Is Darwin's Theory Of Evolution True? Part Two

[buffalo]

The fundamental theorem of natural selection with mutations

Remarkably, Fisher’s theorem by itself illustrates a self-limiting process – once all the bad alleles are eliminated, and once all the individuals carry only good alleles, then there is nothing left to select, and so selective progress must stop. The end result is that the population improves slightly and then becomes locked in stasis (no further change). It is astounding that Fisher’s Theorem does not explicitly address this profound problem! Newly arising mutations are not even part of Fisher’s mathematical formulation. Instead, Fisher simply added an informal corollary (which was never proven), which involved extrapolation from his simple proof. He assumed that a continuous flow of new mutations would continuously replenish the population’s genetic variability, thereby allowing continuous and unlimited fitness increase.

The authors of the new paper realized that one of Fisher’s pivotal assumptions was clearly false, and in fact was falsified many decades ago. In his informal corollary, Fisher essentially assumed that new mutations arose with a nearly normal distribution – with an equal proportion of good and bad mutations (so mutations would have a net fitness effect of zero). We now know that the vast majority of mutations in the functional genome are harmful, and that beneficial mutations are vanishingly rare. The simple fact that Fisher’s premise was wrong, falsifies Fisher’s corollary. Without Fisher’s corollary – Fisher’s Theorem proves only that selection improves a population’s fitness until selection exhausts the initial genetic variation, at which point selective progress ceases. Apart from his corollary, Fisher’s Theorem only shows that within an initial population with variant genetic alleles, there is limited selective progress followed by terminal stasis.

 

[buffalo]

What Junk DNA? It’s an Operating System
Noncoding gene sequences control gene expression and influence disease processes.

Back in the old days, the general wisdom had it that introns loaded into the human genome were basically useless. While some noncoding DNA is transcribed in noncoding RNA, such as transfer RNA, ribosomal RNA, regulatory RNA, or endogenous retroviruses, others produce RNA with no known function or identified utility to the cell.

But over the past few years, as high-powered analytical tools and genomic information have become available, the function of introns, such as transcription factor recognition sequences, has become better understood. And, as John Stamatoyannopoulos, M.D., associate professor of genome sciences and medicine at the University of Washington, points out, while only about 2% of the human genome codes for proteins, “Hidden in the remaining 98 percent are instructions that basically tell the genes how to switch on and off." His laboratory focuses on disease-associated variants in regulatory regions of DNA.

Hidden in the remaining 98% of the genome are the instructions that tell the genes how to switch on and off in different kinds of cells. A chief goal of ENCODE has been to find those instructions and understand how they are written in the genome.

“In essence, these instructions are organized into millions of DNA ‘switches.’ These switches consist of strings of genetic letters, maybe 100 to 200 letters long, that can be thought of as sentences made up of short DNA words. The DNA words function as docking sites for special regulatory proteins,” said Dr. Stamatoyannopoulos.

 

[buffalo]

Reading the genetic code depends on context

The so-called central dogma of molecular biology states the process for turning genetic information into proteins that cells can use. “DNA makes RNA,” the dogma says, “and RNA makes protein.” Each protein is made of a series of amino acids, and each amino acid is coded for by sets of “triplets,” which are sets of three informational DNA units, in the genetic code.

Hughes and Fabienne Chevance worked with a gene in Salmonella that codes for the FlgM protein, which is a component of the bacteria’s flagellum. A mutation that was defective in “reading” a specific codon in the flgM gene only affected FlgM protein production and not other genes that contained the same codon.

“That got us thinking—why is that particular codon in the flgM gene affected and not the same codon in the other genes?” Hughes says. "That’s when we started thinking about context."

The difficulty for natural selection would be in finding codon optimization for a given gene. If the speed through a codon is dependent on the 5′ and 3′ flanking codons, and the flanking codons are dependent on their 5′ and 3′ flanking codons, then selection pressure on a single codon is exerted over five successive codons, which represent 615 or 844,596,301 codon combinations. If modified tRNAs interact with bases in a codon context-dependent manner that differs among species depending on differences in tRNA modifications, ribosome sequences, and ribosomal and translation factor proteins, it is easy to understand why many genes are poorly expressed in heterologous expression systems which codon use is the primary factor in the design of coding sequences for foreign protein expression. The potential impact of differences in tRNA modifications represents a significant challenge in designing genes for maximal expression whether by natural selection or in the laboratory.

