Darwinism and genetics

Started by TheBadger, July 19, 2013, 08:23:53 pm

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TheBadger

July 19, 2013, 08:23:53 pm Last Edit: July 19, 2013, 09:21:46 pm by TheBadger
Hi,

I heard an argument recently about evolutional theory and genetics. I thought it was really interesting. But the discussion did not go on for very long, so I have some questions/statements.
I cant tell you what the show was, I had never seen it before. And I did not recognize any of the people. But I am sure I can relate the important bits pretty accurately. It was a debate between two scientific fields, not a science and a philosophy or religion.

I know there are at least a couple paleontologists, and others from a scientific discipline in this community... So it could be a fun debate!

Anyone in the mood?
It has been eaten.

AP

As a lover of Science I have debated folks before with as much kindness and respect as I could give. I can not go into a debate any time soon as there is way too much going on in my life right now but I have a few folks I like to listen to and or read about but a word of warning as this is not a push to force anyone to follow what I believe personally, after all. It is a choice what one chooses to believe but what you believe will effect how you live your life.

John Lennox, Francis Collins, Kenneth R. Miller, Henry F. Schaefer, III, Sir Robert Boyd, (Old World Folks)... Lord Kelvin, Louis Pasteur, Isaac Newton, Robert Boyle, Blaise Pascal, Galileo Galilei, Johannes Kepler, and Nicolaus Copernicus.

Dune

I'll follow this, but I'm not going to debate either... might throw in a word now and again.

Walli

I think first you need to define, what you mean with Darwinism - because Darwinism is interpreted in different ways.

TheBadger

July 21, 2013, 02:47:11 am #4 Last Edit: July 21, 2013, 03:11:35 am by TheBadger
OK  ;D But this will necessarily be a long post (even for me ;))
So I tried to find the arguments by google, but it was impossible. All I ended up finding was Atheist and religious people pissing on each other.
I have to try to write this out my self as best I can. And thats the reason I asked if there was any interest in this topic... Writing my own ideas and opinions is easy, trying to write representing people I never met is not.
But Here it goes. And hopefully some of you guys can fill in on anything relevant I leave out.

This is not an argument or an attempt to say evolution does not occur in nature. But rather it is an attempt to relay an argument based on provable repeatable sciences that undermines Darwin based evolutional theory. But not the idea of evolution its self. That is, I am not relaying an argument or making one my self that claims one form of life cannot change to become a different form of life. (I really hope that is clear) I am not talking about design, creation, or theory of any kind. I am talking about genetics.

1) First, evolution in simple terms, (and this is where someone else may need to fill in details):
In simple terms, the idea is that in evolution a life form evolves when a species adapts a trait of some kind that is than reproduced in offspring. And which becomes at some point a common trait in all individuals in said species.
For example, an animal needs to eat, and for some reason it needs to eat other animals, so it develops claws to aid it in hunting and killing. (again, just in the simplest terms for brevity). This trait is then found in the animals off spring. And then through the course of time, develops into a perfect example of said trait. This all happens by what is called a positive genetic mutation.


2a) The genetics argument against the above described process. (As I said I could not find the argument on google, so I am putting this together as best I can)

What happens when you make a copy of a copy of a copy of a copy of a copy? The short answer is you get cancer and die, not evolve:
The genetic argument against darwinism and a gene-centred view of evolution.

In nature there are negative genetic mutations and positive genetic mutations. An example of a negative genetic mutation could be "Proteus syndrome" ("Elephant Man"). An example of a positive genetic mutation would be spider man (https://en.wikipedia.org/wiki/Spider-Man) But a real one would be sickle-cell anemia because it "it protects many Africans against malaria". Unfortunately sickle-cell anemia also destroys people.

So let us just assume for the sake of discussion that positive genetic mutation does occur in nature, and that the benefit is handed down to offspring in the same way that we know (and can prove) negative genetics are handed down in nature.

