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TR Memescape

  • I think the biggest problem with TR is that a lot of you dont know how to surrender graciously when youre beat.

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as a once mini-skirt wearing, twist-and-shouting, Beatles-loving teenager
Please post pics.  I'll post some if you post some. Lol
Well if Shapiro is suggesting supernatural forces at work in the cell, then he's moved himself out of the realm of science.

I know of no reason to think that the interactive cognitive and regulatory networks within a cell are not mediated by the same known physical that govern human brains. 

If Shapiro thinks there's a ghost in the machine, he should come right out and say so.

Is there a ghost inside of you?

I happen to think there is, but I don't think you do.

I don't think it's a question for science.  That's the point.  If Shapiro thinks it's a scientific question then he has some more thinking to do. There are no scientific methods for detecting the supernatural, by definition. The best we can do is to say: "we can't explain this yet".  If you and Shapiro want to say "that's because :itsamystery: that's up to you, but at that point you have moved outside science.

But science doesn't stop at "we can't explain this yet".  It keeps on trying.

They've moved outside theology as well. Unless dave wants to claim bacteria have souls (or maybe return to Ye Olde Vis Vitalis days).
Yeah, how exactly does this idea that cells literally think square with Dave's whole humans-are-special thing? Or do thoughts like that never cross the mind of ol' 5th Law Dave?

I'm not sure.  Dave often makes the highly reductionist point that a cell reading a DNA sequence is just like a human reading print because in both cases its the result of clever networks of physical components pushing stuff around.

So I find it odd that I, the materialist, find myself pointing out that the agent in the case of reading is the agent Pingu perceiving and reacting to the external world, while the cell "reading itself" would be more analogous to Pingu qua organism reacting to what I just ate.  I, Pingu, don't direct my stomach to digest what I dump in it.  The body I own does that.  I, Pingu, DO direct my mind to read, mark and inwardly digest a paper by Shapiro.

I don't think the cell has an "I".  But I patently do or I couldn't write this post.  And I is a Strange Loop (as Hofstadter actually wanted to call his book).
It's all biology, right?  According to you anyway.  Which in turn is nothing but chemistry at the bottom of it all, right?  You can't have it both ways.  Either you are a committed materialist.  Or you're not.

Maybe this is the year that you will realize that there is more than just matter / energy?
Dave, the Surgeon General in 1967 said that?

Take a look:

Sounds like more of the same misinterpretation and propagation of myths, very much like you and YEC, Dave.
I dunno.  Here's Shapiro's source ... 389 citations ...
Format: AbstractSend to
Clin Infect Dis. 2001 Mar 1;32(5):675-85. Epub 2001 Feb 23.
Infectious diseases: considerations for the 21st century.
Fauci AS1.
Author information
The discipline of infectious diseases will assume added prominence in the 21st century in both developed and developing nations. To an unprecedented extent, issues related to infectious diseases in the context of global health are on the agendas of world leaders, health policymakers, and philanthropies. This attention has focused both on scientific challenges such as vaccine development and on the deleterious effects of infectious diseases on economic development and political stability. Interest in global health has led to increasing levels of financial support, which, combined with recent technological advances, provide extraordinary opportunities for infectious disease research in the 21st century. The sequencing of human and microbial genomes and advances in functional genomics will underpin significant progress in many areas, including understanding human predisposition and susceptibility to disease, microbial pathogenesis, and the development new diagnostics, vaccines, and therapies. Increasingly, infectious disease research will be linked to the development of the medical infrastructure and training needed in developing countries to translate scientific advances into operational reality.

As for this, "Do you think there's anything he says in there that would come as news to anyone who has at least casually followed microbial genetics for the past 4 or 5 decades?"

It seems that Shapiro would answer "Yes" to this question.  Note what he says ...
In the early days of molecular biology, bacterial geneticists applied conventional evolutionary concepts from the pre-DNA period to explain the evolution of antibiotic resistance. The theory was that mutations could alter the structure of cell components and either block entry of the drugs into the bacteria or prevent their action on cellular targets, such as the enzymes essential to cell wall synthesis. Even if the initial mutation did not confer a high degree of resistance, accumulation of several sequential changes would result in resistance to the antibiotic levels used in clinical medicine. Indeed, a wide variety of laboratory experiments confirmed this theory, and bacterial geneticists isolated the predicted mutant strains. In virtually all cases, the resistant mutants grew less well than the parental sensitive bacteria, leading to the comforting conclusion that resistant bacteria would not significantly accumulate in nature. The degree of confidence was so great that the U.S. Surgeon General in 1967 declared that "the war against infectious diseases has been won" (Fauci 2001).

There were problems both with the science and the new public health policy based on it. The Surgeon General "misunderestimated" the bacteria, which followed their own evolutionary rules and did not listen to what the scientists said they should do. Although experimentally confirmed, the mutation theory of antibiotic resistance failed to account for most cases in the real world. Resistance continued to spread among bacteria isolated in clinics around the globe. Even more ominously, different strains of pathogenic bacteria increasingly displayed resistance to more than one antibiotic at a time. Research pioneered in Japan found that multiple antibiotic resistances could be transferred simultaneously from one bacterial species to another (Watanabe 1967). The DNA agents responsible for this transfer are circular molecules that are called multidrug resistance plasmids, which can move from one cell to another (Clowes 1973; Novick 1980). Moreover, the resultant multiply resistant bacteria were not altered in their cellular structures or inhibited in their growth properties. Rather, they had acquired new biochemical activities that could destroy or inactivate the antibiotics, chemically alter their targets, or remove them from the bacterial cell (Davies 1979; Levy 1998).

