John Harshman

> > It seems quite obvious to me that given a particular

> > creature, such as a bacterium, that the vast majority of possible

> > amino acid sequences/proteins of a given length will have no

> > beneficial function for that creature in its current environment.

>

> Agreed. This is obvious.

>

> > Only a very tiny

> > fraction of the potential amino acid sequences will be recognized by

> > any given bacterium or living cell in any given creature.

>

> Recognized? What meaning are you using for "recognized"?

Take for example the insulin protein.  Not every cell in the body

"recognizes" the insulin amino acid sequence.  Other cells, having the

proper surface receptors, do recognize the insulin protein and perform

various functions when insulin comes around.  So, for some cells the

insulin protein really has no function or meaning while for other

cells it does.  It is like different words for different languages.  A

given word might have some meaning in Spanish, but none in English.

The same is true for protein "words" in living cells.  A given

protein/amino acid sequence might have function or "recognition" for

one cell, but have no function/meaning/recognition for another cell.

If a given part performs some sort of function in a given system of

functional parts, then that part is "recognized" by that particular

system.  The system "knows" what to do with that part.  It "knows"

what function that part has.  For example, the term "recognition" is

often used when describing the interactions of antibodies with

antigens.  When the antibody comes in contact with a particular

antigen that it fits with, the antibody is said to "recognize" the

antigen.  Does this make sense now?

> > Take humans

> > for example.  The vast majority of human DNA does not code for any

> > functional protein much less a beneficially functional protein.  The

> > proteins that are coded for are somewhat plastic, true, but they are

> > also very specific.  If changed or "denatured" to any significant

> > degree, they loose all function.

>

> You are confusing two forms of change. We were talking about mutation.

> Denaturing is a loss of tertiary or quaternary structure, most often as

> a result of heating. Nothing to do with what we are referring to. (Also,

> I don't understand your distinction between "functional" and

> "beneficially functional", or what you mean by "somewhat

>  plastic".)

I mention protein "denaturing" to emphasize the idea that changes in

protein sequence *and* structure affect protein function.  We are

talking about protein function in general here.  Whatever changes a

protein (mutation, heat, chemicals etc) can affect its function in a

given system of function since protein function is dependent upon its

3D shape/structure.

Also, a protein can be functional without being "beneficially"

functional.  For example, a protein can have a "detrimental" function.

> >  This means that the vast majority of

> > potential protein sequences and three-dimensional shapes are worthless

> > to a given human cell.

>

> This is not quite clear, at least the "vast majority" part. There are

> lots of protein sequences that don't do exactly what we would like, but

> it does appear that we can find function from random sequences. See

> this: Hayashi, Y., H. Sakata, Y. Makino, I. Urabe, and T. Yomo. 2003.

> Can an artibrary sequence evolve towards acquiring a biological

> function? J. Mol. Evol. 56:162-168.

Of course one would expect that various random sequences could be

found that do actually have some sort of function in a given cellular

system of function.  Some of these might even have a "beneficial"

function in a given cell and environment.  However, the vast majority

of potential sequences of a given length and 3D structure will not

have a function at all.  You admitted as much above.  When I said, "It

seems quite obvious to me that given a particular creature, such as a

bacterium, that the vast majority of possible amino acid

sequences/proteins of a given length will have no beneficial function

for that creature in its current environment", you said, "Agreed. This

is obvious."  Well then, what are you trying to do here?  You seem to

be contradicting yourself in the same breath.

I see it much like a language system of function.  Pick a given

sequence length of words.  Lets pick a sequence length of 3-letter

words.  How many 3-letter words are defined by the English language

system?  Quite a few, but probably not 17,576 which is the total

number of possible 3-letter words.  Surely there is a sizable

percentage of defined 3-letter words as compared to the total possible

number of 3-letter words... true.  Therefore, it is relatively easy to

change a letter in a 3-letter word and get to a new functional word

such as the evolution of "cat to hat to bat to bad to bid to did to

dig to dog."  However, will this work so easily when we are talking

about say, 6-letter words?  There are 308,915,776 different 6-letter

sequences or potential 6-letter words out there.  Relative to this

number, the number of defined or "functional" 6-letter words in the

English language system of function, are few.  It is much more

difficult to "randomly" pick out of this pile of 6-letter words a word

that will have some sort of function or "recognition" when spoken in

an English speaking crowd.

