New items on my web page
Glenn Morton
http://www.flash.net/~mortongr/micro.htm
Which is a discussion of how microfossils disprove the global flood
http://www.flash.net/~mortongr/paleosol.htm
Which is a discussion by Jonathan Clarke of how paleosols disprove the
concept of a global flood
http://www.flash.net/~mortongr/celltype.htm
a discussion of how animals became more complex over time measured by
the number of cell types the most complex animals in the fossil record
had.
and
http://www.flash.net/~mortongr/gstory.htm
which is the story of why I left young-earth creationism
PZ Myers
>I have put some new stuff on my web page. Items include:
>
>http://www.flash.net/~mortongr/micro.htm
>Which is a discussion of how microfossils disprove the global flood
>
>http://www.flash.net/~mortongr/paleosol.htm
>Which is a discussion by Jonathan Clarke of how paleosols disprove the
>concept of a global flood
>
>http://www.flash.net/~mortongr/celltype.htm
>a discussion of how animals became more complex over time measured by
>the number of cell types the most complex animals in the fossil record
>had.
Thanks for putting that one up...I've heard from several sources,
secondhand, about this idea that the number of cell types shows this
increase. I haven't seen the original source, though -- I'm definitely
going to have to look it up, because I simply don't believe it.
Here's the chart you included:
Porifera 10 cell types 570 myr
Cnidaria 14 cell types 560 myr
Haemocoelic Bilaterian 30 cell types 560 myr
Arthropoda 51 cell types 530 myr
Echinodermata, Annelids 39 cell types 525 myr
Agnatha 64 cell types 510 myr
Cephalopoda 75 cell types 500 myr
Actinopterygii 132 cell types 400 myr
Amphibia 150 cell types 330 myr
Diapsida 154 cell types 300 myr
Aves 187 cell types 150 myr
Hominidae 210 cell types 5 myr
Am I the only one who finds these numbers incredibly fishy? Fish have
fewer cell types than frogs? Birds less than people? There is ONE number
for arthropods, never mind the diversity in *that* group?
I'm very suspicious.
>
>and
>
>http://www.flash.net/~mortongr/gstory.htm
>which is the story of why I left young-earth creationism
>
--
PZ Myers
Glenn Morton
> Am I the only one who finds these numbers incredibly fishy? Fish have
> fewer cell types than frogs? Birds less than people? There is ONE number
> for arthropods, never mind the diversity in *that* group?
>
> I'm very suspicious.
Knowing the mathematics that the authors used to model this, It makes
perfect consistent sense with what we find in the fossil record and how
we think evolution occurred. Evolution started with single celled
animals. They could only remain single cell-type or gain complexity.
THere are no other alternatives.
PZ Myers
Um, no, it doesn't make perfect sense. For instance, the ray-finned
fishes are the product of just as many years of evolution as Homo...so
given your rationale here, why shouldn't we expect them to have an equal
number of cell types?
What's fishy isn't that some lineages should have different numbers of
cell types, but that those lineages should be ranked in that particular
order.
--
PZ Myers
Sherilyn
apparently "nerve cell types are lumped" for the purpose of the
calculation.
--
Sherilyn
Sent via Deja.com http://www.deja.com/
Before you buy.
PZ Myers
>PZ Myers wrote:
[about http://www.flash.net/~mortongr/celltype.htm]
>
>> Am I the only one who finds these numbers incredibly fishy? Fish have
>> fewer cell types than frogs? Birds less than people? There is ONE number
>> for arthropods, never mind the diversity in *that* group?
>>
>> I'm very suspicious.
>
>Knowing the mathematics that the authors used to model this, It makes
>perfect consistent sense with what we find in the fossil record and how
>we think evolution occurred. Evolution started with single celled
>animals. They could only remain single cell-type or gain complexity.
>THere are no other alternatives.
This is a topic in which I've long had an interest, of a peculiar and
morbid sort. It's been a case of occasionally running into these arguments
about cell types, and wondering whether I'm stupidly missing something
obvious, or whether the authors of these claims are the cockeyed ones. I
can't see a middle ground, it's one or the other. Maybe somebody here can
point out how idiotic I must be.
The issue is whether we can identify a good measure of organismal
complexity. One way, you might think, would be to look at the number of
different cell types present. I first ran across this metric in the late
'70s, in JT Bonner's book _On Development: the biology of form_. He has a
number of provocative graphs in that book, that try to relate various
parameters of form to life history and evolution. Some of the parameters
are easy to assess: maximum length, or approximate number of cells (which
is just roughly proportional to volume). Others were messy: number of
different cell types. Bonner didn't push that one too much, just pointing
out that a plot of number of types vs. total number of cells was sorta
linear on a logarithmic plot, and he kept the comparison crude, looking at
a whale vs. a sequoia vs. a sponge, that sort of thing. He also said of
counting cell types that it was "in itself an approximate and arbitrary
task", but doesn't say or cite where the numbers he used came from, or how
they were obtained.
It came up again in Stuart Kauffman's work. He tried to justify his claim
that the number of cell states (or types) in an organism was a function of
the number of genes, and he put together a chart of genome size vs. number
of cell types. It was glaringly bogus. He (or someone) clearly selected
the data, leaving out organisms with what I guess he would consider
anomalous genome sizes -- and Raff and Kaufman thoroughly trashed that
entire line of argument in their chapter on the C-value paradox in
_Embryos, Genes, and Evolution_, showing that one axis of Kauffman's graph
has to be invalid. Nobody has touched on that other axis, the number of
cell types, and I'm still wondering how anybody determined that humans
have precisely 210 different kinds of cells, while flies have 50 (those
numbers seem to have become canonized, by the way -- I've found several
sources that cite them, +/- a bit, but very few say where they came from).
