Fletis Humplebacker wrote:
John Harshman wrote:
Fletis Humplebacker wrote:
Wrong. I've advocated all along at looking at the real data and
you can't avoid the philosophical aspects of evolution since
it is often driven by a philosophical approach.
Can you back that up?
Yes, I've given a few examples of evolutionist filling in the gaps
when the evidence didn't quite support it. That goes back to Darwin.
You have given no such examples, nor have you shown that any of this, if
it exists, is driven by some philosophical approach.
Sure I have. Darwinian Evolution predicts gradual change over long
periods, the fossil record says otherwise so for many people we have
ideology over scientific evidence. In talking to you, you refuse to accept
what the leaders in the field have to say because they are posted
on religious sites. You are putting your ideology over facts.
No, I refuse to accept your interpretation of what they say because it's
wrong, which you could see if you read the entire documents those little
quote mines are taken from. Darwinian evolution predicts gradual change,
true, but the long periods are only with respect to human lifetimes, not
geological eras.
STEPHEN J. GOULD, HARVARD, "The Cambrian Explosion occurred
in a geological moment, and we have reason to think that all major
anatomical designs may have made their evolutionary appearance at
that time. ...not only the phylum Chordata itself, but also all its major
divisions, arose within the Cambrian Explosion. So much for chordate
uniqueness... Contrary to Darwin's expectation that new data would
reveal gradualistic continuity with slow and steady expansion, all major
discoveries of the past century have only heightened the massiveness
and geological abruptness of this formative event..." Nature, Vol.377,
26 10/95, p.682
Gould had an axe to grind. You are right about one thing, that people
tend to interpret data to fit their theories. That's why science is a
social effort and can't depend on one person. Others have shown how
Gould misinterpreted some of what he saw. The Cambrian explosion may
have spawned most phyla, though we can't tell this from the fossil
record, and there are some phyla that clearly did not originate then.
Chordates and the major divisions of Cephalochordata, Urochordata, and
Vertebrata (or at least their stem groups) may well have originated in
the explosion. The explosion may have lasted as little as 5 million
years. But do you have any real idea how long 5 million years is?
Do you ever wonder, by the way, what used to be in the the ellipses in
all these quotes you get from creationist sites?
Preston Cloud & Martin F. Glaessner, "Ever since Darwin, the geologically
abrupt appearance and rapid diversification of early animal life have fascinated
biologist and students of Earth history alike....This interval, plus Early Cambrian,
was the time during which metazoan life diversified into nearly all of the major
phyla and most of the invertebrate classes and orders subsequently known."
Science, Aug.27, 1982
What do you think Cloud and Glaessner meant by "this interval"? They
clearly aren't talking about the Cambrian explosion, because they say
"plus Early Cambrian". I don't know what they mean, but most classes
don't come along until the Ordovician or later, and most orders not
until the late Paleozoic. Also note that they are talking here about
just those phyla with good fossil records.
RICHARD Monastersky, Earth Science Ed., Science News, "The remarkably
complex forms of animals we see today suddenly appeared. ...This moment,
right at the start of the Earth's Cambrian Period...marks the evolutionary
explosion that filled the seas with the earth's first complex creatures. ...‘This
is Genesis material,’ gushed one researcher. ...demonstrates that the large
animal phyla of today were present already in the early Cambrian and that
they were as distinct from each other as they are today...a menagerie of clam
cousins, sponges, segmented worms, and other invertevrates that would seem
vaguely familiar to any scuba diver." Discover, p.40, 4/93
You did this one before. I guess that was before the newest radiometric
dates showed that most of the Early Cambrian came before the Cambrian
explosion. And look at all the ellipses here. If you do this with the
bible, you can come up with stuff like "Luke...I am...your father."
Quote mining is bad practice, especially when you have to stitch
together sentence fragments.
Richard Dawkins, Cambridge, "And we find many of them already in an advanced
state of evolution, the very first time they appear. It is as though they were just
planted there, without any evolutionary history. Needless to say, this appearance
of sudden planting has delighted creationists. ...the only alternative explanation of
the sudden appearance of so many complex animal types in the Cambrian era is
divine creation...", The Blind Watchmaker, 1986, p229-230
I wonder what Dawkins really said.
