Unsatisfactory Scientific Explanations?

[whois]

serious,
i'm sorry, but the wiki article is incorrect.
natual selection doesn't play a dominate role in evolution.

evolution is not a gradualistic paradigm.

nor is it warranted that evolution is an adaptive, progressive paradigm.

for example:
The concept of natural selection as the foundation of evolutionary change has been largely superseded, mostly through the work of Motoo Kimura, Tomoko Ohta, and others, who have shown both theoretically and empirically that natural selection has little or no effect on the vast majority of the genomes of most living organisms.
. . .
Kimura, Ohta, Jukes, and Crow dropped a monkey wrench into the "engine" at the heart of the modern synthesis — natural selection — and then Gould and Lewontin finished the job with their famous paper on “the spandrels of San Marco and the Panglossian paradigm”. The rise of evo-devo over the past two decades has laid the groundwork for a completely new and empirically testable theory of macroevolution, a theory that is currently facilitating exponential progress in our understanding of how major evolutionary transitions happen. And iconoclasts like Lynn Margulis, Eva Jablonka, Marian Lamb, Mary Jane West-Eberhard, and David Sloan Wilson are rapidly overturning our understanding of how evolutionary change happens at all levels, and how it is inherited.
evolutionlist.blogspot.com/2009/11/modern-synthesis-is-dead-long-live.html

 

[whois]

It is not that the paper is wrong or bad, it just over sells it's point.

that's funny, because the paper states the very same thing about the modern synthesis:
We should be equally clear that, in arguing for the necessity of this intellectual transformation, we do not think that those who based their research on the Modern Synthesis were "bad scientists" and those who now abandon it are "good scientists." We are simply offering an overview of how a large number of us have changed our thinking, our biological Weltanschauung.
-ibid.

Let's begin by defining modern synthesis. Wikipedia has a good run down of the key points:

unfortunately, the modern synthesis is no longer valid.
therefor, a definition of it is irrelevant.

 

[[serious]]

serious,
i'm sorry, but the wiki article is incorrect.
natual selection doesn't play a dominate role in evolution.

evolution is not a gradualistic paradigm.

nor is it warranted that evolution is an adaptive, progressive paradigm.

for example:
The concept of natural selection as the foundation of evolutionary change has been largely superseded, mostly through the work of Motoo Kimura, Tomoko Ohta, and others, who have shown both theoretically and empirically that natural selection has little or no effect on the vast majority of the genomes of most living organisms.
. . .
Kimura, Ohta, Jukes, and Crow dropped a monkey wrench into the "engine" at the heart of the modern synthesis — natural selection — and then Gould and Lewontin finished the job with their famous paper on “the spandrels of San Marco and the Panglossian paradigm”. The rise of evo-devo over the past two decades has laid the groundwork for a completely new and empirically testable theory of macroevolution, a theory that is currently facilitating exponential progress in our understanding of how major evolutionary transitions happen. And iconoclasts like Lynn Margulis, Eva Jablonka, Marian Lamb, Mary Jane West-Eberhard, and David Sloan Wilson are rapidly overturning our understanding of how evolutionary change happens at all levels, and how it is inherited.
evolutionlist.blogspot.com/2009/11/modern-synthesis-is-dead-long-live.html

Ok, so you object to the role of selection in evolution. Great! That gives us a place to start.

Let's take an example. How does antibiotic resistance arise and spread?

 

[whois]

Ok, so you object to the role of selection in evolution. Great! That gives us a place to start.

Let's take an example. How does antibiotic resistance arise and spread?

my guess would be by an epigenetic mechanism.

 

[brocke]

What are some topics for which you have found scientific explanations to be unsatisfactory? What is it about the scientific explanations that you've been given that leaves you wanting a better explanation? Are you still in search of more science to back up these explanations or have you given up and left your curiosity unsatisfied on these topics?

Okay haven't read the whole thread so if someone else mentioned this I apologize for repeating.

For me right now there are two things that just leave me wanting a good explanation.