And then Morton mentions this interesting little paper that I hadn't seen
before:
Valentine, JW, AG Collins, CP Meyer (1994) Morphological complexity
increase in metazoans. Paleobiology 20(2):131-142.
[note to Glenn: the citation on your page is incorrect. It's in
Paleobiology, not Paleontology]
Abstract.-The number of cell types required fo rthe constructon of a
metazoan body plan can serve as an index of morphological (or anatomical)
complexity; living metazoans range from four (placozoans) to over 200
(hominids) somatic cell types. A plot of the times of origin of body plans
against their cell type numbers suggests that the upper bound of
complexity has increased more or less steadily from the earliest metazoans
until today, at an average rate of about one cell typer per 3 my (when
nerve cells are lumped). Computer models in which increase or decrease in
cell type number was random were used to investigate the behavior of the
upper bound of cell type number in evolving clades. The models are
Markovian; variance in cell type number increases linearly through time.
Scaled to the fossil record of the upper bound of cell type numbers, the
models suggest that early rates of increase in maximum complexity were
relatively high. the models and the data are mutually consistent and
suggest that the Metazoa originated near 600 Ma, the the metazoan
"explosion" near the Precambrian/Cambrian transition was not associated
with any important increase in complexity of body plans, and that
important decreases in the upper bound of complexity are unlikely to have
occurred.
At least, the paper *sounds* interesting. After reading it, though, I'm
left feeling that it is an awful, lousy bit of work.
The first major flaw: there is no data in the paper. The first figure is a
plot of cell type number against age, in millions of years before the
present -- the numbers and groups described are listed on Glenn Morton's
page. These are the observations against which several computer models
will be compared. These data were not measured by the authors, but were
gleaned from the literature. The sources for these critical numbers are
listed in an appendix, about which more in a little bit.
The bulk of the paper is about the computer models they developed. The
final figure is the same as the first, showing the data points from the
literature with the plot generated by their best-fit simulation
superimposed. It's a very good fit. From this, they make several
conclusions: 1) that their model is in good agreement with the historical
data, 2) that the rate of increase in complexity was greatest near the
origin of metazoans, 3) that that origin was relatively late, and 4) there
was no particular change in rate during the Cambrian explosion. It is a
fine example of GIGO.
The work is completely reliant on the validity of the data about cell type
number, which is not generated by the authors, and worse, which is not
even critically evaluated by the authors. It is just accepted. That data
left me cold, though, with lots of questions.
What is a cell type? There was no attempt to define it. Histologically,
it's a fuzzy mess -- you can go through any histology text and find long
lists of cells types that have been recognized by morphology, location,
staining properties, and so forth. I just skimmed through the index of an
old text I have on hand (Leeson and Leeson), and without trying too hard,
counted a bit more than a hundred distinct, named, vertebrate cell types
in the first 5 pages...and there were 25 more pages to go. What criteria
are the authors using? How well do these superficial criteria for
identification mesh with the molecular reality of the processes that shape
these cells?
Why did they throw out huge categories of cells? The nervous system is
simply not considered -- it's 'lumped'. This seems to me to be grossly
inappropriate. Here is this HUGE heap of cellular diversity, in which half
the genome is involved, and it is discarded in what are supposedly
quantitative models. I can guess that it was thrown out because it is
impossible to quantify...but that doesn't sound like a good excuse if you
are trying to model numbers. Furthermore, they only count cells in adults,
so cell types found only in larvae or juveniles are rejected. Whoops.
Isn't that an admission that complexity in arthropods is going to be
seriously underestimated? I don't know, since they don't say how they
define a cell type.
How did they get these tidy single numbers for a whole group? 'Arthropods'
have only 50 cell types. They admit that "within some groups there is a
significant range of cell type numbers". The range of variation, however,
is not reflected in any of their graphs, nor which groups exhibit this
range. Instead, they say, they picked a representative "primitive number"
of cell types from "the more primitive living forms within each group". I
guess the more primitive living forms haven't done any evolving.
A really bothersome and related point: the high end of their plot is
anchored by the hominids, with 210 cell types and a time of origin within
the last few million years. Remember, they are going to fit all these
computer-generated curves to these data, and they explicitly scale
everything to this endpoint and an earlier one. This point is invalid,
though. We humans don't have any novel cell types that were generated a
few million years ago -- that number of 210 cells ought to be applied to
all of Mammalia, and the time of origin shoved back a hundred million
years. Or more. Is there any reason to think 200 million year old
therapsids were lacking any significant number of histological cell types
found in mammals today?
For that matter, why should we think that these cell type numbers are
anything but arbitrary indicators of the relative amount of time
histologists have spent picking over the tissues of these various
organisms? Do fish really have fewer cell types than mammals, or just
different ones? Fish may lack all the cell types associated with hairs,
but we don't have all the ones that form scales. The authors show
amphibians as being more complex than fish, on the basis of cell type
counts in living forms...and that is completely the reverse of what I
would expect, if I thought there was any difference at all.
What was really the killer for me, and what I was really looking for, was
the primary sources for these numbers. These are listed at the very end,
in a separate appendix. A few are easy: it's not hard to imagine being
able to count all the different cell types in a sponge or a jellyfish. One
is admitted speculation by Valentine -- he estimates the number of cells a
primitive hemocoelic bilaterian must have had. Another, the number of
cells in arthropods, is cited as an unpublished ms by Valentine. However,
almost all of the counts boil down to one source, a critical source I
haven't yet been able to find. This very important paper, that purports to
give cell type numbers for echinoderms, cephalopods, fish, amphibians,
lizards, and birds, is:
Sneath, PHA (1964) Comparative biochemical genetics in bacterial taxonomy.
pp 565-583 in CA Leone, ed. _Taxonomic biochemistry and serology_. Ronald,
New York.