The problem is that negative genetic mutation always results in destruction and so if these traits are handed down they will build up over time.
[attach=1]
http://upload.wikimedia.org/wikipedia/commons/thumb/3/3a/Dihybrid_cross.svg/220px-Dihybrid_cross.svg.png

In the end the destructive negative would overwhelm any positive effect in a species over the course of generations.
So in the image above think of the purple color as multiple sclerosis, breast cancer and schizophrenia (for example). The simple fact is that whatever positives could be handed down, we know that the potential positives are out numbered by definite negatives. That is, you may develop or inherit one time the ability to breath under water. But you will also inherit all of any genetic disorders more often. What I mean is you have the ability to breath under water now (gills) but you will also inherit all of the negatives more often because there are more of them.

We need only look at probability to know with out a doubt that the negative is dominant and the positive is recessive. Therefore over time, genetic mutation will destroy all organic life.

One might say that from the beginning, man has been dying. I am proposing that since mans beginning he has been getting worse not better.
Now while the world may be ancient beyond comprehension, we know that man is not. I am proposing that the first men were superior in nature to modern man. Not inferior as darwinism claims. I am saying we are dying not evolving.

2b)
'science genetics' term meaning:  most variety within a kind results from preeexisting genetic variety; there are fixed limits to biological change; mutations cause genetic information to be lost, not gained.'

2c) Data provided by others"
Researchers on the 1000 Genome Project used genetic data from 179 individuals and found that all had between 40 and 110 potentially disease-causing mutations in their DNA. The individuals had 281-515 actual substitutions each, but the trouble only really started when both parents had passed on a mutation in the same gene. The researchers, estimated, "approximately 400 damaging variants and roughly 2 bona fide disease mutations per individual," according to the American Journal of Human Genetics.

Geneticists Thomas Morgan and Herman Muller conducted a prolonged study of fruit flies (drosophila) looking for traces of evolution. But generation after generation, the uncooperative flies refused to evolve. Eventually they solved the problem, or at least they thought they had. They subjected a pure strain of fruit flies to chemical and radiation treatments. The result was mutilated flies. Flies developed yellow, brown, or purple eyes; or bulging, flat, or dented eyes. Some flies had no eyes. However, despite all the mutated flies that resulted from the experiment no new genetic information evolved and no beneficial mutations occurred and the flies always remained flies. The most important lesson to learn from the fruit fly experiment is the remarkable stability of this species, according to Dr. Jason Richard Boon.

QuoteAnalysis
For evolution to work on a grand scale, where nature transforms a family of animals into a new family of animals, beneficial mutations must appear to add new information to the genetic code. Without mutations, there cannot be any major evolutionary steps. While the weight of scientific evidence demonstrates clearly that the genetic information already existing within a species can contribute variation within animal populations due to natural selection, this process always strains out information and it never adds new genetic information, or previously non-existent coding to the genome. However, while many Darwinists claim that rare, beneficial mutations do exist, the math shows that random mutations result in the net removal of functional programming from the genetic code rather than adding new information to it.
Beneficial mutations are extremely rare. The few mutations that are considered "beneficial" always involve the loss of genetic information and they generally result in the deterioration of the animal's health. We learn in biology class that our genetic code is made up of DNA, the long strands of the nucleotide bases Adenine, Guanine, Thymine, and Cytocine, which are A, G, T, and C for short. These four bases provide the digital code for our system, resembling the way 0s and 1s make up binary code for computers. Within the cell, during the process of translation, these nucleotides are read in groups of three, referred to as codons. Every codon is similar to a small transport vehicle of three letters that code for an amino acid, which go on to make up proteins.
Finally, if neo-Darwinian evolutionary model of origins were history, we should expect to discover a number of beneficial mutations that were the result of added genetic information. However, the weight of scientific evidence demonstrates clearly that we all inherited a damaged, deteriorating version of a once perfect and fully functioning genetic code.



"projects such as ENCODE are showing scientists that they don't really understand how genotypes map to phenotypes, or how exactly evolutionary forces shape any given genome."...In short, the current picture of how and where evolution operates, and how this shapes genomes, is something of a mess."


