Behe's FCT

luca
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Behe's FCT

I've not seen recent topics on evolution here; searched, but nothing found.
What do you think about his definition, the functional coded elements?
What do you think about "academic journals" like bio-complexity.org?
I know, "fecal matter", but could you explain?


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Looks like a way for Behe

Looks like a way for Behe and Dembski to salvage what's left of their scientific reputation.

Maybe we can get someone to submit a paper on alchemy - that fits with Behe's definition of science (at least according to his sworn testimony).

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I had a quick Google on the

I had a quick Google on the topic, and see nothing really new or different in the basic error in his 'reasoning' on 'functional coded elements' , as compared to his ideas on 'irreducible complexity'.

It still doesn''t acknowledge the full implications of the fact that evolution is purposeless, which allows for structures with some specific function to evolve from other structures with quite different functions.

IOW, we would not require that each step of the evolution of some complex functional element to be clearly 'aimed' at the function we currently see. This was clearly identified in the responses to his claims at the Dover trial, when various structures sharing some elements of the infamous 'bacterial flagellum', but serving different functions, were identified. Another fact ID'ers often don't appreciate is that whole sequences can and do occasionally get duplicated, allowing one copy to retain the original function while the other copy can mutate into something else without the organism losing the original function.

As long as the many 'non-functional' parts of the DNA sequence aren't actually harmful, and most aren't, they provide raw material for something to occasional form which does actually 'promote' or otherwise enhance some part of the cellular machinery

The 'information' argument is totally bogus, since a random process can, by definition, produce literally any genetic sequence, quite independent of whether it has significance to us or its 'functionality'. And such a random process, with some degree of selection at each step of replication to filter out clearly dysfunctional versions, but otherwise letting everything else go on, can actually lead to structures and functionality that would be hard or impossible to rationally design. Rational design requires advance knowledge of the functionality of all relevant configurations, but is by that fact limited to 'designs' based on what already exists or is known, or is clearly related to it.

This is why 'genetic algorithms' are used for some complex problems, to randomly explore areas of the possible 'designs' which don't obviously relate to existing ideas. So evolution can, given time, come up with 'designs' that would very hard to come up with rationally.

Evolution is restricted to 'designs' which can be reached via small steps where each step is still a viable organism, so any mutation which would require a number of specific changes to occur at once to avoid some intermediate step which just wouldn't work, is a difficulty.

But this actually supports un-designed evolution, since it explains why there are examples of clearly less-than-optimal 'designs' in the natural world, such as the famous example of the laryngeal nerve of the giraffe, as discussed here, among many other places:

http://scienceblogs.com/grrlscientist/2010/06/the_laryngeal_nerve_of_the_gir.php

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I found this article -

I found this article -

http://www.evolutionnews.org/2010/12/michael_behes_first_rule_of_ad041461.html

Which looks to be a creationist site.

And skimming through the article, Behe is again seeing the evidence he wants to see.  I'd wait for some replication of his experiment from some evolutionary scientists.

I am currently reading How We Know What Isn't So.  The tendency of humans to see only the evidence for their point of view is very strong.  That is the purpose of experimental replication.  If it can't be replicated, it didn't happen.

http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/

And here is Behe himself with a link to the paper.  There are more links on the side bar where Behe addresses some of his critics.

Okay, it sounds like the old creationist "information" argument.  That is, evolution could only happen if there is an "increase" in information.  But Behe is more convoluted than that.  He is saying that over 40 years, he has found increases in genetic information.  Just not very many compared to deletions or changes.  Therefore, the gains he did find must be brought about by an outside agency.  He says this isn't god/s/dess - necessarily.  At least, that is my understanding of his article.

So, does this sound contrived to you?  Evolution is not about how the genome changes - whether there is a change, deletion, or increase.  It is not concerned about "evolving higher orders" or "gaining features" or any of that.   Evolution is all about having grandchildren - being able to produce children who are able to produce children.  Being fit enough to maintain the population.  If not, then either evolution occurs - that is, there is a shift in the population genetics to be better adapted to the environment so those grandchildren can happen - or the organism goes extinct.