1. The results in the Quantum Mechanic Double Slit Experiment.
   How does that stinking electron know it is being watched? Why does it act like a wave when not being detected and then like a particle if it is being detected. I continue to learn more physics and about quantum theory hoping I can come to an explanation myself. I wonder if maybe we are wrong about the quantum theory and there is another explanation we need to figure out. BTW I do accept Quantum Theory as the experimental data does confirm it - right down to the Higgs particle.
2. The recently discovered Holographic Effect. http://www.cornell.edu/video/leonar...ervation-of-information-holographic-principle What does it mean if we can describe all information within a 3D region just on the 2D surface area of that region?

God's creation just continues to amaze me and I am floored by how it was all made to work like a well made machine. It all fits together and functions.

 

[whois]

Ok, so you object to the role of selection in evolution. Great! That gives us a place to start.

Let's take an example. How does antibiotic resistance arise and spread?

BTW, it's kimura that, not only objects, but empirically proved it.

it must be pointed out that his neutral theory has been modified to the nearly neutral theory.

 

[[serious]]

my guess would be by an epigenetic mechanism.

TEM-1 codes for Beta lactamase, the most common form of penicillin resistance. It is a gene.

All enzymatic inactivation of antibiotics known are DNA coded.
Binding site alteration is likewise due to alteration of the DNA coding for that binding site
Active transport of the antibiotic is likewise DNA coded protein

Somewhere out there may be a epigenetic route to antibiotic resistance, but all the ones we've found are genetic.

lets focus just on that TEM gene. It's responsible for 87% of ampicillin resistant e. coli isolated in hospitals. How do you think this gene became so widespread?

 

[whois]

TEM-1 codes for Beta lactamase, the most common form of penicillin resistance. It is a gene.

All enzymatic inactivation of antibiotics known are DNA coded.
Binding site alteration is likewise due to alteration of the DNA coding for that binding site
Active transport of the antibiotic is likewise DNA coded protein

Somewhere out there may be a epigenetic route to antibiotic resistance, but all the ones we've found are genetic.

lets focus just on that TEM gene. It's responsible for 87% of ampicillin resistant e. coli isolated in hospitals. How do you think this gene became so widespread?

first of all, epigenetics is all about genes.
it basically relates to how the environment can switch them on or off.

genes become widespread because they are fixed.
this includes gene acquired by HGT and other sources.
one specific blood group was a result of HGT becoming fixed, and then being further mutated to include similar genes for other blood groupings.

 

[stevevw]

You may not know enough, but physicists do; quantum field theory tells us that the only field with a range and strength relevant to human-scale interactions is the electromagnetic field. The brain does produce EMF, but it's a barely detectable (e.g. by EEG) bioelectric sum of all neural activity. Quantum tunneling, quantum entanglement, time travel, parallel worlds, holographic universe, and so-on, are all irrelevant to this. If you want to know what researchers are speculating about concerning the brain and quantum effects, check out the latest New Scientist issue - it's a 'highly speculative' (and to me unconvincing) hypothesis about the contribution of molecular level quantum effects to neural function in thought and memory.
We do know; everything is quantum mechanical at the lowest level and the theory describing how it behaves is the best tested theory we've ever had. We know very precisely how it behaves; what we don't know is why it behaves like that.

We know some molecular-scale quantum effects are used to optimize some biological functions (e.g. photosynthesis, bird navigation). But the Penrose & Hameroff Orch-OR theory of quantum consciousness mediated by cellular microtubules is more than highly speculative, it's quite implausible; there's no evidence for it, it stretches QM way outside its known bounds, it makes no testable predictions, and it is redundant. If you look for the original paper that phys.org item is based on, you'll find it wasn't a peer-reviewed paper published in an acknowledged journal, but a report of a claimed discovery by a colleague of theirs in a review by Penrose & Hameroff themselves. It was media puffery, an attention grab - but there was nothing to see - which is why, after a brief flurry of interest, it was put back in the 'speculative pseudoscience' bin.

I always thought that most scientists didn't know everything about quantum physics. Thats what I seem to read. As Richard Feynman famously quipped that I can safely say that nobody understands quantum mechanics. How can scientists know exactly how it behaves when part of quantum physics is that they cannot calculate what it will do because there are many possibilities.