:o

P.S. now Im very tired. Some of this was my statements and some not. So if you respond directly to something written here, please make clear exactly what your referring to. It a pretty heavy topic so being focused will help answer my questions... Thinking of this whole post as a question may help.

Cheers to you if you read this far ;D
It has been eaten.

Dune

You are making assumptions that are not correct in my view, they are 'kort door de bocht' (Dutch for too simply stated).
1:
QuoteWhat happens when you make a copy of a copy of a copy of a copy of a copy? The short answer is you get cancer and die, not evolve
It doesn't work that way.
2:
QuoteIn nature there are negative genetic mutations and positive genetic mutations
Not really true; there are mutations, and some will prove negative under certain circumstances, others positive, but under different circumstances that may be the other way round. If certain mutations negatively influence survival and productivity, it will dye out. If certain mutations prove beneficial, it will become a common trait, and more individuals will bear those mutated genes, until circumstances change and it may again turn against them. It's survival of genes in specific circumstances over time, hence evolution. 
3:
QuoteWe need only look at probability to know with out a doubt that the negative is dominant and the positive is recessive
That is not correct, or we won't be here.

This is about all I will say, sorry about that. It would take too much time to discuss this in depth.

Tangled-Universe

Ulco pretty much hits the nail on its head for my first thoughts about reading your posts.
I agree point to point with him.

Especially the latter is a false premise, that we should define negative as dominant and positive as recessive. (which apply to alleles, which is not the same as genes)
Ulco explained that nicely by saying that genetic variations can have their effect in both ways, but that the outcome depends on the conditions rather than the gene itself.
Like Ulco said if that was true then we wouldn't be here. The "negative" wouldn't overwhelm the "positive".
All traits you show, your "phenotype" is a consequence of your dominant alleles.
Following that premise we should be walking failures and then we should also consider the 1000 Genome research research you quoted that ~400 of those are "good genes" then. That doesn't sound very logical, isn't it.

I'm not sure how or where you did get that from.
I don't think it's really important to know where you got it from anyway.
For the moment it seems you're trying to be as neutral as possible :)
I guess a debate is difficult to have when parties are trying to be neutral, that's rather something for a moderator of a debate/discussion, than a participant.

Btw, I'm not sure how serious you can take a genetic research when only using 179 individuals!
Genetics is mostly statistics.
The variation among humans is HUGE.
There are all types of different traits/phenotypes (eye colour, hair colour, just to name the simplest), which alone already make sure you need 100s, probably 1000s of individuals to map the variation and expression of those simple basic traits and to give each gene a statistical probability of being >99% "true".
On top of that you have all kinds of genetic mutations; mutations which shift the reading frame of the gene, single nucleotide polymorphisms, deletions, insertions etc.
Those are all present WITHIN the already present traits/phenotypes WITHIN one race of humans.

Briefly, it takes many thousands of individuals to set up a "reference" genome and even that result will be expressed in a statistical term for each gene.

PabloMack

July 21, 2013, 12:25:19 pm #7 Last Edit: July 21, 2013, 12:50:50 pm by PabloMack
As Dune pointed out, your model is too simplistic. Genes don't work alone. An individual with certain alleles works "better" when in combination with certain alleles of other genes (or certain environments) while they do "not do so well" when in combination with other alleles of those other genes (or other environment). One of my favorites is cycle-cell anemia where the "disease" makes an individual more resistance to malaria. An individual with the "healthy" allele will be much more likely to die of an infection of the Plasmodium protozoan. Interactions between genes, the environment etc. are very complex and the overall well-being and competitiveness of the individual is not so simple to ascertain. The final judge of what survives will be natural selection which itself is unique to a certain place at a certain time. This is all complicated by "luck". The dinosaurs, for example, had superior characterisitics in so many ways above the mammals. This allowed them to dominate all of the open megafaunal niches. The mammals were "forced" into more nocturnal and stealthy roles making extensive use of burrows to avoid the superior dinosaurs during the daylight hours. But by luck, these burrows afforded a protection against the unexpected meteor that wiped out the dinosaurs. Normally, the dinosaurs and other "ruling reptiles" needed little or no shelters because they were well adapted to live without them. So when the meteor came, they had no place to hide. The mammals that survived did so (in part) because they were already hiding from the dinosaurs. This same shelter saved a great number of them from the initial heat and other secondary destructive effects of the meteor strike. Even so, only four of the living thirteen groups of mammals made it across the KT boundary.

