Tally Me Banana: A Question
RobinGoodfellow
little factoid, if such it be, that humans share 50 percent of their DNA
with bananas. I don't remember where exactly I read this, but for some
reason I decided that I had no reason to disbelieve it. That is, until
I mentioned it to a friend with a considerably better grasp of
organismal biology. After getting a good laugh on my behalf, he pointed
out that since plants and animals have diverged a very long time ago in
evolutionary history, such disparate organisms as humans and bananas
wouldn't have such a high degree of genetic identity. Duh!
Anyhow, since that incident, I've been trying to figure out where the 50
percent figure came from. A Google search reveals a bunch of sites
touting this figure (including the usually trust-worthy Wikipedia), but
the only reference ever given is Americans For Medical Progress, a
pro-animal research organization. They use the figure as a means of
justifying that high degree of genetic identity does not mean that
animals are nearly human, since we are "half-way similar" to bananas,
too - but at no point do they give a source of this data.
Unsurprisingly, this figure is also used on creationist sites to counter
the claim that the 98% sequence identity of human and chimp genomes is
in any way significant. However, I could find no support for this
figure in the scientific literature. The papers listed on PubMed that
deal with the banana genome do not compare it to the human genome in any
way. And, if one were to give it a bit of thought (just like I failed
to do), the idea that the typical human and banana genotypes have 50%
sequence identity does seem fairly ridiculous.
So my question is, where did the figure come from? Is this a number
pulled out of thin air by creationists and/or animal research activists,
or does it have some degree of truth to it? For instance, it would make
sense that *some* of the human and banana genes (such as those that are
conserved in all eucarayotic organisms) are at least 50% homologous. It
might also make sense that 50% of human genes have some distanct
homologs or analogous genes in the banana genome. Or it could be
something else. Does anyone have any idea about the source of the 50%
claim, whether it has any legitimacy or not?
PS: I suppose I could run some BLAST searches rather than bother the
good denizens of TO with silly questions. But, if someone already did
all the work, why replicate the effort?
Harlequin
news:br0pa5$ojp$1...@news01.cit.cornell.edu:
> Some time ago, while browsing the web, I came across an interesting
> little factoid, if such it be, that humans share 50 percent of their DNA
> with bananas. I don't remember where exactly I read this, but for some
> reason I decided that I had no reason to disbelieve it. That is, until
> I mentioned it to a friend with a considerably better grasp of
> organismal biology. After getting a good laugh on my behalf, he pointed
> out that since plants and animals have diverged a very long time ago in
> evolutionary history, such disparate organisms as humans and bananas
> wouldn't have such a high degree of genetic identity. Duh!
[snip]
The percent depends on how the measurement is done. After all the
amount of DNA the two species has is different--very different
(or so I am assuming). It much like
creationists disputing the chimp figure because how you deal with
segments that are duplicated or deleted in one species and not
the other affects the percentage.
But lets compare two corresponding DNA segments and assume
no deletions or duplications are present in one but not
the other. The lowest sharing of DNA one could expect
is 25% since totally unrelated DNA has a 25% chance per
base pair for an agreement. (I suppose an "intelligent
designer" could design a 0% for a lark, but evolution
could not.)
Also note that humans and bananas share most of their
evolutionary history.
--
Anti-spam: replace "usenet" with "harlequin2"
"...Everybody has opinions: I have them, you have them. And we are all
told from the moment we open our eyes, that everyone is entitled to
his or her opinion. Well, that's horsepuckey, of course. We are not
entitled to our opinions; we are entitled to our _informed_ opinions.
Without research, without background, without understanding, it's
nothing. It's just bibble-babble...."
- Harlan Ellison
Lane Lewis
"RobinGoodfellow" <lmuc...@yahoo.com> wrote in message
news:br0pa5$ojp$1...@news01.cit.cornell.edu...
> Some time ago, while browsing the web, I came across an interesting
> little factoid, if such it be, that humans share 50 percent of their DNA
> with bananas.
That's backwards, bananas share 50 percent of their genes with humans. Big
difference.
Its really not at all surprising since both bananas and humans are involved
in the cell construction business which require many of the same genes. And
of course we have a common ancestor that bestowed perfectly working genes on
us and the bananas so no reason to change them.
Chimps have approximately 95 percent of the same genes we do which
probably includes the banana genes also.
It is sort of an inside joke since nearly every derived life form has these
same genes for cell reproduction be it banana, tomato or mouse.
3 billion letters in the genome.
only 1.5 percent are genes.
1.5 billion letters (half) are selfish DNA elements that copy themselves but
have no known benefit to us.
Humans and mice share 60 percent of their DNA
At least 99.9 percent of our genes are identical to everyone else's in the
world.
We split off from yeast 1.5 billion years ago.
97 percent of Human DNA has no known purpose.
http://www.pbs.org/wgbh/nova/transcripts/2809genome.html
Lane
RobinGoodfellow
> RobinGoodfellow <lmuc...@yahoo.com> wrote in
> news:br0pa5$ojp$1...@news01.cit.cornell.edu:
>
>
>>Some time ago, while browsing the web, I came across an interesting
>>little factoid, if such it be, that humans share 50 percent of their DNA
>>with bananas. I don't remember where exactly I read this, but for some
>>reason I decided that I had no reason to disbelieve it. That is, until
>>I mentioned it to a friend with a considerably better grasp of
>>organismal biology. After getting a good laugh on my behalf, he pointed
>>out that since plants and animals have diverged a very long time ago in
>>evolutionary history, such disparate organisms as humans and bananas
>>wouldn't have such a high degree of genetic identity. Duh!
>
> [snip]
Thanks for the reply. Please see below:
> The percent depends on how the measurement is done. After all the
> amount of DNA the two species has is different--very different
> (or so I am assuming). It much like
> creationists disputing the chimp figure because how you deal with
> segments that are duplicated or deleted in one species and not
> the other affects the percentage.
