howard hershey
> >>
> >> [snip]
> >> > I didn't know heme was NOT a polypeptide. End of story.
> >> >
> >confused about the number and nature of globin genes involved in the
> >various hemoglobins in different organisms. [He had apparently heard a
> >rumor of a different globin gene being used in embryonic humans.]
>
> In addition to the usual ones mentioned by Fushitani et.al.
Please continue. Use your vast and highly accurate store of knowledge
of hemoglobins and their composition and structure to explain to us poor
ignoramuses how many different genes are involved in the protein
structure of the human hemoglobins, what the homologies are, where the
pseudogenes reside, what changes occur in hemoglobins during
development, and how this all might affect protein/DNA sequence analysis
when comparing the human sequence with the sequences of other animals.
Are "the usual ones mentioned by Fushitani et. al." the total of
sequenceable genes in the hemoglobin protein? Enquiring minds want to
know.
>
> This
> >is even more relevant to discussions of the evolutionary relationships
> >among the proteins, so I would suggest that Peter do a little more
> >reading on these basics before expounding on the defects of certain
> >papers.
>
> Your suggestion is rejected inasmuch as it seems clear that
> you haven't the foggiest idea whether the rumor you
> mention above is true or not.
No, Peter. I know perfectly well the roles of epsilon, delta, A-gamma,
and G-gamma (to be appropriately vague). I am merely giving *you* the
opportunity to amaze us with a clear presentation of the basics of
hemoglobin structure and development in humans (if not in other species;
for example, how much variance exists in different species in the number
of ___-globin genes)? Of course, the fact that you are indicating that
you don't know the roles of the above features (and already have one
mistake to your credit, the aforementioned ignorance of the structure of
heme) might be taken by some as an implicit answer to the question of
"How much of Peter's Post on hemoglobin represents blowing smoke by
someone who doesn't know squat about hemoglobin?" but I am willing to
give you a little more rope (and the opportunity to look up the answers
in those books you claim to have read).
> If it is, Fushitani et al
> were remiss in not mentioning it. If not, then you are
> just blowing smoke in suggesting that my analysis of Fushitani
> et al is flawed in any way at all.
Because I am waiting for *you* to discuss the limitations and problems.
I am, in fact, still waiting for your *analysis* of Fushitani. You
claim that this was done elsewhere than on t.o.
>
> You have yet to make any substantive criticism of that analysis,
> except to suggest REASONS for why the molecular and fossil
> evidence disagree--thereby tacitly conceding the point that
> Moran is a fool to be "bored" with this fact to the point
> of simply stating that the fossil record and molecular evidence
> agree--after having (or so he claims) taught about these things
> for years.
The fossil record and molecular evidence can agree without necessarily
*every* molecule (nor every feature of fossil morphology) agreeing.
Decisions in science are often a matter of the 'weight of evidence'
favoring one solution over another. And the 'weight of evidence' can
change as more information accumulates.
>
> >[snip]
>
[snip - the below shifts to the old endo, ecto problem]
>
> I honestly thought Peter had simply printed a typo - 'endo' for
> >'ecto'. I was wrong. The things you find out when you correct a simple
> >little mistake, especially about how some people respond to being
> >corrected.
>
> Yes, I agreed I was mistaken in thinking it was the standard term.
> But that was not enough for Howard. In scores of posts, despite
> repeated corrections, he kept lying that I think the amnion
> is ectoderm. I do believe he will continue to lie about that.
This may be *deja vu* all over again, but didn't you mean 'endoderm'
rather than 'ectoderm' in the above paragraph? Perhaps *this* time it
really was a typo. I certainly never accused you of thinking the amnion
was ectoderm.
Marquis de Hershey
howard hershey
Peter Nyikos wrote:
>
> howard hershey <hers...@indiana.edu> writes:
>
> >PZ Myers wrote:
> >>
> >> In article <1998013100...@milo.math.sc.edu>, Peter Nyikos
> >> <nyi...@math.sc.edu> wrote:
> >>
> >> [snip]
>
> Correction: not sarcastic at all, as opposed to the sadistic
^^^^^^^^
> repetition of sarcasm on the heme business long after the
> correction was made and acknowledged.
>
[snip]
> >But a statement along the lines that Paul suggested would be acceptable.
[Along the lines that Peter did not (and may still not) understand the
difference between endoderm and ectoderm]
>
> To a sadist like Hershey, nothing less would be acceptable.
^^^^^^
Peter's definition of sadist is someone who points out that Peter is not
the polymath genius he thinks he is, but instead is quite limited in his
knowledge of biology and biochemistry.
howard hershey
> >> ><nyi...@math.sc.edu> wrote:
> >>
> >> >[snip]
> >> >>
> >>
> >> >> I didn't understand the relationship of the basic germ layers of the
> >> >> embryo to one another. End of story.
> >>
> >> That remains to be seen.
>
> As to my understanding back then, that is. By now I'm so
> clear on it, I could describe it blindfolded. The only
> question is whether I was wrong in thinking that the Moore
> theory of amnion production is the correct one, before
> I learned from y'all that there were alternative theories.
Is this the first baby step to saying that you now recognize that the
amnion is lined with ectoderm regardless of how it is formed?
>
> >Only one individual seems to be blind and dense here wrt to what the
> >relationship of the basic germ layers are, and it ain't me and Paul.
>
> None of the three of us is blind to it, period.
One of 'the three of us' is, as long as that 'one of us' continues to
claim that it is reasonable to call the amnion ectoderm.
> As for the
> rest of the people in this ng, none has dared open his/her
> mouth on the subject, not even Wade Hines or Matt Silberstein
> or Jonathan Stone, all of whom have contributed to the
> threads on embyrology.
>
> >Your errors in this area are just as egregious as not knowing that heme
> >is not a peptide when one is discussing hemoglobin.
>
> Though not as egregious as Myers calling the embryonic disk
> "the mammal".
>
> And in any event, that former lack of knowledge is
^^^^^^
What do you mean by *former* lack of knowledge? Are you now saying
that, although it was 'utterly irrelevant to the substantive discussion
on this thread', you now agree that the amnion is lined with ectoderm?
What changed your mind?
> utterly irrelevant to the substantive discussion on this thread.
> You'd admit that if you had an ounce of integrity in you,
> but I wouldn't even credit you with a gram.
>
howard hershey
Peter Nyikos wrote:
>
> howard hershey <hers...@indiana.edu> writes:
>
> >Peter Nyikos wrote:
> >>
> >> howard hershey <hers...@indiana.edu> writes:
> >>
> >> >Peter Nyikos wrote:
> >> >>
> >> >> get...@nobull.net (Cal King) writes:
> >> >>
> >> >> >In article <1998012617...@milo.math.sc.edu>, nyi...@math.sc.edu (Peter
> >> >> >Nyikos) wrote...
> >> >>
> >> >[snip]
>
> I also explicitly point out that it is my view that it
> >wouldn't make any difference which explanation eventually was shown to
> >be correct. Either way, your definition of endoderm
>
> I never posted one. I did carelessly agree to what I thought
> was a carelessly worded statement by you, because I thought
> your intended meaning was different, but when you seized on
> it sadistically, I immediately recanted it. But you continue
> to refer to it as though I hadn't recanted it, dishonest sadist
> that you are.
Perhaps your inability to post a legitimate definition of 'endoderm'
explains why you presented your Peter Principles, which determines what
is called endoderm by the simple process of guessing.
>
> and how it might
> >relate to the amnion reflects a failure on your part to understand even
> >the most minimal principles of embryology,
>
> Who are you, a biologist who hasn't even had the guts to tell
> us what his specialty is, to be drawing such sweeping
> conclusions from my failure to assent to something you
> have never been able to document?
>
> How many colleagues do you have in the biology department?
> How many of them did you turn to for help in supporting
> your unsupported and undocumented claim that the amnion
> would be called ectoderm even if it is produced by
> lamination from the cytotrophoblast?
>
> None, right? You never gave a damn about this issue, did you,
> except as somenthing to bait me with, did you?
No. I first corrected you because I thought you had made a careless
typo. Later, of course, to drop the topic would be tantamount to
accepting asserted ignorance as fact, so I couldn't (and won't) drop it
until you recognized how ignorant it was.
>
> probably because, by being
> >self-taught primarily from a human embryology text, you lack the
> >understanding of the underlying principles and developed your own based
> >on names on pictures.
>
> You are a pathetic excuse for a faculty member. ARE you on
> the I.U. faculty? Or are you just a student?
I am and always will be a student. One *never* ceases being a student
before nature. As for the other part, just consider me as sort of a
third-string benchwarmer of no particular atheletic genius, but a good
understanding of the game. Or don't. I could care less. I have
already expressed my opinion that a PhD and/or faculty status is no
guarantee of knowledge, quality of thought, or civility, and I think you
are an object lesson of the wisdom of that stance.
>
> >> And you two take the tack that I am ignorant of the most
> >> basic embryology through my failure to cave in and agree that
> >> the LATEST texts now have the gospel truth.
> >>
> >My position is now and always has been that you would be just as
> >ignorant of basic embryology if the LATEST texts were wrong.
>
> That and a dollar will get you a cup of coffee.
>
> >> >[snip]
> >> >>
> >> >> And we need to use anatomical insight and fossil evidence too.
> >> >> The fact remains that traditional systematists, vertebrate
> >> >> paleontologists AND cladists have agreed,
> >> >> all through this century (with a few minor exceptions of course)
> >> >> that mammals branched off before squamates.
>
> >Is this consensus based on overwhelming *evidence* (as you claim) or on
> >a consensus based on the *current weight* of evidence. There is a
> >difference.
>
> The former.
So.... Present it. And the timing of the divergences, which is the
point most relevant to the sequencing data.
>
> >> >Nor would it represent the first time that scientists have been shown to
> >> >be wrong when new evidence presented itself. That a consensus had been
> >> >reached on the basis of old data does not make the consensus immune from
> >> >change in the light of new evidence.
> >>
> >> Put that in your posts on embryology and smoke it.
>
> >And what, pray tell, is the *new* evidence you are presenting?
>
> I'm talking about the new evidence Myers was presenting on
> mice, which you've been going on along with.
And does this new evidence support *your* viewpoint?
>
> > You seem
> >to be arguing for a new definition of an old term, endoderm,
>
> I haven't done that in about two months now, and the
> Peter Principles are proof of that.
Which replaces that definition with guesswork and implies that almost
anything could be called endoderm (maybe this, maybe that).
howard hershey
Peter Nyikos wrote:
>
> howard hershey <hers...@indiana.edu> writes:
>
> >Peter Nyikos wrote:
> >>
> >> my...@astro.ocis.temple.edu (PZ Myers) writes:
> >>
> >> >In article <1998020318...@milo.math.sc.edu>, Peter Nyikos
> >> ><nyi...@math.sc.edu> wrote:
> >>
> >> >>my...@netaxs.com (PZ Myers) writes:
> >> >>
> >> >>>In article <1998013100...@milo.math.sc.edu>, Peter Nyikos
> >> >>><nyi...@math.sc.edu> wrote:
> >> >>
> >> >>
> >> >>
> >> >>>> I didn't know heme was NOT a polypeptide. End of story.