What makes you think the Cambrian explosion is at odds with Darwinian
theory? Your problem is that you get all your information from
creationist web sites.
Not exclusively, in fact I've quoted from evolutionists many times.
Almost exclusively quote mines taken from creationist web sites.
Call them whatever you want, it doesn't change the significance of the
meanings. It isn't hard to figure out why they aren't prominent on evolutionist
sites.
Conspiracy again? You don't understand the meanings, as Steven J. Gould
has specifically pointed out to you and other creationists.
I posted many more than just that particular comment by Gould.
If someone doesn't buy the spin it doesn't mean that they didn't
understand the comment.
Whose spin should you buy, if not the author's? Opinions of the state of
science formed by reading carefully selected, mined quotes (especially
the ones full of suspicious deletions) surrounded by creationist
interpretation, are not reliable. You need to read the actual writings
of these authors, in full.
As a start, the Quote Mine Project can help you with some of them:
http://www.talkorigins.org/faqs/quotes/mine/author.html
Yes it is at odds, how can you deny it? The evolutionist community
admits it. Are you ignoring all the quotes that you don't like?
The quotes you are talking about generally have nothing to do with the
Cambrian explosion. They are pretty much all talking about stasis and
punctuation among similar species throughout the history of life.
Some distinctly mentioned evolution in general. I understand that the fossil
record of smooth transitions within a species is rare but not unknown. Gaps
within a species isn't evidence of transitions between species.
That made no sense at all. We're talking about smooth transitions
*between* species, not within them. They are rare but not unknown. More
important, they have nothing to do with the reality of common descent.
You keep falling back on "similar species" as evidence of
transitions. I haven't seen any evidence of one species
changing to another. I'll requote:
Richard Dawkins, Cambridge, "And we find many of them already in an
advanced state of evolution, the very first time they appear."
Which looks an awful lot like an ideological way of looking
at it.
You seem to freely wander between subspecies and phyla without realizing
it. Let's take trilobites. The first trilobites already appear with all
the characteristics of the class, though subsequently species appear in
close temporal (and often spatial) relationships with similar species.
However, these trilobites are distinguished partly by a mineralized
skeleton that makes preservation easy. We have a few clues to
non-mineralized forms in cases of exceptional preservation. One such is
Naraoia. Interestingly, Naraoia does not display *all* the
characteristics of a trilobite, though it has most of them. It's a
transitional fossil. Other transitional fossils embed trilobites within
arthropods, and arthropods within a larger group of "lobopods".
Anomalocaris is a particularly intriguing transitional form, with one
pair of jointed limbs only.
Before that, there are some Precambrian fossils that suggest arthropod
relationships, notably Kimberella, Spriggina, and Parvancorina, though
preservation is not detailed enough to be clear. Fossil tracks that look
like arthropod trails are preserved from the Lat Precambrian, and
increase in size, frequency, and complexity as the Cambrian explosion
approaches. All this is evidence for the existence of trilobites and/or
their ancestors before the explosion.
Is it your view that every species was separately created during the
past 500+ million years?
Not in the strict sense of the word species. I agree that a species
diversifies over time due to the environment they are in. Humans
that are separated change too but that doesn't prove that they came
from apes.
Could you be more specific? How do you recognize separately created
kinds, and distinguish them from species that are related through common
descent? How, for example, did you determine that humans and apes are
not related?
I don't assume that the relation between species exists. Men and
apes aren't the same species, positing that they are related is an
ideological statement.
Communication is being hindered by your use of multiple meanings for
words. You agree that species were not created separately, but then you
claim that being separate species is evidence for separate creation.
Again: how would you determine whether two organisms are or are not
related through a common ancestor? How are you able to apply this to
determine that humans and apes are not related?
http://www.origins.org/articles/john...hofdarwin.html
The reason the theory of evolution is so controversial is that it is the main
scientific prop for scientific naturalism. Students first learn that "evolution
is a fact," and then they gradually learn more and more about what that
"fact" means. It means that all living things are the product of mindless
material forces such as chemical laws, natural selection, and random
variation. So God is totally out of the picture, and humans (like everything
else) are the accidental product of a purposeless universe. Do you wonder
why a lot of people suspect that these claims go far beyond the available
evidence?