True, but while human and chimp genome sizes are very close, the banana
genomes are 20% to 30% percent the size of ours(depending on the species
of the banana). Omitting insertions and deletions in this case when
assessing the similarity between the genomes will greatly distort the
results. (Of course, this may not be the case if you are only trying to
access similarity between actual genes, as opposed to junk DNA - but
that would be a very different measure from the ones used to compare
humans and chimps).
> But lets compare two corresponding DNA segments and assume
> no deletions or duplications are present in one but not
> the other. The lowest sharing of DNA one could expect
> is 25% since totally unrelated DNA has a 25% chance per
> base pair for an agreement. (I suppose an "intelligent
> designer" could design a 0% for a lark, but evolution
> could not.)
>
> Also note that humans and bananas share most of their
> evolutionary history.
Agreed. However, if the bananas are anything like us, than the
overwhelming majority of their DNA is junk, and not under any selective
constraint. And since our two species diverged a long, long time, I
would expect that, when looking at long stretches of aligned DNA,
sequence identity wouldn't be too much above the baseline 25 percent.
But it makes sense that the similariy would be much higher when looking
only at actual genes.
Anyhow, thanks again for the reply.
Cheers, Robin.
dkomo
>
> Some time ago, while browsing the web, I came across an interesting
> little factoid, if such it be, that humans share 50 percent of their DNA
> with bananas.
This sounds apocryphal. The banana genome hasn't even been sequenced
yet.
http://plantbreeding.org/article.php?story_id=145
John Harshman
RobinGoodfellow wrote:
> Some time ago, while browsing the web, I came across an interesting
> little factoid, if such it be, that humans share 50 percent of their DNA
> with bananas. I don't remember where exactly I read this, but for some
> reason I decided that I had no reason to disbelieve it. That is, until
> I mentioned it to a friend with a considerably better grasp of
> organismal biology. After getting a good laugh on my behalf, he pointed
> out that since plants and animals have diverged a very long time ago in
> evolutionary history, such disparate organisms as humans and bananas
> wouldn't have such a high degree of genetic identity. Duh!
This fifty percent figure may well be correct, but it doesn't mean what
you are thinking. It's not sequence similarity, but the possession of
recognizably homologous genes. And these genes may have DNA sequence
similarity considerably less than 50%.
> Anyhow, since that incident, I've been trying to figure out where the 50
> percent figure came from. A Google search reveals a bunch of sites
> touting this figure (including the usually trust-worthy Wikipedia), but
> the only reference ever given is Americans For Medical Progress, a
> pro-animal research organization. They use the figure as a means of
> justifying that high degree of genetic identity does not mean that
> animals are nearly human, since we are "half-way similar" to bananas,
> too - but at no point do they give a source of this data.
> Unsurprisingly, this figure is also used on creationist sites to counter
> the claim that the 98% sequence identity of human and chimp genomes is
> in any way significant. However, I could find no support for this
> figure in the scientific literature. The papers listed on PubMed that
> deal with the banana genome do not compare it to the human genome in any
> way. And, if one were to give it a bit of thought (just like I failed
> to do), the idea that the typical human and banana genotypes have 50%
> sequence identity does seem fairly ridiculous.
>
> So my question is, where did the figure come from? Is this a number
> pulled out of thin air by creationists and/or animal research activists,
> or does it have some degree of truth to it? For instance, it would make
> sense that *some* of the human and banana genes (such as those that are
> conserved in all eucarayotic organisms) are at least 50% homologous. It
> might also make sense that 50% of human genes have some distanct
> homologs or analogous genes in the banana genome.
Bingo. It's the second one. And I do not offhand know where you can find
this information.
John Harshman
Lane Lewis wrote:
> "RobinGoodfellow" <lmuc...@yahoo.com> wrote in message
> news:br0pa5$ojp$1...@news01.cit.cornell.edu...
>
>>Some time ago, while browsing the web, I came across an interesting
>>little factoid, if such it be, that humans share 50 percent of their DNA
>>with bananas.
>>
>
> That's backwards, bananas share 50 percent of their genes with humans. Big
> difference.
>
> Its really not at all surprising since both bananas and humans are involved
> in the cell construction business which require many of the same genes. And
> of course we have a common ancestor that bestowed perfectly working genes on
> us and the bananas so no reason to change them.
>
> Chimps have approximately 95 percent of the same genes we do which
> probably includes the banana genes also.
Not true. Chimps have approximately 100% of the same genes. The 95%
figure is an index of sequence similarity in which indels are counted as
one difference per base of length, i.e. a 500-base indel is counted as
500 site differences.
Lane Lewis
"dkomo" <dk...@concentric.net> wrote in message
news:3FD40447...@concentric.net...
Probably based on the fact that all higher life forms have these same
genes and the banana Genome is very small which gives us the 50 percent
figure. Sequencing will just confirm what has already been discovered
through other types of research.
Lane
RobinGoodfellow
>
> RobinGoodfellow wrote:
[snip]
>>So my question is, where did the figure come from? Is this a number
>>pulled out of thin air by creationists and/or animal research activists,
>>or does it have some degree of truth to it? For instance, it would make
>>sense that *some* of the human and banana genes (such as those that are
>>conserved in all eucarayotic organisms) are at least 50% homologous. It
>> might also make sense that 50% of human genes have some distanct
>>homologs or analogous genes in the banana genome.
>
>
> Bingo. It's the second one. And I do not offhand know where you can find
> this information.
Thanks for confirming this. I tend to think in terms of overall
sequence identities, and so when I came across the 50% figure, that's
what I took it for initially. Ah, well - I guess the banana made a
monkey out of me. Let that be a lesson in trusting web sites.
Cheers,
Robin.
John Harshman
dkomo wrote:
> RobinGoodfellow wrote:
>
>>Some time ago, while browsing the web, I came across an interesting
>>little factoid, if such it be, that humans share 50 percent of their DNA
>>with bananas.
>>
>
> This sounds apocryphal. The banana genome hasn't even been sequenced
> yet.
But you don't have to sequence a genome in order to get a fair estimate
of the percentage of genes in common with humans. A statistical sample
of probes bound vs. probes unbound would do as an approximation.
observa
"Harlequin" <use...@cox.net> wrote in message
news:Xns944AD7DEEC3D8u...@68.12.19.6...
