Genetic Changes In Mice 'Question Evolution Speed'

You may have read it then, but you missed his whole point.

No, I grasped it just fine. His "whole point" is that the genetic variation which natural selection acts upon happens not only at the lowest level of the genetic code (random errors in genetic code), but also at higher molecular levels, including the triggered reshuffling of larger blocks of genetic components (triggered by such things as environmental stresses).

However, again, I must point out that these mechanisms have been recognized for at least three decades, and their effects for at least *eight* decades (e.g. in the work of McClintock).

He has distanced himself from the "traditional" evolutionary viewpoint.

Without trying to be unkind, I'd like to point out that while Shapiro's packaging of these recognized mechanisms under a single somewhat inaccurate label ("21st century view of evolution") and his personal popularizing of it is welcome and useful (since not everyone *has* heard of these mechanisms), it also smacks more than a little bit of self-promotion and self-aggrandizement. Without meaning to minimize Shapiro's solid research in these areas, it looks rather like he's trying to portray himself as being the most vocal head of a "revolution" in science, with the aim of increasing his own career and possible awards. My point in saying this is to highlight the fact that Shapiro has a personal motive in overplaying the alleged "revolutionary" nature of these mechanisms and in puffing up the portrayal of them as being a true "departure" from what you call the "traditional evolutionary viewpoint", when in fact the "traditional" field of evolutionary science has accepted and researched these mechanisms for decades.

A more accurate label than Shapiro's would be, "the latter 20th century view of evolution which will continue to be further researched and developed into the 21st century". But that's not the kind of label that wins science prizes, is it?

Don't misunderstand me -- I'm in no way trying to discredit Shapiro's scientific observations or arguments. In fact, unlike the flawed work of, say, Behe, I think Shapiro's work is quite solid. I'm just saying that one should take care to note the point at which he starts getting into "sales pitch" mode.

I don't deny that this field is a promising one, but it's a mistake to overplay either its "modernity" or the amount of its "departure" from existing and current work. This is just further work in areas that have been accepted and active for decades already.

To be fair, Shapiro himself acknowledges this in his overview of the history of this field. But that doesn't seem to stop him from trying to paint it as a "new millennial" revolution anyway, with a misleading label.

He goes out of his way to establish that the random stochastic mutational mechanism is not the driving mutational force in what we now know of the methods the cell adapt to the environment.

Yes, but I believe you're misunderstanding his point.

Shapiro still credits "random" and "stochastic" changes as the source of the variation which natural selection acts upon, but he bumps it up a few levels and wants to call it by a different name.

Part of the problem is that the word "random" is itself ambiguous, and even in a rigorous context like mathematics means different things in different contexts. Shapiro wants to stress that there are non-random results from the non-random triggers which cause the genetic machinery to *randomly* try new configurations. And that's a good thing, as far as it goes, but it should not lead the reader into thinking that he's talking about some sort of "directed" result, or one that was "pre-planned" or "previously programmed" by design. Shapiro makes this quite clear in an answer he gave during an ISCID interview:

Masciarelli: I'm curious about "their non-random operations." Does 'non-random' suggest that the very instructions for all possible morphological changes are front loaded or pre-programmed into living things, needing only a given catalyst to get things going?
James Shapiro No. Non-random means that they operate under certain conditions (e.g. after genome damage or viral infection) and that these systems make characteristic kinds of changes. When a retrovirus-like element inserts in a new genomic location, it carries with it a defined set of regulatory signals that can affect the reading of nearby DNA sequences in very particular ways. This is an example of non-randomness. In addition, some changes (such as those in the immune system) can be targeted to specific locations by the presence of particular signals in the DNA or by activation of transcription. These phenomena show us that cells are capable of altering their genomes in non-random but not rigidly specified or pre-determined ways.

Note also that here Shapiro is using the word "non-random" to describe processes which help channel results into certain types of outcomes, as opposed to those which would allow *any/all* sort of outcome. But even those types of processes are still "random", just in a different manner.