What makes you think that anyone is teaching that last bit to any students?
I didn't just fall of of the tunip truck on the way into town. Why do you
suppose there is a ID movement regarding public education?
Well, that information is contained in the Wedge document.
http://wiki.cotch.net/index.php/Wedge_document
The purpose is to restore western civilization to its Christian roots.
God forbid.
Not a big fan of the First Amendment, are you?
You lost me there. What's the relevance of the first Amendment?
Restoring western civilization to its (supposed) Christian roots would
require some form of establishment of religion.
Nothing to do with science, you will note. It's all about supposed
cultural benefits, motivated by religion. And science doesn't teach that
the universe is purposeless or that god is out of the picture.
Very true, the problem is that's the way science is erroneously
presented, hence the movement. They are not anti-science. They
are against the 'materialism is the only answer possible' crowd,
who unfortunantly has the reigns in public education.
I have asked you for evidence of this assertion, and you responded with
irrelevancies, then repeated your assertion. No wonder creationism isn't
considered intellectually respectable.
I quoted right out of my science book, you must have mentally
filtered it out and respond with an insult. No wonder some people
can recognize denial when they see it.
You quoted something that says nothing about what you claimed. Merely
supposing that life originated by natural processes does not deny the
existence of god or posit a purposeless universe.
It merely
tries to find testable explanations of past events. God, because of the
vagueness of the concept, is nearly impossible to investigate. You might
as well complain about the atheism of chemistry or physics.
Chemistry? No, I don't see that but philosophy does find it's way
into physics as well when we discuss origins. Many, many theories
abound and are no doubt taught in class. Anything but God.
True, 'god' is vague except within a religion, which is why the
ID supporters use the term Intelligent Designer. That does not
imply any particular religious connotation.
Wink wink, nudge nudge.
I see, so you can't be Jewish, Hindu, Muslim or make up your own
interpretation and believe in an Intelligent Designer? Wink wink indeed.
You could. But the ID movement seems to consist entirely of conservative
Christians (assuming you agree that Moonies count as Christians).
And I repeat: find me anyone who is teaching, in a biology course
anywhere, that humans are the accidental product of a purposeless
universe.
Probably most do by implication, maybe some outright. Believe it
or not I went to school. When one is taught that life formed by
chemical reactions, maybe triggered by lightening and crawled out
of the mud, all on it's own somehow, what do you suppose the message
is? Science can't say for certain that it's all natural (or supernatural)
but look at how hard people fight at the slightest hint of the G word.
Tell me people aren't conditioned.
In other words, you can't support your claim. Noted.
In other words, you can't respond directly to it. Noted. If you
were right there would be no response to the schools by the
IDers. I'll let any reader decide who is in denial.
Fair enough, assuming there are any readers.
Find a biology text that says this. Anything other than an
unsupported claim from a creationist web site.
I'll quote you from my old college book I have right here,
"Fundamentals of Physical Science" page 571:
"Today the nature of life no longer seems as penetrable as it once
did, and the transition from lifeless matter to living matter, though
still hardly an open book, nevertheless seems more to be an
inevitable sequel to to the physical and chemical conditions that
prevailed on the earth some billions of years ago than a supernatural
event".
Notice: no mention of a purposeless universe or the nonexistence of god.
A natural origin of life is quite a different thing.
Please explain how a natural origin can have any purpose.
Or how supernatural events being unlikely does not mean
that no god was involved. Science can't know that because
there's no evidence of it. So explain how thqat doesn't go
beyond scientific claims. Are you a politician?
Nope, nor a theologian. You want to talk to a Christian who believes
this, or read a book by one. I've already recommended such a book, but
there are plenty more. I'll just say that since there is a substantial
body of theology contradicting your claims, and plenty of Christians who
believe both in god and a natural origin of life, there must be
something wrong with your belief in that regard.
