Re: The last ancestor of all life

Seanpit wrote:
Ron O wrote:

Of course antibodies evolve greater specificity for specific antigens
very quickly over just a few generations. This is very easy to explain
because it is based on improved binding of a protein that already
binds, in an beneficial way, to a particular protein antigen sequence.
Every single character change that results in an improvement in
antibody binding to the antigen will be rewarded with improved
reproductive advantages. In this way, the antigen acts as a template
for antibody matching - just like in Dawkins' famous "weasel"
algorithm.

So what? What is the difference to what you claim can't happen? Put
your finger on it and demonstrate that there is some very important
difference. Don't just assert that there is a difference, but
demonstrate it. If you claim that there is a gap of 10 or 20
demonstrate it.

I have, many times. I've shown that the gaps involved between
potential steppingstones along the pathway of higher level functions
are many dozens of residue changes wide:

http://www.detectingdesign.com/flagellum.html

You haven't demonstrated anything of the kind. How did you demonstrate
this? Just pointing out differences doesn't mean anything about
whether those differences were selectable or not for some function.
You basically have to backtrack evolution step by step and determine
how the system functioned at each step. Can you do this? Guys like
Dembski couldn't, Behe couldn't, so if you can, why are you keeping it
such a secret? These guys had to finally admit that to make their
design inference mean what they want it to mean that they had to
demonstrate that all likely evolutionary pathways had probabilities so
small that their notion might begin to look viable. They couldn't tell
anyone what the probability of the existence of their option was to
compare, and they couldn't even calculate the probability of a single
relevant evolutionary pathway. What does that say about your claim?
How do you know that these gaps exist? You first have to determine
what the original design was. Since it is probably billions of years
old and parts have been swapped out, lost, and gained since in the
various lineages how are you going to do that? I'll give you a hint,
you can use the notion of common descent and see how well you can
backtrack the evolution of the flagellum using the existing species
with flagellum. You can determine what parts were added later and what
parts might have been lost if extinction hasn't fuzzed up things too
much. You also have the problem with prokaryotes that they have the
ability to pick up DNA from the environment and stick it into their
genomes. So horizontal transfer is going to knock you and make it
harder to determine a possible pathway. It wouldn't be so hard for an
event that happened within the last 100 million years, but when you go
back that far the molecules start losing their evolutionary
information. Science expects that, but how does your notion of what
happened account for such a snafu in determining the mechanism by which
these systems were designed?

That is only the start. After that you have to determine the starting
materials and how they had to change to make the first flagellum. So
let's see how you did this amazing feat and how you determined that
there were these huge unselectable gaps in the creation of these
systems.

How are you determining that these unselectable gaps exist? You can't
do it can you? Why even claim that you can make such an attempt when
you don't even know the sequence of events that you are trying to prove
couldn't happen?


Not only that, but the antibodies have specificity to the antigens by
chance.

Right . . . but the range that need to be covered in order to have at
least some specificity for all foreign antigen types is limited so that
the immune system needs to produce no more than 20 or so billion
different types of antibody sequences up front. After this initial
casting of the net, at least some of these antibodies will bind to at
least some selectably beneficial degree to any foreign antigen. The
evolution of additional specificity, following this initial exposure,
will happen rapidly.

What is limiting the specificity for foreign antigens? We can make
synthetic antigens that have never been seen in nature before and the
immune system still works on them. New enzmatic activities can be
generated using this system.

Where did you get the 20 billion number? Is it the same for elephants
or whales and mice? The bottom line is that you are saying that
selection can work at a level that makes your probability calculations
bogus. You must know that 10E10 is such a small fraction of the total
protein sequence space of an antibody sequence that your calculations
must be laughable. You also have to remember that the immune system
works nearly every time, so the number of initial protein sequences
that can be selected to do the job is much higher than 1 on average in
any individual at any given time, so you probably have to drop that
number one or two orders of magnitude. That just makes your
calculations even more bogus.