Read more at: Reading the genetic code depends on context

 

[Aloysium]

"Evolution in the sense of common ancestry might be true

Depending on the definition of “common ancestry” I might agree. But, we are not some variation of ape, but a new creation by virtue of our eternal spirit, from God. That’s what defines our parentage.

As close as I can get to that concept is the possibility that Adam was formed through the power of the Holy Spirit utilizing the knowledge contained in the DNA of previously created organisms. There would be no meeting of animal gametes because that would have simply produced another animal. From that original human egg, perfect in its human genetics, male and female versions arose as Eve was cleaved from Adam. We are more than our day to day consciousness would have us think. Near death encounters demonstrate that the roots of memory are the spirit although the brain is required to reformulate them in space and time. What was going on in that relationship with God, the Garden and the source of all our human capacities was Eden. We fell in that state to be born into this fallen world, which would have been very very different had we trusted and loved God and not chosen badly.

Australopithecus, into whose womb the egg would have developed, although not human itself, would have been the model for our eventual form in this now our world, chosen because if its capacity to function within it as an integral participant.

I’m not tied to that vision although it does appeal to my sense of order although it would need work.

With all due respect to our learned teacher, although he qualifies what he means, I think he overvalues the explanatory strength of the standard theory of evolution.

 

[Aloysium]

Dawkins suggested aliens, but those aliens must have evolved.

Francis Crick proposed alien spores rocketed to earth in his book - Life Itself: Its Origin and Nature

 

[edwest211]

Excellent. Thank you. I had been following this and had read how something in a non-coding region was affecting something in a coding region but they have a lot of connections/switches left to identify. Some of what they have learned is that certain switches are involved in human diseases.

 

[edwest211]

He most certainly does. Adam and Eve were both special creations with unique preternatural gifts, including immortality, which were given to them by God. The hominins/hominids were all animals that had humanoid aspects. It’s quite clear that science doesn’t see it this way but I hope this error is discovered.

 

[LeafByNiggle]

In fact my whole argument here is that there is another way, which is precisely what is being explored by many evolutionists today. Specifically, it is a form of evolution first proposed by Lamarck; and it is fundamentally different than the process proposed by Darwin.

I think the process you refer to is that the life experiences of individual organisms impacts the genetic code in a way that makes offspring better able to handle those experiences than their parents, thus making random variation unnecessary. While I can think of several ways in which this is unlikely, my main complaint is that this can only apply to a small subset of adaptations, like a giraffe stretching his neck. Most adaptations don’t make sense under this mechanism. For example, consider the adaptation that created poisonous frogs

What possible life experience would cause a frog to become more poisonous? Unlike a giraffe stretching his neck to reach food, frogs did not decide to “try to be poisonous” so that the act of trying might get reflected in the genes. The only relevant life experience is getting eaten by predators, or not getting eaten. Those that got eaten never had offspring after that, so the life experience of “getting eaten” could not have affected genes. And those that did not get eaten experienced “not getting eaten.”. It is ludicrous to think that the experience of not getting eaten would promote the generation of a poisonous skin. However, Darwinian evolution explains the poisonous frog quite simply. Some frogs were marginally less digestible than others. Natural selection did the rest.

 

[Rau]

I would really like to get away from this argument. It really doesn’t matter what a person believes; all that matters is whether the arguments being made are reasonable. If an atheist argues for Darwinism solely because it reinforces his “God does not exist” beliefs; I don’t care. Either the arguments he uses to support his position are valid or they aren’t; his reasons for proposing them are simply irrelevant.

Evolution as “evil”, as “atheistic”, as a “conspiracy to destroy the faith of Christians”, as “fairytale” as a “rejection of Revelation” is the key theme of a number of posters. Some castigate the Church for not rejecting it as incompatible with Revelation. I don’t think they wish to be silenced.

 

[rossum]

Do you deny the DNA code?

I deny the construction you put on the word “code”. Is the Sun intelligent? Yet sunlight contains coded information which allows astronomers to analyse the chemical composition of the Sun.

You say that “code” requires intelligence, I deny that.

rossum

 

[Techno2000]

While I can think of several ways in which this is unlikely, my main complaint is that this can only apply to a small subset of adaptations, like a giraffe stretching his neck.

So, the food must have slowly grown higher over a period of millions of years to give the giraffe a chance to evolve it’s neck.

 

[Metis1]

1. I don’t see life and matter as synonymous.
2. The two pillars of random mutation and natural selection are valid only in the case of genetic disorder.
3. Similarly, there exists an order to creation, determined by the Word of God, which science will discover once it lets go of the invalid foundations of evolutionary theory.