Multiple antibiotic resistance clearly represented genome change and evolution of a type unimagined in the pre-DNA period. DNA molecules could be transferred "horizontally" between unrelated cells rather than inherited from ancestral cells. Moreover, horizontally transferred DNA could carry complex sets of genetic information encoding multiple distinct biochemical activities. Evolutionary leaps involving several characteristics at once could occur through horizontal DNA transfer.

Over time, it became increasingly clear that bacteria and other microorganisms engage in a great deal of horizontal DNA swapping. In addition, these small cells have an ample toolbox of natural genetic engineering mechanisms to incorporate and rearrange this horizontally acquired DNA (Miller 1998; Shapiro 2011).

So it seems that it took years to figure that the surgeon general's declaration in 1967 was wrong.

No, it did not.  For a start, it looks like he didn't even say it.  But what IS true is that back in the sixties. when people started to worry about bacterial resistance to antibiotics.  And they certainly did - as I have mentioned before, my grandfather was closely involved in the early deployment of penicillin, and both my parents entered medicine in the fifties at the dawn of the antibiotic age - I remember a fat textbook on the shelf at home called Man Against Microbes, so it was something that was literally discussed round the family dinner table in my formative years.  I remember my mother explaining evolution to me in fact, and how bacteria might evolve resistance to antibiotics.  I also remember her saying that the good thing was that because bacteria clone themselves, any mutations conferring resistance would tend to build up in the genome, and make the bacteria overall less fit.

The reason she was wrong in the fifties was the reason Shapiro gives - that people at that stage didn't know that bacteria effectively have sex.  Whereas in people, and other sexually reproducing organisms, mutations don't build up in a single lineage because we can swap them around, people thought that that couldn't happen in bacteria.  But it turned out it can and does, because the bacterial substitute for sex is DNA swappage, aka HGT.  In fact, sex, or at least gamete formation followed by sex, is our brand of HGT.

So it took a while for people to discover this.  Remember that the structure of DNA was only discovered in 1953, right at the beginning of widespread use of antibiotics.  So to have been overoptimistic about antibiotic resistance in the sixties may have been hubristic, it wasn't unreasonable. And it wasn't the only view. I also remember people arguing that bacteria seemed to have evolved to do lots of extraordinary things very nicely, thank you, over the last billions of years, and so expecting them not to evolve to cope efficiently with antibiotics would be wishful thinking. 

And in any case, VoxRat's incredulous question is entirely reasonable. The sixties were half a century ago (I can't believe I'm typing this, as a once mini-skirt wearing, twist-and-shouting, Beatles-loving teenager, but hey).  Cell biologists, biochemists and microbiologists have made extraordinary strides since then.  And actually they were no slouch in the sixties.  If you watch and listen to the narrated version of The Inner Life of the Cell, a lot of the items mentioned were well known about back then.

As were many of the complexities of the neuron.  In another personal anecdote, a couple of girls at my boarding school when I was 11 got a week off school to go to Sweden, because, as I wrote to my parents "their father has won some sort of prize". 

People in the fifties and sixties knew a heck of a lot about the cell and there's been more than half a century of cell biology since.

As for this ...
(1) A given lineage of bacteria can acquire a "novel" function (notably, antibiotic resistance) by horizontal gene transfer.
It's novel to that lineage, but - obviously* it had to evolve somewhere. No one, so far as I know, has proposed a mechanism for process of that evolution other than what you like to sneeringly call "RM + NS".
I agree.

So why were you sneering?  That's exactly what Ayala means by the ultimate source of variation.  Not necessarily the proximal source.
Politics and Current Events / Re: Trumpocalypse
Last post by Faid -
Quote from: AG Jeff "I never met with Russians, I mean I don't recall meeting with Russians, maybe I did, OK I met with Russians" Sessions
The F.B.I. expects every employee to adhere to the highest standards of honesty, integrity and accountability
Spoiler (click to show/hide)
Politics and Current Events / Re: Trumpocalypse
Last post by brugroffil -
I dunno if McCabe has recourse to sue over his pension but I hope so.

I feel kinda sick witnessing someone having their pension shanked like that.  It's something you expect to happen to Walmart managers, not public sector workers.
McCabe should have been fired over the bullshit he pulled in 2016. Comey too.

But he was fired because his wife is a Democrat

E: he also has a net worth of 11m already so I think he's fine, and also like firing Comey I think this will backfire on Trump
Wild guesses department, from around the web:

Keith Schiller, Trump's former long-term bodyguard, may still be on Trump's payroll, and seems a plausible character for the alleged threats delivered to Daniels.

He's getting something like $15k a month direct from the RNC as hush money
not really perfect for this thread but I didn't want to start a new one and it is pretty interesting
Politics and Current Events / Re: Trumpocalypse
Last post by Testy Calibrate -
It's not just New Jersey bridge closures anymore. I'm actually a little surprised no one with potentially damaging information has turned up dead here in America.