I thought Chordates and plants have been separate since the Cambrian
explosion. I don't see how that means we share "...most of our evolutionary
history."
Of course, if there was actual transfer from the Ediacarian fauna, then
perhaps we do.
Alan Jeffery
>
>
>
> --
> Anti-spam: replace "usenet" with "harlequin2"
>
> "...Everybody has opinions: I have them, you have them. And we are all
> told from the moment we open our eyes, that everyone is entitled to
> his or her opinion. Well, that's horsepuckey, of course. We are not
> entitled to our opinions; we are entitled to our _informed_ opinions.
> Without research, without background, without understanding, it's
> nothing. It's just bibble-babble...."
> - Harlan Ellison
>
---
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Matt Penfold
You are aware that a factoid is an untrue fact ?
John Harshman
observa wrote:
Life ~= 4by.
Animal-Plant split ~~= 1by.
3~= most of 4.
[snip]
observa
"John Harshman" <jharshman....@pacbell.net> wrote in message
news:3FD4DEC0...@pacbell.net...
on" until just before the Cambrian explosion. Perhaps I'm just being a
little "chordatist"?
Alan Jeffery
>
> [snip]
Harlequin
news:py8Bb.23340$VV6.5...@news.xtra.co.nz:
[snip]
>> >>Also note that humans and bananas share most of their
>> >>evolutionary history.
>> >>
>> >
>> > I thought Chordates and plants have been separate since the
>> > Cambrian explosion. I don't see how that means we share "...most
>> > of our
> evolutionary
>> > history."
>>
>>
>> Life ~= 4by.
>> Animal-Plant split ~~= 1by.
>> 3~= most of 4.
>>
> Yeah, I figured that. Just thought that there wasn't much evolution
> "going on" until just before the Cambrian explosion. Perhaps I'm just
> being a little "chordatist"?
A metazoaist would be closer. I would add "ist" to whatever the
animal/plant/fungi clade is called.
John Harshman
observa wrote:
More importantly, you're being "eukaryotist". You think evolution isn't
happening unless somebody's growing feet or eyes, but what about all
those bacteria inventing fancy metabolic pathways?
Harlequin
[snip]
>> Yeah, I figured that. Just thought that there wasn't much evolution
>> "going on" until just before the Cambrian explosion. Perhaps I'm
>> just being a little "chordatist"?
>
>
> More importantly, you're being "eukaryotist". You think evolution
> isn't happening unless somebody's growing feet or eyes, but what about
> all those bacteria inventing fancy metabolic pathways?
And a bunch of Eukaryotic clades are left out by this as well.
RobinGoodfellow
> You are aware that a factoid is an untrue fact ?
From our friend, Miriam Webster:
One entry found for factoid.
Main Entry: fac·toid
Pronunciation: 'fak-"toid
Function: noun
Date: 1973
1 : an invented fact believed to be true because of its appearance in
print
2 : a brief and usually trivial news item
I was using the term in the latter sense. But, in all fairness, I
wasn't aware that of the former definition until you pointed it out.
Thanks.
Daniel Harper
Oh, no, those were all intelligently designed. It was only after the
Chordates appeared and arms and legs started growing that evolution could
take place.
--
...and it is my belief that no greater good has ever befallen you in this city
than my service to my God. [...] Wealth does not bring goodness, but goodness
brings wealth and every other blessing, both to the individual and that state.
Plato, quoting Socrates, from The _Apology_
--Daniel Harper
(Change terra to earth for email)
R. Dunno
> Some time ago, while browsing the web, I came across an interesting
> little factoid, if such it be, that humans share 50 percent of their DNA
> with bananas. I don't remember where exactly I read this, but for some
> reason I decided that I had no reason to disbelieve it.
You may find something similar to what you're looking for in
this NOVA transcript.
http://www.pbs.org/wgbh/nova/transcripts/2809genome.html
Do a find on 'banana'.
dkomo
>
> dkomo wrote:
>
> > RobinGoodfellow wrote:
> >
> >>Some time ago, while browsing the web, I came across an interesting
> >>little factoid, if such it be, that humans share 50 percent of their DNA
> >>with bananas.
> >>
> >
> > This sounds apocryphal. The banana genome hasn't even been sequenced
> > yet.
>
> But you don't have to sequence a genome in order to get a fair estimate
> of the percentage of genes in common with humans. A statistical sample
> of probes bound vs. probes unbound would do as an approximation.
>
Ya, come to think of it, I remember hearing about the percent
similarity between human and chimp genomes long before the human (or
chimp) genome was sequenced. It seems like roughly a decade before.
ArWeGod
news:br0pa5$ojp$1...@news01.cit.cornell.edu...
I haven't read the other posts and may be duplicating their thoughts, but it
seems to me we both have things like sugars and carbon in our make up. I
mean, everything on Earth is a carbon - based lifeform, I think. Maybe those
deep sea magna vent organisms are not, but everything else eats something
else to live. You can't eat something that doesn't share something of your
DNA.
-ArWeCarbon
howard hershey
R. Dunno wrote:
Note that they say that humans share 50% of their *genes* with bananas,
not *DNA*. That makes more sense. After all, banana cells have the
same need for mitosis, meiosis, replication, transcription, and
translation as humans do and share the main, and many minor, metabolic
pathways and enzymes (Krebs cycle, amino acid syntheses, etc.). All of
these 'common features and functions of all eucaryotic cells' are
sometimes collectively called "housekeeping" genes.
Some of the genes that differ, of course, would include genes involved
in photosynthesis, manufacturing cell walls, making immunoglobins, and
serum proteins.
Oh, BTW, the current estimates of the *number* of genes in various
eucaryotes and procaryotes are as follows:
Procaryotes: Mycoplasma genitalium, 473; Haemophilous influenzae, 1709;
Bacillus subtilis & Escherichia coli, both about 4000.