You can make up a synthetic antigen that has never been seen
in nature and you will form specific antibodies to it. Not just one,
but many different ones using many different sequences because you can
generate these antibodies in a wide range of different species. So
where did this initial specificity come from?

The initial range of antibody sequences was programmed by design to
produce this range and function of the antibodies and the overall
immune system. The overall immune system function is highly complex and
did not evolve. It was designed. They only aspect of the immune system
that does evolve is antibody specificity for the antigen.

And your evidence for this assertion is....

Oh gee whiz, it looks like all we get is the assertion and nothing
backing it up.

I'd like to see your evidence for the immune system not evolving, when
various taxa don't all have the same immune systems. What do the
differences support? I think that it is some notion called descent
with modification or descent from a common ancestor. You only wish
that the immune systems haven't changed. Why have they changed in such
a way as to support evolutionary ancestral relationships?


How is it different from
taking an existing ATPase and using it to make something like the
flagellar motor?

Because, the function of the flagellar motor is not there originally
like it is for the antibody binding. There is no ATPase that has even
a little bit of the flagellar motility function to start out with.
There is no template upon which to build up the flagellar motility
system one tiny mutation at a time. All these are significant
differences that produce the gap problem for evolution.

The antigen binding ability of the antibody sequence encoded in the
genome doesn't have all the antigen binding capabilities either.
Random mutation of the sequence generates the binding abilities by
chance. A certain number of the variant sequences can bind a given
antigen and usually one wins the race in accumulating new mutations
that improve the antigen binding ability to an immune system effective
level. The new mutations occur in the selected sequence, but they are
still arbitrary with respect to function, right? In what way is this
different from changing an existing ATPase?

Where are the gaps? How did you determine that they exist? Empty
assertion no matter how often repeated is still worthless.


You make these assertions, but you can't back them
up. Why do you think that the assertions are worth anything?

I've shown you example after example. The evidence in literature is
overwhelming. Evolution of functions that cannot use a template just
doesn't happen beyond very low levels of functional complexity - i.e.,
those functions that require a minimum of more than a few thousand
fairly specified bp of DNA. There's not a single example of such a
thing happening in real life nor is this notion statistically tenable
on paper.

Bull pucky, all you have is empty assertion that the gaps exist, you
have never demonstrated that they exist, infact, you have just
demonstrated that you bogus probability argument that you used to
always cough up is bogus, so will we be seeing that probability
argument again in the future? Have you dropped it out of your web
pages?

Show everyone a gap. Put out the sequence and show us the gap that
can't be crossed, and how you determined that it was your type of gap.
Until you can do that, just pointing to the scam systems that
ID/creationist scam artist use doesn't do anything for your argument.
It obvioiusly didn't do anything for the ID/creationists except fool a
lot of rubes. Why would you be using something like the flagellum as
if it meant anything, when the ID scam artists couldn't make anything
out of the argument worth anything. All the flagellar argument was
good for was lying to the creationist rubes through misrepresentation
and lies of ommision. Demonstrate that the flagellar arguments
amounted to anything. Why couldn't they demonstrate that it meant
something in Ohio or Dover? Why keep using an argument that is an
obvious failure? If it was so good, why did the ID/Wedgie creationist
scam artists drop ID for a stupid obfuscation scam that doesn't even
mention that ID ever existed? Go to the Discovery Institute and see
that they are now openly claiming that the creationist replacement scam
is not ID. What does that tell you about the flagellar argument?


The odds that a particular antibody mutation will result in an improved
binding to the antigen are quite high. That is why antibody evolution
happens so rapidly. The problem is that not all functions can evolve
this way - with the use of a template. For example, the flagellar
motility system cannot evolve one residue change at a time via template
matching. There simply is no series of beneficial steps that are
separated by only one or two residue differences in the pathway of
flagellar evolution.

How high are they and why are they different from any other protein
function?

