Darwinism? Tcha... You Know What? Uh-uh!

[catatonic]

I'm pretty well feeling I'd like to move on to economics and someday politics/military.

As for Hobbit's assumption about evolving Nemoy from Where in the World is Carmen San Diego, I love his post 47 but I doubt the eyes/legs everywhere would occur with evolution in view of a UCLA find. UCLA found a gene allowing for the specific placement in legs from amphibians to reptiles. It says the upper legs must be in the same place relative to the body and establishes the 4 legs on a body form as coming from a gene.

Anyway here's my whole argument at all.

Proteins are CPU and software. DNA is memory to make the CPU.
The CPU operates on the memory as it's own software, modifying its creating new hardware capable of eliminating old hardware.

All the commands proteins can do on DNA to mutate it, the only way to avoid the usual microevolution, are like a very basic processor. Many basic processors have multiplication. This is much simpler. Change bit. Concatenate. Separate. Load. Store. Compare. Limited branch on compare. Reverse. Move right. Move left. Did I miss any? All of them are of the wrong order of complexity to get commented/useless memory to come into useful DNA and the ways to program the functioning memory into making a different useful novel protein. It's not really an issue of the software, but the instruction set in memory. This instruction set is too limited to program unless a protein causes a list of steps that has developed in such a way that the modifications of one of those steps fits the new possible hardware into a subclass of useful proteins. That's fine, and I'd love to study it more, but aren't there just one step a protein or group thereof causes and not a list of steps? If a list, I'll have to study more thoroughly to disprove the main argument.

And any evidence on the question for one complements as evidence equally against the other.

Whatever... I don't know if I'll keep commenting.

 

[Harmageddon]

Originally posted by Hobbit
What about a animals with eyes in useless places, or appendages that serve no purpose. There should be millions of those things lying around, but there are NONE.

As I said before, from your perspective on evolution it seems you have no idea.
Take life in caves for example. Today’s caves were carved from bare rock by water a long time ago. Take caves that are cut off from daylight and the river that carved it by a cave in of the original tunnel. In this type of cave, populations of animals are still thriving – and they have been cut off from the rest of the population a long time ago.
In these types of caves you find blind fish (there is no light) but they do have eyes. It does not seem to be the case that losing eyes altogether gives fish a big advantage over the ones that do still produce eyes. Even though you can imagine that this would save vital energy that could be spent better. And energy (resource) is already scarce in these environments.
Keeping eyes around does not seem very intelligent to me at all – if that was a creator’s intention than He is rather cruel. From an evolutionary perspective it makes more sense, as you said.

Originally posted by Hobbit
Geez, crocodiles have been around longer than that, and they still die when flipped on their backs, have stubby legs, and cannot open their jaws if there's even a little pressure holding them shut.

Not a very smart design, I agree. Yet it serves the crocodile well enough to survive.

Originally posted by Hobbit
How does a frickin sponge turn into a vertabrate fish with a hinged jaw, scales, gills, a nervous system, fully formed eyes, a full digestive system, and even air bladders, well, at all, but much less in the space of a mere, at most, 10 million years?

It did not go like this at all. There have been many species between sponges and the first fish. For example: sea snails, crabs and lobsters, tubeworms and all kinds of non-vertebrate organisms.

Originally posted by Hobbit
Only evolutionists believe common descent because there's so little evidence for it. DNA is about the only argument, and it doesn't really prove a whole lot unless you really want it to, because the only way you can believe that DNA proves common descent is if you already believe it's possble for DNA to change over time into the DNA of an entirely different species. Basically, DNA proves evolution is true, given that evolution is true.

Like catatonic has tried to explain, our understanding of evolution took a great leap with the discovery of DNA as the basis of evolution – before that, proteins were thought to be the only key player. The truth is a bit more complicated.

DNA is a strand of nucleotides, that are named either A, T, C or G for their chemical structure. DNA can be translated into messenger RNA (a single strand of nucleotides (DNA is a double strand), by translator RNA. Translator RNA can only transcribe when certain proteins are present that initiate transcription (these proteins together are called the mRNA polymerase complex). When transcription starts translator RNA (which is available in many different forms and each form recognizes three specific nucleotides, for example the sequence TAG or GGT and so on) the transcriptional mechanism makes complementary nucleotides (only the T is translated into a U). These will form the single mRNA strand.