If the Academy meant to teach scientific investigation, rather than to inculcate
a belief system, it would encourage students to think about why, if natural
selection has been continuously active in creating, the observed examples
involve very limited back-and-forth variation that doesn't seem to be going
anywhere. But skepticism of that kind might spread and threaten the whole
system of naturalistic belief. Why is the fossil record overall so difficult to
reconcile with the steady process of gradual transformation predicted by the
neo-Darwinian theory?
Simple: because neo-Darwinian theory doesn't predict a steady process of
gradual transformation.
I suppose it depends on how you define gradual, but the concept
seems to refer to gradual overall change over time in sporatic bursts.
Exactly. "Gradual" to a population geneticist means a few thousand
generations at most, which is much too short a time to register in the
fossil record.
Hmmm. Consider me skeptical on that one.
What, exactly, are you skeptical about here?
What you said. A few thousand generations won't show up in the
fossil record at all?
Yes. Deposition is highly episodic, and so is preservation. The
time-resolution that's possible in the record gets worse as we go back.
One of the best-studied intervals is the K-T boundary, 65 million years
ago, and it's very difficult even there to detect a difference in time
of less than 100,000 years.
It would take exceptional conditions to produce a change,
under selection, that was slow enough to observe, or a preserved
sequence with stratigraphic control precise enough, to observe.
First you say Darwinian doesn't predict smooth transitions and now
you're saying they can't be found anyway. That's covering your bases
pretty well.
I'll try to be clear. Evolution as currently understood does predict
smooth transitions, but it predicts those transitions to happen quickly
in geological terms, such that it would be unlikely (given the nature of
the fossil record) for many of them to be preserved. It's an obvious
effect of the incompleteness of the record and the episodic nature of
change.
So it's too quick to even be recorded so any biological gaps between
species are asserted as being there, and perfectly natural.
No ideology there!
This is merely based on what we know of natural selection, by observing
events in real time, plus what we know of sedimentation, ditto. There is
a whole field, taphonomy, devoted to questions like this. All Eldredge
and Gould did was put the two together for the first time.
There's lots of theories out there but no evidence that natural
forces are the primary cause. It doesn't seem likely to me, it
doesn't seem likely to many, and yes, that includes educated
folks, they aren't all Bible thumping inbred hayseeds.
The evidence that natural processes (or whatever processes there may be)
are the causes of evolution is just not obtainable from the fossil
record. You need to look elsewhere.
I didn't limit my comment to fossil evidence.
OK.
We can observe processes happening
in the present,
No one disputes that.
Well, some creationists do. But I'll accept that you don't.
I haven't seen any creationist make those claims. The
terms micro and macro evolution are used to draw the
distinction.
Creationists often dispute any sort of evolution by reflex. Consider the
common creationist attempts to dismiss the peppered moth story as
incorrect, when it's actually just a very simple example of
microevolution. But this is an irrelevant digression.
and we can look within the genome to infer past
processes. So far, we don't find anything other than mutation,
selection, drift, etc., though there are quite a few bizarre wrinkles.
Perhaps all the processes you suppose, whatever they may be, happened
only in the distant past and are not operating now. But why should that be?
I don't agree that changes within a species is evidence they can
become a different species. Unless you use the term species
in a narrow sense.
I'm not talking just about changes within a species. I'm talking about
differences between species too. There is no sign of any processes other
than the ones we know about already. Though I'm not sure what
creationist processes there would be, or how you would recognize them.
The processes are adaptability, or survival of the fittest. Bigger, faster,
more or less colorful, etc. but no sign of becoming anything but what
they basically were. That's all the creationist can recognize because
that's all there is as far as we know.
The problem here is that "what they basically were" is meaningless.
Little differences can add up to big differences. I don't know where you
would draw the line between still being "what they basically were" and
something new, but whatever it is, there is good evidence for that line
being crossed. Human evolution is a simple example. Keep reading; it's
at the end of this post.
http://cogweb.ucla.edu/ep/Evolution.html
Gradualism. All the way back to Darwin, the notion that changes accrue
gradually over long periods of time has been a central proposition of
evolutionary theory. As Ernst Mayr put it in Animal Species and Evolution
(1963), "all evolution is due to the accumulation of small genetic changes" (p. 586).