TheBadger

Thanks guys! :)
actually I am pretty neutral. I don't have a problem with the truth whatever that is. For me there are two fundamental questions, the how and the why.
The how is biology/science, and the why is metaphysics/philosophy/religion.

From early in my life the why has always been very important to me, its just the question that made me open my eyes. I understand that other people are sparked by the how question. Maybe this is a right brain left brain thing?

I adapted a math phobia very young as a result of some abusive teachers in early education. But as an adult I am far less insecure. Math doesn't trouble me anymore, and I can easily sit down and take the time to learn a formula and learn to use it productively now. And of course as an adult I am less insecure about lots of things compared to a child. So the sciences part of life ultimately hold more interest and use for me now.
I did voluntarily take several lad sciences in college. Geology, botany, ecology. But I was working for a fine art degree in letters, not a science degree.

As an adult the question of how is more important to me now, although personally I still find it the less interesting question. Why is the question that holds all the meaning.

I am neutral because I am not bothered by the seeming conflict between Science and metaphysics.
But what sparked this post (besides the conversation I heard and mentioned in the OP) is that the more I read about the how/science the more I am seeing that it reads an awful lot like religion. Can you believe that as I begin to explore this all with an open mind, I am finding just as many fanatics in "science" as religion?

I am not against "evolution" I think its obvious that evolutions claims of a common origin and biological relationship are true. Simply being a part of the earth and looking at it, it seems true.
And my faith agrees with this. No conflict at all. Ecspt perhaps on the question of when, but truly I dont care about that question very much. I will die when I am around 90 years old or so. That when, is immensely more important to me ;)

My problem is, the more I learn about Darwinism, and modern sciences continued relationship with darwin's ideas. The less I think the study of evolution is about the how, and more about rejecting any claims of why.

Basically I think evolution is a real biological process, my problem is darwinism makes understanding it impossible.
Darwin understood almost nothing about genetics, and yet everything I have been reading about evolution is based entirely on the racist nut-bags ideas. I just don't get that!? Genetics proves there is no such thing as race, or rather, genetics proves there is only one human race.

So this is why I am latching on to genetics as a way to begin to understand all of this. It seems to be the only science that relies less on opinion and personal interpretation.
But everything I have been reading for the last few days seems to create more problems for darwin, but not evolution its self.

QuoteYou are making assumptions that are not correct in my view, they are 'kort door de bocht' (Dutch for too simply stated).
1:
Quote
What happens when you make a copy of a copy of a copy of a copy of a copy? The short answer is you get cancer and die, not evolve
It doesn't work that way.

But that is how cancer happens. And cancer is the most common negative form of genetic mutation.
Cancer shows us how replication of mutated DND destroys the life form.
Yes I put it simply. But I think fundamentally correctly.
http://www.cancerresearchuk.org/cancer-help/about-cancer/what-is-cancer/cells/how-cancer-starts


QuoteWe need only look at probability to know with out a doubt that the negative is dominant and the positive is recessive
That is not correct, or we won't be here.


What you are saying here is that because man is here, and man evolved, therefore evolution is true.

If you can find me one example of a positive genetic mutation in a lab study I would be grateful.

QuoteLike Ulco said if that was true then we wouldn't be here

That is self referential. It does not even begin to be a real argument.
You are saying that you believe darwin is right, and if he was not right you would not be here.
How does that really answer anything?
This is where darwinism starts to sound like religion to me. These are the same kinds of statements Im finding all over the internet.
I think that the only problem with evolution is darwin.

If evolution can ever be proven/disproven, I really feel like genetics is the only way to show it happen, or show that it cannot happen.