That is translated into protein outside the cell’s core by ribosomes (other proteins complexes) that translate each triplet of nucleotides (TAG or GGT) into their respective amino-acids. These are strung together and they form a protein that finally folds itself based on electrostatic interactions and charge separation into its final 3-Dimensional form.

A lot can go wrong in the process, even if it is double checked at every step of the way. Mostly this results in a nonfunctional protein that is terminated and recycled. Sometimes it results in a finished protein that folds wrong – this is the basis of neurodegenerative disease, such as Alzheimer, Parkinson, etc.: protein misfolding.

DNA also is copied when cells divide, by another mechanism. Here again, a lot can go wrong. First, in sexual reproduction, a man and a woman’s DNA mix (the semen and the egg question) in quite radical ways. You as a child of your parents are a product of both, yet you don’t have your father’s exact hair, your mother’s exact nose and so on (not always at least). When this mixing goes wrong, you may end up without eyes, with six fingers, or when entire chromosomes divide a bit too happy, you may become a person that suffers from Down’s syndrome (they have three copies of a certain chromosome, #21, instead of the regular two).

As you see, DNA is quite dynamic: mostly when it comes to the copying or translating of it.

Then there are viruses: some of them possess a little strand of DNA, others only possess RNA. They all require a host (such as a human) to do the copying for them. They may infect cells (if undetected for long enough) and insert their DNA into your own. Then your copying mechanisms make thousands of copies of the virus, the cell in question finally bursts open and the newly hatched viruses seek to infect other cells. This is when you are sick. Your immune-system that may have missed the virus first time around gets to high alert when thousands of the viruses are detected – and as it battles to the death you get a fever from all the effort.

Then we share 98% or so of our DNA with chimpanzees. If you remember, a little error in copying or translation leads to disease, deformities or death in most cases. Even though ~ 2% seems like a little bit, given that we possess several millions of base pairs (the nucleotides of the DNA are paired, A-T and C-G) it is actually quite a lot – over a 100.000 base pairs.

The fact that whole regions of our DNA is made of useless “junk” DNA – dozens of copies of the same sequence after one another, is another hint that not all is as intelligent as it seems.

I hope you understand what I just wrote. If it does not make sense, I’ll see if I can explain better.

 

[Mr.Conley]

Good job, I think you did a great job of explaining the basics of DNA transcription/translation.

 

[Annie]

I know, I'm ignorant. Here's my take on all the nonsense between ID and evolution theory.

Darwin had some things right. Actually he did a pretty good job putting forth a theory on how things got from then to now.

What he/the theory never tried to answer and didn't: What 'created it' to start it all moving...

Literalists will say, Darwin was wrong. All was as was intended, from the beginning.

Some will say, there have been changes, but within the parameters of whatever.

Personally I believe God began life. In what form? I haven't a clue. It changed over time, my belief, according to His plan. Darwin comes close, not perfect, at describing how it all works. Yet, never addressing God's start of the whole process.

My belief, millions of years ago is when it started, not recent as far as inception goes.

 

[PsuedoGhost]

I know, I'm ignorant. Here's my take on all the nonsense between ID and evolution theory.

Darwin had some things right. Actually he did a pretty good job putting forth a theory on how things got from then to now.

What he/the theory never tried to answer and didn't: What 'created it' to start it all moving...

Literalists will say, Darwin was wrong. All was as was intended, from the beginning.

Some will say, there have been changes, but within the parameters of whatever.

Personally I believe God began life. In what form? I haven't a clue. It changed over time, my belief, according to His plan. Darwin comes close, not perfect, at describing how it all works. Yet, never addressing God's start of the whole process.

My belief, millions of years ago is when it started, not recent as far as inception goes.

Exactly. Darwinism and Religion are not mutually exclusive. Evolution has nothign to do with the origins of life, it merely provides a mechanism for life as a cell arriving at life as a human being.