> >> >>>>
> >[snip]
> >> >>
> >> >>I did not make one false statement after another about hemes,
>
> >OTOH, you did display then, and do below, a rather embarrassing lack of
> >knowledge about the genes that code for the various components of the
> >various hemoglobins.
>
> Not where the Fushitani et. al. paper and Moran's false and
> ignorant comments are concerned.
>
> I would suggest something rather basic, like any
> >major modern genetics textbook or molecular biology textbook, before you
> >embarrass yourself further.
>
> Been there, done that.
If you have 'been there' and 'done that', please take this opportunity
to prove your point.
>
[snip]
> >>
> >> On the other hand, Moran took my PARTIAL listing of reptiles
>
> >Just by chance, I printed out a copy of one of the earlier discussions,
> >which shows your exact quote to read:
>
> > This "discovery" is still many years in the future. In the
> > meantime, we have anomalies like the various kinds of hemoglobin
> > ^^^^^^^^^^^^^
> > all agreeing that mammals are more closely related to birds
> > ^^^
> > than birds are to lizards, snakes, or turtles, which is
> > falsified by the fossil evidence.
> > ^^^^^^^^^
>
> Right. Are you under the delusion that crocodilians are listed?
Nope, and the failure to discuss other groups of reptiles which birds
might be more closely related to than mammals does give the misleading
impression, if not the literal statement, that there were no such group
of reptiles to which birds are more closely linked than they are to
mammals. Whether the *partial* listing was meant to give that
misleading impression intentionally is anyone's guess (although *you*
obviously know).
Ooops. I believe you mentioned the separation of pelycosaurs from all
other reptile lineages to be somewhere in the order of 350 mybp and
sphenodon about 100 my later (and, unless my recollection is wrong, from
the 'squamata' rather than from the archosaur lineage). You *were*
somewhat unclear about when the squamata lineage came off. Perhaps you
would like to clarify the relationships and times now? As you
mentioned, there is an overwhelming consensus based on the fossil
record. But I have not heard the evidence on which this is based.
No, Peter. I am giving *you* the opportunity to show that the lack of
knowledge displayed by not knowing that heme is not a peptide was an
aberration. Your failure to take advantage of this opportunity to
'strut your stuff' might be taken by those who do know as a further sign
of limited comprehension on your part, based on the types of questions
you are asking. But I am not responsible for what others think.
Peter Nyikos
my...@netaxs.com (PZ Myers) writes:
>In article <34DFD98F...@ixl.net>, Wade Hines <da...@ixl.net> wrote:
>> Peter Nyikos wrote:
>>
>> > howard hershey <hers...@indiana.edu> writes:
>> > >Peter Nyikos wrote:
>> > >> my...@netaxs.com (PZ Myers) writes:
[Myers, proposing something I should "confess" to]
>> > >> >> I didn't understand the relationship of the basic germ layers of the
>> > >> >> embryo to one another. End of story.
[Nyikos, trying to meet Myers halfway:]
>> > >> That remains to be seen.
[Nyikos, clarifying what "halfway" means:]
>> > As to my understanding back then, that is. By now I'm so
>> > clear on it, I could describe it blindfolded. The only
>> > question is whether I was wrong in thinking that the Moore
>> > theory of amnion production is the correct one, before
>> > I learned from y'all that there were alternative theories.
[...]
>> > None of the three of us is blind to it, period. As for the
>> > rest of the people in this ng, none has dared open his/her
>> > mouth on the subject, not even Wade Hines or Matt Silberstein
>> > or Jonathan Stone, all of whom have contributed to the
>> > threads on embyrology.
>> On the contrary.
Wade meant to say, "Indeed".
>>I have professed to a grand ignorance of embryology
That was part of Wade's contribution to the threads, yes.
>> and even kindly asked for the significance of certain questions to be
>> related so that one as ignorant as I could see what the fuss was about.
>>
>> In response to this, Nyikos ran off a few insults toward the questioner
>> and others responded that they thought there was no grand relevance
>> and that instead the questions were founded on ignorance.
Myers was dissembling when he made that response, since he hasn't
made an appreciable dent in any of my main mysteries labeled by Roman
Numerals, since what little he has posted is marred by highly
dubious blatant assertions. For example, he supposedly knows the
septum primum in humans is NOT homologous to the partial
lungfish atrial septum, but his rationale is completely bogus.
More to the point, he hasn't even TRIED to answer the question of
how the phenomena listed by Roman numerals arose in the course
of evolution, except in Howard Hershey fashion:
There obviously was an easy route up Mount Improbable,
because the view from the top is GREAT.
>If you feel I gave you the runaround on a question about the significance,
>please do ask again and I will try to clarify.
It was indeed a runaround. Myers has claimed these mysteries have
long been solved but his answers were laughably inadequate.
[Hershey:]
>> > >Your errors in this area are just as egregious as not knowing that heme
>> > >is not a peptide when one is discussing hemoglobin.
>> > Though not as egregious as Myers calling the embryonic disk
>> > "the mammal".
>>
>> Wow, then that must be a real whopper. I wonder if it is
>> a.) symantic
>Isn't that a software company?
>> b.) sloppiness
>> c.) wrong
Wrong, dead wrong.
>d.) none of the above. Casual usage,
Blatantly asserted by both Myers and Hershey to be standard,
yet not supported with a scrap of documentation.
a reference to that portion of
>the embryo that will go on to form the adult mammal in a discussion
>that bounced back and forth between fish, frog, avian, and mammalian
>development.
>I *still* do not understand what Peter's objection is. I suspect it
>has something to do with his outrage at embryologists who make distinctions
>between embryonic and extra-embryonic tissues;
Since I have been the one taking Hershey to task for leaving
out the word "extraembryonic", and have never voiced any
objection to making such distinctions, Myers is dissembling big-time
here.
but why that should bother
>him is also incomprehensible to me.
Myers pours on the dissimulation, demonstrating his utter contempt
for the intelligence and conscience of his readers.
Now it's Hines's turn to pour on the dissimulation:
>> I know that heme is rather a basic aspect of hemoglobin.
>> I know that people who argue about molecular phylogenies ought to know
>> about the nature of systematic "errors" in the molecular clock.
Indeed, this whole thread began precisely because there ARE such
errors, including errors that make birds look like they are
more closely related to turtles than to crocodilians, and more
closely related to mammals than to lizards. And the substantive
issue in this thread is nothing more or less than the question
of whether the results of molecular sequencing are "congruent" to the fossil
record. These two examples show it is not.
This means
>> knowing something about function. For instance, those residue which coordinate
>>
>> the heme group are not likely to be flopping back and forth while those which
>> sit in a loop have somewhat greater freedom.
All irrelevant to the main issue, which I've stated in the
preceding paragraph. Hines is indulging in a blatant
fallacy of *argumentum ad ignorantiam* in pretending otherwise.
Sequences aren't just strings
>> of letters. I've said this to Peter before and he got offended.
Because Hines was indulging in a Phantom Error Correction Scam, probably:
pretending I don't know that sequences are more than just lists
of letters, and that some sites are much more likely to be
conserved than others.
>I suspect either of us could say "Good morning!" to Peter, and he would
>get offended.
Only if it was evening. ;-)
>> > And in any event, that former lack of knowledge is
>> > utterly irrelevant to the substantive discussion on this thread.
>> > You'd admit that if you had an ounce of integrity in you,
>> > but I wouldn't even credit you with a gram.
And Hines knows that too, but he doesn't have a gram of integrity
by the looks of it, because he indulges in craven innuendo
to the effect that it IS relevant to the substantive discussion,
without claiming it outright:
>> I realize that anything Peter doesn't know, is by some definition unimportant.
What's the matter with Wade? Why doesn't he lie outright that
heme IS important to the substantive discussion on this thread?
After all, he has two habitual liars, Hershey and Myers, to
back him up if he does lie like that. And I've seen Wade lie
often enough so that it probably wouldn't go against his conscience
if he did that.
[further irrelevant elementary facts by Hines deleted]
>> You can't really begin to believe this until you understand it.
>> Sadly, you will first begin to partially understand it and leap forth with
>> yet another neophyte revalation with which to ridicule the world.
>>
>> One can hardly wait.
>You forgot the <sarcasm> tags.
Part and parcel of his earlier failure to lie outright. He's
relying on innuendo to the effect that he is being sarcastic
about me, but he isn't willing to even label it as such.
Peter Nyikos -- standard disclaimer --
Professor, Dept. of Mathematics
University of South Carolina
Columbia, SC 29208
Peter Nyikos
howard hershey <hers...@indiana.edu> writes:
>Peter Nyikos wrote:
>>
>> howard hershey <hers...@indiana.edu> writes:
>>
>> >PZ Myers wrote:
>> >>
>> >> In article <1998013100...@milo.math.sc.edu>, Peter Nyikos
>> >> <nyi...@math.sc.edu> wrote:
>> >>
>> >> [snip]
>> >> > I didn't know heme was NOT a polypeptide. End of story.
>> >> >
>> >There were a few other places in that post where Peter also seemed
>> >confused about the number and nature of globin genes involved in the
>> >various hemoglobins in different organisms. [He had apparently heard a
>> >rumor of a different globin gene being used in embryonic humans.]
>>
>> In addition to the usual ones mentioned by Fushitani et.al.
>Please continue.
I decline the invitation, which was made in bad faith, as
the sequel [mostly deleted] shows.
>Are "the usual ones mentioned by Fushitani et. al." the total of
>sequenceable genes in the hemoglobin protein? Enquiring minds want to
>know.
If you don't know the answer, why ask me? Read the paper
by Fushitani et.al. and see whether they missed any. Ask
Certified Senior Mandarins of Science [tm] Paul Myers
or Laurence A. Moran if you aren't sure.
>> This
>> >is even more relevant to discussions of the evolutionary relationships
>> >among the proteins, so I would suggest that Peter do a little more
>> >reading on these basics before expounding on the defects of certain
>> >papers.
>>
>> Your suggestion is rejected inasmuch as it seems clear that
>> you haven't the foggiest idea whether the rumor you
>> mention above is true or not.
>No, Peter. I know perfectly well the roles of epsilon, delta, A-gamma,
>and G-gamma (to be appropriately vague). I am merely giving *you* the
>opportunity to
Talk about things Fushitani et.al never mentioned? No thanks.
amaze us with a clear presentation of the basics of
>hemoglobin structure and development in humans (if not in other species;
>for example, how much variance exists in different species in the number
>of ___-globin genes)?
Fushitani et.al. listed the ones for betas and alphas. See if
they missed any. By the way, they only gave data for alpha
sequencing, and didn't indicate why. Maybe you can enlighten
us. After all, you are a Certified Mandarin of Science but
since you are too cowardly to tell us whether "Academic"
means "Faculty" in the U. of Indiana website, I cannot
give you the Senior label. But you can ask the two certified
Senior Mandarins if you are not sure.
>"How much of Peter's Post on hemoglobin represents blowing smoke by
>someone who doesn't know squat about hemoglobin?"
None of it, since I know all I need to know in order to
talk about the evolutionary trees Fushitani et. al. drew
up as they relate to the main issue on this thread, which
I just got done relating in followup to Senior Mandarin Myers.