In contrast, the fossil record suggests long periods of stasis followed by brief
periods of rapid change - what Niles Eldredge and Stephen J. Gould dubbed
punctuated equilibrium. This data has sometimes been taken as evidence
against the neo-Darwinian model by people who believe the order of nature is
due to the intentional act or acts of a supernatural being. Within the scientific
tradition, the relative lack of continuous change in the fossil record is interpreted
as evidence that speciation events have typically taken place in small populations
over relatively short periods of time.
As you suggested above, all this is due to a confusion over timescales
and the meaning of "gradual". Even to Eldredge and Gould, "brief periods
of rapid change" encompassed thousands of years. In fact, one of the
main problems of the fossil record is figuring out why change is so
slow, when natural selection is capable of driving change much, much
faster than we observe there.
I think about that almost every time I purchase groceries.
I notice you often resort to inane quips. Do they help you avoid
thinking about this sort of thing?
I haven't exactly avoided it so far. You think it's natural, I don't.
That doesn't mean that you thought about it and I didn't.
You don't wonder why change is so slow. You claim it can't happen at
all. Different thing.
How would the theory fare if we did not assume at
the start that nature had to do its own creating, so a naturalistic creation
mechanism simply has to exist regardless of the evidence? These are the
kinds of questions the Darwinists don't want to encourage students to ask.
True, because they're stupid "Have you stopped beating your wife?" sorts
of questions.
Not so fast there. I think we both went to school. I definitely got
the idea that only natural means were at play for the creation
of life, it's transformation and the universe. I understand not teaching
any religious interpretations but science cannot honestly make those
claims.
As for the universe, you'll have to check with somebody else. I only
deal with biology, with a little geology on the side. Natural processes
are all we can profitably investigate, and so we do. This has nothing to
do with a "purposeless universe". But that's theology, not biology.
Since a great many Christians have no problem with a natural course of
evolution, or even a natural origin of life, that much must be clear.
Evolution is subject to interpretation, so is religion, including
Christianity. But no Christian would attribute life to natural causes.
Plenty of them do, in fact.
I've never once heard that and I've heard one extreme of Christianity
to the other. I don't think you can support that.
Read Kenneth Miller's book.
Many Christians believe that god operates
through natural causes.
That's a contradiction.
Take it up with them.
Perhaps you would not consider them real
Christians. Read Kenneth Miller's book Finding Darwin's God, for example.
If you paraphrased it accurately I would have problems with it.
Not at issue. You said that there were no such Christians. You can
either accept that there are such Christians, or you can redefine
"Christian" so as to exclude such people. Pick one.
Changing the subject for a minute, how old do you think the earth and
universe are?
According to the oracles of Zoaraster....just kidding. I am an older
earther. I do believe in evolution to some extent but don't see the
evidence for macro-evolution. If I ever do see it I'll need even
more convincing that it was a natural outcome of the existence of
matter. For me, the odds are too great.
There are many separable questions here. There is no good way to
demonstrate that only natural causes were operating in the evolution of
life, so I won't try. Let's concentrate on what I can show, and that's
common descent. That much is clear: all life is descended from common
ancestors. There is some weird hanky-panky going on at the bottom of the
tree (among all those gene-exchanging bacteria), but nearer the top,
it's simpler. All animals (Metazoa), for example, are descended from a
single common ancestor, and we know many of the details of this tree of
descent. We can't rule out that some of the mutations during that long
history were directly caused by divine intervention. (How could we?) But
the history itself is clear.
Well, I can't buy the macro-mutation thing. But like life itself, too many
things need to happen concurently for anything to function. Most
mutations are detrimental, not helpful. and things like limbs turning
into flippers is too much a stretch for me. At some point the legs are
going to be less than efficient as legs and the creature needs to
survive for thousands of generations in a dog eat dog world.
I don't like macromutations either. But your other assertions are wrong.
Most mutations are in fact neutral, neither helpful nor harmful.