 

[Harmageddon]

Probably no-one took notice, but I actually made a mistake concerning translator DNA (it was late last night, and the beer didn't help). The rest is correct, although I made some adjustment to the Chimp part, that makes it clearer.

Hey, it's my job.

DNA is a strand of nucleotides, that are named either A, T, C or G for their chemical structure. DNA forms a double helix structure, and the nucleotides are paired: A-T and C-G. DNA can be translated into messenger RNA (a single strand of nucleotides – DNA is a double strand), by a complex of proteins that may initiate transcription (these proteins together are called the mRNA polymerase complex). Usually a stimulus of the cell is required, that is transmitted from the exterior of the cell to the core (nucleus) and transcription then commences. The transcriptional mechanism makes complementary nucleotides, so for every “C” it encounters it makes a “G” and for every “T” it makes an “A” (only when an "A" is encountered, it is translated into a “U” instead of a "T"). These will form the single mRNA strand.

The mRNA strand is translated into protein outside the cell’s core by ribosomes (other proteins complexes) and translator RNA (which is available in many different forms that each recognizes a specific sequence of three nucleotides, for example the sequence AAG, AUG or GCG and so on) that translate each triplet of nucleotides into their respective amino-acids – the building blocks of proteins. These are strung together and they form a protein that finally folds itself based on electrostatic interactions and charge separation into its final 3-Dimensional form.

Then we share 98% or so of our DNA with chimpanzees. If you remember, a little error in copying or translation leads to disease, deformities or death in most cases. Even though ~ 2% seems like a little bit, given that we possess several millions of base pairs it is actually quite a lot – over a 100.000 base pairs. And this accounts for the differences between us – the hair (although we have the exact same amount of hair, it is thinner and shorter), the language, the size of our brains. It also accounts for the similarities that should be obvious, compared to a fish or dog.

The fact that whole regions of our DNA is made of useless “junk” DNA – dozens of copies of the same sequence after one another, that are probably the result of mismatched copies, is another hint that not all is as intelligent as it seems.

Darwin did not know about DNA. Darwin just speculated upon the mechanism behind the diversity of finches he saw on a particular Island (a "closed" system, a bit like the cave). His theory has been adjusted over the years, but the core concept is quite workable and seems to be correct.

Thing is, Darwins theory severely undermined the church's take on creation at the time, which was that in six days about six thousand years ago we were created. It had been found that the Universe itself and the earth were billions of years old, and then Darwin postulated that in the process of creation, evolution, not God, was the key principle. If species can evolve and give rise to other species all by themselves, God is irrelevant.

 

[catatonic]

I don't want blood on my hands from a big dual specialization of political parties over ID and evolution, leading to loss of communication, leading to unnecessary war... so I censored myself. It's already happening that conservatives specialize science out of the picture too much and liberals the same with religion. This leads to loss of communication among those who won't go out in the fray, which can cause unnecessary war. For instance, liberals often dismissed Bush's religious justification for war. Gathering among themselves, they weren't challenged, regardless of the trth.

I would say to go easy on that last statement: "If species can evolve and give rise to other species on their own, God is irrelevant." Taking the most upsetting-to-Christians, stripped-down, secular, unnecessarily liberal, scientific concept of God I can picture, that God is a garbage, left-over programming object made by neural firing objects in our brain that resulted from pure evolution, even defective evolution threatening the planet if you like (I aim to please everyone), this programming object of neural patterns is not irrelevant. Lets potentially upset Christians more for your sake, and say this programming object whose variable name is "God" is an evolutionary mechanism to... to... OK I've never once studied neurotheology (yes neurotheology is real) say "God" started as an effort to say there was consciousness in a Venus figurine or a bail of hay. How does this cause natural selection of people and of "God"? Well for starters, people might have been very dumb that long ago... or not necessarily dumb but just very ignorant. Some people could claim their ancient dildo had its dildo-God, keeping it safe, increasing their fitness for reproduction. Accumulating resources is another fine use increasing fitness for reproduction. As people evolve either through knowledge or genetics, this simple stuff doesn't work, and people start to make predictions so they can show "God". Through more and more interaction with this programming object, people become more and more directly conscious of it. People start to claim they are "God". Then people realize claiming to be "God" image is more useful. Maybe at this point, they still don't know what they are talking about. Just last year, more powerful uses of this "programming object" have been used to change society, I think in an overwhelming advanced way, by brand new claims. Amazing what people can seem to think up as far as the evolutionists are concerned, so if "God" is just a programming object in the brain and people see that, does that end the relevance of "God"? Still, in this absolute extreme of negativity, I would argue nay. People can study where the programming object derived from, and call their bail of hay more from a relevant evolutionary mechanism than their neighbor, use it to accumulate wealth in the name of the purpose of where the programming object derived from, claim to be more part of it, and then more an image of it, and brand new claims can come up... I'm babbling.