It has been eaten.

TheBadger

It is like medicine! too many sick people and not enough doctors!... There are too many questions and not enough scientists!

I wish I was filthy rich. I would fund research on questions that interest me. There is a lot of money being poured into research now. But not enough, I think.
Sadly, the only way I think these questions will get more funding, is if someone thinks of a way to weaponize it :-[ Same with space exploration. We need to find aliens to start a war with, then we will see better advances in space exploration. :-\

Before I said that only genetics offers real hope for any real answers. But really, probably, space exploration will help too.

I want answers now! You know what I mean? But darwin creates more questions than answers, once you start questioning beyond the basics, no one has any answers. And of course religion does not even make an effort about biology.
It has been eaten.

Dune

Sorry guys, this is getting too much for me. I want to create, not debate. Interesting to follow though.

TheBadger

Quote from: Dune on July 21, 2013, 04:25:09 pm
Sorry guys, this is getting too much for me. I want to create, not debate. Interesting to follow though.


Create is an interesting choice of words Ulco.

But you are right, I probably just need to spend the next 15 years reading. If by my death time, I feel satisfied by the answers I found, so be it.
If not, I guess that is normal.

Never mind.
:)
It has been eaten.

Tangled-Universe

I think evolution is a self-organising force, driven by chance because of environmental conditions.
The self-organising force driving evolution, I think, is similar to entropy, nature's tendency to smooth things out to get an equal energy balance, in
turn driven by thermodynamical laws.

If you look at nature as a whole then you can see the entire earth, without humans or only a small population of humans, is a perfectly stable and balanced biotope with a netto energy excess of 0. Everything is recycled or re-used.
Within this biotope we can see "evolution", where one creature is adding to the left side of the scale/balance and the other to the right side of the scale balance. Their netto result is still 0.

That's what nature is about.
It doesn't like to have a whif of gas sitting in a corner of your room, it makes it spread everywhere.
That spread happens kind of randomly and similar to evolution it IS that aspect which makes it difficult to accept for many people, because when applying evolution you will have to accept that at least a part of the driving mechanism is chaos/randomness and that's exactly what religious people don't believe in.

Quote from: TheBadger on July 21, 2013, 01:25:59 pm
Thanks guys! :)
actually I am pretty neutral. I don't have a problem with the truth whatever that is. For me there are two fundamental questions, the how and the why.
The how is biology/science, and the why is metaphysics/philosophy/religion.
I am neutral because I am not bothered by the seeming conflict between Science and metaphysics.


You can easily substitute metaphysics with religion here or rather philosophy.
Metaphysics is metaphysics, because it can't be called science since metaphysics doesn't use certain steps involved to call the findings "scientific".
Actually there's no real conflict between the two because metaphysical thinking is essential to (performing) science.
Metaphysics is about the questions, the why, and science is about both why and how where it lends it's "why" from the metaphysical approach, but uses methods (experiments) to support the metaphysical core of why we're performing science -> to understand (our) nature.

This is reasoning from the scientific point of view, but there's hardly any arguing possible against science, since it has proven itself zillion times to be a truthful method of describing the universe we live in and all we see and do (not) understand.

Quote from: TheBadger on July 21, 2013, 01:25:59 pm
But what sparked this post (besides the conversation I heard and mentioned in the OP) is that the more I read about the how/science the more I am seeing that it reads an awful lot like religion. Can you believe that as I begin to explore this all with an open mind, I am finding just as many fanatics in "science" as religion?


Science is not religion. Period.
However,....defending the scienfitic methods can be seen like being religious over it.
But then one can ask why a person would consider such a person being religious over it.
Because he can't persuade him? Because he can't deny that science gave as so much to make our lives easier and better.
(except for PRISM and the global crisis, lol)

See the above paragraph. Science has proven itself way too much to be questioned at all.
That we can't explain all aspects of our universe by using science, yet, does absolutely not mean that science is a believe or not a good tool.
Science and technology go hand in hand and it is especially this bond which allowed us to progressively acquire knowledge.
Science needs to evolve too ;)
Following this topic, for example:
The first human genome to be sequenced cost >$100k and took many months.
Now it costs <$5000 and takes a  couple of days.
Improved technology as a product of science.
Not only does it allow to do more in less, eventually it will allow us to explore the most complex interactions and connection of genes with their environment.
We will just have to wait for more computing power and more cheaper and faster sequencing to then analyze this huge heap of genetic information. And interesting answers and questions will be found, no doubt.