Eucaryotes: Saccharomyces cerevisiae (yeast), 6241; Oxytrichia similis
(a ciliate protozoan), 12,000; Drosophila melanogaster (insect), 13,601;
Caenorhabditis elegans (roundworm, nematode), 18424; chordates
(including mouse, fugu, and human), about 70,000 (estimates run from
30,000 to 100,000 because of difficulty in identifying all genes in a
sequenced genome); Arabidopsis thaliana (a small weed), 16,000-33,000
(range also due to difficulty in identifying genes); Nicotiana tabacum,
43,000.
Many of the genes and gene functions found in E. coli also are
"housekeeping genes" found in and shared by all eucaryotes.
Given their penchant for polyploidy, I would actually expect some plants
(especially ferns) to have more genes than humans. Note that the
numbers of genes do not correlate strongly with intuitive ideas about
'complexity'. In particular, there is little difference in any of the
chordates (from fugu fish to man), chordates have only 2-4 times as many
genes as a simple nematode, plants have more genes than flies and worms
and, in the case of tobacco, chordates have only twice as many genes (or
equivalent numbers if the lower estimates are correct).
puppe...@hotmail.com
> But lets compare two corresponding DNA segments and assume
> no deletions or duplications are present in one but not
> the other. The lowest sharing of DNA one could expect
> is 25% since totally unrelated DNA has a 25% chance per
> base pair for an agreement. (I suppose an "intelligent
> designer" could design a 0% for a lark, but evolution
> could not.)
I suspect that the 25% figure may not be representative.
Though I have not done any reading on the specific question.
But, as my admitedly sketchy understanding goes, there are
many "words" in DNA that are repeated fairly often. That is,
DNA is not random. For example, the coding for a specific
amino acid is the same. (I'm not at all sure about that one,
but I'm going to run with it anyway.) So when a banana wants
a particular amino acid, and a human wants that one also,
then the same word is going to be written.
So, I'm guessing that the 25% (from there being essentially
four "letters" that can be written in DNA) may not be a good
estimate. Though, just off, I can't say what should be a
good estimate. I can imagine that it could be much higher
or much lower depending on how the words line up, how often
each appears, etc.
Socks
John Harshman
dkomo wrote:
Yes, that was from DNA hybridization, which essentially turns the whole
genome into a set of probes. However, that measures the sequence
similarity of homologous sequences, quite a different thing from the
banana comparision.
Philip Deitiker
<lmuc...@yahoo.com> did some sarious thank'n and scribbled:
Identity can be described as a function of strengency. If
you for example search the human genome with any genome
using 16 nt sequences you will find alot of identity.
That is because humans have 10E9 bp of DNA which goes 2
directiosn approximately 10E10 nt. The possible combinations
of nt are:
Length combinations
1. 4
2. 16
3. 64
4. 256
5. 1024
6. 4096
7. 16384
8. 65536
9. 262164
10. 1048576
11. 4194304
12. 16177716
13. 67108864
14. 268435456
15. 1073741824
16. 4294967296
Therefore if you are searching say with 16 nt string one
genome with another you expect ~50% identity for no more
than random reasons.
Certain proteins are rather invariable, like the histone
and actin genes, therefore the coding sequences does not
change, and the ntSequence will change at a minority of
wobble positions.
Therefore one expects a combination of random and
selective events to create identity, and depending on the
strengency of the argument of identity. This argument of
identity has been going on in the feild of molecular
evolution/biology/genetics for some time, and there are a
wide range of feelings on the topic of strengency. However
if one accepts the single common origin of all life and that
in the early stages of life replicative elements were
duplicated in an expanding genome, it means that most
elements can be related by the identity argument sometime.
(In fact 1000s of identity arguments can be made in each
genome).
My point of view on this topic is that identity is something
that is statistcally unquestionable relationship. For
example a p-Value in the 10E-30 range for two sequences.
This is not however the end of the argument. I may be able
to establish identity between say Human and Chimp for some
sequence, the grab gorilla and use the apes to create a
parsimony tree and also create a consensus sequence. I can
then use that consensus sequence to scan other critters and
repeat the process going down various trees until I reach a
point in which my query can give no other matches with other
queries, at which point what it does match the p-values will
rise and you can then define a cluster of identity within a
genome. You can take this information and look to see where
else the various intermediates appear in the genome
(duplications) and also track those genes as they evolve.
With this approach you can go very far back into evolution;
however the limitation is the number of species, genera, and
large taxa that have gone extinct, at some point
you go back far enough the the assymetric expansion within
the extant taxa all fuse together and are distal to proximal
extant taxa.
Particular examples of this are the structural
similarities of Legheamoglobins and Hemoglobins and
Myoglobins. These proteins can be shown to be similar at the
secondary and tertiary levels, but all identity at the
primary sequence level is lost. There is a claim that all
heme-binding proteins are related (hemoglobins, giant
hemoglobins, cytochromes, . . . . . . )
At the nt level the identity is virtually non-exisitent.
There is no way yet to take a consensus nt sequence and
create a correct 3 dimensional structure of a protein it
would encode; however there is sufficient evidence in the
3-D structures of many living organisms to show similar
origins and to do primative gene allignments based on the
tertiary structures. If there is a strong selective
constraint on the structures, such as histones, the task is
easy. If there is are no strong selective constraints, such
as on the rod region of myosin and paramyosin, the task is
much more difficult.
I suspect that as the number of genomes expand one will
see alot more identity matches bases on functionally similar
or derivative structures that shared common origin in the
past. Identity has to be qualified in several ways so that
these different levels of identity will not be confused.
howard hershey
howard hershey wrote:
>
> R. Dunno wrote:
>
>
>>RobinGoodfellow <lmuc...@yahoo.com> wrote:
>>
>>
>>>Some time ago, while browsing the web, I came across an interesting
>>> little factoid, if such it be, that humans share 50 percent of
>>>their DNA with bananas. I don't remember where exactly I read
>>>this, but for some reason I decided that I had no reason to
>>>disbelieve it.
>>
>>
>>You may find something similar to what you're looking for in this
>>NOVA transcript.