It's a paper about bacterial taxonomy? And biochemistry? The only
discussion in the text of the Valentine paper about this source mentions
that it compares DNA content to cell type number, a measure that Raff and
Kaufman have shown most emphatically to be invalid. And it's from 1964,
although the author seems to still be around and active in bacterial
taxonomy and molecular biology right up until at least a few years ago. He
doesn't look like a histologist or comparative zoologist though, that's
for sure.
It's from 1964. Oh, boy. I did manage to track down a copy of this volume
in a library a few miles away, but I haven't yet been able to get out and
read it. I'm not too inclined to even try right now, because this appendix
also has a little subscript in fine print at the bottom...virtually every
source in this list, including Sneath, is marked with an asterisk, and the
fine print tells us that that means "estimates NOT [my emphasis]
documented by lists of cell types or by references to published
histological descriptions". In other words, there ain't no data there,
either.
I'm afraid to look up Sneath, for fear that it will turn out to be an
estimate of cell number derived from measures of DNA content, with a bit
of subjective eyeballing tossed in. At least that would explain why
Kauffmann could find a correlation between DNA content and complexity,
though.
From my perspective right now, this whole issue of cell type number is
looking like a snipe hunt, a biological myth that is receding away as I
pursue it. Does anybody know any different?
--
PZ Myers
Sherilyn
"PZ Myers" <my...@mac.com> wrote in message
news:myers-11010...@bio-32.bio.temple.edu...
[...]
>
> The issue is whether we can identify a good measure of organismal
> complexity. One way, you might think, would be to look at the number of
> different cell types present. I first ran across this metric in the late
> '70s, in JT Bonner's book _On Development: the biology of form_. He has a
> number of provocative graphs in that book, that try to relate various
> parameters of form to life history and evolution. Some of the parameters
> are easy to assess: maximum length, or approximate number of cells (which
> is just roughly proportional to volume). Others were messy: number of
> different cell types. Bonner didn't push that one too much, just pointing
> out that a plot of number of types vs. total number of cells was sorta
> linear on a logarithmic plot, and he kept the comparison crude, looking at
> a whale vs. a sequoia vs. a sponge, that sort of thing. He also said of
> counting cell types that it was "in itself an approximate and arbitrary
> task", but doesn't say or cite where the numbers he used came from, or how
> they were obtained.
I'm reading the appendix "The Chemistry of Life" in Behe's book at the
moment, and came across one interesting metric, without any source citation
but I expect he knows his stuff: "The amount of DNA in a cell varies
_roughly_ with the complexity of the organism. Bacteria have about several
million nucleotides of DNA. the amount of eukaryotic DNA ranges from a low
of several tens of millions of nucleotides in fungi to a high of several
hundred billion in some flowering plants. Humans come in at around three
billion nucleotides."
Darwin's Black Box p268 para 2.
[Emphasis on _roughly_ is mine; I don't want to be accused of implying that
Behe means to promote this as a serious metric for complexity, he's just
describing a rough correspondence with illustrations.]
PZ Myers
<Sher...@sidaway.demon.co.uk> wrote:
>"PZ Myers" <my...@mac.com> wrote in message
>news:myers-11010...@bio-32.bio.temple.edu... [...]
>>
>> The issue is whether we can identify a good measure of organismal
>> complexity. One way, you might think, would be to look at the number
>> of different cell types present. I first ran across this metric in
>> the late '70s, in JT Bonner's book _On Development: the biology of
>> form_. He has a number of provocative graphs in that book, that try
>> to relate various parameters of form to life history and evolution.
>> Some of the parameters are easy to assess: maximum length, or
>> approximate number of cells (which is just roughly proportional to
>> volume). Others were messy: number of different cell types. Bonner
>> didn't push that one too much, just pointing out that a plot of
>> number of types vs. total number of cells was sorta linear on a
>> logarithmic plot, and he kept the comparison crude, looking at a
>> whale vs. a sequoia vs. a sponge, that sort of thing. He also said
>> of counting cell types that it was "in itself an approximate and
>> arbitrary task", but doesn't say or cite where the numbers he used
>> came from, or how they were obtained. [...] I'm reading the appendix
>> "The Chemistry of Life" in Behe's book at the moment, and came
>> across one interesting metric, without any source citation but I
>> expect he knows his stuff: "The amount of DNA in a cell varies
>> _roughly_ with the complexity of the organism. Bacteria have about
>> several million nucleotides of DNA. the amount of eukaryotic DNA
>> ranges from a low of several tens of millions of nucleotides in
>> fungi to a high of several hundred billion in some flowering plants.
>> Humans come in at around three billion nucleotides." Darwin's Black
>> Box p268 para 2.
>
>[Emphasis on _roughly_ is mine; I don't want to be accused of implying
>that Behe means to promote this as a serious metric for complexity,
>he's just describing a rough correspondence with illustrations.]
There is an intuitive correspondence: more complex organisms ought to
require a more elaborate set of instructions. Unfortunately for the
tidiness of the metric, lots of organisms that we would consider to be
rather simple have an extremely wordy and apparently sloppy instruction
booklet. Even where we like to pretend that the measure has some meaning
(such as for our own personal species), the instructions seem to be so
heavily larded with what we think is probably useless garbage that it
makes it useless for making comparisons. Are we mammals really more
complex than birds? That's what DNA content says. Or are their genomes
just a little more efficiently coded?