I'm more familiar with the human species and haven't seen
more beneficial mutations compared to helpful ones.
Those are the same thing. What did you actually mean? At any rate, most
mutations are visible only if you look inside the genome. They have no
phenotypic effects.
Limbs
did turn into flippers, and there is excellent documentation from
genetic data for this.
Genetic data reveals former forms of a limb?
No. It reveals relationships of common descent. If an animal with
flippers and an animal with limbs are related by common descent, then
either flippers turned into limbs, or limbs into flippers. Greater
sampling of species can reveal which was which, and it turns out to be
the latter. This is supported by fossil evidence too, as it happens.
Exactly how that happened is another question.
But there is no reason to suppose that intermediates would be less than
efficient.
It defies logic.
Why?
Clearly, sea lion flippers are intermediate between dog legs
and dolphin flippers.
I like the way that you say clearly. Are sea lions on their way
to being dogs or dolphins or are they stuck in the intermediate
stage being happy with their limbs just the way they are?
Who knows? They work fine as it is, but they might return to the land or
become even more aquatic, given a change in conditions. But aren't their
legs intermediate? They work as legs, just barely, on those occasions
when the animals venture onto shore. They work well as flippers in the
ocean, though not as well as the fins of dolphins. What is that other
than intermediate?
But do sea lions have any problem surviving? There
are all manner of functional intermediates in the world today, despite
what you may believe.
Let's say that was true for the sake of argument. Up to and including
the halfway point between the dolfin or dog and the sea lion how did
the critter excel in it's environment?
This is known as the Zeno strategy. For every intermediate I bring up,
you can talk about the gap between the intermediates. Every new
intermediate creates two more gaps. Apparently, the only evidence that
you would believe would be a movie showing one animal morphing into
another. This will not be forthcoming, but you should ask yourself why
you make such unreasonable demands, far beyond what you would expect in
any other case.
We don't know every single branch in that big tree, but we know some
beyond doubt. One of the best known, and perhaps most interesting to
you, is the relationship of humans and their various primate cousins.
Are you fanning the flames?
Just stating facts. If you don't want to believe it, you need to find a
way to ignore all the evidence.
What evidence?
See below for a small sample.
You may not like that, but the genetic evidence is overwhelming. I could
show you gene after gene that gives the same result.
Chimps have 48 chromosomes and humans have 46, I believe.
Does your record show how the change occurred?
Indeed it does, very nicely. Two ape chromosomes fused into one human
chromosome, which still retains a sequence resembling a pair of
telomeres, the stuff that's on the end of a chromosome, right at the join.
Here's a pretty good description of the evidence:
http://www.gate.net/~rwms/hum_ape_chrom.html
I'll look into it.
And I couldn't show
you a single gene that gives a different result. If you want, I could
start showing you the actual data, though you would need a bit of
education before you could understand it.
I appreciate that, I got me a ride set up to the big city libery on the next
hay wagon out. Just picture Jed Clampet looking at the cement pond
for the first time.
Buried in that aw shucks stuff, was there a serious request for data?
You betcha.
Here you go.
[You need to view this in a font in which all the characters take up the
same amount of room. If you view it in a proportionally-spaced font,
both the tree and the DNA sequence will fail to line up properly.]
Evidence for human relationships to the other apes.
But first, a primer on DNA and how it can be used to understand
phylogenetic relationships. If you understand
this already, skip ahead to "Here is a set of DNA sequences" below the
dotted line.
DNA is double helix, each half being a twisted string of chemicals,
called bases or nucleotides, on a backbone. The bases come in four
flavors, each with a slightly different chemical formula, which can be
represented as single letters: A, C, G, or T, from the first letters of
each chemical's name. Because each of the two strings completely
determines the other one, we can ignore one of them, and because of
DNA's beads-on-a-string structure, we can completely describe a given
gene by a linear sequence of the four bases. So if I tell you that the
DNA sequence in some gene in some species is AAGAAGCTAGTGTAAGA, I have
completely described that particular part of the DNA molecule.