>>
>>http://www.pbs.org/wgbh/nova/transcripts/2809genome.html
>>
>>Do a find on 'banana'.
>
>
> Note that they say that humans share 50% of their *genes* with bananas,
> not *DNA*.
I should have said that bananas share 50% of their *genes* with humans.
Otherwise the math won't work, assuming that bananas have half as many
genes as humans.
mel turner
wrote...
[snip]
>> Also note that humans and bananas share most of their
>> evolutionary history.
>
>I thought Chordates and plants have been separate since the Cambrian
>explosion.
Long before that. Their last common ancestor would have been some
Precambrian unicellular eukaryote.
http://tolweb.org/tree?group=Eukaryotes&contgroup=Life
http://www.ucmp.berkeley.edu/alllife/eukaryotasy.html
I don't see how that means we share "...most of our evolutionary
>history."
Well, maybe not necessarily "most", but very likely "more than
half".
If the earliest fossils of multicellular animals are less than 600
million years old,
http://www.ucmp.berkeley.edu/vendian/critters.html
and we allow another several hundred million years before that for the
time of the last common ancestor of plants and animals [perhaps 1500
mya might be a generous enough estimate? That's getting a bit close to
the earliest probable eukaryotic microfossils, IIRC], the first strong
evidence of cellular life would reportedly still be 2000 million years
or so older than that.
http://www.ucmp.berkeley.edu/bacteria/bacteriafr.html
http://www.talkorigins.org/origins/geo_timeline.html
>Of course, if there was actual transfer from the Ediacarian fauna, then
>perhaps we do.
I'm not sure I follow. The Ediacarian things were already
multicellular animals [if animals is what they are]; the LCA of
animals and green plants was unicellular and much earlier.
cheers
observa
Well, yes that as well. But the real mistake I made was forgetting that
*most* evolution actually occurred before the development of the Cambrian
metazoa. In other words, all those changes required to give rise to them.
<Wipes egg off face> I mean. let's face it. The Cambrian explosion gave
rise to all the body plans that now exist. Since then it just been bigger
and hairiier.
Alan Jeffery
Lilith
<snip>
> Thanks for confirming this. I tend to think in terms of overall
> sequence identities, and so when I came across the 50% figure, that's
> what I took it for initially. Ah, well - I guess the banana made a
> monkey out of me. Let that be a lesson in trusting web sites.
There are a limited number of banana fruit sequences in NCBI. For one
species, Musa acuminata (edible banana), there are in the low 100's of
unique genic sequences that are not retroposons, genetic markers,
patents, or repeats, including sequences from subspecies (such as
plantain). Of these ~100, a significant number are only partial genic
sequences. (as an aside, most genes deposited as sequence seem to have
something to do with ripening).
When you try to find the sequences most similar to banana in the
public database, plants like maize pop up (there are a limited number
of plant sequences deposited at NCBI).
For fun, here's the banana vs human acs
(1-aminocyclopropane-1-carboxylate synthase) gene, a random gene I
picked out from Musa.
The similarity between these two genes is measured by how often the
sequences "agree", even if they're randomly hitting the same
nucleotide along the sequence. This gene, encoding an enzyme, has some
recognizable conserved regions and the degree of match between the two
is 40%.
For anyone who's interested, the ID lines follow, before the alignment
of the two genes.
banana acs: AJ605082.1| Musa acuminata mRNA for
1-aminocyclopropane-1-carboxylate synthase (acs gene)
human acs: BC020197.1| Homo sapiens 1-aminocyclopropane-1-carboxylate
synthase, mRNA (cDNA clone MGC:31771 IMAGE:3632065), complete cds
....|....| ....|....| ....|....| ....|....| ....|....|
10 20 30 40 50
human acs CCGAGTGCCA GCACCGCCTC CTCCAGCTCC GCCAAGTAGG TGGGATCCAC
banana acs ---------- ---------- ---------- ---------- ----------
....|....| ....|....| ....|....| ....|....| ....|....|
60 70 80 90 100
human acs TACTTTGCAG AGGAGGAAGC CGTTCAGGCC TCCCTCTGTG CACTTTGCAA
banana acs ---------- ---------- ---------- ---------- ----------
....|....| ....|....| ....|....| ....|....| ....|....|
110 120 130 140 150
human acs AAGCCTCTGC CCTTCCATCT CGAATCCCTT GGCGCCGATC ACACTTCCTC