Quote from: TheBadger on July 21, 2013, 01:25:59 pm
My problem is, the more I learn about Darwinism, and modern sciences continued relationship with darwin's ideas. The less I think the study of evolution is about the how, and more about rejecting any claims of why.


Why do you think so?

Do you think scientist who research evolution are actually researching to disprove religious people?
Don't worry, they absolutely don't waste their time on this.

The continued relationship between darwinism and science is only because scientific methods support the idea by providing proof/evidence, not only from the biological realm of science, but also geology for example.
Geologists study the drift of continents, for example, and using genetic studies you can show when certain species with a common ancestor became separated and you can overlay that with geologists data.

Quote from: TheBadger on July 21, 2013, 01:25:59 pm
Basically I think evolution is a real biological process, my problem is darwinism makes understanding it impossible.
Darwin understood almost nothing about genetics, and yet everything I have been reading about evolution is based entirely on the racist nut-bags ideas. I just don't get that!? Genetics proves there is no such thing as race, or rather, genetics proves there is only one human race.


You should really stop calling it darwinism, but rather "evolution". Since that's the easiest concept and basically what this whole discussion is about: is evolution true or not.
Darwinism is a populistic term.

Quote from: TheBadger on July 21, 2013, 01:25:59 pm
Yes I put it simply. But I think fundamentally correctly.
http://www.cancerresearchuk.org/cancer-help/about-cancer/what-is-cancer/cells/how-cancer-starts


Can you explain again, why you think it's fundamentally correctly?

Because I think it is not.

You imply all cancers are genetically inheritable.

Quote
What you are saying here is that because man is here, and man evolved, therefore evolution is true.


No we're not. That's what you make of it.

We applied your reasoning to how the world would look if it would be true.

Quote
If you can find me one example of a positive genetic mutation in a lab study I would be grateful.


Seemingly you still didn't let the positive/negative mutation thing go. It's pretty senseless Michael. Evolution can't be understood by scoring individual outcomes of genes. It's the end result which matters, because that determines survival.

You should keep another thing in mind:

You have evolution and you have evolution.

The evolution we're discussing here, I THINK, is the "big one" of the two.
Why do animals have certain traits, how did those improve their survival and how does these mechanisms work.

The evolution you're sometimes trying to mix into here is the "small one".
If I were to have cancer, then that cancer has evolved (evolution) in my body.
That's a different kind of evolution, small scale, in a different context.
There may be overlap with the "big one", but there are plenty of environmental factors present causing cancer, like smoking/drinking/drugs.
There doesn't have to be an evolutionary (big one) mechanism behind it. Not all cancer, at all, is inhereted.

However, some are, like some forms of intestinal and breast cancers.

And it's hard to say, so forgive me for that, but in a natural environment, without medical science, those persons would die and thus the genetic background causing that cancer will also disappear.

Tangled-Universe

This is a nice accessible read about:
http://learn.genetics.utah.edu/content/begin/cells/organelles/

I'd recommend to read the "It's just a theory" paragraph so many times until you can read it out loud by heart ;)

And something less accessible to read, on the how's, a review published in Nature (highly positioned scientific journal):
http://www.nature.com/scitable/content/endosymbiotic-gene-transfer-organelle-genomes-forge-eukaryotic-13997492

Both links are about how eukaryotic (mammalian) cells got prokaryotic (bacterial) cell's organelles like mitochondria, the energy-producing factories within our cells.
These findings are one of the strongest evidence available on evolution.

Dune

Agreed, just didn't want to write all that down  :P Thanks, Martin.