I used the parallel worlds, hologram worlds, time travel ect because they are some of the things used to describe and address how the quantum world acts. Scientists seem to have to reach out beyond the classical physics to be able to explain how quantum physics works. Thats why I ask if there may be some unknown aspect of how our brains work at a quantum level that may be beyond the calculations we can know at the moment. I did a bit of investigation and although you say that the article for ORC OR by Penrose & Hameroff is pseudoscience there is other peer reviewed work out there supporting similar stuff.

Keeping time: could quantum beating in microtubules be the basis for the neural synchrony related to consciousness?
http://www.ncbi.nlm.nih.gov/pubmed/25012713
Though the authors of this paper disagree with Penrose & Hameroff conclusions they still believe that the quantum brain and consciousness is a valid field of study and present their own findings.
Quantum models of the mind: are they compatible with environment decoherence?
http://www.ncbi.nlm.nih.gov/pubmed/15524544
Reply to criticism of the ‘Orch OR qubit’ – ‘Orchestrated objective reduction’ is scientifically justified
http://www.sciencedirect.com/science/article/pii/S1571064513001917

 

[[serious]]

first of all, epigenetics is all about genes.
it basically relates to how the environment can switch them on or off.

genes become widespread because they are fixed.
this includes gene acquired by HGT and other sources.
one specific blood group was a result of HGT becoming fixed, and then being further mutated to include similar genes for other blood groupings.

If you are using a definition of epigenetics that does not require heritable changes, but rather includes any environmental impact on expression, that's fine. Such a broadened use of the term is really only a new buzzword applied to a very old idea. Response to the environment has always been a part of the modern definition of life.

 

[FrumiousBandersnatch]

yes, it does seem you know a lot about the modern synthesis, and its foundations.
unfortunately genomics and other disciplines have overturned many important assumptions of the modern synthesis in the last decades of the 20th century.
give the following a read:
www.ncbi.nlm.nih.gov/pmc/articles/PMC2222615/

Strange as it may seem, I continued to take an interest in the field after finishing formal education.

The article is a reasonably good history of developments to date, and how it continues to develop and integrate wider areas of the sciences as technology gives us greater detail and depth (although I agree with some of Eugene Koonin's criticisms). There is always a problem with labeling an era as if it has clear and distinct boundaries, but the particular problem with the label 'Modern Synthesis' is the hubristic 'modern' - it was modern for 50 or 60 years... The usage I most often hear that accounts for more recent developments in molecular genetics, genomics, symbiogenesis, epigenetics, and so-on, is the 'New Modern Synthesis' - presumably because 'Post-modern Synthesis' is too redolent of postmodernism...

But less of the semiotics - how does your post, with its implication that I'm somehow educationally stuck in the 1970's, address any of my points concerning the apparent lack of understanding of basic genetics in your posts?

since some genes are conserved, then science apparently know what these genes are.
what are these genes specifically, HOX genes perhaps?

Yup, HOX genes are highly conserved. You can access a fairly comprehensive list in the Ultraconserved Element Database.

 

[FrumiousBandersnatch]

BTW, it's kimura that, not only objects, but empirically proved it.

it must be pointed out that his neutral theory has been modified to the nearly neutral theory.

We already dealt with Kimura - he has suggested new mechanisms that drive molecular-level evolution. He specifically states that at the phenotypic level, natural selection is the primary evolutionary driver.

 

[whois]

The usage I most often hear that accounts for more recent developments in molecular genetics, genomics, symbiogenesis, epigenetics, and so-on, is the 'New Modern Synthesis' - presumably because 'Post-modern Synthesis' is too redolent of postmodernism...

personally i prefer extended synthesis, because that's exactly what it is

But less of the semiotics - how does your post, with its implication that I'm somehow educationally stuck in the 1970's, address any of my points concerning the apparent lack of understanding of basic genetics in your posts?

and?
what exactly are you saying here?
you give me a chance to demonstrate why your reasoning is wrong with you very next quote:

Yup, HOX genes are highly conserved. You can access a fairly comprehensive list in the Ultraconserved Element Database.

like you mentioned above, it appears i lack a "basic understanding".
it doesn't take a rocket scientist to realize that these genes that are conserved, traceable through millennia, are the very same genes that MUST change in order to comport with common decent.