As I said earlier:
>> If it is, Fushitani et al
>> were remiss in not mentioning it. If not, then you are
>> just blowing smoke in suggesting that my analysis of Fushitani
>> et al is flawed in any way at all.
>Because I am waiting for *you* to discuss the limitations and problems.
>I am, in fact, still waiting for your *analysis* of Fushitani.
Already done. If you want more details than you see here
in talk.origins, have a look at my posts in sci.bio.systematics,
on the thread, "Molecular methods (was: Benton's book)"
where I discuss the paper in depth with people who don't
have a militantly anti-Nyikos agenda.
The discussion overflowed into "birds and crocs (but not really)",
and despite the thread title (for which I was not responsible)
I gave data for birds and crocs (and turtles and Sphenodon) in
a neat little tree giving some of the bootstrap values
for NJ and MP which you can look up in Deja News if you are interested.
But you aren't interested, are you?
You
>claim that this was done elsewhere than on t.o.
Right. Here's a small sample to bore you to death:
===================== begin excerpt
See the above paper, where the performance is mixed. Five incorrect
(IMO) groupings had bootstrap values over 50 for NJ. Removing the
viper led to a much more sensible arrangement--except that the
bootstrap NJ value for grouping non-lizards, including mammals,
away from lizards shot up to 80. With the viper included,
it was below 40. But then, how can you trust a system
which puts the viper as more closely related to horses and
humans than to ANY of the other reptiles, including lizards?
To be sure, the bootstrap values for putting the viper with
us were below 40%, but that was what was keeping
the bootstrap value for the {birds, crocodilians, mammals,
turtles, Spenondon} group away from lizards from shooting up to 80.
=========================== end of excerpt
Are you snoring yet?
>> You have yet to make any substantive criticism of that analysis,
>> except to suggest REASONS for why the molecular and fossil
>> evidence disagree--thereby tacitly conceding the point that
>> Moran is a fool to be "bored" with this fact to the point
>> of simply stating that the fossil record and molecular evidence
>> agree--after having (or so he claims) taught about these things
>> for years.
>The fossil record and molecular evidence can agree without necessarily
>*every* molecule (nor every feature of fossil morphology) agreeing.
Moran used the word "congruent" and claimed the Fushitani et.al.
paper shows it--which, of course, it does not.
>> >[snip]
>>
>[snip - the below shifts to the old endo, ecto problem]
>>
>> I honestly thought Peter had simply printed a typo - 'endo' for
>> >'ecto'. I was wrong. The things you find out when you correct a simple
>> >little mistake, especially about how some people respond to being
>> >corrected.
>>
>> Yes, I agreed I was mistaken in thinking it was the standard term.
>> But that was not enough for Howard. In scores of posts, despite
>> repeated corrections, he kept lying that I think the amnion
>> is ectoderm. I do believe he will continue to lie about that.
>This may be *deja vu* all over again, but didn't you mean 'endoderm'
>rather than 'ectoderm' in the above paragraph? Perhaps *this* time it
>really was a typo.
It sure was, and I thank you for catching it.
As to why that was a lie, it (1) leaves out an all-important
conditional clause and (2) I have merely said it would
be reasonable to *call* it that if the conditional referred
to in (1) is satisfied.
>Marquis de Hershey
Nice sense of humor.
Peter Nyikos
howard hershey <hers...@indiana.edu> writes:
>Peter Nyikos wrote:
>>
>> howard hershey <hers...@indiana.edu> writes:
>>
>> >PZ Myers wrote:
>> >>
>> >> In article <1998013100...@milo.math.sc.edu>, Peter Nyikos
>> >> <nyi...@math.sc.edu> wrote:
>> >>
>> >> [snip]
>>
>> Correction: not sarcastic at all, as opposed to the sadistic
> ^^^^^^^^
>> repetition of sarcasm on the heme business long after the
>> correction was made and acknowledged.
>>
>[snip]
>> >But a statement along the lines that Paul suggested would be acceptable.
>[Along the lines that Peter did not (and may still not) understand the
>difference between endoderm and ectoderm]
>>
>> To a sadist like Hershey, nothing less would be acceptable.
> ^^^^^^
>Peter's definition of sadist is someone who points out that Peter is not
>the polymath genius he thinks he is, but instead is quite limited in his
>knowledge of biology and biochemistry.
Of course, Hershey is dissembling. My definition of sadists includes,
but is not confined to, people who, like Hershey, will habitually
and publicly lie about others to force those others to "confess" to
things they never did and to opinions they don't hold.
I may have been premature when I compared him, months ago,
to the people who hounded Thomas More (as shown in _A Man
for All Seasons_) to assent to things his conscience wouldn't
allow him to assent to. But Hershey seems determined to
prove the analogy right.
If the USA were ever to become a Jacobin-style nation where
people can be tried for treason for doing politically
incorrect things, I do believe Hershey would be glad to
do the following analogy to a court testimony by Richard
Rich, who perjured himself in order that Thomas More be
found guilty of high treason and executed:
PROSECUTOR: Please recount your conversation with the prisoner.
HERSHEY: I put the following question to him: if the National
Academy of Sciences were to declare that an amnion formed
by unfolding of somatopleure is ectoderm, would you agree?
PROSECUTOR: And his answer to that?
HERSHEY: He agreed. Then he said, "I will put to you a higher
case. Suppose the National Academy of Sciences were to declare
that the eye of an octopus is homologous to the eye of a human
being. Would you agree to that?"
NYIKOS: That is correct, and you said...
JUDGE: SILENCE! Let the witness continue.
HERSHEY: Then I said, "I will put to you an intermediate
case. Suppose the National Academy of Sciences were
to declare that an amnion formed by delamination from
a cytotrophoblast were homologous to one formed by spreading
from the epiblast. Would you agree?
PROSECUTOR: And what did he say to that?
HERSHEY: <swallowing> He said "NAS has not the authority."
PROSECUTOR: <feigned surprise> WHAT????
HERSHEY: <softly> NAS has not the competence...or words to
that effect.
PROSECUTOR: He committed high treason against NAS! Your honor,
I have no further questions of the witness.
Peter Nyikos
howard hershey <hers...@indiana.edu> writes:
>Peter Nyikos wrote:
>>
>> howard hershey <hers...@indiana.edu> writes:
>>
>> >Peter Nyikos wrote:
>> >>
>> >> my...@netaxs.com (PZ Myers) writes:
>> >>
>> >> >In article <1998013100...@milo.math.sc.edu>, Peter Nyikos
>> >> ><nyi...@math.sc.edu> wrote:
>> >>
>> >> >[snip]
>> >> >> I didn't know heme was NOT a polypeptide. End of story.
>> >> >>
>> >[snip]
>> >>
>> >> >> I didn't understand the relationship of the basic germ layers of the
>> >> >> embryo to one another. End of story.
>> >>
>> >> That remains to be seen.
>>
>> As to my understanding back then, that is. By now I'm so
>> clear on it, I could describe it blindfolded. The only
>> question is whether I was wrong in thinking that the Moore
>> theory of amnion production is the correct one, before
>> I learned from y'all that there were alternative theories.
Note how Hershey avoids dealing with the question, and asks
a disingenuous question:
>Is this the first baby step to saying that you now recognize that the
>amnion is lined with ectoderm regardless of how it is formed?
It is not a step in that direction at all, since I've repeatedly
made clear to you the Moore theory conditional. It's right
there in the Peter Principles ("formed by delamination..."), which
I now update as follows:
The First Peter Principle of Extraembryonic Membrane Formation:
To insist that an amnion or Heuser's membrane formed by
delamination from the cytotrophoblast
is homologous to one formed by folding
of somatopleure, and to insist that the amnion is
comprised of ectoderm AND Heuser's membrane of endoderm
if both delamination theories are correct,
is to promote the words "homologous" and "ectoderm"
and "endoderm" beyond their levels of competence.
The Second Peter Principle of Extraembryonic Membrane Formation:
To insist that an amnion or Heuser's membrane formed by
delamination from cytotrophoblast
is NOT homologous to one formed by folding
of somatopleure, and to insist that BOTH are comprised of
extraembyronic endoderm in such an event, is probably to promote the
terms "homologous" and "extraembyroninc endoderm" beyond their
levels of competence, but the case isn't as open-and-shut as in
the First Peter Principle of Extraembryonic Membrane Formation.
NOTE: In the first principle, the two "insist that"s describe something
Hershey has insisted on, and the only rationale for his discrepancy
between amnion and Heuser's membrane that he has given (IIRC) is his
own brainchild, the so-called "crayon test" which is applied to
these things but not to the extraembryonic mesoderm which borders
the epiblast and cytotrophoblast.
>> >Only one individual seems to be blind and dense here wrt to what the
>> >relationship of the basic germ layers are, and it ain't me and Paul.
>>
>> None of the three of us is blind to it, period.
>One of 'the three of us' is, as long as that 'one of us' continues to
>claim that it is reasonable to call the amnion ectoderm.
Where do you see me claiming it above? Anyway, I have repeatedly
given my conditions for saying WHY I think it reasonable, but
you have not assented, probably because you want to reserve
to yourself the right to misrepresent it hundreds of times
without having to actually quote the thing you deliberately
misrepresent.
Even though I told you and Myers the rationale is only about
20 lines long, you have NOT agreed to repost it every
time you make disparaging remarks about it.
>> As for the
>> rest of the people in this ng, none has dared open his/her
>> mouth on the subject, not even Wade Hines or Matt Silberstein
>> or Jonathan Stone, all of whom have contributed to the
>> threads on embyrology.
>>
>> >Your errors in this area are just as egregious as not knowing that heme
>> >is not a peptide when one is discussing hemoglobin.
>>
>> Though not as egregious as Myers calling the embryonic disk
>> "the mammal".
>>
>> And in any event, that former lack of knowledge is
> ^^^^^^
>What do you mean by *former* lack of knowledge?
Exactly as described at the beginning: I did not know that
Moore's statement that the amnion is formed in humans
by delamination from cytotrophoblast is highly controversial
among embryologists.
Henry Barwood
Peter Nyikos wrote:
> Of course, Hershey is dissembling. My definition of sadists includes,
> but is not confined to, people who, like Hershey, will habitually
> and publicly lie about others to force those others to "confess" to
> things they never did and to opinions they don't hold.
And exactly when did you confess to these things you never did and to
opinions you do not hold?
Rest snipped.
Barwood
Peter Nyikos
Another followup to a post on the thread, "Hemoglobin Genes and the
Fossil Record" in which I catch Hershey insincerely (IMO) paying
lip service to the principle that a Ph.D. in biology is no
guarantee of knowledge, etc. There is also an incredibly
egregious use by Hershey of the False Dichotomy fallacy.
howard hershey <hers...@indiana.edu> writes:
>Peter Nyikos wrote:
>>
>> howard hershey <hers...@indiana.edu> writes:
>>
>> >Peter Nyikos wrote:
>> >>
>> >> howard hershey <hers...@indiana.edu> writes:
>> >>
>> >> >Peter Nyikos wrote:
>> >> >>
>> >> >> get...@nobull.net (Cal King) writes:
>> >> >>
>> >> >> >In article <1998012617...@milo.math.sc.edu>, nyi...@math.sc.edu (Peter
>> >> >> >Nyikos) wrote...