--
PZ Myers
mel turner
wrote...
[big snip of POTM-worthy material]
>What was really the killer for me, and what I was really looking for,
was
>the primary sources for these numbers.
[snip]
>However,
>almost all of the counts boil down to one source, a critical source I
>haven't yet been able to find. This very important paper, that purports
to
>give cell type numbers for echinoderms, cephalopods, fish, amphibians,
>lizards, and birds, is:
>
>Sneath, PHA (1964) Comparative biochemical genetics in bacterial
taxonomy.
>pp 565-583 in CA Leone, ed. _Taxonomic biochemistry and serology_.
Ronald,
>New York.
Just checked, and it's in the bio library in this same building. I'll
just wander over and check it out... [done; it's now open next to me]
>It's a paper about bacterial taxonomy? And biochemistry?
Yep. A review-type paper. The relevant part is in a final section headed
"Implications for the study of higher organisms". It's a couple pages of
text with 2 graphs and one table.
The section starts out pretty silly: "To understand genetic homologies,
we will need to know the quantitiy of genetic information and its change
during evolution. It may not be long before we can read the genetic
message of DNA. The work of Beer (9) shows that the electron microscope
now possesses almost this capability." Huh? DNA sequence analysis by
EM??
Yep. Or, there's no original data. Here's the relevant text:
"Although there are many possible correlations, for example, that
between cell size and DNA content (135), it seems plausible to suggest
that the amount of DNA is largely determined by the amount of genetic
information that is required and that this will be greater in the more
complex organisms. Fig. 38-2 shows the distribution of DNA contents of
haploid nuclei taken from the literature, mostly from several compendia
(4,10,87,128,134,135). The haploid nucleus was chosen for uniformity,
and because the genetic information in diploids is presumably mostly
reduplicated. The values are plotted against the number of
histologically distinguishable cell types in the life cycle of the
organism (suggested by a figure of Zimmerman (141)). This number is some
measure of complexity, and was estimated from standard textbooks
(5,13,85,126). In Fig. 38-2 organisms incapable of independent
multiplication (e.g., viruses) have been assigned to the 0.1 cell level.
The values for some well-known organisms are shown in Fig. 38-3."
Fig. 38-2 is a graph of number of cell types (Y-axis) vs. log content of
DNA/gamete, with a extra superimposed x-axis of "number of bits" ("one
nucleotide pair = two bits").No species names are indicated, but there
are clusters of multiple separate points plotted for "mammals", "birds",
"fish", "angiosperms", "bacteria" "algae & fungi", "viruses", etc.
[oddly, he scores "RNA viruses" as having DNA content].
Fig. 38-3 purports to show "the histological complexity of some
well-known organisms" with a log graph placing examples like "Man,
Mammals" at the top with ca. 200 cell types, and "birds", "reptiles",
"amphibia", "fish" [again, no species names] just below that, then
various cited generic names of plants animals, protists and bacteria
[e.g., Pteromyzon (sic), Sepia, Helix, Ranunculus, Polypodium,
Escherichia, etc.; about 50 taxa altogether]. Strictly unicellular
organisms with different cell types during the life cycle [cysts,
spores, gametes, etc. are properly scored as having histological
complexity; e.g., Plasmodium scored with ca. 6 cell types]
There's also discussion of the significance of the reported rough
correlation of complexity and DNA content, a suggestion that
histologically complex organisms should require disprortionately many
times the DNA amounts of simple ones [cell specialization and
regulation], a mention of some plants and amphibia with 'unexplained'
very large DNA contents, and a page of stuff on base-pair changes,
informational "bits", & Kimura.
Table 38-3 "estimated amount of genetic and phenetic change in
vertebrate evolution" looks pretty odd indeed [especially in a paper on
bacterial biochemistry!]; it apparently tries to say something about
times of origin and amounts of DNA change [% and in "bits"] for classes,
orders, families, genera, species.... a bit dubious, to put it mildly.
Looking at the References list for the anatomical data sources cited for
Figs 38-2 and 38-3, the "standard textbooks" were indeed just that:
5. Andrew, W. 1959. Textbook of Comparative histology. Oxford Univ.
Press, London
13. Borradaile, L.A., L.E.S. Eastham, F.A. Potts, & J. T. Saunders.
1941. The Invertebrata: A manual for the use of students. 2nd ed.
Cambridge Univ. Press, Cambridge.
85. Maximow, A.A. & W. Bloom. 1940. A textbook of histology. W. B.
Saunders Co., Philadelphia.
126. Strasburger, E., L. Jost, H. Schenck, & G. Karsten. 1912. A
textbook of botany. 4th English ed. Maximillian & Co. Ltd. London.
The Zimmerman citation from above is:
Zimmerman, W. 1953. Evolution: Die Geschichte ihrer Probleme und
Erkenntnisse. Alber, Freiburg & Munchen 623 pp.
>I'm afraid to look up Sneath, for fear that it will turn out to be an
>estimate of cell number derived from measures of DNA content,
No, it seems he wasn't guilty of that, at least it's claimed to be
derived from anatomical texts.
>with a bit of subjective eyeballing tossed in.
That's entirely possible. It seems likely to me that the cited texts
wouldn't actually have provided Sneath with taxonomic lists giving all
the numbers of different cell types; he probably had to estimate them
from the anatomical descriptions.
>At least that would explain why
>Kauffmann could find a correlation between DNA content and complexity,
>though.