 

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BobSpence1 wrote:IOW, we

BobSpence1 wrote:

IOW, we would not require that each step of the evolution of some complex functional element to be clearly 'aimed' at the function we currently see. This was clearly identified in the responses to his claims at the Dover trial, when various structures sharing some elements of the infamous 'bacterial flagellum', but serving different functions, were identified. Another fact ID'ers often don't appreciate is that whole sequences can and do occasionally get duplicated, allowing one copy to retain the original function while the other copy can mutate into something else without the organism losing the original function.

 

I noticed on  Behe's blog, he has a picture of that artist's rendition of a bacterial flagellum.  You would think it has been refuted often enough that he would give it up.  But no.......

 

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behehehe

cj wrote:
Okay, it sounds like the old creationist "information" argument. That is, evolution could only happen if there is an "increase" in information.
Yes, but at this point what I usually reply is: do speciation cares? No. Even if there was only "loss of FCTs" a certain number of mutations could lead to a different variety.

BobSpence1 wrote:
Rational design requires advance knowledge of the functionality of all relevant configurations, but is by that fact limited to 'designs' based on what already exists or is known, or is clearly related to it.

What I ask usually to ID'ers is: since there could be almost only losses, but microevolution could adapt organism to small changes, is there the future written in the DNA?


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luca wrote:cj wrote:Okay, it

luca wrote:

cj wrote:
Okay, it sounds like the old creationist "information" argument. That is, evolution could only happen if there is an "increase" in information.
Yes, but at this point what I usually reply is: do speciation cares? No. Even if there was only "loss of FCTs" a certain number of mutations could lead to a different variety.

 

My point.  A different variety is a different variety - regardless of how it got there.

 

luca wrote:

BobSpence1 wrote:
Rational design requires advance knowledge of the functionality of all relevant configurations, but is by that fact limited to 'designs' based on what already exists or is known, or is clearly related to it.

What I ask usually to ID'ers is: since there could be almost only losses, but microevolution could adapt organism to small changes, is there the future written in the DNA?

 

To some extent, there is.  A plant could not become an insect.  The energy costs are too high to make that many changes.  Evolution is ruled by thermodynamics just like every other process ever observed.

Evolution works on the structures of DNA the organism has.  And if the organism loses a structure - it de-evolves - it can not regain that exact same structure.  I don't remember precisely, but my professor had an example of an insect that lost a structure (wings?), then evolved a similar but not exactly the same structure from a different starting point.  Over millions of years, of course.  See The Panda's Thumb for another example and discussion.

(Coda: I know not all evolutionary scientists agree with Stephen Jay Gould's theories.  But his articles for the general public are very readable and usually address basic uncontroversial evolutionary theory.)

 

-- I feel so much better since I stopped trying to believe.

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Since we know with certainty

Since we know with certainty that genetic sequences can accidentally or otherwise be repeated in the process of DNA replication, a gene can get definitely gain more raw 'information".

Interaction with the environment selects out the "useful" variations, so that is the source of the new 'information' that Behe is thinking of.

Even the growth of an organism from a single fertilized cell to an adult represents a massive increase of information associated with that organism, so we see a violation of Creationists' ideas every day.

In the sense as defined in physics, the quantity of 'information' within a closed system is constant, but it is only the quantity of data required to describe the position/momentum of each fundamental particle that is conserved.

Since the position/momentum of the particles can and usually is constantly changing, the content of that information is changing all the time, so there is nothing at that level to block any increase of complexity of any form, as long as we have the same number of total particles, and entropy rules are observed, so any local decrease of entropy represented by some emergent structure is supplied by available energy from elsewhere in the system.

The stubborn blindness to such basic FACTS that these guys display is fascinating, and depressing. Especially when they appear to have some scientific education.

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 Hold the phone! Our boy

 Hold the phone! Our boy has gone mainstream on this one. Here is the actual paper if anyone want to spend a couple of hours wading through twenty plus pages of molecular genetics:

 

http://www.lehigh.edu/~inbios/pdf/Behe/QRB_paper.pdf

 

While he is introducing the new terminology of an “FCT”, it is really quite similar to the older concept of a genetic allele. The difference (as I read that paper) is that instead of just saying that there might be several similar alleles of a basic gene, he is looking at the specific molecular distinctions between related genetic loci.