>> >> >>
>> >> >[snip]
>[snip]
>>
>> I also explicitly point out that it is my view that it
>> >wouldn't make any difference which explanation eventually was shown to
>> >be correct. Either way, your definition of endoderm
>>
>> I never posted one. I did carelessly agree to what I thought
>> was a carelessly worded statement by you, because I thought
>> your intended meaning was different, but when you seized on
>> it sadistically, I immediately recanted it. But you continue
>> to refer to it as though I hadn't recanted it, dishonest sadist
>> that you are.
>Perhaps your inability to post a legitimate definition of 'endoderm'
You haven't posted a legitimate definition either, nor have
you posted one of "homologous", so I am one up on you.
Here, I'll post a NECESSARY condition (though not a sufficient
one, not by a long shot) for something to be called
*embryonic* ectoderm: it originates in epiblastic cells.
And here's a SUFFICIENT condition (though not necessary, not
by a long shot) for something to be called "endoderm": it originates
in hypoblastic cells.
To try and make me "define" something which is so much an arbitrary
convention as to cause Arey to put `ectoderm' in inverted
commas when applied to the amnion, suggests that you are a mediocre
scientist who looks upon science as a mere career and propaganda
to be his profession.
>explains why you presented your Peter Principles, which determines what
>is called endoderm by the simple process of guessing.
You are indulging in an incredibly unscientific and egregious
False Dichotomy fallacy. The Peter Principles up to now
have only had to do with the solitary question of whether
AMNION is endoderm under a theory of amnion formation that you yourself don't
subscribe to; to extend this one isolated case to a general
theory about what is endoderm is the mark of either a
worse-than-mediocre scientist or a highly dishonest propagandist
(probably both).
Now I've added Heuser's membrane to the principles. Let's
see what new ways you conjure up for deceiving people about
them.
>> and how it might
>> >relate to the amnion reflects a failure on your part to understand even
>> >the most minimal principles of embryology,
>>
>> Who are you, a biologist who hasn't even had the guts to tell
>> us what his specialty is, to be drawing such sweeping
>> conclusions from my failure to assent to something you
>> have never been able to document?
The thing you have never been able to document is that the
amnion would be called "ectoderm" even if it is formed
by delamination from the cytotrophoblast.
>> How many colleagues do you have in the biology department?
>> How many of them did you turn to for help in supporting
>> your unsupported and undocumented claim that the amnion
>> would be called ectoderm even if it is produced by
>> lamination from the cytotrophoblast?
>>
>> None, right? You never gave a damn about this issue, did you,
>> except as somenthing to bait me with, did you?
>No. I first corrected you because I thought you had made a careless
>typo. Later, of course, to drop the topic would be tantamount to
>accepting asserted ignorance as fact, so I couldn't (and won't) drop it
>until you recognized how ignorant it was.
The ignorance is on your part, and the part of your colleagues
if you turned to them for help, for insisting that the
amnion would be called "ectoderm" even if it is formed
by delamination from the cytotrophoblast, in the absence
of ability to find justification for it.
>> probably because, by being
>> >self-taught primarily from a human embryology text, you lack the
>> >understanding of the underlying principles and developed your own based
>> >on names on pictures.
>>
>> You are a pathetic excuse for a faculty member. ARE you on
>> the I.U. faculty? Or are you just a student?
>I am and always will be a student. One *never* ceases being a student
>before nature.
Nice, but evasive.
As for the other part, just consider me as sort of a
>third-string benchwarmer of no particular atheletic genius, but a good
>understanding of the game.
The propaganda game. If you think science is a game, then
you are indeed a careerist rather than a professional.
Or don't. I could care less. I have
>already expressed my opinion that a PhD and/or faculty status is no
>guarantee of knowledge, quality of thought,
If that were your opinion, you wouldn't be jeering at me so
much for daring to take issue with you and Myers, nor
insisting that I assent to something you are unable
to document [see above] just on your say-so.
No, Hershey, you are banking on most people regarding you
as a professional biologist and taking your word on issues
where we differ. Otherwise you wouldn't be lying so much
about me, day in and day out, hardly caring whether you
make mistakes in biology because you can always jeer at
me for my past mistakes.
or civility, and I think you
>are an object lesson of the wisdom of that stance.
No, you think that since I am a mathematician rather than
a professional biologist, my opinions on embryology count
for nothing even though I've demonstrated more competence
here on Usenet than you have.
As I was saying earlier:
>> >> And you two take the tack that I am ignorant of the most
>> >> basic embryology through my failure to cave in and agree that
>> >> the LATEST texts now have the gospel truth.
>> >>
>> >My position is now and always has been that you would be just as
>> >ignorant of basic embryology if the LATEST texts were wrong.
See? You have done nothing worthy of note in the way of
demonstrating my ignorance except to (1) indulge in
dozens of repetitions of the same misrepresentations
of where I stand and (2) to keep insisting that I
agree with your undocumented claim just on your say-so.
In other words, you think I am ignorant because I disagree
with you on things you can't prove, and because my Ph.D.
is not in biology. At least, the preponderance of evidence
points to that, and I'd like to see you even try and reason
otherwise. [Note: I said "reason" not "argue". Dost understand
the difference, knave?]
[deletia of things to be dealt with on original thread]
>> > You seem
>> >to be arguing for a new definition of an old term, endoderm,
>>
>> I haven't done that in about two months now, and the
>> Peter Principles are proof of that.
>Which replaces that definition with guesswork and implies that almost
>anything could be called endoderm (maybe this, maybe that).
There you go again with your atrocious false dichotomy.
Peter Nyikos -- standard disclaimer --
Peter Nyikos
This is my second and final followup to a post in which Hershey
used an incredibly egregious fallacy of False Dichotomy. I
exposed that on the thread, "Fallout from the embryology threads, Part 2",
and now I deal with the tiny bit of his post that is on-topic
for *this* thread.
howard hershey <hers...@indiana.edu> writes:
>Peter Nyikos wrote:
>>
>> howard hershey <hers...@indiana.edu> writes:
>>
>> >Peter Nyikos wrote:
>> >>
>> >> howard hershey <hers...@indiana.edu> writes:
>> >>
>> >> >Peter Nyikos wrote:
>> >> >> And we need to use anatomical insight and fossil evidence too.
>> >> >> The fact remains that traditional systematists, vertebrate
>> >> >> paleontologists AND cladists have agreed,
>> >> >> all through this century (with a few minor exceptions of course)
>> >> >> that mammals branched off before squamates.
>>
>> >Is this consensus based on overwhelming *evidence* (as you claim) or on
>> >a consensus based on the *current weight* of evidence. There is a
>> >difference.
>>
>> The former.
>So.... Present it. And the timing of the divergences, which is the
>point most relevant to the sequencing data.
Timing has to be couched in terms of geological periods, since
dating on those differs. By the way, if you read the Fushitani
et.al. paper you would know that their theory does NOT make
use of "biological clock" models of gene change.
Anyway, the bottom line is that I have never seen a book
or paper on paleontology that put the divergence between
birds and lizards earlier than the Permian, nor one
that put the one between birds and mammals later than
the Pennsylvanian. Yes, these are adjacent periods,
but usually there is a comfortable margin in any given
book or paper. For instance, a diagram in the paper by
Michael Benton in [1] puts the divergence between
birds and mammals in the LOWER MISSISIPPIAN, while that
between birds and lizards goes in the lower Permian.
Carroll's text [2] agrees with the latter but puts
the former divergence in the *lower* Pennsylvanian,
and that's where most paleontologists today put it.
[1] _Origins of the Higher Groups of Tetrapods: Controversy and Consensus_,
ed. by Hans-Peter Schultze and Linda Trueb, co. 1991, Cornell
University Press, at p. 328.
[2] Robert H. Carroll, _Vertebrate Paleontology and Evolution_,
Published in 1988 by W. H. Freeman and Co., New York.
>> >> >Nor would it represent the first time that scientists have been shown to
>> >> >be wrong when new evidence presented itself. That a consensus had been
>> >> >reached on the basis of old data does not make the consensus immune from
>> >> >change in the light of new evidence.
>> >>
>> >> Put that in your posts on embryology and smoke it.
>>
>> >And what, pray tell, is the *new* evidence you are presenting?
>>
>> I'm talking about the new evidence Myers was presenting on
>> mice, which you've been going on along with.
>And does this new evidence support *your* viewpoint?
It is essentially irrelevant to it, as I've been explaining. It does
nothing to alleviate the lack of consensus on how the HUMAN
amnion forms. Yet Myers was quite dogmatic in falsely claiming
that it outdated statements by Keith L. Moore on how the human
amnion is formed.
Peter Nyikos -- standard disclaimer --
Wade Hines
Peter Nyikos <nyi...@math.sc.edu> writes:
>>In article <34DFD98F...@ixl.net>, Wade Hines <da...@ixl.net> wrote:
Many insults, accusations, revisions and translations deleted.
>Now it's Hines's turn to pour on the dissimulation:
>>> I know that heme is rather a basic aspect of hemoglobin.
>>> I know that people who argue about molecular phylogenies ought to know
>>> about the nature of systematic "errors" in the molecular clock.
>Indeed, this whole thread began precisely because there ARE such
>errors, including errors that make birds look like they are
>more closely related to turtles than to crocodilians, and more
>closely related to mammals than to lizards. And the substantive
>issue in this thread is nothing more or less than the question
>of whether the results of molecular sequencing are "congruent" to the fossil
>record. These two examples show it is not.
If I contort my hand the right way in front of the slide
projector I cast a shadow like a dogs head. This doesn't mean
my hand is homologous to the head of a dog.
If you don't understand what a protein does and how it works
you ought to be careful about looking at sequences and saying
much about them. As Nyikos didn't know what heme was, it's a
fair guess he doesn't understand much about the function of
hemoglobin and what factors, such as mudualtion of O2 affinity
through pH, would be expected to work against simplistic
clock assumptions. It seems he is too blind to even get a
glimpse of the cliff he keeps stepping over. ASCII allignments
of sequences is not the point Peter.
>>> This means knowing something about function. For instance,
>>> those residue which coordinate the heme group are not
>>> likely to be flopping back and forth while those which
>>> sit in a loop have somewhat greater freedom.
>All irrelevant to the main issue, which I've stated in the
>preceding paragraph. Hines is indulging in a blatant
You may not understand the relevance but believe it or not,
that doesn't make it irrelevant. That's always been so hard
for you to understand, that things you don't understand
might well be important.
>fallacy of *argumentum ad ignorantiam* in pretending otherwise.
>>> Sequences aren't just strings
>>> of letters. I've said this to Peter before and he got offended.
>Because Hines was indulging in a Phantom Error Correction Scam, probably:
>pretending I don't know that sequences are more than just lists
>of letters, and that some sites are much more likely to be
>conserved than others.
It goes way beyond that Peter.
>>I suspect either of us could say "Good morning!" to Peter, and he would
>>get offended.
>Only if it was evening. ;-)
And it's always evening somewhere.