1.They are not synonymous but they certainly relate, as living forms are largely composed of matter. If matter within us changes, and it does over time, then we and other life forms must logically change as well.

2.What you call “genetic disorder” could be bad news, no news (recessive), or good news. It is the “powerhouse” that adds new “energy” to the gene pool. Without it, evolution would be extremely limited. You might consider googling “genetic mutations”.

3.The “foundations” have been very well established for well over a century now, but it was even known before that that life forms change. For examples, google “speciation”. Even the Wiki article on that is quite decent.

OTOH, there is not one shred of objectively-derived evidence for a theistic causation of life forms or our universe, so if one accepts it, they must do so on the basis of faith, not empirical evidence. Personally, I have no problem with religious faith, including my own, but I also know its highly variable from one person to another, thus it cannot be used as a basis for science. About half of American scientists are theists, so the two can be paired.

 

[buffalo]

If I make a code how do you read it?

 

[buffalo]

The giraffe also eats from the ground. The blood pressure must be regulated. It is much higher when the giraffe’s head is fully upright. Learn about the mechanisms that must have “evolved” to protect the giraffe when it moves his head to the ground.

Of course, we know evolution did it.

 

[buffalo]

Evolution has no empirical evidence either, that is observable, repeatable and predictable. It is a worldview.

 

[Metis1]

BTW, one thing I’m thankful for is that at least the Catholic Church and most of its leaders, including recent popes, and most of its congregants worldwide accept that evolution of life forms has indeed happened and that God caused it all. The fundamentalist Protestant church I grew up in was quite anti-science, which is one reason why I left it.

Life evolves, and of that there simply is no doubt. We can debate the details, but the handwriting has been clearly on the wall for over a century now. In order for some to try and negate this, frankly they have to lie and/or parrot someone else’s lies, often drawing up absurdities about how dumb, corrupt, or monolithic scientists are. Of course they cannot prove it, but they parrot it nevertheless.

As one who’s studied and been involved in science for over 50 years, I can easily vouch for the fact that these conspiracy theories are bogus and disingenuous. Even one who reads “Scientific American” once in a while can read how scientists often disagree with each other.

Anyhow, any religion or denomination that teaches that life forms have not evolved is a bogus religion or denomination as Truth is not relative.

So, I just leave it at that and move on. I’ll deal with serious questions if I feel like it, but I will not deal with those who lie or parrot lies.

 

[Metis1]

BTW, here’s from the Smithsonian Institute in D.C. that deals with this topic: http://humanorigins.si.edu/evidence

BTW, I’ve spent many an hour there and on multiple occasions.

 

[AIPM1615]

I’m coming into the conversation a bit late, so forgive me if I missed something here.

Giraffes did not develop long necks because they were “stretching to reach food.” Physical changes as a result of life experience are not passed along to offspring. If my arm were to be amputated, my kids are not then more likely to be born without an arm. If I stare at the solar eclipse and go blind, my children won’t be born blind (at least, not as a result of the eclipse).

According to the theory of evolution, the long necks developed because as the ideal food source–trees–grew taller, the ancient giraffes with longer necks (thanks to genetic variation) were better suited to reach them. After millions of years, the long-necked giraffes survived and continued to become taller, while their ancestors didn’t.

I’m probably preaching to the choir but ya know.

 

[Ender]

Let’s verify that they didn’t “screw it up” before speculating about what it would mean.

No. Let’s address what it would mean first. Noble has claimed that acquired characteristics can be inherited, which is what Lamarck said. This is an entirely different mechanism for evolution than what Darwin proposed. If the experiment is valid, does it support this claim? If it doesn’t then does it have any significance at all?

If it lacks significance even if it is valid then we don’t need to concern ourselves with it.

 

[goout]

They are scientists. Many are atheists, but not all. Prediction: when this all settles in there will be some conversions.

The sad fact of that matter is that the positions your propose as a Catholic, scandalize others.

And I do not know why you grin about it. This is sad and tragic.

On the one hand, we would like others to look at the world around us, and at human beings, with the Catholic Church, in a reasonable way.
Take gender issues for instance. The Church has a proposition to make that is well-founded on reason and common sense.

And then we have Catholics that undermine those positions.
It’s scandalous to others looking for answers. It contributes to the un-reason of our culture. It marginalizes Catholic thought. It’s nothing to grin about.