The odds that a mutation will result in improved antibody-antigen
binding, when the initial binding isn't the most ideal, are extremely
good - perhaps as high as 1 in 2 or 3 mutations to begin with.

Where is your Nobel prize or at least a peer reviewed publication on
the subject? You must have one if you have the evidence to back up
this assertion. If it is this low what does that tell you about your
bogus protein probability arguments? Have you removed them from your
web page? The relevant mutations have to increase the binding enough
to be detected by the selection process. I don't know how much that
is, but your estimate is probably to high in the number of mutations
that will do the job. It is more likely that additional selectable
mutations do not have to be any more probable than the mutations that
generated the initial binding sequence by chance. All you have to do
is get the final sequence in less than 10E12 events. Your original
10E10 estimate above is likely too high. That might be closer to the
estimate for getting the final product. You have to factor in the
reality that it takes up to a couple of weeks to generate the final
antibody product. You have a lot of cell divisions inbetween.


The reason for this is the same reason why Dawkins' "weasel" program
works so well. Every single character in a random sequence that gets
mutated to match the template is selected for improved reproductive
fitness. In this particular example, the odds that a mutation will
change a character that isn't "right" to the correct type of character
for that position is no less than 1 in 27. Those are extremely good
odds and result in very rapid evolution of a random sequence to "match"
the template sequence.

Actually you are the one that keeps harping on the inadequacy of the
"weasel" program by using the scam argument about language and words
that have to go in a certain order. Now you seem to be admitting that
proteins aren't like that. So have you removed those bogus arguments
from your web page? Selection works on function of the protein
sequence. It isn't a language and we haven't even begun to map out the
potential. A lot of mutations work to change or enhance function
because that is simply the way that it is. The antibody system
demonstrates that empirically. We can't predict what changes will do
what but the system wouldn't work if it wasn't true. That is the
bottom line that you want to ignore.


Now, when it comes to the flagellar system, there is no template with
which to compare every single residue difference and select every
single residue change as an improvement or a detriment. Without this
template, the finding of the next beneficial steppingstone starts to
involve more and more non-beneficial changes. And, this gap of
non-beneficial changes grows linearly with each increase in the minimum
size and specificity requirement of the functional system. A linear
increase in these minimum requirements translates into an exponential
increase in the random walk/random selection time needed before success
can be realized - on average.

What is the template for the antibody response when you can use a
synthetic antigen that has never been seen in nature before? The
antibody gene can no more see the future than an ATPase.

No matter how many times you repeat worthless assertions, they remain
worthless. Demonstrate that the gaps exist. This is a neat trick for
the flagellum because you first have to demonstrate how the ATPase
changed even in your model. Your designer obviously took an existing
ATPase and changed it a little to get what he wanted, so what were
those changes, and point out the "gaps" that could not be crossed using
mechanisms that we know exist. You don't even have a mechanism that
you can point to, so what is your assertion about some designer doing
it worth? Heck, you don't even have any evidence that your designer
even exists. Behe admitted in court under oath that the designer could
be dead. The reason for this seem to be that he can't tell if the
designer is doing anything today. All his bogus arguments depend on
things that happened hundreds of millions of years ago like the blood
clotting system, the Cambrian explosion half a billion years ago, and
way back to the bacterial flagellum. What did the original flagellum
look like over a billion years ago? How do you know that it was
designed if you don't know that simple piece of information?


Since you can't demonstrate that any other protein sequence
isn't just as plastic and variable when it comes to doing things, what
is your beef?

Oh, but I can. Do you realize that every single antigen will have at
least some match to an antibody of a well-working immune system?
Consider then your notion that all other systems of function will be
just as easily found by looking at a really simple one that is not
based on template matching - like the lactase function. Many types of
bacteria simply cannot evolve the relatively simple lactase function
despite high mutation rates and a high selective advantage if the
lactase function were ever realized. Some bacteria have been observed
to be lactase negative for over 40,000 generations of time in specific
experimental conditions. Others have been lactase negative for over 1
million generations according to hospital logs.