Peter Nyikos
howard hershey <hers...@indiana.edu> writes:
>Peter Nyikos wrote:
>>
>> howard hershey <hers...@indiana.edu> writes:
>>
>> >Peter Nyikos wrote:
[irrelevant argument about hemes deleted]
>> >> On the other hand, Moran took my PARTIAL listing of reptiles
>>
>> >Just by chance, I printed out a copy of one of the earlier discussions,
>> >which shows your exact quote to read:
>>
>> > This "discovery" is still many years in the future. In the
>> > meantime, we have anomalies like the various kinds of hemoglobin
>> > ^^^^^^^^^^^^^
>> > all agreeing that mammals are more closely related to birds
>> > ^^^
>> > than birds are to lizards, snakes, or turtles, which is
>> > falsified by the fossil evidence.
>> > ^^^^^^^^^
>>
>> Right. Are you under the delusion that crocodilians are listed?
>Nope, and the failure to discuss other groups of reptiles which birds
>might be more closely related to than mammals
I discussed them in timely fashion, and Moran continued his
below-35-IQ simulation about me talking about reptiles, period.
does give the misleading
>impression, if not the literal statement, that there were no such group
>of reptiles to which birds are more closely linked than they are to
>mammals. Whether the *partial* listing was meant to give that
>misleading impression intentionally is anyone's guess (although *you*
>obviously know).
You are dissembling, beyond a reasonable doubt. With my demonstrated
knowledge of paleontology it would be unthinkable for me to
be leaving crocodilians out unless I MEANT to leave them out.
>> Here is what I say Larry did:
>>
>> >> to jump to the conclusion that I was saying birds are closer
>> >> to mammals than they are to ALL reptiles,
>>
>> >Larry replied:
>> > I pointed out that Peter's statement was not correct.
>> > The various kinds of hemoglobin do not all agree that
>> > ^^^^^^^^^^^^^ ^^^
>> > mammals are more closely related to birds than birds
>> > are to reptiles.
>> > ^^^^^^^^
>>
>> In other words, since I left crocodilians out, Larry is
>> either NOT disagreeing with me (if he means "all reptiles")
>> or saying something false (if he means "some reptiles").
You had no comment to this, and it doesn't take a rocket
scientist to figure out why not.
>> >> while taking
>> >> the Fushitani et. al. statement "birds form a sister
>> >> group with other reptiles but not with mammals" to mean
>> >> what the authors implicitly intended it to mean, namely
>> >> that the alpha globins showed birds form a sister group
>> >> with SOME reptiles (Sphenodon and maybe turtles
>>
>> >Even aside from the fact that your original statement, by using the
>> >ambiguous (in common useage) term 'lizard' which could, in context, be
>> >read as meaning all reptiles,
>>
>> You are lying, shamelessly lying. When it is used with turtles
>> and snakes as I did, it cannot mean that. And you are confusing common
>> usage of "lizard" with the latin suffix "saurus" which is a different
>> matter altogether.
Amazing. You didn't even have anything to say to this,
although it makes nonsense of what you wrote
up there about misunderstandings.
>> I do think Larry pointed out that the
>> >quote was in error because it was based on the more limited amount of
>> >older data.
>>
>> That was one of the few correct things he did.
>>
>> >Turtles are one of the groups you explicitly mentioned in your quote,
>> >Peter.
>>
>> Indeed, and Larry is not SO stupid as to think, despite this,
>> that "lizards" meant "reptiles."
Here too. Amazing.
>> > Sphenodon was not mentioned,
>>
>> Because the earlier studies did not mention it. Duh.
>>
>> >but you clearly think it to be a
>> >later divergence than 'lizards' and thus can be subsumed in that
>> >grouping.
>>
>> Wrong. I think no such thing.
>Ooops. I believe you mentioned the separation of pelycosaurs from all
>other reptile lineages to be somewhere in the order of 350 mybp and
>sphenodon about 100 my later (and, unless my recollection is wrong, from
>the 'squamata' rather than from the archosaur lineage).
It's irrelevant; the number in both cases is significantly
lower than for mammals.
You *were*
>somewhat unclear about when the squamata lineage came off. Perhaps you
>would like to clarify the relationships and times now?
Well, it is generally believed by paleontologists that Sphenodon and lizards
form a clade, but I wasn't counting on that because the evidence
seems not so strong as for the two main places where alpha
hemoglobin disagrees with the fossil record. (At least,
that's my amateur paleontologist-of-4-decades humble opinion.)
So they may have branched off from archosaurs together or may not, but
in any event the one that branched off earlier from them
still did so about 100 mya later than mammals did by most estimates.
As you
>mentioned, there is an overwhelming consensus based on the fossil
>record. But I have not heard the evidence on which this is based.
Start with the two books I used as references in my
post of a few minutes earlier. Chase down references. Enjoy.
[...]
>> Matt's statement, and Larry's statement, that it is in
>> agreement with the fossil record, is wrong; you will
>> not find a single book or paper on vertebrate paleontology
>> that agrees with it.
>>
>> >and that the distances separating the divergence points of the
>> >squamate, mammalian, and avian lineages are *so* large that only
>> >something highly unusual could give a false molecular phylogeny,
>>
>> I never said that. I find nothing unusual in false readings
>> of molecular phylogeny.
Cat got your tongue, Howard?
>> >> >Figured out what fetal hemoglobin is, yet?
[...]
>> >> In humans? The Fushitani et. al. study trumpeted
>> >> by Moran didn't touch it with a ten foot pole.
>> >>
>> >> Curious sidelight: they did give a table showing only one
>> >> alpha (adult) and one beta (ditto) having been detected in
>> >> mammals, although in a footnote they say that the number of
>> >> Hb components should be taken as minima. On the other hand,
>> >> two pages later they say:
>> >>
>> >> (1) Claimed that the results suggest embryonic and adult alpha globin genes
>> >> were "acquired by gene duplication of the ancestral gene before the
>> >> divergence of amniotes took place."
>> >>
>> >> (2) Made the following remark about crocodilians, which are
>> >> no more and no less amniotes than humans are:
>> >>
>> >> The embryonic alpha chanin of crocodilians may
>> >> exist, but it has not yet been found, or, alternatively,
>> >> it is possible that crocodilians have lost the
>> >> corresponding embryonic alpha globin gene.
>> >>
>> >> Apparently they assumed that the reader would draw the
>> >> obvious parallel with mammals, because they made no mention
>> >> of them at this juncture.
Either that, or it was a case of too many cooks spoiling the
broth.
>> >No comment, except to say that Peter should really do some reading of
>> >something other than 20 year old biochemistry textbooks. A recent
>> >review article on comparative molecular biology of the hemoglobins
>> >wouldn't hurt either.
>>
>> In other words, you have no substantive comment to make
>> and are just being your usual sadistic self.
>No, Peter. I am giving *you* the opportunity to show that the lack of
>knowledge displayed by not knowing that heme is not a peptide was an
>aberration. Your failure to take advantage of this opportunity to
>'strut your stuff' might be taken by those who do know as a further sign
>of limited comprehension on your part, based on the types of questions
>you are asking.
Only to someone pathetically ignorant of the issues,
and impressed by all the irrelevant stuff you throw into
post after post to strut *your* stuff on mostly elementary
things that were not a matter of discussion. Even Dan
Hughes caught onto that aspect of your BSing.
> But I am not responsible for what others think.
You are in part, by not admitting that your idiocy about
me not strutting my stuff is a bunch of misdirection.
Peter Nyikos -- standard disclaimer --
University of South Carolina
howard hershey
Peter Nyikos wrote:
>
> howard hershey <hers...@indiana.edu> writes:
>
> >Peter Nyikos wrote:
> >>
> >> howard hershey <hers...@indiana.edu> writes:
> >>
> >> >Peter Nyikos wrote:
>
> [irrelevant argument about hemes deleted]
>
> >> >> On the other hand, Moran took my PARTIAL listing of reptiles
> >>
> >> >Just by chance, I printed out a copy of one of the earlier discussions,
> >> >which shows your exact quote to read:
> >>
> >> > This "discovery" is still many years in the future. In the
> >> > meantime, we have anomalies like the various kinds of hemoglobin
> >> > ^^^^^^^^^^^^^
> >> > all agreeing that mammals are more closely related to birds
> >> > ^^^
> >> > than birds are to lizards, snakes, or turtles, which is
> >> > falsified by the fossil evidence.
> >> > ^^^^^^^^^
> >>
> >> Right. Are you under the delusion that crocodilians are listed?
>
> >Nope, and the failure to discuss other groups of reptiles which birds
> >might be more closely related to than mammals
>
> I discussed them in timely fashion, and Moran continued his
> below-35-IQ simulation about me talking about reptiles, period.
What this means is that Peter clarified what he meant when he was
prodded to do so by Larry. Peter qualified his statement (when prodded)
to the extent that he agreed that crocodiles are more closely related to
birds than birds are to mammals. That Sphenedon is more closely related
to birds than birds are to mammals. But, of course, turtles are also in
the group of current species that the alpha globin evidence indicates is
closer to birds than to mammals. And that *was* a group Peter
specifically mentioned which makes his statement, *as written*, false
and misleading, which is all that Larry pointed out. Besides, you only
have presented the current data for alpha globins (well, actually Larry
is the one who did this). And your statement requires that beta globins
also show the same pattern of "all agreeing that mammals are more
closely related to birds than birds are to (lizards and its derivative
snakes) and turtles (if you still want to hang on to this group as being
more closely related to mammals than to birds). You have presumably
asserted that this too must be true by your use of the term "the various
kinds of hemoglobin all agree.." but have not presented any supporting
evidence aside from a nearly decade old article. Has no data on
beta-globins been gathered since then? Perhaps you want to revise your
original statement to something like the following?: There is currently
a potential discrepancy between the fossil evidence (which *at present*
tends to indicate that the lineage of reptiles leading to current snakes
and lizards diverged from the lineage of reptiles that led to birds
*after* the divergence of the lineage of reptiles that led to mammals)
and the sequence data that we currently have for alpha globin (which
*ambiguously* may indicate that the lineage leading to mammals may have
occurred *after* the divergence of the lineage leading to current
lizards and snakes from a primitive stock and that the lineage that led
to birds (archosaurs) and the lineage that led to mammals had a more
recent common ancestor than did birds and lizards.
This restatement of your comment does several things. It clarifies what
the discrepancy (not anomaly) really is (a question about the nature of
the divergence points of the most ancestral members of the various
lineages in question). It does not *automatically* conclude that the
divergence points indicated by the *current* fossil evidence is "an
unalterable absolute truth" which supercedes all other evidence. It
points out that the data is and can be ambiguous (both fossil, molecular
phylogeny, and morphology of survivors of the lineages) and that this is
a case which will be eventually resolved by the cumulative weight of
data from all this sources (including sequencing data from other
molecules) rather than by any single bit of data. It points out the
tentativeness of the *current consensus*.
>
[snip]
> >>
> >> >Larry replied:
> >> > I pointed out that Peter's statement was not correct.
> >> > The various kinds of hemoglobin do not all agree that
> >> > ^^^^^^^^^^^^^ ^^^
> >> > mammals are more closely related to birds than birds
> >> > are to reptiles.
> >> > ^^^^^^^^
> >>
> >> In other words, since I left crocodilians out, Larry is
> >> either NOT disagreeing with me (if he means "all reptiles")
> >> or saying something false (if he means "some reptiles").
