Unsatisfactory Scientific Explanations?

Paul of Eugene OR said:

The question makes no sense. Empirical physics, by definition, is physics done according to what works. So if you are trying to find a solution to a physics question, you are by definition doing empirical physics. So the answer to "why limit oneself to only empirical physics" would be . . . because there is no other kind of physics.

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equations on paper are theoretical.
it's the actual testing of these equations that makes them empirical.
quantum physics is a perfect example of this.
actual testing shows that photons somehow "know" they are being observed.
further equations show that the events of today affect the past.
the first is empirical, it's been demonstrated, the second remains to be seen (to my knowledge).
BTW, einstein questioned quantum physics up until the very end, saying it was either outright wrong, or incomplete.
strange stuff for sure.

FrumiousBandersnatch said:

I can't speak for hypothetical aliens - you seem to know them better than I; it might not be intuitively obvious from a superficial explanation - it's a simple principle with profound implications over geological time, but I expect that if he had access to the available evidence, a little study should convince him that it's possible, and it happened. Alternatively, a technologically competent alien might run a simple computer simulation and discover the power of replication with heritable variation and selection.

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Frumious,
First off you cite computer simulation as one reason that your principle is good yet reality and computer sims are two different things. Artificial simulations can tell us of some accidental aspects of nature but certainly not what is substantial to nature... this is to use Aristotle's philosophical language. The principle you say you've adopted is at the level of substance (corporeal, physical or empirical) in that it tries to encompass all of nature's unfolding and change.

Here I might add that the very word bantied about by the two opposing sides of this issue, termed evolution, comes from the Latin evolvere; that is simply... to unfold. Now to unfold implies something exists that can by its nature do just that. Yet on the athiest side we have those who try to deny the existence of a creator implying the principle explains its own existence... in other words the principle moves beyond science (especially physics) into the realm of metaphysics and theology.

My main point here is that even if evolution is part of reality within the true and limited sense I indicate above it cannot, even in principle, eliminate the need for a cause, more importantly a first cause that is by defintion uncaused.

Ratjaws said:

Frumious,
First off you cite computer simulation as one reason that your principle is good yet reality and computer sims are two different things.

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true.
although computer simulations have great value, they cannot model the unknown.
a computer built specifically to play chess couldn't tell you what 2+2 is.
this is one area that humans are light years ahead of computers, computers simply cannot "guess", they must follow a programmed plan verbatum.
of course, they can generate and use random numbers, but this too must follow a program or plan.

Gentle Lamb said:

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?

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Leslie,
I love your question! I wonder what brings you to ask it? It is much needed in our extremely scientificly centered culture... which I might add somewhat shockingly... has been very miseducated on the limits of true empirical science. I can only give a cursory answer here precisely because the topic includes... well really everything. Or at least this is how so many poorly educated persons have been lead to believe. I watch with fasination movies of the 40's, 50's 60's, 70's, and on up to now... that when they treat of the physical sciences it would seem an ultimate principle in-and-of itself.

Here lies the rub, where the physical sciences goe so too does metaphysics as well as the theological sciences. To affirm limits for each is good rationality yet ask an average person, whether religious, non-religious or irreligious, college degree or not, and you find will their understanding as sadly lacking as in the political realm we now find where Americans don't even know of or understand the founding principles of this country and sadly are giving away their freedom in the name of rights and equality. I digress a little here only to show that societal ignorance spans not just the subject here but in all areas of knowledge.

As for those limits, modern science deals with strictly observable subjects whereas metaphysics (of the Greek or even the Eastern Asian type), like empirical science, start with what is observable but don't end there.One might say philosophical musing moves from what is accidental (in Greek: the accidens) to nature to what is substantial. Now of course the theological sciences deal with what is revealed yet this touches on what is observable by definition since God has created.

So generally speaking I find these three main areas of science (sciencia: knowledge) while they have their centers of concern, overlap and are also limited, as they should be. But of course I should add here that the theological sciences have been rightly called the Mother of all the Sciences in that they deal with ultimate things more directly and affirmatively than the other two observable sciences (physics and metaphysics).

