Bacteriophages, Budding Yeast, and Behe’s Vindication

https://evolutionnews.org/2018/11/bacteriophages-budding-yeast-and-behes-vindication/

@Agauger writes:

(I’ll bet you didn’t know that bacteria have their own little viruses, called bacteriophages, that make them sick and kill them.)

yes, I do and here is an interesting paper on bacteriophages and how they cooperate to suppress Crispr-Cas9

https://www.cell.com/cell/fulltext/S0092-8674(18)30738-4

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To piggy-back onto @Patrick 's question/comment - @Agauger, do you think point mutations that alter phage receptors are more important and durable evolutionary mechanisms for achieving phage resistance than CRISPR? Also, in your opinion, is CRISPR an example of a gain of function, modification of function, or loss of function adaptation (roughly in the parlance of Behe’s 2010 paper and, I presume, his book)?

I am trying to wrap my mind around Behe’s assertions, and a discussion of phage might help here. Thanks.

Am I alone in finding it amusing that (according to the cell.com article) “some phages produce anti-CRISPR (Acr) proteins”? I suppose I have a quirky sense of humor but I think it comical that microorganisms have become so annoyed at humans intruding upon their genetic affairs that they have struck back and tried to lock their doors! They’d prefer that we mind our own business. :wink:

[Yes, I’ve taken huge anthropomorphic liberties which have no basis in fact. But I enjoy myself. This is another topic where a The Far Side type of cartoonist could have a lot of fun, such as imagining a truce called between the bacteria and bacteriophages so that they can discuss mutual defenses against increasingly annoying CRISPR experiments. One hapless bacterium, the low guy on the totem pole, gets drafted to wear a poorly tailored “protein coat” which bacteria and phage scientists have crafted to ward off CRISPR intrusions. While the tailor makes final adjustments, the reluctant bacterium looks at himself in a full-length mirror and says, “Yeah, but the cuffs are too long and it makes me look like I have no waist at all!”]

As to the Evolution News & Views article, the spin is about what I would expect. This brings to mind a topic which we should perhaps discuss in its own thread someday: Does Evolution News & Views often appear to operate at cross-purposes to the objectives and effectiveness of Discovery Institute scientists? If not for ENV muddying the waters, would DI scientists have a better chance of getting a hearing? (That’s a question, not a statement with an agenda. I just wonder about the “disconnect” I often sense between ENV and DI scholars.)

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Heck, even a statistician knows that! I would bet you a cup of coffee (via $10 Starbucks gift card) that Ann does too.

But you have to take me up on it before Ann responds. :slight_smile:

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Behe tends to cherry pick the data. He will only talk about examples that he can call a loss in function, and will avoid examples that are clear increases in function, such as Turf13.

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I’m sure she does. And I’d bet that Patrick thinks so too. I assumed that Patrick was just being “Patrick” in his usual having-fun, mischievous sort of way.

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Ahh, turns out this was a quote from Ann’s ENV article, and not an example of @Patrick -ing! :slight_smile:

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@Agauger, I’m having difficulty following what you are saying.

In the paper, he summarized years of work by geneticists on numerous bacteria and viruses, and laid out this principle, the First Rule of Adaptive Evolution:

This looks like a sentence fragment that doesn’t complete the “First Rule”.

Behe was pointing out an inconvenient truth . Much of evolution occurs by loss of function

I’m also curious why you characterize stating the obvious as an “inconvenient truth”.

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Don’t be silly. I am enterily sure @Agauger knows about bacteriophages. We have even discussed them here before. We can disagree with her but do not call her ignorant, especially on things she is obviously knowledgeable about.

I just edit the OP to make it quote, clarifying she is not ignorant here.

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{sigh} so much for my getting free coffee! :wink:

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@swamidass, once again we all got fooled by the attribution-bug in this forum’s software. As @cwhenderson pointed out, that was actually a quote from @Agauger’s ENV article, not a remark by Patrick!

That bug has “bugged” me every since I first saw it confusing dialogue on the Biologos forum. Until that bug gets repaired, we must diligently manually edit our quote-tags! (Fortunately, it becomes a natural habit after a while. I now give it little thought when I’m grabbing text to quote. I just fix it, as I’ve done in the above by making it say “Not-Patrick”.)

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Thanks, Patrick. An interesting paper indeed.

Great fleas have little fleas

Upon their backs to bite 'em,

And little fleas have lesser fleas,

And so ad infinitum

Attributed to various writers with slight variations. This version appears in De Morgan’s "A Budget of Paradoxes.

"

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@cwhenderson

If you read the rest of the piece I think your question will be answered. I agree, Mike’s phrasing can be confusing. Rather than a declarative sentence, see it as an imperative.

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Use of the phrase “inconvenient truth” suggests that the obvious fact that it is simpler genetically to break than to build is something that scientists would prefer to overlook, rather than explore. I don’t think that is a fair assessment.

Additionally, since you did say “Behe was pointing out an inconvenient truth. Much of evolution occurs by loss of function” (my emphasis), then I’m sure you would concede that molecular alterations to DNA are not always of the demolition variety. Every so often, a bridge does indeed get built. This tends to work against the possibly over-simplified argument you are proposing.

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Software bug - blame the atheist for it. :rofl:

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I should point out that “break” is very poorly defined in this context. The analogy to real world objects (blowing up a bridge, versus building one) are highly misleading.

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@cwhenderson

Yes Even Behe himself acknowledges gain of function mutations do exist. And the extensive quotes I made indicated a majority but not all mutations were loss of function.

Fair enough. A perhaps prejudicial turn of phrase. Scientists do acknowledge it, at least some. But not on Panda’s Thumb, I’ll wager.

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I’m highly doubtful of the dig on Panda’s Thumb. @Art cut his teeth their, and I am sure he would agree.

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@swamidass
You are not going to get me to back off here. @Art may have been civil, others definitely were not. And I highly doubt they discussed the fact that most mutations are loss of function, and that many evolutionary diversifications are due to loss of function mutations, unless they discussed it in the context of Behe’s paper.

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Well that is sadly true. I’m sorry about this.

I guess i’m not really qualified to make a full throated defense of them. I think the absence of public Christians among them undermined their case in religious audiences too.

Regardless, do you understand why this observation is not troubling to evolutionary science? Do you know why we think Behe’s argument doesn’t follow from this observation, and Behe is not at all vindication?

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