 

He is quite open about information being copied, changed and deleted as well. That and he never mentioned design or irreducible complexity even once. Although it was Dembski who came up with the idea of information not increasing.

 

An FCT (if I am following him) is a change in genetic information and can be of varying size from a single codon to a whole genome copy coming into existence.

 

I don't know how much I am willing to buy into what he is saying but it does not come off as scientifically dishonest like his performance in Dover did.

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The intro to that

The intro to that paper:

Quote:

Adaptive evolution can cause a species to gain, lose, or modify a function; therefore, it is of basic interest to determine whether any of these modes dominates the evolutionary process under particular circumstances. Because mutation occurs at the molecular level, it is necessary to examine the molecular changes produced by the underlying mutation in order to assess whether a given adaptation is best considered as a gain, loss, or modification of function. Although that was once impossible, the advance of molecular biology in the past half century has made it feasible. In this paper, I review molecular changes underlying some adaptations, with a particular emphasis on evolutionary experiments with microbes conducted over the past four decades. I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre-existing molecular function, and I discuss the possible reasons for the prominence of such mutations.

Seems like he is trying a more subtle approach than before, by admitting that evolution can occasionally lead to real increase of functionality.

But he is trying to show that the process 'seems' to be dominated by changes which involve a "loss of function", therefore hinting that a general progression from very simple forms to 'advanced' forms of life is very unlikely without some kind of intervention.

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Quote:Quote:What I ask

Quote:
Quote:
What I ask usually to ID'ers is: since there could be almost only losses, but microevolution could adapt organism to small changes, is there the future written in the DNA?

To some extent, there is. A plant could not become an insect. The energy costs are too high to make that many changes. Evolution is ruled by thermodynamics just like every other process ever observed.

Yes, but what I meant was that bacteria could adapt to something *new*, like eating nylon, and in this perspective, organism has to evolve to situations not seen before BUT they do it mostly (ID says) by losing functions, so here there are the "future" genes.

Quote:
I don't know how much I am willing to buy into what he is saying but it does not come off as scientifically dishonest like his performance in Dover did.

But he is. He is "reinterpreting" experiments like Lenski's LTEE to tell us there are no "news" that can come from evolution (expecially from macro).

Also, about FCT, there is the problem, maybe written around here somewhere, that a single gene could be involved in more that one function, which is something, if I understood well, that is not covered by FCT's definition.


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I just realized, he

I just realized, he says:

Quote:

I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre-existing molecular function

By categorizing functional changes as 'loss', 'modification' and 'gain', he is confusing the issue. A 'modification' of an existing genetic mechanism is precisely how evolution normally works to achieve a NEW function. 'Loss' is what happens when unused functionality withers away, like our appendix.

And OF COURSE most change we see will appear as 'modifications' of existing functions. The evolution of a NEW function, such as the ability to breathe air, may require some specific set of new functions which could be more clearly seen as 'new', but they would still be achieved by duplication and modification of existing functions. Once some ability to absorb oxygen from the atmosphere as well as from water solution emerged, the whole progress to purely air-breathing creatures would be 'just' modification (refinement and improvement) of the air breathing mechanism, accompanied by 'loss' of the ability to 'breathe' under water.

So what Behe describes is entirely consistent with natural evolution - life only need to 'gain' functions relatively infrequently, most of the time it will appear as simply 'modification'.

If the new function is sufficiently different form the old function, and the old function is still needed, old versions of the genes involved will still persist, in addition to the new 'modified' ones. This IS evolution.

In pursuing this argument he is clearly trying to cast doubt on the ability of 'natural' evolutionary processes to lead to the emergence of 'higher' life forms from simpler forms. But all he is doing is documenting the way evolution works, the relative frequency of what he categorizes as 'gains' being all that is necessary.

Look at the evolutionary 'tree': most of it is just extending branches rather than 'forks'.

 

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BobSpence1 wrote:I just

BobSpence1 wrote:

I just realized, he says:

Quote:

I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre-existing molecular function

By categorizing functional changes as 'loss', 'modification' and 'gain', he is confusing the issue. A 'modification' of an existing genetic mechanism is precisely how evolution normally works to achieve a NEW function. 'Loss' is what happens when unused functionality withers away, like our appendix.