Yet when I point out that empirical science is limited I certainly don't mean it is of no value to us. It in fact gives us means to control and manipulate corporeal or physical nature.It "sees" within the accidens of nature (Aristotle's nine categories) but does not move down to substance, at least not directly. It is the job of philosophical science to tell us directly about substantial nature. So when someone tells us that science proves there is no such thing as a soul they leave science and step into the metaphysical realm. They misuse empirical science by acrediting to it what it does not have since a soul by definition cannot be observed directly... that is be quantified or measured as the empirical sciences must..

Likewise when someone tells us they have found another atomic particle, meaning they've peered deeper into the core of physical reality and now see ultimate essence, they move into the realm of being that the observable sciences cannot deal with directly. It is simply not proper for natural science to give us esse. Matter and energy don't explain themselves nor can calling their substance atoms or force be rooted in what is essential. This I might add is why from Einstein's theories we find scientists moving away from the firmness of reality toward it's mutableness. We have a whole branch of physics that uses tools of math to study nature calling it relative. Statistics come to mind here because at the atomic level of nature we find being is less determined and more probabalistic.

We encounter becoming less certain at the atomic level because we take what we observe to be real in the sense we do everyday things like a ball after being thrown arching to the ground. Our models of physical reality at this level are just that... models. Herein lies the confusion as students are taught what empirical science gives us is essential. It is not rather it is how what is substantial interacts with instruments... atomic "particles" striking a plate give us an indication of their existence as light. Yet these partieles as we invision them have never been seen in the literal sense of that ball. We envision planetary systems of balls or particles yet nature does not show us this in any direct sense.

To my mind what the Greeks gave, especially Aristotle (and Saint Thomas Aquinas subsequently); his ideas of substance and accidens, potency and act and his form and matter, all explain better what is happening at this level as opposed to the materialistic view of science. We are "seeing" at the atomic level of nature forms moving from potency to act... that is coming into being in a way they were not before. The same being essentially morphing (note here morph is the Greek word for form) into something new while staying the same. This is much like the caterpillar turning into a butterfly. It changes at the surface level but is essentially the same being. It could only do so if it had within it what it later becomes. Likewise for the small acorn that becomes a huge oak tree. Particles at the atomic level are simply matter taking on new forms; the idea of which of course leaves nature more complex and ambigious... shall I say mysterious. This is why, I suspect, non-Christians view the world as particulate or energetic when probing deeper into nature and why it is so disconcerting to find that instead of empirical physical science giving us more firm ideas of nature, that is being more precise, we have gone in the other direction. Science reached it's limit and metaphysics, being abandoned by modern disciples and teachers of the scientific method, have less certainty rather than more. It's their view that is flawed and not the science which is being used improperly and beyond its limits.TCB alias Ratjaws@aol.com

whois said:

true.
although computer simulations have great value, they cannot model the unknown.
a computer built specifically to play chess couldn't tell you what 2+2 is.
this is one area that humans are light years ahead of computers, computers simply cannot "guess", they must follow a programmed plan verbatum.
of course, they can generate and use random numbers, but this too must follow a program or plan.

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Agreed Whois, this is why I understand that artificial intelligence in the sense of say, Arnold Schwarzenegger's Terminator, is impossible. Computers by definition are artificial and cannot move across the infinite void to living matter, let alone a second leap to intelligent living matter. What is behind them is a human mind as you say and so they can imitate but not become human. They can be programmed to look like but cannot change their essence from machine to person. I laugh at people who constantly cite computers playing chess better than the one they are programmed to imitate but this only proves they are good at repetitive tasks. Chess is a look forward game that requires seeing as many combinations of moves as possible then making the best one. This kind of task therefore requires no intelligence and so a machine can be programmed to do it and even be better than the chess masters. Notice we move from machanical-electrical matter to material organized as life, to life that has immaterial intelligence. There is no way to scale these barriers contrary to popular belief.. TCB ratjaws@aol.com

Ratjaws said:

Agreed Whois, this is why I understand that artificial intelligence in the sense of say, Arnold Schwarzenegger's Terminator, is impossible. Computers by definition are artificial and cannot move across the infinite void to living matter, let alone a second leap to intelligent living matter. What is behind them is a human mind as you say and so they can imitate but not become human. They can be programmed to look like but cannot change their essence from machine to person. I laugh at people who constantly cite computers playing chess better than the one they are programmed to imitate but this only proves they are good at repetitive tasks. Chess is a look forward game that requires seeing as many combinations of moves as possible then making the best one. This kind of task therefore requires no intelligence and so a machine can be programmed to do it and even be better than the chess masters. Notice we move from machanical-electrical matter to material organized as life, to life that has immaterial intelligence. There is no way to scale these barriers contrary to popular belief.. TCB ratjaws@aol.com

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i guess the concept we are discussing here is creativity.
there is no doubt that computers can display signs of learning and intelligence, but i seriously question whether they can be truly creative.
another area where humans outrank computers is processing density.
just the ability of taking a "snapshot" of your field of view and instantly analyzing it is still far beyond current computing ability.
not to mention picking a random object in that field of view and ad libing about it.
all this, at a few hundred hertz, 3 pounds, and 20 watts, completely outstrips even the most advanced super computer.

will any of this ever be achieved?
not with current technology.
the only way this will be achieved is by a fundamental breakthrough in computing concepts and architecture.
frankly, i can't envision a computer operating on an arbitrary set of guidelines, which must happen if computers were to become truly human.
creativity, resourcefulness, instincts, a computer simply cannot come up with this stuff on its own.

whois said:

the question is, are the accumulation of these variations over time responsible for the diversity of life we see.

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That question has been answered, "yes", since Darwin.

eldridge would make no such assertion if the fossil record showed this.

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The work of gould and Eldridge explained why new species seem to appear suddenly. Neutral, non-selective changes in allele frequency are the most common, and are not reflected in the fossil record.

these gaps in the record are the most likely reasons PE and HGT were introduced, and accepted.

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Yes!

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.
evolutionlist.blogspot.com/2009/11/modern-synthesis-is-dead-long-live.html

there are other sources too, some may be found on google perhaps.

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Most of the genomes of organisms are non-coding, and changes to this part of a genome would have no impact on selection, would have no phenotypical effect on morphology or function, and would not be evidenced by speciation. In other words: Changes to the non-coding and non-regulating genome, while causing a change in allele frequency would not result in speciation.

Ratjaws said:

Computers by definition are artificial and cannot move across the infinite void to living matter, let alone a second leap to intelligent living matter.

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There is no difference between living and non-living matter, just as there is no difference between the maple wood in a plank and the maple wood in a chair. "Life" is a set of chemical reactions, "an orderly decay of energy states", a pattern of flows of matter, electrical charge and heat.

whois said:

i understand that.
the question is, are the accumulation of these variations over time responsible for the diversity of life we see.
eldridge would make no such assertion if the fossil record showed this.
these gaps in the record are the most likely reasons PE and HGT were introduced, and accepted.

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.
evolutionlist.blogspot.com/2009/11/modern-synthesis-is-dead-long-live.html

there are other sources too, some may be found on google perhaps.

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Another thing is, that fossilized bones, will not show different skin / hair colour / organ developments
(changes) . As evolution, takes place at a cellular level and thus skeletal changes (if any) took place
over much greater time periods
An ability to attain faster escape speeds (an advantage for 'prey' ) would not be so-obvious
in an examination of fossils, ~more powerful muscalature, could also mean increased body mass / weight

Hidden Evolution (?)

davedajobauk said:

Another thing is, that fossilized bones, will not show different skin / hair colour / organ developments
(changes) . As evolution, takes place at a cellular level and thus skeletal changes (if any) took place
over much greater time periods
An ability to attain faster escape speeds (an advantage for 'prey' ) would not be so-obvious
in an examination of fossils, ~more powerful muscalature, could also mean increased body mass / weight

Hidden Evolution (?)