Rather, you included turtles.
>
[snip]
>
> >Ooops. I believe you mentioned the separation of pelycosaurs from all
> >other reptile lineages to be somewhere in the order of 350 mybp and
> >sphenodon about 100 my later (and, unless my recollection is wrong, from
> >the 'squamata' rather than from the archosaur lineage).
>
> It's irrelevant; the number in both cases is significantly
> lower than for mammals.
>
> You *were*
> >somewhat unclear about when the squamata lineage came off. Perhaps you
> >would like to clarify the relationships and times now?
>
> Well, it is generally believed by paleontologists that Sphenodon and lizards
> form a clade, but I wasn't counting on that because the evidence
> seems not so strong as for the two main places where alpha
> hemoglobin disagrees with the fossil record. (At least,
> that's my amateur paleontologist-of-4-decades humble opinion.)
> So they may have branched off from archosaurs together or may not, but
> in any event the one that branched off earlier from them
> still did so about 100 mya later than mammals did by most estimates.
And I would probably agree that the *current* fossil evidence *best*
supports the view that squamata diverged from the lineage that
eventually led to archosaurs after that parent lineage diverged from the
pelycosaurs. But stating that it was 100 my *between* these two events
is, I would hazard a guess, rather more tenuous and ambiguous (a new
fossil find could at any time reduce that time in half or less) than you
think. Such a statement would require that the fossil record of these
events be sufficiently complete to be sure that the time indicated
reflected the true timing of initial divergence rather than the oldest
known 'lizard-like' ancestor. That is one of the reasons for trying to
analyze these questions using different types of data (like molecular
sequences) with different types of problems in analysis. If these
different types of data largely agree (are congruent), even if not every
data point in either morphology, fossil evidence, or sequencing agrees,
we can reach a consensus. If there are discrepancies, that may require
*re-thinking* our previous consensus. Perhaps the fossil record is
incomplete and our assumption that the earliest currently known species
is, in fact, close to the branching point is mistaken. Perhaps there
are problems with using alpha globin for molecular sequencing.
Discrepancies are useful tests of our current consensus based on the
weight of the evidence.
But you seem to be implying that you have data that produces an
overwhelming consensus that the divergence points are at least 100
million years and that the record is well enough understood that it is
unlikely for this to be off by, say, one geological era.
>
> As you
> >mentioned, there is an overwhelming consensus based on the fossil
> >record. But I have not heard the evidence on which this is based.
>
> Start with the two books I used as references in my
> post of a few minutes earlier. Chase down references. Enjoy.
>
> [...]
>
> >> Matt's statement, and Larry's statement, that it is in
> >> agreement with the fossil record, is wrong; you will
> >> not find a single book or paper on vertebrate paleontology
> >> that agrees with it.
> >>
> >> >and that the distances separating the divergence points of the
> >> >squamate, mammalian, and avian lineages are *so* large that only
> >> >something highly unusual could give a false molecular phylogeny,
> >>
> >> I never said that. I find nothing unusual in false readings
> >> of molecular phylogeny.
And I also find nothing unusual in false understandings of lineage
divergence points based solely on the current (and incomplete) fossil
record and analyses of the morphology of current organisms (e.g. fish) -
in addition to false readings from molecular phylogeny.
[snip the rest, to be covered later]
howard hershey
Peter Nyikos wrote:
>
> howard hershey <hers...@indiana.edu> writes:
>
> >Peter Nyikos wrote:
> >>
> >> howard hershey <hers...@indiana.edu> writes:
> >>
> >> >Peter Nyikos wrote:
>
> [irrelevant argument about hemes deleted]
>
>
> [...]
> >> >> In humans? The Fushitani et. al. study trumpeted
> >> >> by Moran didn't touch it with a ten foot pole.
A study of alpha-globins (which is, of course, what they did) wouldn't.
However, someone with minimal knowledge of human (and mammalian)
hemoglobin would know this.
> >> >> Curious sidelight: they did give a table showing only one
> >> >> alpha (adult) and one beta (ditto) having been detected in
> >> >> mammals, although in a footnote they say that the number of
> >> >> Hb components should be taken as minima.
Yes. It should be taken as a minima. How many alpha genes are there in
humans? What is the variance in the number of alpha genes in
vertebrates?
> >> >>On the other hand,
> >> >> two pages later they say:
> >> >>
> >> >> (1) Claimed that the results suggest embryonic and adult alpha globin genes
> >> >> were "acquired by gene duplication of the ancestral gene before the
> >> >> divergence of amniotes took place."
Yes. Why do you find this problematic?
> >> >> (2) Made the following remark about crocodilians, which are
> >> >> no more and no less amniotes than humans are:
> >> >>
> >> >> The embryonic alpha chanin of crocodilians may
> >> >> exist, but it has not yet been found, or, alternatively,
> >> >> it is possible that crocodilians have lost the
> >> >> corresponding embryonic alpha globin gene.
> >> >>
> >> >> Apparently they assumed that the reader would draw the
> >> >> obvious parallel with mammals, because they made no mention
> >> >> of them at this juncture.
What parallels do you *think* they want the reader to make, since they
didn't actually make these parallels themselves? That it is possible
for independent loss of genes to occur?
> Either that, or it was a case of too many cooks spoiling the
> broth.
>
> >> >No comment, except to say that Peter should really do some reading of
> >> >something other than 20 year old biochemistry textbooks. A recent
> >> >review article on comparative molecular biology of the hemoglobins
> >> >wouldn't hurt either.
> >>
> >> In other words, you have no substantive comment to make
> >> and are just being your usual sadistic self.
>
> >No, Peter. I am giving *you* the opportunity to show that the lack of
> >knowledge displayed by not knowing that heme is not a peptide was an
> >aberration. Your failure to take advantage of this opportunity to
> >'strut your stuff' might be taken by those who do know as a further sign
> >of limited comprehension on your part, based on the types of questions
> >you are asking.
Don't you think that knowing a little bit about the structure of the
family of genes involved in hemoglobin might be somewhat important in
correctly interpreting an analysis of the sequences? It might even rank
right up there with knowing what heme is and why it is a poor candidate
for sequencing.
>
> Only to someone pathetically ignorant of the issues,
> and impressed by all the irrelevant stuff you throw into
> post after post to strut *your* stuff on mostly elementary
> things that were not a matter of discussion. Even Dan
> Hughes caught onto that aspect of your BSing.
Are you comparing yourself to someone who repeatedly asserts an ability
to calculate *absolute* fitnesses (independent of environmental
conditions) without ever telling us how to actually do so? I agree that
there is some similarity.
>
> > But I am not responsible for what others think.
>
> You are in part, by not admitting that your idiocy about
> me not strutting my stuff is a bunch of misdirection.
I am merely trying to decide whether you know enough about the
proteins/genes you are analyzing the sequence of to say anything
relevant or whether you are merely blindly doing math on sequences.
howard hershey
Peter Nyikos wrote:
>
[snip]
>
> howard hershey <hers...@indiana.edu> writes:
>
> >Peter Nyikos wrote:
> >>
> >> howard hershey <hers...@indiana.edu> writes:
> >>
> >> >Peter Nyikos wrote:
> >> >>
> >> >> howard hershey <hers...@indiana.edu> writes:
>
> >> >>
> >> >> >Peter Nyikos wrote:
>
> >> >> >> And we need to use anatomical insight and fossil evidence too.
> >> >> >> The fact remains that traditional systematists, vertebrate
> >> >> >> paleontologists AND cladists have agreed,
> >> >> >> all through this century (with a few minor exceptions of course)
> >> >> >> that mammals branched off before squamates.
> >>
> >> >Is this consensus based on overwhelming *evidence* (as you claim) or on
> >> >a consensus based on the *current weight* of evidence. There is a
> >> >difference.
> >>
> >> The former.
>
> >So.... Present it. And the timing of the divergences, which is the
> >point most relevant to the sequencing data.
>
> dating on those differs.
earliest currently *known* member of the lineage that led to current
lizards, the earliest currently known member of the the lineage that led
to current mammals, the earliest currently known member of the lineage
that led to current birds? I am truely surprised.
> By the way, if you read the Fushitani
> et.al. paper you would know that their theory does NOT make
> use of "biological clock" models of gene change.
All sequencing analyses make use of features and assumptions of the
"biological clock" models of gene change, especially the idea that most
of the observed changes are effectively neutral. Not all of them try to
use the sequences to determine actual points in time and that is not
what I expected. But the expected results would differ significantly if
the time point of separation of the lineage that led to birds from the
lineage that led to lizards (and snakes) was close to the time point of
separation of both from the lineage that led to mammals or relatively
far apart. These time points would be estimates based on the earliest
currently known member of these lineages (with more ambiguity on the
older side than on the more recent side, of course).
>
> Anyway, the bottom line is that I have never seen a book
> or paper on paleontology that put the divergence between
> birds and lizards earlier than the Permian, nor one
> that put the one between birds and mammals later than
> the Pennsylvanian. Yes, these are adjacent periods,
> but usually there is a comfortable margin in any given
> book or paper. For instance, a diagram in the paper by
> Michael Benton in [1] puts the divergence between
> birds and mammals in the LOWER MISSISIPPIAN, while that
> between birds and lizards goes in the lower Permian.
> Carroll's text [2] agrees with the latter but puts
> the former divergence in the *lower* Pennsylvanian,
> and that's where most paleontologists today put it.
That's your overwhelming evidence of clear-cut uncontrovertible
consensus? Two diagrams in books that even disagree with each other and
place the divergence in adjacent gelogical eras? I am not saying that
the order of divergence they give is wrong, only that it is clear that
the fossil evidence is not a completely unambiguous set of data on the
older end and one should not treat it as being the only possible true
result against which all other data must either agree or be totally and
irretrevibly false and misleading. At least, you have yet to convince
me that this is the case with this particular set of divergences. And I
actually could be convinced.
>
> [1] _Origins of the Higher Groups of Tetrapods: Controversy and Consensus_,
> ed. by Hans-Peter Schultze and Linda Trueb, co. 1991, Cornell
> University Press, at p. 328.
>
> [2] Robert H. Carroll, _Vertebrate Paleontology and Evolution_,
> Published in 1988 by W. H. Freeman and Co., New York.
>
> >> >> >Nor would it represent the first time that scientists have been shown to
> >> >> >be wrong when new evidence presented itself. That a consensus had been
> >> >> >reached on the basis of old data does not make the consensus immune from
> >> >> >change in the light of new evidence.
[snip]
Peter Nyikos
For some reason, my posts to this thread haven't been showing
up lately in my newsreader. I'll check Deja News and see whether
I can figure out what's been posted and what hasn't. If you
have any posts to this thread to which you haven't seen a reply
to from me, feel free to repost them.
howard hershey <hers...@indiana.edu> writes:
>Peter Nyikos wrote:
>>
>> howard hershey <hers...@indiana.edu> writes:
>>
>> >Peter Nyikos wrote:
>> >>
>> >> howard hershey <hers...@indiana.edu> writes:
>> >>
>> >> >Peter Nyikos wrote:
>>
>> [irrelevant argument about hemes deleted]
>>
>>
>> >> >> >Figured out what fetal hemoglobin is, yet?