And OF COURSE most change we see will appear as 'modifications' of existing functions. The evolution of a NEW function, such as the ability to breathe air, may require some specific set of new functions which could be more clearly seen as 'new', but they would still be achieved by duplication and modification of existing functions. Once some ability to absorb oxygen from the atmosphere as well as from water solution emerged, the whole progress to purely air-breathing creatures would be 'just' modification (refinement and improvement) of the air breathing mechanism, accompanied by 'loss' of the ability to 'breathe' under water.

So what Behe describes is entirely consistent with natural evolution - life only need to 'gain' functions relatively infrequently, most of the time it will appear as simply 'modification'.

If the new function is sufficiently different form the old function, and the old function is still needed, old versions of the genes involved will still persist, in addition to the new 'modified' ones. This IS evolution.

In pursuing this argument he is clearly trying to cast doubt on the ability of 'natural' evolutionary processes to lead to the emergence of 'higher' life forms from simpler forms. But all he is doing is documenting the way evolution works, the relative frequency of what he categorizes as 'gains' being all that is necessary.

Look at the evolutionary 'tree': most of it is just extending branches rather than 'forks'.

 

What Bob said. 

 

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 OK, I am not going to go

 OK, I am not going to go so far as to say that the guy is not up to something. He may well be. Certainly his track records speaks badly on him not having an agenda.

 

In all honesty, I kind of agree with bobspence, except that I see him as having a different agenda here.

 

One of the points which came out of the Dover case was that there are no peer reviewed papers on the matter. Well now there is one.

 

If he can bitchslap dembski into doing something similar, then, well, we will have a very different problem to deal with than the Dover case gave us.

 

Here is the deal: We need to be ready for that when it comes. The more that we press for good arguments the more we can expect what we require.

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 OK, I am not going to go

 OK, I am not going to go so far as to say that the guy is not up to something. He may well be. Certainly his track records speaks badly on him not having an agenda.

 

In all honesty, I kind of agree with bobspence, except that I see him as having a different agenda here.

 

One of the points which came out of the Dover case was that there are no peer reviewed papers on the matter. Well now there is one.

 

If he can bitchslap dembski into doing something similar, then, well, we will have a very different problem to deal with than the Dover case gave us.

 

Here is the deal: We need to be ready for that when it comes. The more that we press for good arguments the more we can expect what we require.

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AIG,I can see how it is

AIG,

I can see how it is 'reasonable' to see this paper as more vaild scientifically than stuff he has done previously, but he still seems to me be laboring a point which is not as significant as he thinks, or wants to think. After what he has done in the past, and having seen him interviewed, I find it difficult to accept it really is as clearly thought out as he probably believes it is.

I was going to say it is not quite as 'intellectually honest' as he thinks it is, but that is probably unfair. He almost certainly thinks he is doing legiitimate science, but I see logical flaws in it, as I pointed out, related to objectively assessing what 'modifications' count as 'gains', or just modications', and the assumed implications of the rates of 'gains' vs just 'modifications, or even 'losses'.

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 Bob, I think that you

 Bob, I think that you misunderstood me.

 

Creationism failed at court so they used ID as a new strategy. That did not work out so well and “they” tried ID as the next strategy.

 

ID failed at court.

 

Ever since the Dover trial, I have found myself waiting to see the next strategy. This may be it.

 

If it is, then we need to counter it rationally.

 

Don't get me wrong, I have many thoughts on this paper but let us get to the “new strategy” first.

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Ok...Do you agree or not

Ok...

Do you agree or not that the problems I pointed out with this account, that the 'observations' of the relatively low proportion of 'gains' do not present a necessary problem for 'unguided' evolution, do at least constitute a pre-emptive strike at the new strategy?

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 I am not clear on how

 I am not clear on how addressing Dembski affects the work of Behe.

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Behe did it

The aim is always the same, the strategy I think is just a little more subtle.
The point is always to eliminate Darwin from human knowledge. Obviously they don't understand that theory of evolution and Darwin are not the same thing. If not they would not use the word 'darwinists'.
What Behe tried to do, and expecially how this study is used, is to affirm that now there is "proof" that evolution could not do what it says, because, essentially, ID'ers think there are sufficient laboratory tests to deprecate macroevolution. No "new functions", no "new species", nothing...