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Increased muscle mass, would likely be needed to increase the speed of prey, since the muscle, is what is creating the force to propel the prey. With increased musculature, typically comes increased bone mass, so the structure can withstand the forces created to propel the prey.

whois said:

i guess the concept we are discussing here is creativity.
there is no doubt that computers can display signs of learning and intelligence, but i seriously question whether they can be truly creative.
another area where humans outrank computers is processing density.
just the ability of taking a "snapshot" of your field of view and instantly analyzing it is still far beyond current computing ability.
not to mention picking a random object in that field of view and ad libing about it.
all this, at a few hundred hertz, 3 pounds, and 20 watts, completely outstrips even the most advanced super computer.

will any of this ever be achieved?
not with current technology.
the only way this will be achieved is by a fundamental breakthrough in computing concepts and architecture.
frankly, i can't envision a computer operating on an arbitrary set of guidelines, which must happen if computers were to become truly human.
creativity, resourcefulness, instincts, a computer simply cannot come up with this stuff on its own.

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But there is nothing to stop that from happening down the road . . . and so it will happen.

Gracchus said:

That question has been answered, "yes", since Darwin.

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answering yes to a question is by no means empirical evidence.
according to the following, there is no empirical evidence for the major transitions of evolution:
www.researchgate.net/publication/15314671_The_Major_Evolutionary_Transitions

The work of gould and Eldridge explained why new species seem to appear suddenly. Neutral, non-selective changes in allele frequency are the most common, and are not reflected in the fossil record.

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gould and eldridge introduced PE, not the neutral theory.
granted, the neutral theory probably explains why PE happens, but even this cannot be the entire explanation.
HGT was introduced for a reason, and so far no one has offered an adequate explanation as to why.
science has to somehow know the difference between an HGT gene and a mutated one.

Most of the genomes of non-living organisms are non-coding, and changes to this part of a genome would have no impact on selection, would have no phenotypical effect on morphology or function, and would not be evidenced by speciation. In other words: Changes to the non-coding and non-regulating genome, while causing a change in allele frequency would not result in speciation.

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i'm going to assume you made a mistake in this part of your post.
non-living organisms?

Paul of Eugene OR said:

But there is nothing to stop that from happening down the road . . . and so it will happen.

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i agree it COULD happen, it's a stretch to say it will.
i will almost bet it will not happen by anything man can come up with, it will almost certainly be modeled on "biotronics", a melding of already existing biology with electronics.
IOW, it will have to come from already existing life.

whois said:

answering yes to a question is by no means empirical evidence.
according to the following, there is no empirical evidence for the major transitions of evolution:
www.researchgate.net/publication/15314671_The_Major_Evolutionary_Transitions

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What that link said was:

ABSTRACT

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There is no theoretical reason to expect evolutionary lineages to increase in complexity with time, and no empirical evidence that they do so. Nevertheless, eukaryotic cells are more complex than prokaryotic ones, animals and plants are more complex than protists, and so on. This increase in complexity may have been achieved as a result of a series of major evolutionary transitions. These involved changes in the way information is stored and transmitted.

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The Major Evolutionary Transitions - ResearchGate. Available from: http://www.researchgate.net/publication/15314671_The_Major_Evolutionary_Transitions [accessed Nov 14, 2015].

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It doesn't say that there is no evidence for major transitions. It says that there is no reason to expect increase in complexity. On the other hand it is easier for simple things to become more complex than to become simpler. That is why most life, by volume, is bacteria.

gould and eldridge introduced PE, not the neutral theory.
granted, the neutral theory probably explains why PE happens, but even this cannot be the entire explanation.

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Changes in allele frequency occur all the time, but most of these changes are neutral and do not lead to selective changes in phenotype. Thus, evolution usually happens without changes leading to speciation, or leaving evidence in the fossil record.

HGT was introduced for a reason, and so far no one has offered an adequate explanation as to why.

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Horizontal gene transfer has been observed in bacteria, and less commonly in plants. It was not "introduced". It was observed. Bacteria are even less picky about sex partners than plants or people. A fertile hybrid that could interbreed with parent stock can cause horizontal gene transfer, but that seems to be very rare, even in plants.

science has to somehow know the difference between an HGT gene and a mutated one.

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The term "gene" is usually reserved for coding DNA. Because of the redundant coding not all mutations, even to coding DNA, cause changes to phenotype.

i'm going to assume you made a mistake in this part of your post.
non-living organisms?