Different species have slightly different sequences, and when we line up
the corresponding sequences from different species, the patterns of
bases (letters) at each position (or site) in the sequence can tell us
about their relationships. Consider a set of 5 species. At any
particular position in the sequence each species has either A, C, G, or
T. For my purposes I don't care about the particular bases, only about
the patterns of similarity, so I'm going to use a different symbolism to
describe those patterns. I'll use lower case letters to represent
identical bases. So if I say a position has pattern xxxyy, I mean that
the first three species have one base and the last two have another. The
real bases could be TTTCC, GGGAA, or any other combination. There
are many possible patterns: xxxxx, xyzyz, xyxyy, etc. But only a few of
them can be used to determine relationships. It should be obvious that
xxxxx, all bases the same, tells us nothing. If only one base differs,
such as xyxxx, that also tells us nothing except that one species is
different from all the rest; but we already knew it was a separate
species. The only patterns that make a claim of relationships are those
in which two species have one base, and the other three have another:
xxyyy, xyxyx, xxyxy, and so on. (Actually, patterns like xxyzz tell us
something too, just not enough for my current purposes.) Why is this?
Because such patterns split the species into two groups, implying a tree
that looks something like this:
y x If all the species on the left have state y, and
\ / all the species on the right have state x, then
\ / somewhere in the middle (the branch marked *),
y__\_____/ there must have been a change in that site --
/ * \ a mutation -- either from y to x or x to y
/ \ (we can't tell which from this information).
/ \
y x
A little further note: the patterns that I represent in rows above
(xxyyy, etc.) are shown in columns in the DNA sequences below. That is,
in the sequences below, you read across to find the sequence in a single
species, but you read down to read the contents of a single site in five
species. So the first column of the sequence, reading down, would be
AAGAG, which is an xxyxy pattern.
-------------------------------------------------------
Here is a set of DNA sequences. They come from two genes named
ND4 and ND5. If you put them together, they total 694 nucleotides. But
most of those nucleotides either are identical among all the species
here, or they differ in only one species. Those are uninformative about
relationships, so I have removed them, leaving 76 nucleotides that make
some claim. I'll let you look at them for a while.
[ 10 20 30 40 50]
[ . . . . .]
+ 1 2++ 3 11 +4 3 ++ 52+1 2615+4 14+ 3 3+6+
gibbon ACCGCCCCCA TCCCCTCCCT CAAGTCCTAT CCAATCTACT GTACTTTGCC
orangutan ACCACTCCCA CCCTTCCTCC TAAGACTCAC ACAACTCGCC ACACCTCGTC
human GTCATCATCC TTCTTTTTTT AGGAATTTCC TCTCTCCGTC ACGCTCTACT
chimpanzee ATTACCATTC CTTTTTTCCC CGGATTCTCC CTTCTTCATT ATGTCTCATT
gorilla GTTGTTATTA CCTCCCTTTC AAGAACCCCT TTCACCTATC GCGTCCCACT
[ 60 70 ]
[ . . ]
+++ +++1 + + 2 + +++
gibbon CCTACAGCCC AGCCAAACGA CACTAA
orangutan CCTACCGCCT AGCCATTTCA CACTAA
human CCCCTTATTT TCTTGTCCGG TGACCG
chimpanzee TTCCTCATTT TCTTACTCAG TGACCG
gorilla TTCCTTATTC TTTCGCCTAG TGATTA
I've marked with a plus sign all those sites at which gibbon and
orangutan match each other, and the three African apes (including
humans) have a different base but match each other. (That's the xxyyy
pattern mentioned above) These sites all support a relationship among
the African apes, exclusive of gibbon and orangutan. You will note there
are quite a lot of them, 23 to be exact. The sites I have marked with
numbers from 1-6 contradict this relationship. (Sites without numbers
don't have anything to say about this particular question.) We expect a
certain amount of this because sometimes the same mutation will happen
twice in different lineages; we call that homoplasy. However you will
note that there are fewer of these sites, only 22 of them, and more
importantly they contradict each other. Each number stands for a
different hypothesis of relationships; for example, number one is for
sites that support a relationship between gibbons and gorillas, and
number two is for sites that support a relationship between orangutans
and gorillas (all exclusive of the rest). One and two can't be true at
the same time. So we have to consider each competing hypothesis
separately. If you do that it comes out this way:
hypothesis sites supporting pattern
African apes (+) 23 xxyyy
gibbon+gorilla (1) 6 xyyyx
orangutan+gorilla (2) 4 xyxxy
gibbon+human (3) 4 xyxyy
gibbon+chimp (4) 3 xyyxy
orangutan+human (5) 2 xyyxx
orangutan+chimp (6) 2 xyxyx
I think we can see that the African ape hypothesis is way out front, and
the others can be attributed to random homoplasy. This result would be
very difficult to explain by chance.