banana acs -AA-----G- ---------- C--AG----T ---GG-TAT- -CAA------
....|....| ....|....| ....|....| ....|....| ....|....|
160 170 180 190 200
human acs TGCCTGGAAA CCTGGAGCCG TCTCTCGCGA GACGTCCTCC GCCCTGTAGA
banana acs ---C--GC-A ----GA---G --TA-CGCG- GG-GGCAG-C AG-CTGCTT-
....|....| ....|....| ....|....| ....|....| ....|....|
210 220 230 240 250
human acs AGGCCGTTTC GGTTCTTCGT GCGCGGTAGC CGCCCCACTT GCGGGATTCC
banana acs ----C---TC C-TTCTTC-T TCTC--T--- ------GCTC GC-----TTC
....|....| ....|....| ....|....| ....|....| ....|....|
260 270 280 290 300
human acs AAGGCCTCAT CGAGTGCGGG TATCTGGCTG TGGATTCGCC GCCGTCCTGC
banana acs --AGCCTTTT C-----C-GG TACGTACCTG -AGA-T---- AACGG---G-
....|....| ....|....| ....|....| ....|....| ....|....|
310 320 330 340 350
human acs TGGACGCCTG GAGGCTCGAA CCCCGCCGCC CCCCTACCCC AGGCTTTACT
banana acs T---CACAT- GAGGATC-TA ---------- ----TGGCG- AGG----AG-
....|....| ....|....| ....|....| ....|....| ....|....|
360 370 380 390 400
human acs CCCACCCCGG CTTCCGCCCA CTGTGCTGCC CTTCCTCGGA CCTGGGCTGT
banana acs --CACCCAA- -ATCAG---- C--AGATCCT C-T-CTCGGA TCGCGACCAA
....|....| ....|....| ....|....| ....|....| ....|....|
410 420 430 440 450
human acs CGGGAGAGCT GGAGATGTTC ACCCTTCCTC AAAAGGACTT CAGGGCTCCC
banana acs CGACGGCCAT GGCGA-G--- A-AC-TCCTC -------CTA CT----T---
....|....| ....|....| ....|....| ....|....| ....|....|
460 470 480 490 500
human acs ACCACCTGTC TGGGCCCCAC CTGCATGCAG GACCTGGGCA GTAGCCATGG
banana acs --C-GATGGC T-GG-AAGGC CTACGAGAAG GATCCTTTC- -CA-CCTCAC
....|....| ....|....| ....|....| ....|....| ....|....|
510 520 530 540 550
human acs GGAAGATCTG GAAGGAGAAT GCTCCAGAAA ACTGGACCAG AAGCTGCCAG
banana acs CGATAACCCC -ACGG-G--- G-----GTC- A-T----C-C AAA-TGG--G
....|....| ....|....| ....|....| ....|....| ....|....|
560 570 580 590 600
human acs AGCTCCGTGG AGTGGGTGAT CCTGCCATGA TCTCCTCTGA TACCTCCTAC
banana acs A-C-TC--GC AGA-----AA A---CCA-GC T-TTCCCTCG -A-CTTG-A-
....|....| ....|....| ....|....| ....|....| ....|....|
610 620 630 640 650
human acs CTGTCCTCTA GAGGAAGAAT GATTAAATGG TTCTGGGATT CAGCTGAGGA
banana acs ---T-C-C-- ----GAGACT GGATGAA--- ------G--- -A----A-GA
....|....| ....|....| ....|....| ....|....| ....|....|
660 670 680 690 700
human acs GGGCTACAGG ACCTACCACA TGGATGAGTA TGATGAGGAC AAGAACCCCA
banana acs A-CCCACAGG --CTTCGATC TGCA--CCGA AGAAGGGGTC T-----CAGA
....|....| ....|....| ....|....| ....|....| ....|....|
710 720 730 740 750
human acs GTGGCATCAT TAACTTGGGC ACCAGTGAGA ACAAACTCTG CTTTGACCTG
banana acs GT-TCAA-AG -CAATT-GCC AACTTTCAG- ---GATTATC A--TGGCCTC
....|....| ....|....| ....|....| ....|....| ....|....|
760 770 780 790 800
human acs CTGTCCTGGC GGCTGAGTCA GCGCGACATG CAGAGGGTGG AGCCATCCCT
banana acs CCAGCCTT-- --CC--GA-A AGGCCATC-G C--------- --CCAGTTCA
....|....| ....|....| ....|....| ....|....| ....|....|
810 820 830 840 850
human acs GCTGCAGTAT GCTGACTGGA GGGGACATCT GTTCCTCCGG GAGGAAGTGG
banana acs --TGGAG-AA G--G--T-GA AAGGAG---- G-ACGAGCC- -A-GATTTGA
....|....| ....|....| ....|....| ....|....| ....|....|
860 870 880 890 900
human acs CCAAGTTCCT GTCTTTCTAC TGCAAGAGCC CAGTACCCCT CAGACCAGAG
banana acs CCCAG--ACC --GCATC--G T-GATGAGCG GCGGA--GC- C--ACC----
....|....| ....|....| ....|....| ....|....| ....|....|
910 920 930 940 950
human acs AATGTGGTTG TCCTGAATGG TGGTGCCTCG CTCTTCTCTG CTCTGGCCAC
banana acs ------GGCG --CT-CA--- -GGAA----- ACCATCGC-- CTTTT-GC-C
....|....| ....|....| ....|....| ....|....| ....|....|
960 970 980 990 1000
human acs GGTGCTGTGT GAGGCCGGGG AGGCTTTCCT GATCCCCACC CCTTACTATG
banana acs TG-GC----T GATCCTGGCG AGGCCTTCTT GATTCCAACG CCATATTAT-
....|....| ....|....| ....|....| ....|....| ....|....|
1010 1020 1030 1040 1050
human acs GCGCTATCAC ACAGCACGTG TGTCTCTATG GCAACATCCG GCTGGCCTAT
banana acs CCGGGGTT-- -C--GATC-G AG--AC--TT ----CAGGTG GAGGACAGGA
....|....| ....|....| ....|....| ....|....| ....|....|
1060 1070 1080 1090 1100
human acs GTCTACCTGG ACAGTGAGGT CACTGGGCTA GACACACGCC CCTTCCAGCT
banana acs GTTCAGCTCC TCCC-CA-TT CACTGCCACA GTTCCAACAA G-TTCAAGAT
....|....| ....|....| ....|....| ....|....| ....|....|
1110 1120 1130 1140 1150
human acs CACAGTGGAG AAGCTGGAGA TGGCCCTGAG AGAAGCTC-A CTCTGAGGGT
banana acs CACCCAAGCC GCACTGGAGA CTGCTTATAG AAAGGCTCGA AACTCACACA
....|....| ....|....| ....|....| ....|....| ....|....|
1160 1170 1180 1190 1200
human acs GTGAAGGTCA AAGGCCTCAT CCTCATCAGC CCCCAGAACC CTCTGGGTGA