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Thank you! That editing mistake has been corrected.

Gracchus said:

What that link said was:

It doesn't say that there is no evidence for major transitions.

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it does indeed say there is no empirical evidence for increasing complexity.
not only that, but also no reason to expect it.
doesn't the theory of evolution give us every reason in the world for this increase?
yet this paper says there is no reason to.

On the other hand it is easier for simple things to become more complex than to become simpler. That is why most life, by volume, is bacteria.

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well see, this is another thing, the genomes of bacteria are MORE complex than that of humans.
complexity, in this regard, is measured by the ability of codons to code for more than one protein.

Changes in allele frequency occur all the time, but most of these changes are neutral and do not lead to selective changes in phenotype. Thus, evolution usually happens without changes leading to speciation, or leaving evidence in the fossil record.

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the fact still remains that the majority of genes that are fixed are done so by drift, not natural selection.

Horizontal gene transfer has been observed in bacteria, and less commonly in plants. It was not "introduced". It was observed. Bacteria are even less picky about sex partners than plants or people. A fertile hybrid that could interbreed with parent stock can cause horizontal gene transfer, but that seems to be very rare, even in plants.

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i'm not doubting HGT, i'm asking how scientists knows this happened millions of years ago as opposed to mutated.
in this regard, HGT of the past is an assumption, not a verified fact.

The term "gene" is usually reserved for coding DNA. Because of the redundant coding not all mutations, even to coding DNA, cause changes to phenotype.

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genes are genes, coding or non coding.
if they are non coding genes, then they are called that.

Thank you! That editing mistake has been corrected.

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okay, i'll get to it.

davedajobauk said:

We could imply that evolution provided the means (from early days) to pick up and utilize tools

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I do not think we could imply that at all. Around 40,000 years ago you have three artifacts that began to show up. A fish hook made out of bone, a fishing net & sowing needles. With these three tools or artifacts man was able to come up out of africa and pretty much take over the area that Neanderthal man was living. In what way does evolution make it possible for man to make a fishing net and thus feed a lot more people then before?

whois said:

it does indeed say there is no empirical evidence for increasing complexity.
not only that, but also no reason to expect it.
doesn't the theory of evolution give us every reason in the world for this increase?
yet this paper says there is no reason to.

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Perhaps I am confused as to whether you mean molecular or cellular complexity?

well see, this is another thing, the genomes of bacteria are MORE complex than that of humans.
complexity, in this regard, is measured by the ability of codons to code for more than one protein.

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In the big picture, eukaryotes are a minor aberration, and multicellular organisms even more rare.

the fact still remains that the majority of genes that are fixed are done so by drift, not natural selection.

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genes are genes, coding or non coding.
if they are non coding genes, then they are called that.

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Let us be clear:

A gene is a locus (or region) of DNA that encodes a functional RNA or protein product, (emphasis mine) and is the molecular unit of heredity. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic traits.

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https://en.wikipedia.org/wiki/Gene

So if it does not code it is not a gene, it is non-coding DNA. If it is not expressed phenotypically, it is not rally a gene. I will try to be more precise in future.

i'm not doubting HGT, i'm asking how scientists knows this happened millions of years ago as opposed to mutated.

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The presence of long strings of non-coding DNA in unrelated lineages is evidence of HGT or retro-viral insertions.

in this regard, HGT of the past is an assumption, not a verified fact.

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In science, a fact is an observation. A hypothesis is a testable explanation of facts. A theory is a body of well-tested and un-falsified hypotheses.
HGT is an observed mechanism that explains the identical sequences of non-coding DNA, DNA that cannot be expressed phenotypically or subject to selection.
If you have a better explanation for long sequences of non coding DNA in unrelated lineages than HGT or retro-viral insertion, then, trot it out.

Gracchus said:

Most of the genomes of organisms are non-coding, and changes to this part of a genome would have no impact on selection, would have no phenotypical effect on morphology or function, and would not be evidenced by speciation. In other words: Changes to the non-coding and non-regulating genome, while causing a change in allele frequency would not result in speciation.