>> [...]
>> >> >> In humans? The Fushitani et. al. study trumpeted
>> >> >> by Moran didn't touch it with a ten foot pole.
>A study of alpha-globins (which is, of course, what they did) wouldn't.
They also wrote quite a bit about beta-globins, but did not
do a phylogenetic analysis of them.
However, someone who actually looked at the paper would know this.
And someone who read the paper might even wonder why they didn't
include beta globins in their study.
>> >> >> Curious sidelight: they did give a table showing only one
>> >> >> alpha (adult) and one beta (ditto) having been detected in
>> >> >> mammals, although in a footnote they say that the number of
>> >> >> Hb components should be taken as minima.
>Yes. It should be taken as a minima. How many alpha genes are there in
>humans? What is the variance in the number of alpha genes in
>vertebrates?
Ask Fushitani et.al. They didn't get into that problem in the
paper, except to mention two alpha globins that have been
found in some amniotes but not others.
>> >> >>On the other hand,
>> >> >> two pages later they say:
>> >> >>
>> >> >> (1) Claimed that the results suggest embryonic and adult alpha globin genes
>> >> >> were "acquired by gene duplication of the ancestral gene before the
>> >> >> divergence of amniotes took place."
>Yes. Why do you find this problematic?
"before the divergence of amniotes" is the curious part. Not one
single mammal has been found (to their knowledge, anyway) to
have more than one alpha globin.
>> >> >> (2) Made the following remark about crocodilians, which are
>> >> >> no more and no less amniotes than humans are:
>> >> >>
>> >> >> The embryonic alpha chain of crocodilians may
>> >> >> exist, but it has not yet been found, or, alternatively,
>> >> >> it is possible that crocodilians have lost the
>> >> >> corresponding embryonic alpha globin gene.
>> >> >>
>> >> >> Apparently they assumed that the reader would draw the
>> >> >> obvious parallel with mammals, because they made no mention
>> >> >> of them at this juncture.
>What parallels do you *think* they want the reader to make, since they
>didn't actually make these parallels themselves? That it is possible
>for independent loss of genes to occur?
Perhaps. But one would think they would have written "mammals or
crocodilians" in both places. As it is, the reader is left wondering
whether the failure to find an embryonic alpha in *any* mammals
might be due to a colossal oversight on the part of biochemists,
rather than due to the loss of the gene. After all, what's the
ratio of people studying the hemoglobins of one mammal or another
to the ratio studying the hemoglobins of crocodilians?
>> Either that, or it was a case of too many cooks spoiling the
>> broth.
I'm inclined towards this view. Different authors responsible
for writing different parts of the paper.
>> >> >No comment, except to say that Peter should really do some reading of
>> >> >something other than 20 year old biochemistry textbooks. A recent
>> >> >review article on comparative molecular biology of the hemoglobins
>> >> >wouldn't hurt either.
>> >>
>> >> In other words, you have no substantive comment to make
>> >> and are just being your usual sadistic self.
>>
>> >No, Peter. I am giving *you* the opportunity to show that the lack of
>> >knowledge displayed by not knowing that heme is not a peptide was an
>> >aberration. Your failure to take advantage of this opportunity to
>> >'strut your stuff' might be taken by those who do know as a further sign
>> >of limited comprehension on your part, based on the types of questions
>> >you are asking.
>Don't you think that knowing a little bit about the structure of the
>family of genes involved in hemoglobin might be somewhat important in
>correctly interpreting an analysis of the sequences?
Alas, one would have to write to the authors themselves. Too
little raw data appears in the paper for a reader to figure it
out for themselves. It's not at all like the complete listing
of amino sequences for the 14 serine proteases in the
Doolittle-Feng article. Now there's something a specialist
could really sink his teeth into--but I'm not a specialist
and neither is anyone else here except possibly Hines, Svetlov,
Moran, and Thomas.
[stupid wisecrack deleted]
>> Only to someone pathetically ignorant of the issues,
>> and impressed by all the irrelevant stuff you throw into
>> post after post to strut *your* stuff on mostly elementary
>> things that were not a matter of discussion. Even Dan
>> Hughes caught onto that aspect of your BSing.
>Are you comparing yourself to someone who repeatedly asserts an ability
>to calculate *absolute* fitnesses (independent of environmental
>conditions) without ever telling us how to actually do so?
If even HE can see you are indulging in irrelevant
window dressing, there must be something to it, eh?
[stupid wisecrack based on the equivocation inherent in "compare"
deleted]
>> > But I am not responsible for what others think.
>>
>> You are in part, by not admitting that your idiocy about
>> me not strutting my stuff is a bunch of misdirection.
>I am merely trying to decide whether you know enough about the
>proteins/genes you are analyzing the sequence of to say anything
>relevant
Then you are going about it the wrong way. First read
the paper to figure out just what kind of knowledge
is really relevant to it.
> or whether you are merely blindly doing math on sequences.
Dead giveaway that you haven't read the paper yet.
Peter Nyikos -- standard disclaimer --
howard hershey
Peter Nyikos wrote:
>
[snip]
> >Perhaps your inability to post a legitimate definition of 'endoderm'
>
> You haven't posted a legitimate definition either, nor have
> you posted one of "homologous", so I am one up on you.
>
> Here, I'll post a NECESSARY condition (though not a sufficient
> one, not by a long shot) for something to be called
> *embryonic* ectoderm: it originates in epiblastic cells.
It is more important *where* it is at the two and/or three layered stage
of the embryo. First you need to know when this stage is and to define
its layers.
>
> And here's a SUFFICIENT condition (though not necessary, not
> by a long shot) for something to be called "endoderm": it originates
> in hypoblastic cells.
Again, it is more important *where* it is at the two and/or three
layered stage of the embryo.
>
> To try and make me "define" something which is so much an arbitrary
> convention as to cause Arey to put `ectoderm' in inverted
> commas when applied to the amnion, suggests that you are a mediocre
> scientist who looks upon science as a mere career and propaganda
> to be his profession.
It suggests to me that you are a mathematician without a clue and with a
real tin ear when it comes to reading human embryology textbooks for med
students.
>
[snip]
>
> The thing you have never been able to document is that the
> amnion would be called "ectoderm" even if it is formed
> by delamination from the cytotrophoblast.
Is all that tissue on the 'inside' or 'gut side' of the two and three
layered embryo or is it on the 'outside' or epidermal side of same?
>
[snip Peter playing the 'what kind of a biologist are you' authority
game]
> Or don't. I could care less. I have
> >already expressed my opinion that a PhD and/or faculty status is no
> >guarantee of knowledge, quality of thought,
>
> If that were your opinion, you wouldn't be jeering at me so
> much for daring to take issue with you and Myers, nor
> insisting that I assent to something you are unable
> to document [see above] just on your say-so.
>
> No, Hershey, you are banking on most people regarding you
> as a professional biologist and taking your word on issues
> where we differ.
I certainly hope not.
> Otherwise you wouldn't be lying so much
> about me, day in and day out, hardly caring whether you
> make mistakes in biology because you can always jeer at
> me for my past mistakes.
>
> or civility, and I think you
> >are an object lesson of the wisdom of that stance.
>
> No, you think that since I am a mathematician rather than
> a professional biologist, my opinions on embryology count
> for nothing even though I've demonstrated more competence
> here on Usenet than you have.
I judged the quality and value of your opinions on embryology based
solely on the data presented to me here on the Usenet compared mostly to
the knowledge in my head (with an occassional peek at a book). I found
it wanting. That they were the opinions of a rank amateur in biology
who got his information from a few readings of text books didn't, by
itself, matter to me one bit. Even ranker amateurs than you can get
things right (or wrong) by sheer guesswork without even touching a
textbook. If you had gotten it right I would have agreed with you.
That your opinions were often misreadings, misunderstandings, strange
interpretations, and overgeneralizations of that literature, OTOH, did
matter to me.
I am perfectly happy to present my views and let readers judge the
competence of my posts as they will; they can always do the reading to
check up on either me or thee. And if I am wrong (certainly not
impossible) I don't mind being corrected, unlike some individuals who
take it rather personally. And there are people posting here with
enough experience in embryology or biochemistry or geology or whatever
to correct any major (and even some minor) mistakes I make. That one of
those experts (Paul) has only rarely disagreed with me is comforting in
that it indicates I am getting at least the basics basically right, but
he is certainly willing to disagree if he thinks I am wrong (and he has
done so) and I am certainly willing to disagree with him if I think he
is wrong. OTOH, we *both* think that a lot of what *you* have been
posting is just plain wrong-headed and off-the-wall and bizarre. Again,
the congruence between Paul and me is comforting *because* neither of us
is in a conspiracy to make you look silly or to claim your ideas to be
nonsense. You seem to be doing a good enough job of that all by
yourself.
>
[snip tedious rest]
howard hershey
howard hershey wrote:
>
> Peter Nyikos wrote:
> >
> [snip]
> > howard hershey <hers...@indiana.edu> writes:
> >
> > >Peter Nyikos wrote:
> > >>
>
> > >Perhaps your inability to post a legitimate definition of 'endoderm'
> >
> > You haven't posted a legitimate definition either, nor have
> > you posted one of "homologous", so I am one up on you.
> >
> > Here, I'll post a NECESSARY condition (though not a sufficient
> > one, not by a long shot) for something to be called
> > *embryonic* ectoderm: it originates in epiblastic cells.
>
> It is more important *where* it is at the two and/or three layered stage
> of the embryo. First you need to know when this stage is and to define
> its layers.
> >
> > And here's a SUFFICIENT condition (though not necessary, not
> > by a long shot) for something to be called "endoderm": it originates
> > in hypoblastic cells.
>
> Again, it is more important *where* it is at the two and/or three
> layered stage of the embryo.
That is, of course, most true in vertebrates with regulative
determination. In ascidians, nematodes, and molluscs, the endoderm and
ectoderm are determined to a greater extent by oocyte morphogens. But I
do think Peter was concerned with the human embryo, which is quite
regulative.
> >
[snip rest]
> >
> [snip tedious rest]
howard hershey
Peter Nyikos wrote:
>
[snip]
> howard hershey <hers...@indiana.edu> writes:
>
> >Peter Nyikos wrote:
> >>
> >> howard hershey <hers...@indiana.edu> writes:
> >>
> >> >Peter Nyikos wrote:
> >> >>
> >> >> howard hershey <hers...@indiana.edu> writes:
> >> >>
> >> >> >Peter Nyikos wrote:
> >>
> >> [irrelevant argument about hemes deleted]
Namely that Peter asked a question which clearly demonstrated that he
had not a clue what the chemical nature of heme was. Given that level
of 'knowledge' as his knowledge base, one might reasonably not consider
Peter as a highly reliable source when it comes to the nature of
hemoglobin, an interpretation further strengthened by the questions he
asks (and the ones he doesn't answer) below. I was not asking whether
these topics were covered by Fushitani, et. al. in their narrowly
focused research paper (not a review article) where their addition to
the literature was a couple of new alpha sequences. Peter seems to
think that every research article (intended for other professionals)
should also review the basics in such simple and complete detail that
rank amateurs can jump in at the professional level. That is why I
asked Peter some pretty simple and basic questions about hemoglobin that
most molecular biologists (not even experts in sequencing and
hemoglobin) would know the answer to. They would have learned it from
introductory undergrad and/or grad classes in molecular biology and this
information can be found in most recent (since the mid 1980s at least)
textbooks and are regularly reveiwed and updated in the scientific
literature. Peter's reply is basically that he couldn't find the
answers in the Fushitani paper. I wouldn't expect it there. It is
simply the kind of basic background information I would expect one to
*already have* or *be willing to learn* if one is making an absolutist
assertion of conflict between sequencing analysis of these proteins and
the ONE TRUE divergence pathway indicated by the fossil record (I
presume), a claim in a nearly decade old article in a book about
hemoglobin that Peter seems to think has remained unchanged with no
significant added data since then.