No, Sneath also concluded
"It can be shown that the DNA content is roughly proportional to
histological complexity.", and
"There is a correlation between the histological complexity of organisms
and the DNA content of their gametes, which presumably is related to the
amount of genetic information required for specialization in higher
organisms. The theoretical information content varies from about 10 4
bits for the smaller viruses to about 10 11 bits for some vertebrates
and angiosperms." [the 4 and 11 are superscript exponents, of course]
>From my perspective right now, this whole issue of cell type number is
>looking like a snipe hunt, a biological myth that is receding away as I
>pursue it. Does anybody know any different?
Gee, how can you possibly say that? It all looks so rock-solid...
cheers
PZ Myers
mtu...@snipthis.acpub.duke.edu (mel turner) wrote:
>In article <myers-11010...@bio-32.bio.temple.edu>,
>my...@mac.com wrote...
>
>[big snip of POTM-worthy material]
>
>>What was really the killer for me, and what I was really looking for,
>>was the primary sources for these numbers.
>
>[snip]
>
>>However, almost all of the counts boil down to one source, a critical
>>source I haven't yet been able to find. This very important paper,
>>that purports to give cell type numbers for echinoderms, cephalopods,
>>fish, amphibians, lizards, and birds, is:
>>
>>Sneath, PHA (1964) Comparative biochemical genetics in bacterial
>>taxonomy. pp 565-583 in CA Leone, ed. _Taxonomic biochemistry and
>>serology_. Ronald, New York.
>
>Just checked, and it's in the bio library in this same building. I'll
>just wander over and check it out... [done; it's now open next to me]
Hooray! You saved me some work...thanks!
>
>>It's a paper about bacterial taxonomy? And biochemistry?
>
>Yep. A review-type paper. The relevant part is in a final section headed
>"Implications for the study of higher organisms". It's a couple pages of
>text with 2 graphs and one table.
>
>The section starts out pretty silly: "To understand genetic homologies,
>we will need to know the quantitiy of genetic information and its change
>during evolution. It may not be long before we can read the genetic
>message of DNA. The work of Beer (9) shows that the electron microscope
>now possesses almost this capability." Huh? DNA sequence analysis by
>EM??
Weird. You gotta use a scanning tunneling scope, right?
"Estimated from standard textbooks"...that's a bit of a worry. So the
data that all this is based on may not exist at all -- it's just the
result of a most unscientific survey of cell types listed in textbooks.
I just checked my library's online catalog, and we have all of the
above. I'll take a look tomorrow and see how explicitly those magic
numbers are laid out.
>
>126. Strasburger, E., L. Jost, H. Schenck, & G. Karsten. 1912. A
>textbook of botany. 4th English ed. Maximillian & Co. Ltd. London.
>
>The Zimmerman citation from above is:
>Zimmerman, W. 1953. Evolution: Die Geschichte ihrer Probleme und
>Erkenntnisse. Alber, Freiburg & Munchen 623 pp.
Oh, great. This afternoon I faced the prospect of having to dig up an
old 1964 paper on bacterial biochemistry; now you tell me I have to go
read a 600 page book from 1953 in German, no less.
>
>>I'm afraid to look up Sneath, for fear that it will turn out to be an
>>estimate of cell number derived from measures of DNA content,
>
>No, it seems he wasn't guilty of that, at least it's claimed to be
>derived from anatomical texts.
That's good. Although it's still not clear who the primary source for
these numbers is.
[snip]
>
>>From my perspective right now, this whole issue of cell type number is
>>looking like a snipe hunt, a biological myth that is receding away as I
>>pursue it. Does anybody know any different?
>
>Gee, how can you possibly say that? It all looks so rock-solid...
Oh, right. Of course.
--
PZ Myers
mel turner
my...@mac.com wrote...
[big snip]
>>The Zimmerman citation from above is:
>>Zimmerman, W. 1953. Evolution: Die Geschichte ihrer Probleme und
>>Erkenntnisse. Alber, Freiburg & Munchen 623 pp.
>
>Oh, great. This afternoon I faced the prospect of having to dig up
an
>old 1964 paper on bacterial biochemistry; now you tell me I have to
go
>read a 600 page book from 1953 in German, no less.
Well, you probably don't have to read the German. Zimmerman's a
classic source of some interesting, idiosyncratic ideas about
morphology, evolution & development [the Telome Theory in botany,
some pre-cladistic hints at phylogenetics, etc.] but Sneath just
cited an unspecified figure [restored]:
>The values are plotted against the number of
>histologically distinguishable cell types in the life cycle of the
>organism (suggested by a figure of Zimmerman (141)).
So maybe Sneath just looked at the pictures.
cheers
*Hemidactylus*
No but I'm ready to babble a little (intoxicated by Li and Graur's
_Fundamentals of Molecular Evolution_ and Gerhart and Kirschener's _Cells,
Embryos, and Evolution_) . Can cell types be rigidly defined. Intuitively
they are defined by the subset of genes they express related to other cells,
but I'd assume cells could blend together in that there is overlap of
expression. Cells might have a characteristic molecular repertoire or at
least the molecular components shared with other cells come together in a
somewhat unique way to help define a subtype. In neurons, there are
differences in the particular array of membrane receptors expressed and the
way they branch and communicate with other cells, which brings us to an
inportant consideration not of cellular subtypes, but the way they mesh
together and form composites such as tissues and organs. Here we might get
into modularity and compartmentalization. I'm kinda thinking of collinearity
and Hox compartmentalization right now. In the brain you've got some
compartmentalizing early in development as the zootypical genes (emx and otx,
Hox'es et al) are expressed. Later on you get networks or synaptic
associations between neurons. I'm tempted to bring JZ Young's mnemon into the
mix here, but I'll not get this far in depth. Memory might be a matter of
co-opting cellular components just like anything else, but employing these
components in novel ways.