For example, consider a box which contains 10 rubber balls, each of a different color. Kick the box in the absence of gravity, and the balls will bounce around for a while and eventually come to rest at random locations within the box (slowed to a stop by air resistance). Their final locations will be random, distributed across the entire volume of the box. Now repeat the experiment with gravity present. The balls will fly around the box for a bit, but when they come to rest, they will all be found resting only on the bottom of the box. However, their positions on the bottom of the box will still be randomly distributed. Nonetheless, although the outcome is indeed "random" in both cases, in the second case one can still correctly say that their final resting places are "non-random" in the sense that at least their vertical position is now constrained to be somewhere on the bottom of the box (as opposed to say, floating near the top of the box as was possible in the first case). (And note that even the first case is not "purely random", since the nature of the results are constrained by the walls of the box.)

This is the manner in which Shapiro uses the term "non-random". The results are still random, but are simply more constrained than the other sorts of random processes (e.g., point mutations) which Shapiro compares them to. There's nothing wrong with the way Shapiro uses the terms, as long as the reader understands his usage properly.

The same goes for "stochastic". This too is a term that is highly dependent upon context. Shapiro chooses to use it with the meaning, "random walk", as he makes clear several times in his paper:

"... this capability removes the process of genome restructuring from the stochastic realm of physical-chemical insults to DNA and replication accidents."
"The conventional view is that genetic change comes from stochastic, accidental sources: radiation, chemical, or oxidative damage, chemical instabilities in the DNA, or from inevitable errors in the replication process."
"...vision of evolutionary engineering that postulates a more regular principle-based process of change than the gradual random walk of 19th and 20th Century theories."

Again, though, Shapiro overplays the degree to which the "conventional view" relies upon direct pointwise mutation of DNA -- larger scale changes have long been understood to play a large role. And he again underplays the manner in which random change (which he now places primarily at the "building block" level) is itself a "stochastic process" in his own model of genetic change (albeit in the more general meaning of the term, not his "random walk" connotation).

For example, from his paper:

"If it is true, as all sequencing projects indicate, that genomes are composed of Lego-like assemblies of smaller and larger modular genetic elements (segments of protein coding sequences, regulatory sites, repetitive DNA elements, chromatin domains), then it follows that a major source of genetic novelty must be the rearrangement of these modular components."
"Natural selection following genome reorganization eliminates the misfits whose new genetic structures are non-functional."

This makes quite clear that Shapiro understands that the reshuffling of the "Lego-like assemblies" of the genetic code is done in a random (non-directed, combinatorial) fashion, the results of which have to be "weeded" by natural selection because they still often produce "misfits whose new genetic structures are non-functional". This is, frankly, traditional evolutionary theory just knocked a few levels up the chemical heirarchy.

That's not to say that Shapiro isn't correct in pointing out that the timing of these reshuffling events is less than totally random (since they are often triggered by external conditions) and that the results are less random than pointwise DNA mutation (since they are likely to be more constrained to "useful" results due to their higher-level action on the genome). These are important points, and should well be heeded (even especially by creationists, who will find the implications contrary to their "evolution can't work fast or well" positions). But the point is that it's hardly a major departure from "traditional" evolutionary processes. It still entails the 140+ year old process of genetic variation, amplified by reproduction, and acted upon by natural selection. Shapiro is just pointing out (most probably correctly) that higher-level genetic variation plays a very significant role when compared to low-level genetic variation. That's not to say that low-level genetic variation is out the window, however, because many studies of molecular evolution in the history of life on Earth has provided clear evidence of the strong role of basepair DNA mutation as well.

Evidence after piece of molecular evidence now bolsters that viewpoint.

Yes it does. Your point?

Having established that as the mechanism any postulation of how that mechanism came about then belongs in the range of just-so.

This is an empty claim of yours, which hand-waves away the amount of research which has been done on the topic. This view rests on far more than "just-so" scenarios.