 

[Harmageddon]

To catatonic (thanks for the babbling reply) and whomever it may concern:

I did not mean to say that God is irrelevant, period. I just stated that the implications of Darwin’s theory of natural selection were regarded by the powers that were (the Catholic Church) that God seemed irrelevant if Darwin was correct.

I agree with you that estranging the Christians or followers of other mono- or polytheistic faiths from the scientific community, and vice versa is not a very fruitful way forward. Instead, communications should at some point reach a higher level.

A large part of the problem is that (in my experience) Christians or other believers don’t know anything about the theory of evolution, only that it is a theory and that therefore they should not bother with it. Christians of course may have felt the same but then the other way around. The Catholic Church, rightfully so, thought otherwise – it does imply a significantly smaller role for God to play in the theater of life.

Look, personally, I don’t know whether there is a God or not – it is I think impossible to know – but I do think that God is not necessary for the Universe, earth and all life to exist. Whether or not He/She is pulling the strings after all is in my view irrelevant. Let me explain.

Suppose there is a God that created everything, and views us as the most lovable part of his entire creation (quite a Narcissist worldview). Then what does this say about God, and what does it say about us?

About God, in whose image we were created, we can say that he is humanoid in his natural form and that God is a thinking entity with a consciousness. We cannot say that God is infinitely good, since we aren’t either. Actually, most Christians believe we are inherently evil, and we need to deserve our place at Gods table by being true believers and by doing good deeds (according to Jesus at least). This means that God is Him/Herself inherently evil as well, and that God is striving to do good all the time, like we are supposed to be doing.

What does it say about us, humans? We have been privileged to be the most lovable species in all of creation and what do we do with it? We rape our planet of its resources, we are rapidly destroying the environment that is home not only to us, but countless other life-forms, and we wage wars amongst one another since the dawn of time. This quite fits the image of an evil God. Not to discredit the minority that is actually truly good-hearted, like Gandhi for example.

Then again, we may all be a part of God, and thus we may influence one another. The more evil we get the more evil God gets and vice versa. This would be true for good as well of course.

But it is written that God is good. So where does this fit the image of God and us? In other words, what would be Gods reason to create lesser copies of Him/Her and make them evil? People say it is because God is testing humanity to see if we are worthy of His creation. But God is supposedly all-knowing. He would already know if we were worthy or not – it makes no sense to test us if God already knows the outcome. And if God doesn’t know it, because of our free will, then God is not all-knowing. Thus, there is plenty of controversy on the existence of God.

From this I conclude that God is insofar irrelevant as to my behavior. I think that it is in humanity’s best interest to try and follow the wise words of the supposed only true son of God, Jesus, who said we should really try to love one another, and stand up to injustice, evil and oppression. That is a philosophy I can live with, whether there is a God, whether God is evil or good is, to me, irrelevant.

 

[catatonic]

Development:

new york times

Scientists Say They’ve Found a Code Beyond Genetics in DNA

Published: July 25, 2006

Researchers believe they have found a second code in DNA in addition to the genetic code.
Skip to next paragraph
Loren Williams/Chemistry and Biochemistry, Georgia Institute of Technology

In a living cell, the DNA double helix wraps around a nucleosome, above center, and binds to some of its proteins, known as histones.

