We donʼt see genes or organisms simply popping into existence out of nowhere. They all appear to have natural lineages. Connections abound in nature, not disconnections and miracles. Hereʼs what Intelligent Design advocates WANT to say happened, notice how unconcerned they are with continuing to examine all the connections in nature, and how eager they are to promote disconnections in nature and miracles:
“Michael Behe told us his hypothesis a few years ago. We both took part in a week–long lecture series on the intelligent design debate at Hillsdale College. After Michael Beheʼs lecture, some of us pressed him to explain exactly how ‘irreducibly complex’ mechanisms arose—mechanisms that cannot, according to Behe, be explained as products of evolution by natural selection. He repeatedly refused to answer. But after a long night of drinking he finally answered: ‘A puff of smoke!’ A physicist in the group asked, Do you mean a suspension of the laws of physics? Yes, Behe answered. Not very persuasive as a scientific answer.” —RBH July 9, 2012
Reminds me of what Berlinski wrote:
“Before the Cambrian era, a brief 600 million years ago, very little is inscribed in the fossil record; but then, signaled by what I imagine as a spectral puff of smoke and a deafening ta–da!, an astonishing number of novel biological structures come into creation, and they come into creation at once.” —Berlinski, “The Deniable Darwin” (June 1996), Commentary magazine. Oh, and Berlinski and Stephen C. Meyer are wrong about the Cambrian providing evidence of I.D., simply repeating an old creationist lie.
There is no evidence of things popping into existence via Beheʼs puff of smoke. But there is endless evidence of natural connections, i.e., of atoms and molecules naturally interacting and nudging each other, and organisms naturally replicating, dividing into individuals and new species, with only a select number of each new generation of organisms passing along their genes to future generations—the rest unable to leap over the many hurdles nature puts in the way (from zygote to the age of sexual reproduction), and hence a large percentage usually die off or leave behind smaller proportions of offspring than others.
Compare the pro–I.D. stance with that of BIOLOGOS. The latter was founded by a leader of the Human Genome Project, and it is an organization of Christians who are scientists who support evolution and critically analyze I.D. arguments.
Biologist Jeffery P. Schloss used to be a senior member of the pro–I.D. Discovery Institute but left after the Instituteʼs film, Expelled, was released, and he wrote a lengthy review and rebuttal of the filmʼs arguments. Schloss has since joined BIOLOGOS.
DNA does not copy itself perfectly. Study all the mutations that happen during meiosis. Study the variety of known mutations and mutagenic substances inside cells, and mutagentic energies that enter cells from the outside. Most mutations do not appear to be guided, and most mutations appear to be neutral, no great benefit or harm.
Speaking of genetic diversity, all the cells in your body are not uniquely your own. Your DNA and identity are not as entwined as once thought. In fact most people have multiple genomes floating around inside them. Nature is more malleable than we previously thought (speaking of natureʼs malleability, one might even note instances of whole genome duplication events with subsequent mutations and whittling down).
Some people have undergone rare mutations even today that lead to things like people who are super tasters, super hearers, or super seers who can see with greater resolution, or who can distinguish a wider spectra of colors. Such people exist, do some googling. One can also read about the evolution of our own tri–color vision, related to a gene duplication event in our monkey ancestors, apparently humans with greater color detecting abilities underwent a recent added gene duplication event with subsequent minor mutations and the mutated protein molecule in their retina now absorbs slightly different spectra of light, adding to their color sensing spectra.
Which isnʼt to say we are ALL headed in the direction of becoming super seers and super tasters, etc. The mutation that led to the ability to digest milk sugar spread quickly after the domestication of cattle and the drinking of milk began in one part of the world, but has not yet spread to everyone on earth, especially some people in parts of Asia.
Also, evolution via mutation being what it is, some species are better endowed than the human species in key cognitive regions:
If I.D. were true and every single mosquito had the same intelligently amazing non–Darwinian ability to adapt, why was DDT still so great at killing millions of them until that odd random mutation took decades to spread throughout the gene pool? Keep in mind also how many mosquito eggs a female lays each generation and how many of them simply perished without leaving behind their genes. A mosquito happened to be born with multiple copies of the esterase gene that helps detoxify DDT. That one mosquito got lucky. We also now know that there is more than one mutation that can accomplish greater survival of DDT (I.D.ists employ phony statistical arguments, as if thereʼs only a single target and a single arrow that has to hit the exact center of that target, and then they ask, “what are the odds?” But nature doesnʼt work that way. Nature has redundancies, and keeps mutating. And as I said most mutations are neutral). For instance a cotton budworm at some point was born with a mutation that changed the target of the DDT poison. A housefly was born with a mutation that altered the proteins that transport the DDT poison. So we know a variety of possible mutations could reduce the killing effects of DDT, and only one of those different mutations has to occur in order for the organism to develop some resistance, and of course the organism that survives gets to continue passing that gene along while all the rest that did not experience that mutation died or left behind far fewer offspring.
We donʼt know all the possible mutations that might allow Plasmodium (the malaria parasite) to survive anti–malaria. drugs either. See this recent Take Down Of Beheʼs Argument That Malariaʼs Resistance To A Drug Could Not Have Evolved, “New research on the evolution of drug resistance in malaria contradicts Michael Beheʼs claims in The Edge of Evolution.”
See also, “Natural selection in the time of cholera. Using a recently developed computational method, the researchers have been able to detect patterns of strong natural selection left behind in the genomes of a population that has been contending with cholera for generations.”