One could point out, however, that the ID presumption is the view which far more heavily rests on a "just-so" foundation, given that it just reflexively declares a "must have been designed, and the designer must have been the God the Christian Bible" default response in the face of any natural observation which appears more complex than the speaker personally believes might have arisen naturally.

Again, your reputation rests heavily on the nature of your response.

You can ask me in a civil manner and I'll consider a response.

You disgust me.

No one is obligated to respond to a pompous simian.

small amount of effort it takes to do more than just read the "did so/did not"

I take it your response is "did not."

But then, random insults are far easier than real discussion, aren't they?

Juging from your posts, yes.

Juging

Judging.

I think you hitta nerve...

Maybe. It was Friday night and hedonist inhibitions tend to get washed or smoked away on the weekend.

The difference is, we usually give the reasons for our insults

Oh, I see. If you can self-justify, it's ok.

This calls for a top ten reasons why Evos throw insults.

10: Civilization is for peopole
9: It's how Mother kept Father in line
8: I attend a rough public school.
7: It was passed down by angry monkeys

6: My tremendous intelligence has been insulted
5: Everybody else really is stupid
4: It is the proper response to a disagreement
3: It's Friday or Saturday night and inhibitions are low
2: A nerve was hit
1: It's what you do when you don't know the answer.

"Sure, we sometimes insult. The difference is, we usually give the reasons for our insults" - Itchy

Give me one reason why we should not raise the issue of your conduct with the owners of this site, and ask them to consider your permanent banishment as an obvious disruptor?

This is what I meant by "run to Mama."

Hypocrites like you exhibit a mean thuggery, spewing bile and insults 10:1, unable to persuade, barely able to reason, resort to the abuse button if not allowed to control and dominate.

You quite obviously attempt to undermine discussion by disrupting it with your obsessive-compulsive behavior.

By your standard, 90% of the evos on this thread should be banned. Unbelieveable world-class hypocrisy! You don't find the creationists threating the abuse button when they don't get their way.

Grow up.

That wasn't what I was asking for.

I was asking for one evolutionist poster on FR who contribute less worth than you do, and contribute more insults. Since you claim the higher moral ground, it should be easy to name names.

You really should keep up with current scientific data Mr. Itchy

I always wondered what happened to Itchy Brother.

This calls for a top ten reasons why Evos throw insults.

This on my personal web site is all the "science" I have learned from creationists in four years.

In short, there tends to be a side that says, "Earth to Bozo! There's an external world and it's fighting for your attention."

Nice essay. Thanks for posting the link!

FR Rules Itchy 4got to read:

Do "take it to the Alley" - The Alley (now known as the Smokey Backroom) is a public chat room. A link to it is provided on the latest posts page. Invite people there if you want to talk things over or settle a score, so to speak, off site. (which we are)

Do use common sense - (Yes, please do. Spewing evolunacy shows a distinct lack of it.)

Do stay on topic - (This one will find you scrolling up to see just what was the topic again?)

Don't be a whiner - learn to live with it, or move along. (yep, them's the actual words. just do it)

Looks to me like you qualify as a knuckle dragging rule breaker Meester Itchy.

carry on!

"That wasn't what I was asking for.

I was asking for one evolutionist poster on FR who contribute less worth than you do, and contribute more insults. Since you claim the higher moral ground, it should be easy to name names."

You either are kidding or hopelessly blind. You type as if your ilk doesn't do the same/worse.

Take another look sparky. We are 2 guys. There are many more of you spewing low grade insults and inserting snooty remarks in every post. Although you outnumber us in quantity, we kick your asses in quality.

If such weren't the case, we wouldn't see so much whining from the chimp section.

"Nice essay. Thanks for posting the link!"

back to that ol' butt kissing routine again, eh balrot?

You must either be the team mascot or the cheerleader.
Either way, the pigtails are you!

Evo-spellchecker?

Evo-spellchecker?

We don't claim to be descendants of ape men so it must be theirs.