IMO there's a lot which goes into "morphological complexity" and I've only
scratched the tip of the iceberg, oddly contemplating memory as an example,
yet if treating the mind as an organ isn't too off base, so be it.
I don't know if genome size is an appropriate metric because of the junk or
selfish DNA which rides along with the coding genome or that subset of the
genome which produces RNA, some of which codes for amino acids. Would actual
number of coding genes be a better metric than genome size? Should coding
genes be broken apart into groups which lead to proteins and those which
don't? There are also regulatory sections which might influence phenotype
without producing RNA.
Maybe morphological or phenotypic complexity only roughly approximates genic
complexity (as opposed to genomic size). The size of the genome might vary
between closely related species, but what about the number of coding genes?
Maybe phenotypic or morphological complexity are more of a matter of how the
genes are used, rather than sheer numbers.
--
Scott Chase
John Harshman
<my...@mac.com> wrote:
> In article <85gdj...@news2.newsguy.com>, "Sherilyn"
> <Sher...@sidaway.demon.co.uk> wrote:
>
> >"PZ Myers" <my...@mac.com> wrote in message
> >news:myers-11010...@bio-32.bio.temple.edu... [...]
> >>
> >> The issue is whether we can identify a good measure of organismal
> >> complexity. One way, you might think, would be to look at the number
> >> of different cell types present. I first ran across this metric in
> >> the late '70s, in JT Bonner's book _On Development: the biology of
> >> form_. He has a number of provocative graphs in that book, that try
> >> to relate various parameters of form to life history and evolution.
> >> Some of the parameters are easy to assess: maximum length, or
> >> approximate number of cells (which is just roughly proportional to
> >> volume). Others were messy: number of different cell types. Bonner
> >> didn't push that one too much, just pointing out that a plot of
> >> number of types vs. total number of cells was sorta linear on a
> >> logarithmic plot, and he kept the comparison crude, looking at a
> >> whale vs. a sequoia vs. a sponge, that sort of thing. He also said
> >> of counting cell types that it was "in itself an approximate and
> >> arbitrary task", but doesn't say or cite where the numbers he used
> >> came from, or how they were obtained. [...] I'm reading the appendix
> >> "The Chemistry of Life" in Behe's book at the moment, and came
> >> across one interesting metric, without any source citation but I
> >> expect he knows his stuff: "The amount of DNA in a cell varies
> >> _roughly_ with the complexity of the organism. Bacteria have about
> >> several million nucleotides of DNA. the amount of eukaryotic DNA
> >> ranges from a low of several tens of millions of nucleotides in
> >> fungi to a high of several hundred billion in some flowering plants.
> >> Humans come in at around three billion nucleotides." Darwin's Black
> >> Box p268 para 2.
> >
> >[Emphasis on _roughly_ is mine; I don't want to be accused of implying
> >that Behe means to promote this as a serious metric for complexity,
> >he's just describing a rough correspondence with illustrations.]
>
> There is an intuitive correspondence: more complex organisms ought to
> require a more elaborate set of instructions. Unfortunately for the
> tidiness of the metric, lots of organisms that we would consider to be
> rather simple have an extremely wordy and apparently sloppy instruction
> booklet. Even where we like to pretend that the measure has some meaning
> (such as for our own personal species), the instructions seem to be so
> heavily larded with what we think is probably useless garbage that it
> makes it useless for making comparisons. Are we mammals really more
> complex than birds? That's what DNA content says. Or are their genomes
> just a little more efficiently coded?
Or do they just have less junk DNA (unless that's what you mean)? I for
one doubt sincerely that mammals are more complex than birds. You *might*
be able to devise a valid comparison metric by counting the number of
proteins coded for in a genome. Obviously there are definitional problems,
and obviously there are few organisms for which we can apply this metric
as yet. For a few more organisms you could count ORFs as a proxy, and for
many more you could count the size of the single-copy nuclear genome,
estimable by looking at the reassociation kinetics of cellular DNA. The
last metric is doable and makes (I think) a decent definition of genetic
complexity. Gets rid of the junk and also conveniently takes care of gene
families/multiple-copy genes (the more different, the more they contribute
to perceived genome size). I don't know of any publications on the
subject, though. How do you like that notion?
--
*Note the obvious spam-defeating modification
to my address if you reply by email.
PZ Myers
<harshman.diespamdi...@snfca030-0377.splitrock.net>,
harshman....@sjm.infi.net (John Harshman) wrote:
>In article <myers-8E71DA....@netnews.netaxs.com>, PZ Myers
><my...@mac.com> wrote:
>
>> In article <85gdj...@news2.newsguy.com>, "Sherilyn"
>> <Sher...@sidaway.demon.co.uk> wrote:
>>
>> >"PZ Myers" <my...@mac.com> wrote in message
>> >news:myers-11010...@bio-32.bio.temple.edu... [...]
>> >>
>> >> The issue is whether we can identify a good measure of organismal
>> >> complexity. One way, you might think, would be to look at the number
>> >> of different cell types present. I first ran across this metric in
>> >> the late '70s, in JT Bonner's book _On Development: the biology of
>> >> form_. He has a number of provocative graphs in that book, that try
>> >> to relate various parameters of form to life history and evolution.