What did Hall find? He found that E. coli and two other species of
bacteria could evolve lactase function in a single mutational step.
How many bacteria did he test? Probably less than 20, right? What is
that in number of protein sequences? Only about 40,000 total protein
sequences tested and in a small number of bacterial species he could
find 3 that did not have lactase activity, but could develop that
activity in one or two mutations. Even if he tested 100 species that
would only be testing 200,000 protein sequences. Proteins seem to be
pretty darn plastic to me.

Hall's experimental design would not detect those species that needed
more than two mutations to get function.


Scientists like Barry Hall have referred to these bacteria as having
"limited evolutionary potential". Now Ron, what is it, exactly, that
limited the evolutionary potential of these bacteria? What made them
incapable of evolving the lactase function despite the significant
advantage that they would have gained if they were able to do so?

The experimental design was a single step selection. They had to
develop the ability in a single plating. A bacteria only has around
2000 protein sequences. Even on the antibody scale this is a low
number of initial sequences. To do the experiment correctly you would
have to grow the bacteria that didn't pass the first test in a
chemostat where the bacteria could live and divide slowly if they could
not metabolize lactose. The population would be kept constant in size
(fresh medium is added and bacteria are constantly being removed) and
you would start to accumulate mutations and you would generate a
population like you would see in the wild (approaching mutation
selection balance). Eventually the bacteria would begin dividing more
rapidly (this has been observed in just about any chemostat experiment
ever done) and it would be found that the bacteria were now genetically
different than the orignal clones used at the beginning of the
experiment. If lactose was used, my expectation would be that the
bacteria will have developed lactase ability. Hall didn't do this
experiment, but that is how it works in nature.


The fact is that if anything in the bacterial genome of these limited
bacteria were just one or two residue changes away from the lactase
function, the lactase function would have evolved - and quickly. We
know this because such an experiment has been done and was successful.
So, the fact that many types of bacteria cannot evolve the lactase
function can only mean one thing. There is a larger gap between what
they have and the minimum requirements of the relatively simple single
protein lactase function.

What do you expect? There are only 2000 protein sequences in each
bacteria, and Hall got his trick to work in 3 out of the species that
were tested. Why isn't that enough for you? Do you realize how few
protein sequence had to be tested to get those three? It makes your
estimate of 10E10 estimate for antibodies look pretty far out of whack
with reality doesn't it? Hall probably only tested less than a million
protein sequences and got three to work.


In other words, this is proof of a gap problem starting out at a
relatively low level of functional complexity. There are just no two
ways about it.

In other words, since this has been explained to you repeatedly, the
gap seems to exist only in your head.


And, therein lies the gap problem.

Demonstrate that there are gaps. Point them out and show us how big
they are. Since you have never been able to do this for even a gap of
three mutations, what is your argument worth?

What is really sad is that you are using the ID scam of the flagellum
when you know that you can't trust the ID/creationist scam artists
anymore than you can trust the junk on your web page. If any of this
stuff was worth anything you wouldn't be dinking around using bogus
arguments from people that you know have lied to you for years. They
had their chance in Ohio and Dover to demonstrate that they had an
argument about the flagellum, but what did they come up with? Behe's
excuse for putting forward such a bogus argument was that he could test
it like in science fiction even though he couldn't test it in reality.
How bogus is that? Fictional testing is just what you do when you make
these bogus assertions and you never back them up. The flagellar
argument never amounted to anything. You know this for a fact because
the ID scam artist that lied to you about it quietly dropped the ID
scam for a replacement scam that doesn't even mention that ID ever
existed. You kept believing the junk even after Ohio when they were
not able to come up with a scientific theory of ID to teach, and you
even tried to defend ID after Dover. What is wrong with you? When the
scam artist that fooled you have moved on to another scam, what the
heck do you think that you are doing beating a dead horse?