Let's try a statistical test just to be sure. Let's suppose, as our null
hypothesis, that the sequences are randomized with respect to phylogeny
(perhaps because there is no phylogeny) and that apparent support for
African apes is merely a chance fluctuation. And let's try a chi-square
test. (I'm not going to explain chi-square tests here; just understand
that it's a statistical test that tells us the probability that we would
see the patterns we see if sequence differences were random.) Here it is:
hypothesis obs. exp. (obs.-exp)^2/exp.
African apes (+) 23 6.29 44.4
gibbon+gorilla (1) 6 6.29 0.0
orangutan+gorilla (2) 4 6.29 0.8
gibbon+human (3) 4 6.29 0.8
gibbon+chimp (4) 3 6.29 1.7
orangutan+human (5) 2 6.29 2.9
orangutan+chimp (6) 2 6.29 2.9
sum 44 44 53.7*
(*This column is rounded, so it doesn't quite add up here.)
These are all the possible hypotheses of relationship, and the observed
number of sites supporting them. Expected values would be equal, or the
sum/7. The important column is the third one, which is a measure of the
"strain" between the observed and expected values. The larger the sum of
this column ("the sum of squares"), the greater the strain. There are 6
degrees of freedom (meaning that if we know 6 of the observations, we
automatically know the 7th), and the sum of squares is 53.7. That last
number gets compared to a chi-square distribution to come up with a P value.
It happens that P, or the probability of this amount of asymmetry in the
distribution arising by chance, is very low. When I tried it in Excel, I
got P=8.55*10^-10, or 0.000000000855. That's pretty close to zero, and
chance can be ruled out with great confidence.
Having ruled out chance, now the question is how you account for the
pattern we see. I account for it by supposing that the null hypothesis
is just plain wrong, and that there is a phylogeny, and that the
phylogeny involves the African apes, including humans, being related by
a common ancestor more recent than their common ancestor with orangutans
or gibbons. How about you?
By itself, this is pretty good evidence for the African ape connection.
But if I did this little exercise with any other gene I would get the
same result too. (If you don't believe me I would be glad to do that.)
Why? I say it's because all the genes evolved on the same tree, the true
tree of evolutionary relationships. That's the multiple nested hierarchy
for you.
So what's your alternative explanation for all this? You say...what?
It's because of a necessary similarity between similar organisms? But
out of these 76 sites with informative differences, only 18 involve
differences that change the amino acid composition of the protein; the
rest can have no effect on phenotype. Further, many of those amino acid
changes are to similar amino acids that have no real effect on protein
function. In fact, ND4 and ND5 do exactly the same thing in all
organisms. These nested similarities have nothing to do with function,
so similar design is not a credible explanation.
God did it that way because he felt like it? Fine, but this explains any
possible result. It's not science. We have to ask why god just happened
to feel like doing it in a way that matches the unique expectations of
common descent.
By the way, if you want to see the full data set I pulled this from, go
he
http://www.treebase.org/treebase/console.html
Then search on Author, keyword Hayasaka. Click Submit. You will find
Hayasaka, Kenji. Then click on Search. This brings up one study, in the
frame at middle left. Click on Matrix Fig. 1 to download the sequences.
You can also use this site to view their tree. The publication from
which all this was drawn is Hayasaka, K., T. Gojobori, and S. Horai.
1988. Molecular phylogeny and evolution of primate mitochondrial DNA.
Mol. Biol. Evol., 5:626-644.