>> >> Some of the parameters are easy to assess: maximum length, or
>> >> approximate number of cells (which is just roughly proportional to
>> >> volume). Others were messy: number of different cell types. Bonner
>> >> didn't push that one too much, just pointing out that a plot of
>> >> number of types vs. total number of cells was sorta linear on a
>> >> logarithmic plot, and he kept the comparison crude, looking at a
>> >> whale vs. a sequoia vs. a sponge, that sort of thing. He also said
>> >> of counting cell types that it was "in itself an approximate and
>> >> arbitrary task", but doesn't say or cite where the numbers he used
>> >> came from, or how they were obtained. [...] I'm reading the appendix
>> >> "The Chemistry of Life" in Behe's book at the moment, and came
>> >> across one interesting metric, without any source citation but I
>> >> expect he knows his stuff: "The amount of DNA in a cell varies
>> >> _roughly_ with the complexity of the organism. Bacteria have about
>> >> several million nucleotides of DNA. the amount of eukaryotic DNA
>> >> ranges from a low of several tens of millions of nucleotides in
>> >> fungi to a high of several hundred billion in some flowering plants.
>> >> Humans come in at around three billion nucleotides." Darwin's Black
>> >> Box p268 para 2.
>> >
>> >[Emphasis on _roughly_ is mine; I don't want to be accused of implying
>> >that Behe means to promote this as a serious metric for complexity,
>> >he's just describing a rough correspondence with illustrations.]
>>
>> There is an intuitive correspondence: more complex organisms ought to
>> require a more elaborate set of instructions. Unfortunately for the
>> tidiness of the metric, lots of organisms that we would consider to be
>> rather simple have an extremely wordy and apparently sloppy instruction
>> booklet. Even where we like to pretend that the measure has some meaning
>> (such as for our own personal species), the instructions seem to be so
>> heavily larded with what we think is probably useless garbage that it
>> makes it useless for making comparisons. Are we mammals really more
>> complex than birds? That's what DNA content says. Or are their genomes
>> just a little more efficiently coded?
>
>Or do they just have less junk DNA (unless that's what you mean)?
I think it's what I meant.
>I for
>one doubt sincerely that mammals are more complex than birds.
I do, too. However, by the metric of DNA content or the even more
dubious measure of 'cell type number', birds are less complex.
>You *might*
>be able to devise a valid comparison metric by counting the number of
>proteins coded for in a genome. Obviously there are definitional problems,
>and obviously there are few organisms for which we can apply this metric
>as yet. For a few more organisms you could count ORFs as a proxy, and for
>many more you could count the size of the single-copy nuclear genome,
>estimable by looking at the reassociation kinetics of cellular DNA. The
>last metric is doable and makes (I think) a decent definition of genetic
>complexity. Gets rid of the junk and also conveniently takes care of gene
>families/multiple-copy genes (the more different, the more they contribute
>to perceived genome size). I don't know of any publications on the
>subject, though. How do you like that notion?
It sounds interesting. Do any of the more molecularly inclined
participants in this newsgroup know if something similar has been
attempted?
--
PZ Myers
PZ Myers
<hemida...@my-deja.com> wrote:
[snip]
>No but I'm ready to babble a little
So what else is new?
>(intoxicated by Li and Graur's
>_Fundamentals of Molecular Evolution_ and Gerhart and Kirschener's
>_Cells, Embryos, and Evolution_).
G&K also parrot the dogma that flies have 50-80 cell types and
vertebrates have 200. Interestingly, they say their example, Xenopus,
has 200, rather than mammals.
>Can cell types be rigidly defined.
That's the question.
>Intuitively they are defined by the subset of genes they express
>related to other cells,
Or is there more to it than that? Does developmental lineage and history
impose other patterns of information on cells than just which genes are
active and suppressed?
>but I'd assume cells could blend together in
>that there is overlap of expression. Cells might have a characteristic
>molecular repertoire or at least the molecular components shared with
>other cells come together in a somewhat unique way to help define a
>subtype. In neurons, there are differences in the particular array of
>membrane receptors expressed and the way they branch and communicate
>with other cells, which brings us to an inportant consideration not of
>cellular subtypes, but the way they mesh together and form composites
>such as tissues and organs. Here we might get into modularity and
>compartmentalization. I'm kinda thinking of collinearity and Hox
>compartmentalization right now.
This is all well and good, but we have a problem. This issue of the
number of cell types has been brought up in the context of data from the
early '60s, or as Mel Turner has now found, data from the '50s and
earlier. The numbers that are found in the literature are not based on
patterns of gene expression. I don't know what the heck they are based
on.
>In the brain you've got some
>compartmentalizing early in development as the zootypical genes (emx
>and otx, Hox'es et al) are expressed. Later on you get networks or
>synaptic associations between neurons. I'm tempted to bring JZ Young's
>mnemon into the mix here, but I'll not get this far in depth. Memory
>might be a matter of co-opting cellular components just like anything
>else, but employing these components in novel ways.
The nervous system raises all kinds of other hairy questions about cell
types. There are so many of them! Or, at least we think there are so
many of them. What if morphologically diverse cells all represent the
same single cell type at the molecular level, but have been warped in
different ways by different histories? For example, I'm thinking of
those large dorsal interneurons in the zebrafish hindbrain that are in
that lovely metameric ladder. Maybe they are completely identical in
terms of what genes are active, but because one is in a position to
receive inputs from cranial ganglia V, VII, and VIII, while another sees
just V and VII, they grow into a Mauthner cell and a MiD2, respectively.
They sure look different, but maybe they aren't.
>
>IMO there's a lot which goes into "morphological complexity" and I've
>only scratched the tip of the iceberg, oddly contemplating memory as
>an example, yet if treating the mind as an organ isn't too off base,
>so be it.
>
>I don't know if genome size is an appropriate metric because of the
>junk or selfish DNA which rides along with the coding genome or that
>subset of the genome which produces RNA, some of which codes for amino
>acids. Would actual number of coding genes be a better metric than
>genome size?
What do you do with polyploid lines, then?