These are my own arguments Ron. They are not based on the arguments of
others - not when it comes to genetics at least. I came up with these
ideas all by myself after doing my own research into the problem. I
really don't care if I'm the only one left to say so. The ToE just
doesn't make rational sense. It is statistically untenable and I'm
truly amazed that you and many other otherwise intelligent people have
been so taken in by it.

Even if you came up with this junk independently you have the problem
that every other creationist scam artist or incompetent rube that has
tried to use them has failed to come up with any arguments worth
talking about. So it doesn't matter does it. Failure is failure
whether you blame yourself or someone else.

You really do need some help. Just look at the reality around you. If
your arguments were worth anything, what happened in Dover? Why did
the ID/creationist scam artists that perpetrated the flagellum scam
switch scams back in 1999 if they really had an argument that they
could support? Sure they played fast and loose with the truth and kept
scamming everyone about ID, but what happened in Ohio? Why didn't they
give the rubes a scientific theory of ID to teach to to kids? What
happened in Dover? What happened to the previous batch of
prevaricators that called themselves creation scientists? You have all
this history to look at and you can be amazed that there are people
that disagree with your view of reality? Fool me once shame on me,
fool me twice shame on you, fool me three times and what? You have
probably been scammed more than three times, so what is your excuse?


This is just sad and at some level you know it. If creationist like
yourself had valid arguments we would all know about it by now. Get a
clue and get some help. I can't believe that there isn't someone that
you trust that can set you straight about this. It is black and white
that you have been scammed. If it wasn't Dover and Ohio would have
totally different outcomes.

Not true. The ToE isn't just a cold rational "scientific" notion. It
is believed with a strong passionate faith by the mainstream scientific
community. It has taken on religious devotion. Such devolution is not
easily overcome - even by the strongest rational scientific evidence to
the contrary.

Biological evolution has the facts backing it up. What do you have?
It doesn't matter what some people have fallen into in terms of belief.
You can believe things that are true and you can be like you.

The difference is that one group can back up what they claim and the
other can't. Besides what about all those theistic evolutionists that
worry the ID scam artists? If there was a better explanation would
they still believe that evolution happened? Why would it matter to
them?


What an idiot, or is it simple dishonesty this time?

Well, I can assure you that I'm being quite honest in these threads.
So, I guess I'm left with the "idiot" option? ; )

Basically, you are worse off then an idiot. The insanity defense is
about all you have left.

LOL - bummer ; )

You only wish. Get someone that you trust to go over this situation
with you. Have them explain just what the bogus failure of ID,
scientific creationism, etc. means to your arguments. At least have
them explain to you why your gap argument is total bull pucky. Just
ask them to verify that your gaps exist.


You are too far gone for it to be simple
incompetence at this point, and at some level you probably know it. Do
you want me to quote your defense of ID when you claimed that you could
do better than the rubes that ended up taking the replacement scams
from the guys that you still think have valid arguments? Do you still
think that you could do better than the ID scam artists did in Ohio and
Dover?

Actually I don't think the outcome would have been any different if I
had presented my ideas in Ohio or Dover. I think this whole thing is
far beyond rational presentation of ideas. It is about one religion
vs. another. And yes, the ToE is held with just as much passion,
fervor and faith by you guys as any religious belief.

Only because the side that you are on is beyond rational argument. It
doesn't matter to you that you can't back up what you claim. Point out
a single demonstration of your gaps that is equivalent to the molecular
evidence in demonstrating common descent.

You can't do that can you? What does it tell you when you have nothing
worth comparing to the evidence that you don't like? It isn't rational
thought that makes you reject it. Try to be honest with yourself. You
have claimed that you have evidence for your explanation that is as
good as the evidence science has for common descent, so why have you
never put it forward? This should tell you something about the
dishonesty that you have to live with in order to keep believing what
you do, so what is rational about lying to yourself? If you really had
this stuff you could present it. Since you don't have it, what does
that tell you about your option?