Mutations come in many sizes, from simple point mutations in DNA to the duplication of whole genes or other parts of the genome, to whole chromosome duplication events, to whole genome duplication events. Once you have such extra genetic material you have redundant genes for evolution to continue working on, usually via neutral mutations, since as I said most mutations are neither horribly deleterious nor marvelously beneficial.
Another way to gain extra genetic material is via swapping DNA packets like bacteria do continually. Or in the case of the human genome via invasions of viruses or bacteria whose RNA or DNA gets incorporated into a human germ cell in the gonads (testes/ovaries), which is the only way such extra DNA will get passed on to future generations, i.e., if that particular egg or sperm forms a viable zygote in future.
In many cases there are not only neutral mutations, but also degrees of functionality or dysfunctionality when it comes to proteins formed by mutated DNA. Itʼs not a simple matter of the protein being either on or off, active or inactive. Thereʼs degrees. For instance, a simple frame shift mutation in one bacterium allowed it to obtain some energy from partially digesting a man–made substance, nylon, reducing it to a gooey slime. This bacterium was discovered in a bin of discarded nylon at a factory. But it does not break down the nylon wholly, only partially, so it is a partially effective mutation. Mutations need not start out wholly effective, and as I said, neutral mutations are slightly changing the genome all the time as well, raising the chances for unforeseen future changes.
There is a known estimate of human genome mutations that accumulate per generation. I believe this estimate has been further substantiated by the 1000 genomes project which analyzed the whole genomes of over 1000 individuals from around the world. And that estimate of naturally occurring mutations per generation greatly exceeds what would have been needed to provide enough mutations to transform our great ape ancestors into modern day human beings over a period of about five million years. (Keep in mind that the genetic distance from modern day humans to modern day chimpanzees is greater than the distance from either of us to our common ancestor because both humans and chimps have continued to mutate in their own unique ways after splitting off from a common ancestor. And even though the genetic distance has grown between us and chimps, we are still as close to chimp DNA as the DNA of sibling species of fruit flies are to one another.)
All living things are mashups and mixes of genetic material that has been traded between replicators over untold eons. The human genome contains both viral and bacterial genes, and the amount of viral genetic material that has wheedled its way inside our cells is equal to or exceeds the number of genes that make us peculiarly human.
The simplest replicators are not viruses but transposons, transposable genetic elements (TE) or retrotransposons which are DNA sequences that can change its sequence within the genome sometimes causing or reversing mutations and altering the cellʼs genome size. These transposons have been found inside viruses that infect other viruses, which in turn affect amoebas that infect human beings. As one microbiologist put it, “I think itʼs difficult to see where one organism begins and another one ends, we are only beginning to appreciate how intertwined these layers of organisms are in large flora and fauna.” [from “The Dexter of Parasites” on the Stuff to Blow Your Mind podcast for Nov 14, 2013, the podcast also discusses a species of wasp that lays its eggs inside caterpillars that have already been infected by wasp eggs, but the larva of this species of wasp not only eats the caterpillar but also the larva of the other wasp species whose eggs hatched earlier inside the caterpillar, basically hot parasite on parasite action]
We even know via experiments that a single strand of RNA (usually taken from a virus) can make more strands that then make more strands in test tubes filled with that strand & some basic building block molecules & a little zinc as a catalyst. So a single strand of RNA can self–replicate. They even put some RNA dissolving chemicals in one of those test tubes (a dilute amount of chemical that was poisonous to RNA) and then siphoned out of the tube any RNA strands that survived and placed them in a fresh test tube to produce more strands, and then slowly increased the dosage of the poison, and then took out any surviving RNA strands and placed them in a fresh test tube to make more RNA, etc., until an RNA strand that was more highly resistant to the poison was produced, demonstrating the naturally growing adaptability of a strand of RNA to poisonous chemicals over several generations and via a selection of surviving strands.
Viruses. Viruses are so adaptable they can have either RNA or DNA as their genetic material (in other words their nucleic acid may be single– or double–stranded). The entire infectious virus particle, called a virion, consists of nucleic acid covered by an outer shell of protein. The simplest viruses contain only enough RNA or DNA to encode 4 proteins. But the largest known virus, the Pandora salinus virus, is larger than many bacteria and contains more than 2,500 genes! Nor do viruses have proof reading mechanisms, so more mutations occur in them each generation than other replicators on earth. Also, giant viruses are known to be infected by much smaller viruses that invade them! Hot virus on virus action.
Viruses are the most abundant replicators on earth, with each drop of healthy sea water containing exponentially larger numbers of viruses than either bacteria (prokaryotes) or single–celled organisms (eukaryotes). Viruses attack other viruses, prokaryotes, eukaryotes, and the Archaea (single–celled organisms that were recently discovered to constitute their own separate kingdom of living things neither bacterial nor eukaryotic).
Bacteria. Most bacteria are larger than most viruses. Bacteria passively absorb genetic material they happen to run into. And they actively exchange packets of genetic material. This means they are filled with loads of odd genetic material at all times. And keep in mind how many countless viruses and bacteria are perishing every second on earth (never passing along their genetic material to future generations, while others are busy producing far more offspring than others) and you begin to realize just how much genetic shuffling and natural selecting has been going on for a long time. In fact for the majority of biological history on earth there was nothing but single–celled organisms on earth. Multicelluar organisms havenʼt been around nearly as long as single–celled organisms. So however amazing the internal architecture of single–celled organisms, they had a long long time to develop that internal architecture—far longer than the time multi–cellular organism have been around.
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