So yes, one would expect that there would be "lots of protein

sequences" that could be picked at random out of a mix of protein

"words" that would have some function for a given cell in a given

environment.  However, I am willing to bet that these functions are

usually quite simple, having to do with enzymatic activities that

require relatively short amino acid sequences to perform them (like

3-letter words).  Such functional sequences would be found to be

relatively common in a random mix of proteins.  However, when one

starts increasing the complexity, the difficulty for picking a protein

with a function of higher complexity becomes more and more difficult

(As with the challenge of picking, at random, a functional 6-letter

word from a mix of 6-letter sequences).  It might not be "impossible"

to randomly pick such a sequence, but it would take a lot longer time

to be successful on average.

The average time involved becomes the problem because, with increasing

complexity, the total number of sequences with potential function

decreases dramatically leaving larger and still larger gaps in

function between those sequences that would actually have function for

a given cell in a given environment.  The random drift or "selection"

involved in getting from one sequence with function to any other

sequence with a different function of comparable complexity requires

greater and still greater amounts of time.

> And the introduction of 3-D shapes only confuses the question.

Actually, the 2-D sequence of proteins really is not what does the

job.  The 3D structure is what really matters when it comes to protein

function.  The same sequence can be folded in different ways.  And,

depending upon which way the protein is folded; function may be gained

or lost.  Proteins do not always spontaneously fold in the proper way

to realize their function.  There are other proteins that fold new

proteins as they are made.  If the 3D structure of a particular

protein is "unfolded" and then allowed to "refold" by itself, it most

likely will not fold properly and its function will be lost.  So,

really, we talk about the 2D sequence because it is easier to talk

about, but in reality, the 3D structure is very important to function

and only compounds the problem of complexity since even more

differences can be realized for a given amino acid sequence than a

simple 2D sequence analysis would suggest.  For a 2D sequence of 10

amino acids, the total number of potential proteins is:

10,240,000,000,000 (~10 trillion).  However, the total number of

different proteins would actually be much higher than this because of

all the added differences in 3D structures that are not being included

in the total number.  This makes for even less of a chance of picking

those sequences/3D structures of amino acids that actually have some

sort of function, much less beneficial function, for a given cell in a

given environment.

> > As far as demonstrating a negative (ie: A lack of a functional path

> > between two different proteins), it is impossible this side of

> > eternity.  A negative finding never means that a positive finding is

> > impossible.  However, the likelihood that a negative finding will

> > occur can be calculated.

>

> If it can, then you haven't done it yet. This remains to be seen.

Well, of course I disagree.  Can you prove that these gaps do not

exist or explain how they might not exist?  For example, can you show

how a relatively complex function, such a bacterial motility (Any

type, not necessarily flagellar motility), could evolve where no

genetic gaps in function would need to be crossed?  There are those

who suggest that there is no goal in evolution.  Therefore, the

testing of a specific "goal" such as the evolution of a specific

function, such as motility, is not a valid challenge of evolution

since a given type of bacteria may evolve other equally complex

functions before motility is ever evolved.