banana acs TTCGA-GTCA AAGGAATCGT GGTGACCAAG CCATCGAACC CTCT--G-G-
....|....| ....|....| ....|....| ....|....| ....|....|
1210 1220 1230 1240 1250
human acs TGTATACTCC CCT-G-AAGA GCTACA-GGA GTA-CCTGGT ---ATTTGCC
banana acs -G--CACAAC CATGGACAGA GACACGCTGA GAACCCTAGT CAGCTTCGTC
....|....| ....|....| ....|....| ....|....| ....|....|
1260 1270 1280 1290 1300
human acs AAGAGGCACA GGCTGCATGT GATTGTGGAT GAGGTCTACA TGTTGTCCGT
banana acs AACGAGAAAA GGATGCACTT GGTGTGCGAC GAGGTCTTCT CCGGAACCGT
....|....| ....|....| ....|....| ....|....| ....|....|
1310 1320 1330 1340 1350
human acs GTTTGAGAAG TC-TGTTGGG T-ACCG-CAG TGTCCTAAGC CTGGAAAGGC
banana acs CTTCGACAAG CCGAGTTACG TGAGCGTCGC CGAGGTGATC C--AAGACGA
....|....| ....|....| ....|....| ....|....| ....|....|
1360 1370 1380 1390 1400
human acs TCCCTGACCC CCAGA-GGAC CCATGTGATG T-GG--GCAA -C-CAGCAAG
banana acs TCCCT-ACTG CGACAGGGAT CTGATTCACA TCGCCTACAG CCTCTCCAAG
....|....| ....|....| ....|....| ....|....| ....|....|
1410 1420 1430 1440 1450
human acs GACTTCGGGA TGTCTGGGCT CCGCTTTGGC ACGCTGTACA CAGAAAACCA
banana acs GACCTGGGCG TCCCTGGCTT CCGCGTCGGC GTCATATACT CCTACAACGA
....|....| ....|....| ....|....| ....|....| ....|....|
1460 1470 1480 1490 1500
human acs GGATGTGGCC A-CTGC-CGT GGCTTCCCTC TGCCGCTACC ACGGCCTCAG
banana acs CGCCGTGGTC AGCTGCGCGA GGAAGATGTC GAGCTTCGGA CTGGTCTC-G
....|....| ....|....| ....|....| ....|....| ....|....|
1510 1520 1530 1540 1550
human acs TGGCTTGGTC CAGTACCAGA TGGCACAGCT GCTCCGGGAC CGTGACTGGA
banana acs TCGC-AGACG CAGCACCTGC TCGCTTCCAT GTTGGGAGAC GAGGAGTTCA
....|....| ....|....| ....|....| ....|....| ....|....|
1560 1570 1580 1590 1600
human acs TCAACCAGGT GTACCTGCCG GAAAACCATG CCCGGCTCAA GGCTGCCCAC
banana acs -CCA-CAAGT -TTCTTAGCG ACGAGCCGGA CGAGGTTGTG CGGGCGGCGC
....|....| ....|....| ....|....| ....|....| ....|....|
1610 1620 1630 1640 1650
human acs ACCTATGTCT CAGAAGAGCT TAGGGCATTG GGGATCCCCT TCTTGAGTCG
banana acs AGGGTCTTTA CGGACGGCCT CAAGCGAGTC GGGATTCATT GCTTGGACGG
....|....| ....|....| ....|....| ....|....| ....|....|
1660 1670 1680 1690 1700
human acs TGGGGCTGGC TTCTTCATCT GGGTTGACTT GAGAAAGTAC CTGCTCAAGG
banana acs CAATGCGGGT CTCTTCTGCT GGATGGACTT GAGGCCGT-- -TGCTGAA-G
....|....| ....|....| ....|....| ....|....| ....|....|
1710 1720 1730 1740 1750
human acs GCACCTTTGA GGAGGAAATG CTGCTCTGGC GCCGCTTTTT GGACAACAAG
banana acs G-AAGC--GA CGGTGGAG-G CGGAGCT--C -CGGC--TGT GG----C---
....|....| ....|....| ....|....| ....|....| ....|....|
1760 1770 1780 1790 1800
human acs GTGCTGCTGT CCTTTGGCAA GGCCTTCGAG TGTAAAGAGC CTGGTTGGTT
banana acs G-GGTG--AT --CAT--CAA CGACGT-GAA GCTCAACA-T CTCGCC-GG-
....|....| ....|....| ....|....| ....|....| ....|....|
1810 1820 1830 1840 1850
human acs TCGCTTTGTC TTCTCAGACC AGGTCCACCG GCTTTGCCTG GGGATGCAGA
banana acs --G----GTC GTC-CTT-CC ACTGCT--CG GA---GCC-- -GG--G--G-
....|....| ....|....| ....|....| ....|....| ....|....|
1860 1870 1880 1890 1900
human acs GGGTCCAGCA GGTGCTTGCA GGCAAATCCC AAGTGGCAGA AGACCCCCGT
banana acs TGGTTCAG-- GGTG--TGCT ------TCGC CA-----ACA TGG---ACGA
....|....| ....|....| ....|....| ....|....| ....|....|
1910 1920 1930 1940 1950
human acs CCCTCTCAGA GCCAGGAGCC AAGTGACCAA CGCAGGTGAG CTGGTC-ATT
banana acs ------CACG GCCA--TG-- -A-AGATAG- CGCTGAGGAG --GATCGAGA
....|....| ....|....| ....|....| ....|....| ....|....|
1960 1970 1980 1990 2000
human acs GTCTCGTGGC CAGAGGGCCC AGCAGCCACT GTGGACCTGG GGCGTTCTGG
banana acs GTTTCGT--- -----GTACC GGGAG--AAC ---GA-C--- -GCCG-CT--
....|....| ....|....| ....|....| ....|....| ....|....|
2010 2020 2030 2040 2050
human acs GGCTGCAGAA GACTGACTGT GGATGTGCCA TTTGCCAGGA AGGTATCTAA
banana acs -G-TGCAGGC GAA-GA---- --ACAAG--A ---GG-AGGT -GGGA-CG-A
....|....| ....|....| ....|....| ....|....| ....|....|
2060 2070 2080 2090 2100
human acs CTTGGCTTTG TGCCTGAAGA ACTGTTTCTT GTCTTTCGCT GTAGCAGTGG
banana acs A---GCGCTG CGGCT---GA GCT-TGCCTC GTCGGAGGTT CGAGGA-TCC
....|....| ....|....| ....|....| ....|....| ....|....|
2110 2120 2130 2140 2150
human acs GAAACTCCTT AAGCTGTGGT TCAGCCTGGG CCCTCCCTCT CTCCTATTAA
banana acs G-ACCATCAT GA-CAC---C ACATCTGATG TCTCCCCACT CGCC---T--
....|....| ....|....| ....|....| ....|....|
2160 2170 2180 2190
human acs ACAAAACTAG GAGAGTCAAA AAAAAAAAAA AAAAAAAAAA
banana acs ------CT-- ---AGTTCAA GCCGCC---- ----ACCTGA
John Harshman
observa wrote:
This assertion has two problems. First, how to define body plans.