 

[whois]

We already dealt with Kimura - he has suggested new mechanisms that drive molecular-level evolution. He specifically states that at the phenotypic level, natural selection is the primary evolutionary driver.

kimura isn't the only scientist that says natural selection is not the dominate force in regards to evolution.
now, if you want me to understand this, then explain it so i can.

 

[FrumiousBandersnatch]

I always thought that most scientists didn't know everything about quantum physics. Thats what I seem to read. As Richard Feynman famously quipped that I can safely say that nobody understands quantum mechanics.

That's true; also, knowing isn't understanding.

How can scientists know exactly how it behaves when part of quantum physics is that they cannot calculate what it will do because there are many possibilities.

It is a probabilistic, stochastic regime, like thermodynamics. In QM the probability of various outcomes of a measurement can be very precisely determined, but not predicted for any particular instance. Similarly, in thermodynamics, the position and velocity of individual molecules and particles is unpredictable, effectively random, but the behaviour of the bulk is precisely calculable and predictable. The reason our world is so seemingly deterministic at human scales is this bulk effect averaging out all the little quantum uncertainties.

I used the parallel worlds, hologram worlds, time travel ect because they are some of the things used to describe and address how the quantum world acts.

They're not relevant.

Scientists seem to have to reach out beyond the classical physics to be able to explain how quantum physics works. Thats why I ask if there may be some unknown aspect of how our brains work at a quantum level that may be beyond the calculations we can know at the moment. I did a bit of investigation and although you say that the article for ORC OR by Penrose & Hameroff is pseudoscience there is other peer reviewed work out there supporting similar stuff.

I've looked too. Nothing that isn't highly speculative, or has any convincing evidence in support, or can explain how the claimed effect actually influences the brain. Just because the quantum world is counter-intuitive it doesn't mean it's random magic that could do anything.

Though the authors of this paper disagree with Penrose & Hameroff conclusions they still believe that the quantum brain and consciousness is a valid field of study and present their own findings.

Yup, that's the beauty of science - there are always people prepared to pursue their personal predilections - although they often turn out to be wild goose-chases. There's no good reason to suspect quantum effects need play any role in brain function, beyond classical chemistry, but some brave souls are determined to try and find one. The problem for them is that by starting with a claim for which there is no clear rationale or evidence, it's very hard to construct a testable hypothesis; so they end up looking for evidence that looks as if it might support the claim (e.g. microtubules) and get into all kinds of problems with interpretation - to a man with a hammer, everything looks like a nail.

 

[FrumiousBandersnatch]

it doesn't take a rocket scientist to realize that these genes that are conserved, traceable through millennia, are the very same genes that MUST change in order to comport with common decent.

I suspect even a rocket scientist would understand that, for example, all eukaryotes have eukaryotic cells in common, with similar cellular structures and metabolic mechanisms, and this suggests that the genes that control basic cellular structure and metabolism will be highly conserved, while genes that control development in other respects may not be. The genes that are conserved are genes that comport with common descent because they don't change significantly; they're evidence of common descent.

 

[FrumiousBandersnatch]

kimura isn't the only scientist that says natural selection is not the dominate force in regards to evolution.
now, if you want me to understand this, then explain it so i can.

As I understand it, Kimura says that mutation is the source of genetic variation and natural selection and genetic drift are the main forces leading to changes in allele frequency. Natural selection is predominant at the phenotypic level and neutral genetic drift is predominant at molecular level.

So in terms of the evolution of species (phenotypic variation), he says natural selection is the driving force. Neutral mutations at molecular level don't affect this; they're neutral.

You seem to think I have this wrong; I don't think so, but you may be right - if so, you should be able to quote or link to some Kimura references that contradict my current understanding of his work.

 

[whois]

I suspect even a rocket scientist would understand that, for example, all eukaryotes have eukaryotic cells in common, with similar cellular structures and metabolic mechanisms, and this suggests that the genes that control basic cellular structure and metabolism will be highly conserved, while genes that control development in other respects may not be. The genes that are conserved are genes that comport with common descent because they don't change significantly; they're evidence of common descent.

keep in mind i'm using common decent in the macro evolutionary sense.
if these genes aren't changed, then the body plans aren't changed either.
science has already stated they can trace these genes through millennia.
some of them all the way back to bacteria.
this does not imply a changing body plan, in fact it implies the exact opposite.

at the very least it is further proof that macro evolution is not accumulating micro evolution.
it certainly seems to support what eldridge says of the record.