This is a great argument.  For one thing, without a goal to defend,

there is no need to move goal posts as YECs are so often accused of

doing.  Just because a particular function does not evolve, such as

the lactase function in certain of Hall's bacteria, does not mean that

evolution is having problems.  It only means that evolution does not

need to travel down any particular path, regardless of the benefits

that would be realized if that path was traversed.  Well, Ok... lets

go there.  Naturalistic evolution obviously does not "know" which path

to choose.  It can go down any path in any direction and eventually

get somewhere with some beneficial function.  Sure it can.  However,

what if each starting point is completely surrounded by a huge ocean

of neutral function or nonfunction?  Consider that if there were 1

million defined 6-letter words that each word would, on average, be

surrounded by 300 non-defined words.  No matter which way evolution

went, odds are that it would quickly run into a gap of nonfunction

that separates current function from new function.  Try it.  Starting

with a 6-letter word, how far can you go before you are blocked by a

gap of nonfunction?  Now, if that seems hard, try to evolve a larger

sequence of letters, such as a sentence of words, one letter at a time

and see how far you can go before you are blocked by sequences of

nonfunction.

> How do you

> know there are such gaps? For eyesight, it has certainly been shown that

> there is a continuous series of slight morphological variants, each

> advantageous, from a patch of light-sensitive cells to a camera eye.

A series of morphologic variants that appear to follow a smooth

evolution of very small steps is deceptive in that is covers up the

complexity of the genetics involved.  If in fact every "slight"

morphologic variant was the result of an equivalently "slight" change

in the genetic code then you would be correct in your statement that

such a series of morphologic variants give convincing evidence of

common descent.  However, there are several problems with such an

automatic assumption.  One problem is that apparently small

morphologic changes often require relatively large changes in the

underlying genetic code.  The same is true for computer functions.

Apparently "simple" or "small" changes in a program's function often

require comparably large changes in the underlying code.  For example,

going from a "simple" eye spot or collection of light sensitive cells

to a slightly concave eye cavity spot, seems morphologically simple,

but the genetics involved are quite complex. All the cells involved in

the formation of this cavity must be programmed to relate with the

other cells in this area in a very specific way to form this

concavity.  This orchestration requires many very specific genetic

changes.  Gaps in beneficial function are certainly involved.  Another

problem is that function is arbitrarily attached to code.  Very

different codes can and do code for the same or similar functions and

very similar codes can and do code for very different functions.

Because of this arbitrary nature of code, a change in the code will

probably not result in an equivalent change in code function or

"morphology".  Very small changes in code can result in huge changes

in morphology.  Also, very large changes in code might not change

morphology/function very much at all.

An argument based on morphology alone might seem compelling if that is

all that one had, but we know more now than Darwin knew.  We know that

there is an underlying code or genotype that gives rise to morphology

or phenotype.  If you can explain, genetically, how the gaps between

these various "small" differences in morphology can be explained, then

you would certainly win the Nobel Prize. As of yet, I have found no

detailed genetic explanation or real-time experiment that explains or

demonstrates how the evolution of morphologic variants, such as the

morphologic eye variants or various bacterial motility systems,

evolved or even could have evolved.

> I'm

> sure you are familiar with How would one go about demonstrating that

> there are or are not such gaps with respect to feathers?

Yes, try to evolve a feather or a feather-like structure or to

estimate how long it would take based on genetic sequence analysis,

mutations rates, functional genetic intermediates, and the length of

the average genetic pathway to such a function in a given creature.

Detail the genetic codes involved in coding for feathers and then

compare these codes to the codes that are available in other

non-feathered creatures and see if a genetic path could be detailed

and how long it would take to cross this path.

> We do know that

> feathers arose in a bipedal, non-flying dinosaur. That seems clear

> enough.

Oh really?  How so?  Is there a gradual step-by-step demonstration of

this evolution in the fossil record?  Not any more than could be

detailed various creatures all living at the same time today.  It is

the same argument as the evolution of simple to complex eyes.  Get a

bunch of different kinds of eyes and line them up in a morphologic

sequence from more "simple" to more "complex".  Obviously, once this

lineup is complete, the conclusion must follow that the simple eyes

gave rise to the more complex eyes.  This might seem reasonable at

first glance, but this is not necessarily a correct conclusion.

Practically any collection of objects can be categorized in such a

manner, but this does not mean that these various object arose via

common descent... especially if the mechanism to adequately explain

such variations is weak.  For example, the various books on my

bookshelf can be categorized in this manner, and just as convincingly,

from more "simple" to more "complex."  But, this does not mean that

the more complex books arose via common descent from the less complex

books even if the changes between them seem to be relatively small.