The genetic code specifies all the proteins that a cell makes. The second code, superimposed on the first, sets the placement of the nucleosomes, miniature protein spools around which the DNA is looped. The spools both protect and control access to the DNA itself.

The discovery, if confirmed, could open new insights into the higher order control of the genes, like the critical but still mysterious process by which each type of human cell is allowed to activate the genes it needs but cannot access the genes used by other types of cell.

The new code is described in the current issue of Nature by Eran Segal of the Weizmann Institute in Israel and Jonathan Widom of Northwestern University in Illinois and their colleagues.

There are about 30 million nucleosomes in each human cell. So many are needed because the DNA strand wraps around each one only 1.65 times, in a twist containing 147 of its units, and the DNA molecule in a single chromosome can be up to 225 million units in length.

Biologists have suspected for years that some positions on the DNA, notably those where it bends most easily, might be more favorable for nucleosomes than others, but no overall pattern was apparent. Drs. Segal and Widom analyzed the sequence at some 200 sites in the yeast genome where nucleosomes are known to bind, and discovered that there is indeed a hidden pattern.

Knowing the pattern, they were able to predict the placement of about 50 percent of the nucleosomes in other organisms.

The pattern is a combination of sequences that makes it easier for the DNA to bend itself and wrap tightly around a nucleosome. But the pattern requires only some of the sequences to be present in each nucleosome binding site, so it is not obvious. The looseness of its requirements is presumably the reason it does not conflict with the genetic code, which also has a little bit of redundancy or wiggle room built into it.

Having the sequence of units in DNA determine the placement of nucleosomes would explain a puzzling feature of transcription factors, the proteins that activate genes. The transcription factors recognize short sequences of DNA, about six to eight units in length, which lie just in front of the gene to be transcribed.

But these short sequences occur so often in the DNA that the transcription factors, it seemed, must often bind to the wrong ones. Dr. Segal, a computational biologist, believes that the wrong sites are in fact inaccessible because they lie in the part of the DNA wrapped around a nucleosome. The transcription factors can only see sites in the naked DNA that lies between two nucleosomes.

The nucleosomes frequently move around, letting the DNA float free when a gene has to be transcribed. Given this constant flux, Dr. Segal said he was surprised they could predict as many as half of the preferred nucleosome positions. But having broken the code, “We think that for the first time we have a real quantitative handle” on exploring how the nucleosomes and other proteins interact to control the DNA, he said.

The other 50 percent of the positions may be determined by competition between the nucleosomes and other proteins, Dr. Segal suggested.

Several experts said the new result was plausible because it generalized the longstanding idea that DNA is more bendable at certain sequences, which should therefore favor nucleosome positioning.

“I think it’s really interesting,” said Bradley Bernstein, a biologist at Massachusetts General Hospital.

Jerry Workman of the Stowers Institute in Kansas City said the detection of the nucleosome code was “a profound insight if true,” because it would explain many aspects of how the DNA is controlled.

The nucleosome is made up of proteins known as histones, which are among the most highly conserved in evolution, meaning that they change very little from one species to another. A histone of peas and cows differs in just 2 of its 102 amino acid units. The conservation is usually attributed to the precise fit required between the histones and the DNA wound around them. But another reason, Dr. Segal suggested, could be that any change would interfere with the nucleosomes’ ability to find their assigned positions on the DNA.

In the genetic code, sets of three DNA units specify various kinds of amino acid, the units of proteins. A curious feature of the code is that it is redundant, meaning that a given amino acid can be defined by any of several different triplets. Biologists have long speculated that the redundancy may have been designed so as to coexist with some other kind of code, and this, Dr. Segal said, could be the nucleosome code.

 

[Harmageddon]

Thanks for posting, catatonic, this is science at it's best!

Step by step pieces start falling in their place, as science unravels more and more about the fabric of life and the universe. Magnificent stuff this.

And it confirms several theories, while others are now debunked.
And that is in my humble view the only way to seriously consider the origins of life, the universe, and everyting else - not to dismiss philosophy by the way, since ideas first have to be cooked up before they can be scientifically tested.

Nice.