>Should coding genes be broken apart into groups which
>lead to proteins and those which don't? There are also regulatory
>sections which might influence phenotype without producing RNA.
>
>Maybe morphological or phenotypic complexity only roughly approximates
>genic complexity (as opposed to genomic size). The size of the genome
>might vary between closely related species, but what about the number
>of coding genes? Maybe phenotypic or morphological complexity are more
>of a matter of how the genes are used, rather than sheer numbers.
I'm still looking for an objective measure of morphological/phenotypic
complexity before anyone starts trying to correlate it with that other
problem area, genomic complexity. Which is more complex, a frog or a
mouse? How do you tell?
--
PZ Myers
Richard Harter
>In article
><harshman.diespamdi...@snfca030-0377.splitrock.net>,
>harshman....@sjm.infi.net (John Harshman) wrote:
>>I for
>>one doubt sincerely that mammals are more complex than birds.
>
>I do, too. However, by the metric of DNA content or the even more
>dubious measure of 'cell type number', birds are less complex.
I dunno, one could probably make a good case that birds are less
complex than mammals. They have a less complex and cumbersome
reproductive system than mammals and they don't have complex
dentition.
Richard Harter, c...@tiac.net
http://www.tiac.net/users/cri
Tick tock, Tick tock, the hours run on
Like little mice under the feet of elephants.
PZ Myers
(Richard Harter) wrote:
>On 11 Jan 2000 21:08:38 -0500, PZ Myers <my...@mac.com> wrote:
>
>>In article
>><harshman.diespamdi...@snfca030-0377.splitrock.net>,
>>harshman....@sjm.infi.net (John Harshman) wrote:
>
>>>I for
>>>one doubt sincerely that mammals are more complex than birds.
>>
>>I do, too. However, by the metric of DNA content or the even more
>>dubious measure of 'cell type number', birds are less complex.
>
>I dunno, one could probably make a good case that birds are less
>complex than mammals. They have a less complex and cumbersome
>reproductive system than mammals
A *different* reproductive system. If you start tallying it up piece
by piece I wouldn't presume to predict which one would be most complex.
>and they don't have complex
>dentition.
And we mammals don't have as complex a respiratory system. But how do
you know that a beak doesn't require a more elaborate set of
instructions to specify it? Maybe teeth are algorithmically cheap.
To me, the point is that we don't have any robust criteria for
determining whether one organism is more complex than another. All we
can do is eyeball them and express an opinion. And when scientists start
plotting those kinds of opinions as single points on a chart and
matching computer models to them and using them as 'data' to make
estimates about metazoan origins, maybe a few warning bells ought to go
off.
--
PZ Myers
howard hershey
>
> In article
> <harshman.diespamdi...@snfca030-0377.splitrock.net>,
> harshman....@sjm.infi.net (John Harshman) wrote:
>
> ><my...@mac.com> wrote:
> >
> >> In article <85gdj...@news2.newsguy.com>, "Sherilyn"
> >> <Sher...@sidaway.demon.co.uk> wrote:
> >>
> >> >"PZ Myers" <my...@mac.com> wrote in message
> >> >news:myers-11010...@bio-32.bio.temple.edu... [...]
> >> >>
>
> >I for
> >one doubt sincerely that mammals are more complex than birds.
>
> I do, too. However, by the metric of DNA content or the even more
> dubious measure of 'cell type number', birds are less complex.
>
> >be able to devise a valid comparison metric by counting the number of
> >proteins coded for in a genome. Obviously there are definitional problems,
> >and obviously there are few organisms for which we can apply this metric
> >as yet. For a few more organisms you could count ORFs as a proxy, and for
> >many more you could count the size of the single-copy nuclear genome,
> >estimable by looking at the reassociation kinetics of cellular DNA. The
> >last metric is doable and makes (I think) a decent definition of genetic
> >complexity. Gets rid of the junk and also conveniently takes care of gene
> >families/multiple-copy genes (the more different, the more they contribute
> >to perceived genome size). I don't know of any publications on the
> >subject, though. How do you like that notion?
>
> It sounds interesting. Do any of the more molecularly inclined
> participants in this newsgroup know if something similar has been
> attempted?
>
bacteria, brewer's yeast, and C. elegans. Basically I don't think there
is much difference between mammals wrt the number of functional genes
they have, but I would imagine problems in making these counts. I would
certainly want to include most genes in gene families as independent
(especially those involving transmembrane receptors) because the
individual genes often perform specific different functions (from minor
isozyme effects to major functional differences). But telling when
members of the same gene family start serving radically different
functions is not easy just from an ORF count or sequence similarity
(e.g., hemoglobin and myoglobin). Should two genes that produce the
same functional protein but that are transcribed in different tissues
(or for different functions -- e.g., crystallins) be counted once or
twice? Many of the homeobox genes in mammals would be problematic
here.
Does a gene that produces one polypeptide that gets cleaved to produce
several different active peptides count as one gene or several?
The HOX clusters of mammals arose by duplication and/or polyploidy and
the genes often have partially overlapping functions. How much
functional duplication is too much for a gene to be counted as an
independent gene or, instead, as a mere duplication of an existing
gene? Many plants have undergone polyploidy more recently and the
number of genes that are mere duplicates is massive.
And then there are the FUN (function unknown) genes -- about 20-30% of
yeast genes are FUN and in many cases, disruptive null mutation has no
effect. Some of these genes may, in fact, be pure fluff, serving no
utile function. Others may be important in environments other than the
one in the lab.
But it is the amount of redundancy and duplication in most metazoan
genomes that will be the big stumbling block to an accurate comparison
of 'complexity' between metazoans (except for some broadbrush findings)
IMVVHO.
> --
> PZ Myers