You see, without an ability to detail a mechanism of change, the

differences and similarities, by themselves, do not necessarily

support the position of common descent.

> Whether they arose by natural selection, or by any naturalistic

> pathway, is difficult to determine. I suppose you could, if you liked,

> support some kind of theistic evolution in which God gives the

> occasional nudge to get a genome across some functional gap. I'm not

> sure where you would find evidence for it, as there is for selection,

> and I'm pretty sure you would reject such a theory anyway. Right?

The evidence that you have is one of morphology alone, not of

genetics.  The morphologic evidence is not compelling enough to

adequately support the theory of common descent.  You need genetic

evidence or some way to explain how the genetic gaps can be crossed.

Also, I find the standard interpretation of fossils and the geologic

column unconvincing and quite biased or colored by the a priori

assumptions of evolution and naturalism.  I see no clear evidence that

feathers must have evolved from featherless creatures.  The fossil

record is a static record and is thus quite limited in what it can

tell us about the lives and changes of creatures over time.  You need

real-time examples detailing the actual genetic changes in life forms.

 Relying on morphology is easy to do, but it is rather weak when it

comes to explaining how the genetic codes themselves evolved via some

naturalistic process.

> >  If you think that a neutral gap in function

> > that requires just one protein sequence is hard to cross, try crossing

> > a gap that requires the evolution of multiple proteins to cross where

> > hundreds or even many thousands of neutral mutations are needed.

>

>

> I agree that this scenario sounds unlikely. I just don't agree that it

> is necessary.

Why not?  What *genetic* explanation do you have to account for the

differences then?

> > If there were such a path from scales to feathers, then we should be

> > able to quickly demonstrate such evolution in real time.

>

> I deny that there is any such expectation. Why should there be? Are you

> saying that we should be able to demonstrate every possible occurrence

> in the lab? Why? If we are talking about something that took millions of

> years, why should we be able to do it in one or two? And this assumes

> that we know what steps are necessary, which we don't, at least not yet.

If it took millions of years... why did it take so long if there was a

beneficially functional path each step (mutation) of the way?

> You have the kernel of an interesting point there, and it's been a

> conundrum of evolution for some time. Why is evolution so slow over the

> long term, when natural selection is so fast? I think there are several

> reasons: waiting for mutations, waiting for the environment (internal

> and external) to change so that new selective pressures are seen, and

> following a twisty path around constraints rather than the straight path

> you seem to think is the only possible one. It's an interesting problem,

> but not as you seem to think a disproof of the efficacy of selection.

Mutations occur quite rapidly.   For humans, the average mutation rate

is around 250 mutations per individual per generation.  In a large

population, such mutations, if a fair proportion were directed in some

way, would result in rapid evolution along a great variety of

evolutionary paths.  Feathers, wings, eyes, legs, arms, and a host of

potentially beneficial functions would evolve in short order.  The

problem is that the path is quite "twisty" indeed.  The path is not

straight.  That is the problem.  The path is very curvy because of the

random drift problem.  If each and every step is not selectively

advantageous, then evolution starts to wander around a neutral sea of

function.  The wandering is very curvy or nonlinear.  In fact, it is

such a curvy path that millions, billions, and trillions upon

trillions of years are simply not enough to traverse this path.  The

"efficacy of selection" is dependent upon nature's ability to select

between different genetic changes.  If the changes are "neutral" in

function then natural cannot select between different genetic

sequences that have the same function (or nonfunction).  At this point

the "efficacy" of natural selection is severely limited.

> > There are gaps between various functions that

> > require a lot of time to cross.  In fact, many of these gaps seem so

> > wide that billions or even many trillions upon trillions of years are

> > simply not enough.

>

> If there are, name one and show the evidence that it is such a gap.

I already have.  Depending on the complexity of the function in

question, the evidence for non-evolution can be found in comparing