If you do, why don't you consider that to be insanity? Just
think if it was someone else. Get someone you trust to clue you in,
and if you want to claim honesty and integrity, put up front on your
web page that even you don't trust the junk in it. If you trusted it
you would be able to demonstrate that it means what you think, and if
you could do that we wouldn't have any arguments.

There is a big difference between presenting very good evidence and
getting someone else who is strongly biased against it to accept it for
what it really is. You can only lead a horse to water you know . . .

What a dishonest cop out. You first have to present the evidence and
see what happens. All you do is obfuscate the issues. We don't see
positive evidence for what you think happened, do we. Where is it for
your alternative to common descent?

You aren't leading horses to water, you are only deluding yourself with
stupid obfuscation ploys when you know that your ideas can't stand the
same amount of scrutiny that you are putting on what you don't want to
believe. Science has evidence to evaluate, what do you have?


And, remember Ron, many very good ideas were scoffed to scorn
originally by the mainstream scientists of the day. Be careful when
you call someone an idiot or insane. Sometimes, these "crazy" people
are actually right after all.

This is true, but you have to get your ideas out there. Obfuscation
isn't presenting new ideas. What is your bogus probability argument
except obfuscation? What is the dumb antibody prevarications? Where
is your evidence and the ideas that you want to back up? Why don't we
ever see them? Why is all you want to do is tear down someone elses
ideas? You can't scorn what doesn't exist. There was no scientific
theory of intelligent design, was there? Even the godfather of the ID
scam (Philip Johnson) admits that there never was and there isn't one
currently after Dover, so there didn't seem to be any ideas worth
scorning except the scam. You aren't putting your ideas out there, you
are just obfuscating an issue that you can't deal with. "Crazy" would
be a polite term for what you do.

I've taken more time than I usually do and been nicer than I usually am
to people like you because I think that you really do need some help.
I don't believe that you are some dishonest smuck just trying to foist
off some political scam like guys like Dembski and Johnson. What do
you think of the Wedge document? What do you think about being lied to
about ID? For some reason you can't evaluate this material in a
rational manner. It doesn't matter how often you get lied to and
misled it all just gets put on the back burner and ignored to push your
original beliefs. You can't deny that you can't trust creationist
sources of information and your source is no different. The simple
reason for this is that reality doesn't match up with what you want to
believe. It is that simple, and at some level you know it, but you
can't bring yourself to believe it. Things would be different if the
ID/creationist claims had been verified instead of being shown to be
bull pucky, but we do not live in that reality, do we?

Ron Okimoto


Ron Okimoto

Sean Pitman
www.DetectingDesign.com

.

Relevant Pages

  • Re: The Relationship of Gaps to Thresholds
    ... size (or average gap size) that says something else. ... the average gap size between potentially beneficial ... potentially beneficial sequences for a protein of length 1000 aa ... sequence space, ...
    (talk.origins)
  • Re: The Strawman Defense: Use at all times - it just in case
    ... A deletion mutation that removes 3 nt is no ... > sequence will actually exist, intact, within a given gene pool. ... >>> My neutral gap theory does not require multiple steps to cross the gap. ... >> new protein. ...
    (talk.origins)
  • Re: The Relationship of Gaps to Thresholds
    ... other than a fair degree of sequence similarity. ... Your MATH explicitly says that the size of the gap needed to be ... is roughly 30% of the total size of the end protein. ... start at some average distance away (that distance being a function of ...
    (talk.origins)
  • Re: Ron Okimoto and the Gap Problem
    ... 400 aa from the Lac Z starting sequence. ... The ebg sequence didn't evolve from a LacZ sequence. ... No matter how you arrange the residues, a 50aa protein just ... beneficial gap problem - i.e., the exponential decline in the odds ...
    (talk.origins)
  • Re: Most valuable poster
    ... nylonase or lactase evolution examples. ... residues), you have the ability, so you say, to tell us *exactly* what ... the average gap size is based on the size of the end product. ... recognizable sequence homologs or recognizable intermediate functions. ...
    (talk.origins)