 

[FrumiousBandersnatch]

keep in mind i'm using common decent in the macro evolutionary sense.
if these genes aren't changed, then the body plans aren't changed either.
science has already stated they can trace these genes through millennia.
some of them all the way back to bacteria.
this does not imply a changing body plan, in fact it implies the exact opposite.

As I already explained, the genes that control the stuff that changes very little - e.g. cell type, structure, and metabolism, obviously change very little themselves (conservation). The genes that control phenotypic variation at the body plan level vary according to that variation because they determine that variation. This is not difficult to grasp.

at the very least it is further proof that macro evolution is not accumulating micro evolution.

Nope.

Still waiting for your Kimura quotes or links to show how I've misunderstood his ideas.

 

[stevevw]

That's true; also, knowing isn't understanding.
It is a probabilistic, stochastic regime, like thermodynamics. In QM the probability of various outcomes of a measurement can be very precisely determined, but not predicted for any particular instance. Similarly, in thermodynamics, the position and velocity of individual molecules and particles is unpredictable, effectively random, but the behaviour of the bulk is precisely calculable and predictable. The reason our world is so seemingly deterministic at human scales is this bulk effect averaging out all the little quantum uncertainties.

But isn't that what some are saying about quantum physics that its the observer that is determining the final effects. So what is averaged out that we end up seeing is only seen that way because it is us that is determining that. But up until that point at least in the quantum world and to some point leading up to what we see there are many possibilities. What we end up seeing isn't what happens in the lead up. So therefore some come up with the many world idea to address this. In another parallel world someone may end up seeing and experiencing a different end result.

They're not relevant.

OK well I thought they were some of the ideas scientists used to address the quantum effect of many possibilities. It helps solve the problems of uniting classical physics with quantum physics.
http://www.livescience.com/48806-parallel-worlds-quantum-mechanics-theory.html

I've looked too. Nothing that isn't highly speculative, or has any convincing evidence in support, or can explain how the claimed effect actually influences the brain. Just because the quantum world is counter-intuitive it doesn't mean it's random magic that could do anything.

Of course this is what quantum physics seems to provoke in people and even scientists. The point is if they are having to reach for these ideas then something is causing them to do so. They are merely trying to unite things together and the only way to do so is to appeal to these ideas beyond the logical realms. Afterall if we go back to the point of where something comes from nothing and this is where things have to go then it has to have something beyond logic and beyond the classical physics to be able to explain things. This is the point where scientists are hitting and constantly having to consider this in their equations now with the universe and physics itself.

Some say that there are some scientists who are speculating about quantum woo and pseudoscience by bringing in these far fetched ideas. But even the mainstream science is more or less coming up with the same sort of speculations. Things like multiverses, hologram worlds, string theory, black holes, worm holes, ect are along the same lines. Yet even prominent scientists are using this type of language.

Yup, that's the beauty of science - there are always people prepared to pursue their personal predilections - although they often turn out to be wild goose-chases. There's no good reason to suspect quantum effects need play any role in brain function, beyond classical chemistry, but some brave souls are determined to try and find one. The problem for them is that by starting with a claim for which there is no clear rationale or evidence, it's very hard to construct a testable hypothesis; so they end up looking for evidence that looks as if it might support the claim (e.g. microtubules) and get into all kinds of problems with interpretation - to a man with a hammer, everything looks like a nail.

I think this was how any science began and was looked upon. This is especially true with the quantum world. Look at the ideas that some of the great scientists have had like Schrodinger. If you read some of the articles and even papers on the subject many mainstream scientists have suggested contradictory things like there is no big bang according to quantum physics, the universe is a big 2D TV screen in a hologram universe.

Maybe the answer has to be in some far fetched explanation because what we are seeing points in that direction. So even though some are saying that the brain cannot be linked with the quantum world at the moment who knows what we will find in a couple of years time. I think thats why some are speculation that the brain maybe connected to the quantum world because there is a rational. That rational started with the findings of quantum physics with things like the observer effect and that everything has to have started in the quantum world even our brains.