Second, a majority of phyla having no fossil records or very sparse
ones, how do you tell whether or not they arose in the Cambrian? And of
course there are a few with good fossil records that most certainly did
not arise in the Cambrian, including all plant phyla.
And the divergence between animals and plants probably arose long before
the Cambrian -- that was my 1by estimate above.
observa
Well, maybe a lot of body plans did arise before the Cambrian, but do we
have any evidence? Based on a statement of Gould's (can't remember the
book - its the one where he has the essay about the fella who discovered the
Burgess Shale - I think). Also, what we do know about the Ediacaran flora
and fauna tends to indicate, for the fauna at least, that it appeared to be
based on quite different body plans from those which arose during the
Cambrian. Do we have any fossil specimens that are undoubtably animals, and
are also pre-Cambrian?
But back that issue that gave rise to this discussion. I have no idea
whether the "basic " genomes (?) DNA sequences (?) (I'm not a specialist
here) could have crossed the "barrier" from the Ediacaran extinction to the
Cambrian explosion, but it appears possible they did. I don't think
everything was wiped out.
John Harshman
observa wrote:
I was talking mostly about *after* the Cambrian. Plants arose after, as
did bryozoans, and we have no good evidence about many of the other
metazoan phyla. (There is also a problem with what "arose" means;
divergence of two groups may have a very different time frame from the
origin of the defining characters of either of them.)
> Based on a statement of Gould's (can't remember the
> book - its the one where he has the essay about the fella who discovered the
> Burgess Shale - I think).
You are almost certainly thinking of Wonderful Life. What statement, though?
> Also, what we do know about the Ediacaran flora
> and fauna tends to indicate, for the fauna at least, that it appeared to be
> based on quite different body plans from those which arose during the
> Cambrian. Do we have any fossil specimens that are undoubtably animals, and
> are also pre-Cambrian?
Yes, we do. The least controversial would be the phosphatized metazoan
embryos from the late Precambrian. Many of the Ediacaran species are
interpreted as metazoans of various sorts, with various degrees of
confidence; unfortunately, Ediacaran preservation is generally nowhere
near as detailed as Burgess preservation.
> But back that issue that gave rise to this discussion. I have no idea
> whether the "basic " genomes (?) DNA sequences (?) (I'm not a specialist
> here) could have crossed the "barrier" from the Ediacaran extinction to the
> Cambrian explosion, but it appears possible they did. I don't think
> everything was wiped out.
Of course they did. Nobody thinks that life began all over during the
Cambrian. All Cambrian organisms had ancestors in the Precambrian.
observa
"Arose" - sloppy use of word. Should have said developed.
>
> > Based on a statement of Gould's (can't remember the
> > book - its the one where he has the essay about the fella who discovered
the
> > Burgess Shale - I think).
>
>
> You are almost certainly thinking of Wonderful Life. What statement,
though?
No, not Wonderful Life. I don't have it, and haven't read it. One of his
essay compendia - like "Bully for Brontosuarus".
>
> > Also, what we do know about the Ediacaran flora
> > and fauna tends to indicate, for the fauna at least, that it appeared to
be
> > based on quite different body plans from those which arose during the
> > Cambrian. Do we have any fossil specimens that are undoubtably animals,
and
> > are also pre-Cambrian?
>
>
> Yes, we do. The least controversial would be the phosphatized metazoan
> embryos from the late Precambrian. Many of the Ediacaran species are
> interpreted as metazoans of various sorts, with various degrees of
> confidence; unfortunately, Ediacaran preservation is generally nowhere
> near as detailed as Burgess preservation.
>
> > But back that issue that gave rise to this discussion. I have no idea
> > whether the "basic " genomes (?) DNA sequences (?) (I'm not a specialist
> > here) could have crossed the "barrier" from the Ediacaran extinction to
the
> > Cambrian explosion, but it appears possible they did. I don't think
> > everything was wiped out.
>
>
> Of course they did. Nobody thinks that life began all over during the
> Cambrian. All Cambrian organisms had ancestors in the Precambrian.
>
Stanley Friesen
>> Also note that humans and bananas share most of their
>> evolutionary history.
>
>I thought Chordates and plants have been separate since the Cambrian
>explosion. I don't see how that means we share "...most of our evolutionary
>history."
Life originated around 3 to 4 *billion* years ago. Plants and animals
have been separate for around a billion (well before the Cambrian
actually). This leaves around 2 to 3 billion years of common heritage -
two to three times longer than the time since the split.
The peace of God be with you.
Stanley Friesen
Elessar
<snip>
> This leaves around 2 to 3 billion years of common heritage
Banana ... split ... oh never mind.
--
Laurie R
RobinGoodfellow
About 18% percent of the time, actually. However, for random 32 nt
strings, this probability drops to around 0.2%, and by the time you are
comparing 100 nt stretches, the odds of >50% identity between two
randomly selected sequences are pretty much nil.
Yeah, I think this example is really cool. Leghemoglobins and
Myoglobins have nearly indistinguishable tertiary structure, yet their
level of sequence identity is pretty much what you'd expect when you
align two random sequences. A great illustration of how "accomodating"
certain folds can be.
ArWeGod
news:br9jha$r814$1...@ID-195053.news.uni-berlin.de...
I think you are on to something. Banana. Cow. Pineapple.
Someone else will have to take it from here...
Traklman
>From: "ArWeGod" ArWeGod?@sbcglobal.net
>Date: 12/11/2003 6:07 AM Central Standard Time
>Message-id: <%9ZBb.37038$um7....@newssvr29.news.prodigy.com>
Banana. Banana. Cherry -damn!
Friggin' one-armed bandits.