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i think that what is being said here is, genes are fixed as a matter of course, no matter what or where they are.
there are only 2 ways these genes will be eliminated, by the ability of DNA to repair itself, or if these fixed genes somehow interferes with reproduction.
natural selection probably plays a very minor role in selection because of the organisms ability to adapt to the environment.

i say the above for 2 reasons.
first is the molecular clock hypothesis of genes.
this implies genes become fixed simply because that's what they do.

second is, it's becoming apparent that evolution is not an adaptionist paradigm.
the genomes of organisms along the timeline and their apparent decreasing complexity supports this.
the genomes of life show little, if any, signs of optimal design.
in this regard, evolution programs such as boxcar2d do not realistically model evolution.

Gracchus said:

Perhaps I am confused as to whether you mean molecular or cellular complexity?

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don't feel bad.
i've seen threads go on page after page arguing what complexity is, even smith in the referenced paper has questions about it.
i ran across a very good definition the other day, a month ago i guess, but i don't think i saved the page it was on.
even if i did save it, it would be hard to find it because i don't have a directory structure for my evolution folder.
i have well over 200 megabytes of web pages and PDFs in my folder, have any idea how many items that is?
anyway, this definition was on the gene scale and mentioned something about the ability to code for an increasing number of proteins.
the more proteins it could code for, the more complex it was.
it might seem obvious to biologists, but i now understand why bacteria is considered more complex than humans.
bacteria contains very little, if any, non coding sequences.

Let us be clear:
https://en.wikipedia.org/wiki/Gene

So if it does not code it is not a gene, it is non-coding DNA. If it is not expressed phenotypically, it is not rally a gene. I will try to be more precise in future.

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yes, please.

The presence of long strings of non-coding DNA in unrelated lineages is evidence of HGT or retro-viral insertions.

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hmmm . . .
okay, i reluctantly agree, but i have doubts.
the above might be an explanation for sequences, but not for a single gene event.
then again, a single base pair change, which could be a mutation, can change an entire sequence.
your hypothesis is questionable.

In science, a fact is an observation. A hypothesis is a testable explanation of facts. A theory is a body of well-tested and un-falsified hypotheses.

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a hypothesis must also be able to be falsified in order to be a valid hypothesis.
this is one of the reasons creationism creeps into debates such as this, and please don't.

HGT is an observed mechanism that explains the identical sequences of non-coding DNA, DNA that cannot be expressed phenotypically or subject to selection.
If you have a better explanation for long sequences of non coding DNA in unrelated lineages than HGT or retro-viral insertion, then, trot it out.

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like i said earlier, i'm not doubting it happens, but i do question how scientists actually knows this stuff happened so long ago.
a single base pair mutation can screw up an entire sequence, and a single gene can be easily seen as mutated instead of HGT.
gene duplication can also be a factor.

FrumiousBandersnatch said:

The TOE doesn't take such a purposeful or intentional stance; initially cells didn't stick together from any innate instinct or recognition of strength in numbers, but by chance genetic changes to the cell wall components that made them more likely to stick together than separate. In places where this clustering was advantageous, cells with these modifications survived better than those without, and a clustering population would develop. In places where it wasn't advantageous, they'd die out, leaving just the single cell version.

It's been observed in the lab, where by manipulating the environment they grow in, populations of yeast cells that clump together have been bred from cells that didn't clump together. It's not yet clear whether this is a completely new trait for this particular yeast, or a reactivation of a distant ancestral trait.

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Frumious,
What you say here has bothered me for a long time in that we have two branches of science in conflict with each other, of which no one notices. Here you say chance is a prime element of evolutionary theory leading to what you term advantage, yet the theory which environmentalism asserts says that all life is in a chain and it is bad for any one species to disappear. Thus evolutionary theory wants the weaker species to die while environmental theory teaches we must protect the weak. Due to this oversight proponents of each theory tend to use the other as support for their own. How can the same scientific insight give us both theories?

Also you contradict yourself initially saying "cells didn't stick together from any innate instinct" then you say "It's not yet clear whether this is a completely new trait for this particular yeast, or a reactivation of a distant ancestral trait." Clearly an ancestral trait is an innate instinct. Why would one look for traits if it is chance that drives the advantageous change?