> >>
> >> >> >> >Figured out what fetal hemoglobin is, yet?
> >> [...]
> >> >> >> In humans? The Fushitani et. al. study trumpeted
> >> >> >> by Moran didn't touch it with a ten foot pole.
>
> >A study of alpha-globins (which is, of course, what they did) wouldn't.
>
> They also wrote quite a bit about beta-globins, but did not
> do a phylogenetic analysis of them.
Why would they? This is a research paper, not a review of the
literature. I would imagine that a recent review of the literature will
be one of the early citations in the article. It typically is in
research articles.
>
> However, someone who actually looked at the paper would know this.
>
> And someone who read the paper might even wonder why they didn't
> include beta globins in their study.
>
> >> >> >> Curious sidelight: they did give a table showing only one
> >> >> >> alpha (adult) and one beta (ditto) having been detected in
> >> >> >> mammals, although in a footnote they say that the number of
> >> >> >> Hb components should be taken as minima.
>
> >Yes. It should be taken as a minima. How many alpha genes are there in
> >humans? What is the variance in the number of alpha genes in
> >vertebrates?
>
> Ask Fushitani et.al. They didn't get into that problem in the
> paper, except to mention two alpha globins that have been
> found in some amniotes but not others.
>
> >> >> >>On the other hand,
> >> >> >> two pages later they say:
> >> >> >>
> >> >> >> (1) Claimed that the results suggest embryonic and adult alpha globin genes
> >> >> >> were "acquired by gene duplication of the ancestral gene before the
> >> >> >> divergence of amniotes took place."
>
> >Yes. Why do you find this problematic?
>
> "before the divergence of amniotes" is the curious part. Not one
> single mammal has been found (to their knowledge, anyway) to
> have more than one alpha globin.
Was that protein or gene or adult protein or adult gene?
What do you call the human zeta globin gene (on chromosome 16), derived
from beta or alpha? How many alpha globin *genes* (on chromosome 16) do
humans have?
>
> >> >> >> (2) Made the following remark about crocodilians, which are
> >> >> >> no more and no less amniotes than humans are:
> >> >> >>
> >> >> >> The embryonic alpha chain of crocodilians may
> >> >> >> exist, but it has not yet been found, or, alternatively,
> >> >> >> it is possible that crocodilians have lost the
> >> >> >> corresponding embryonic alpha globin gene.
> >> >> >>
> >> >> >> Apparently they assumed that the reader would draw the
> >> >> >> obvious parallel with mammals, because they made no mention
> >> >> >> of them at this juncture.
>
> >What parallels do you *think* they want the reader to make, since they
> >didn't actually make these parallels themselves? That it is possible
> >for independent loss of genes to occur?
>
> Perhaps. But one would think they would have written "mammals or
> crocodilians" in both places.
Which would be misleading, since it is just possible that it may not be
true. But you can discuss the nature of embryonic and adult alpha and
beta globins at this point, to demonstrate your knowledge of at least
the situation in humans.
> As it is, the reader is left wondering
> whether the failure to find an embryonic alpha in *any* mammals
> might be due to a colossal oversight on the part of biochemists,
> rather than due to the loss of the gene. After all, what's the
> ratio of people studying the hemoglobins of one mammal or another
> to the ratio studying the hemoglobins of crocodilians?
>
> >> Either that, or it was a case of too many cooks spoiling the
> >> broth.
>
> I'm inclined towards this view. Different authors responsible
> for writing different parts of the paper.
I guess I will have to read the article (and perhaps a recent review or
two) myself to be sure. I don't have much faith in your ability to
comprehend what you read, since you have been having some difficulty
with reading comprehension lately. And given your demonstrated (or not)
knowledge base wrt to the nature of heme or even human alpha globins and
their genes, the odds of *some* problem in reading comprehension of this
article is almost a certainty.
>
> >> >> >No comment, except to say that Peter should really do some reading of
> >> >> >something other than 20 year old biochemistry textbooks. A recent
> >> >> >review article on comparative molecular biology of the hemoglobins
> >> >> >wouldn't hurt either.
> >> >>
> >> >> In other words, you have no substantive comment to make
> >> >> and are just being your usual sadistic self.
> >>
> >> >No, Peter. I am giving *you* the opportunity to show that the lack of
> >> >knowledge displayed by not knowing that heme is not a peptide was an
> >> >aberration. Your failure to take advantage of this opportunity to
> >> >'strut your stuff' might be taken by those who do know as a further sign
> >> >of limited comprehension on your part, based on the types of questions
> >> >you are asking.
>
> >Don't you think that knowing a little bit about the structure of the
> >family of genes involved in hemoglobin might be somewhat important in
> >correctly interpreting an analysis of the sequences?
>
> Alas, one would have to write to the authors themselves. Too
> little raw data appears in the paper for a reader to figure it
> out for themselves. It's not at all like the complete listing
> of amino sequences for the 14 serine proteases in the
> Doolittle-Feng article. Now there's something a specialist
> could really sink his teeth into--but I'm not a specialist
> and neither is anyone else here except possibly Hines, Svetlov,
> Moran, and Thomas.
I think you need to remove Thomas from that list, if you are referring
to Julie Thomas. I have seen no evidence of her being able to analyze
sequence data. But, as I am sure you know, all the sequences in these
papers are available on line from the usual data banks. If you wish to
reanalyze them, it is a relatively simple task to get the complete
protein or DNA sequences in a computer useable form.
>
[snip]
howard hershey
Did they look at human genes? BTW, there *is* reason not to be overly
concerned (at the protein level) about the fact that there might be more
than one gene encoding adult human alpha (I am not saying there is. I
haven't read THE paper, after all, so how could *I*, mediocre biologist
- but superior sadist - that I am, possibly know more about hemoglobin
than Peter. Aside from knowing that you can't sequence heme, of course.
:-)). There can't possibly be a human embryonic alpha globin. Peter
says so, after all. :-) *And* we haven't even *begun* to discuss the
beta globins. I wonder what Peter *knows* about those genes that ain't
so. So far we have a fairly consistent track record.
> >> >> >> (2) Made the following remark about crocodilians, which are
> >> >> >> no more and no less amniotes than humans are:
> >> >> >>
> >> >> >> The embryonic alpha chain of crocodilians may
> >> >> >> exist, but it has not yet been found, or, alternatively,
> >> >> >> it is possible that crocodilians have lost the
> >> >> >> corresponding embryonic alpha globin gene.
> >> >> >>
> >> >> >> Apparently they assumed that the reader would draw the
> >> >> >> obvious parallel with mammals, because they made no mention
> >> >> >> of them at this juncture.
>
[snip]
>
> >> >> >No comment, except to say that Peter should really do some reading of
> >> >> >something other than 20 year old biochemistry textbooks. A recent
> >> >> >review article on comparative molecular biology of the hemoglobins
> >> >> >wouldn't hurt either.
> >> >>
> >> >> In other words, you have no substantive comment to make
> >> >> and are just being your usual sadistic self.
Yep. And you are falling for it, hook, line, and sinker. Despite my
rather broad hints that a little review of the literature might be
helpful before you start writing (It certainly would have been a bit
less embarrassing).
> >> >No, Peter. I am giving *you* the opportunity to show that the lack of
> >> >knowledge displayed by not knowing that heme is not a peptide was an
> >> >aberration. Your failure to take advantage of this opportunity to
> >> >'strut your stuff' might be taken by those who do know as a further sign
> >> >of limited comprehension on your part, based on the types of questions
> >> >you are asking.
>
> >Don't you think that knowing a little bit about the structure of the
> >family of genes involved in hemoglobin might be somewhat important in
> >correctly interpreting an analysis of the sequences?
>
> Alas, one would have to write to the authors themselves. Too
> little raw data appears in the paper for a reader to figure it
> out for themselves. It's not at all like the complete listing
> of amino sequences for the 14 serine proteases in the
> Doolittle-Feng article. Now there's something a specialist
> could really sink his teeth into--but I'm not a specialist
> and neither is anyone else here except possibly Hines, Svetlov,
> Moran, and Thomas.
>
> [stupid wisecrack deleted]
****** that must have been the last sentence of that paragraph****
> Don't you think that knowing a little bit about the structure of the
> family of genes involved in hemoglobin might be somewhat important in
> correctly interpreting an analysis of the sequences? It might even rank
> right up there with knowing what heme is and why it is a poor candidate
> for sequencing.
*********************
>
> >> Only to someone pathetically ignorant of the issues,
> >> and impressed by all the irrelevant stuff you throw into
> >> post after post to strut *your* stuff on mostly elementary
> >> things that were not a matter of discussion. Even Dan
> >> Hughes caught onto that aspect of your BSing.
>
> >Are you comparing yourself to someone who repeatedly asserts an ability
> >to calculate *absolute* fitnesses (independent of environmental
> >conditions) without ever telling us how to actually do so?
>
> If even HE can see you are indulging in irrelevant
> window dressing, there must be something to it, eh?
>
> [stupid wisecrack based on the equivocation inherent in "compare"
> deleted]
**** the 'wisecrack' must have been the last sentence****
> Are you comparing yourself to someone who repeatedly asserts an ability
> to calculate *absolute* fitnesses (independent of environmental
> conditions) without ever telling us how to actually do so? I agree that
> there is some similarity.
********************
>
> >> > But I am not responsible for what others think.
> >>
> >> You are in part, by not admitting that your idiocy about
> >> me not strutting my stuff is a bunch of misdirection.
>
> >I am merely trying to decide whether you know enough about the
> >proteins/genes you are analyzing the sequence of to say anything
> >relevant
>
> Then you are going about it the wrong way. First read
> the paper to figure out just what kind of knowledge
> is really relevant to it.
I don't need to read the paper to know that you are not competent to
comment on the genes (or heme) of hemoglobin and can't even read a
research paper without committing some rather egregious
misinterpretations due to your lack of knowledge about hemoglobin (such
as your comments about the numbers of mammalian alpha genes). How many
alpha globin gene sequences did you say there are in the thirty kb
cluster on chromosome 16 of humans? How many are pseudogenes and what
are the sources of the pseudogenes? How many of these genes function
(produce a protein) and what function do they have and when? What is
the variance in the number of alpha genes in vertebrates and what effect
might that have on sequence analysis?
>
> > or whether you are merely blindly doing math on sequences.
>
> Dead giveaway that you haven't read the paper yet.
When I have some time. When you do, I suggest you read up a little bit
on the nature of the globins in humans, at the very least.