An August 25, 2012 Washington Post article talked about a superbug outbreak at the NIH. The article highlighted the problem that we are running out of useful antibiotics. Antibiotic resistance is an evolutionary question of great practical importance. I have recently been asked and agreed to sign on to petitions requesting that antibiotic use in animals be banned for the sake of human health.
There is no evolutionary phenomenon we understand better than multiple antibiotic resistance in bacteria. It has been occurring virtually synchronously with the development of molecular genetics for 60 years. For public health as well as scientific reasons, antibiotic resistance was a major focus of the first decades of molecular biology.
Let us use this well-studied phenomenon to disentangle some of the thorny questions raised and debated in my most recent two blogs dealing with evolutionary processes (you can read them here and here). Our knowledge of the underlying cell and molecular biology makes it possible to discuss these questions in terms of specific experimental results rather than abstract principles.
The chief factor in the rapid evolution of multiple antibiotic resistance is the presence of sequences encoding resistance mechanisms on transmissible plasmids (Watanabe 1967). It was my PhD supervisor, Bill Hayes, who first demonstrated the existence of transmissible plasmids. They have proved to be extremely important evolutionary tools in bacteria.
Working under minimalist conditions (Bill initially had to make his own petri dishes by cutting the bottoms off glass vials), he demonstrated that sexual recombination in E. coli required an infectious factor that he called F, for fertility (Hayes 1968). Bill demonstrated that F was independent of the E. coli chromosome by studying the kinetics of its spread in a bacterial population. He found that F could replicate and spread though the population far faster than the 30 minute division time of the bacteria. This kind of autonomously replicating element came to be called a plasmid (Novick 1980).
A graph showing the spread of an antibiotic resistance plasmid in the absence of antibiotic is included in Watanabe's Scientific American article on transmissible antibiotic (Watanabe 1967). This result is significant because it shows how the mobility apparatus of the plasmid can operate to distribute the plasmid and make it spread through an unselected population of bacteria. Later, when antibiotic is applied, a large fraction of the population is already resistant.
In my recent blogs, a number of commentators asserted that the source of variation is immaterial to evolution because natural selection works on any variants that appear. But, as I pointed out in the first blog on superbugs, cells which can only modifying their existing genomes cannot achieve the same high levels of antibiotic resistance as cells that can pick up DNA from outside. Moreover, they are certainly not able to establish a resistant population prior to encountering selection as quickly as cells that have received a resistance plasmid.
Acquiring DNA from other cells, "horizontal transfer," occurs among bacteria most commonly by plasmids. However, bacterial cells can also take DNA up directly from the environment or receive it by viral infection. All these processes have been amply documented to occur in nature.
The F plasmid that Bill Hayes identified did not carry any antibiotic resistance sequences. So it is important to ask how those particular sequences came to be associated with transmissible plasmids. The answer leads us to two intriguing natural genetic engineering systems, transposons and integrons.
Transposons are segments of DNA that have the capacity to move (or "transpose") from one location in a genome to another (Cohen and Shapiro 1980). In order to make an antibiotic resistance sequence itself part of a transposon, it is sufficient to surround it by two copies of an existing transposon. This sometimes occurs normally as part of the transposition process, but other classes of transposons have been found already associated with antibiotic resistance sequences incorporated inside.
Once an antibiotic resistance determinant has the capacity to transpose, it is easy to see that it can insert into a plasmid and become transmissible to other cells. This is clearly the source of many resistance plasmids. The resistance determinants can be observed moving between plasmids (Hedges and Jacob 1974) and from plasmids to other components of the bacterial genome, such as the chromosome or viral DNA (Bukhari 1977).
In a fascinating example of genetic specialization, the structures known as "integrons" have been found to exist inside plasmids, transposons, and even bacterial chromosomes. Identified initially by Ruth Hall and her colleagues in the 1990s (Hall and Stokes 1993), integrons are DNA platforms for accumulating cassettes containing the sequences encoding proteins for antibiotic resistance, bacterial virulence, and other properties. These cassettes can accumulate and build up a number of multi-resistance DNA sequences.
Faced with such a powerful bacterial toolbox for accumulating and spreading antibiotic resistance, it is no wonder that we have been caught off guard underestimating the capacity of these small cells to evolve high levels of resistance quickly. Many questions remain to be clarified, such as where the resistance sequences themselves arose, but the DNA manipulation virtuosity of the bacteria should give us pause in thinking we have yet plumbed the depths of the evolutionary process.
REFERENCES
Bukhari, A. I., J.A. Shapiro, and S. L. Adhya (Eds.) (1977). DNA insertion elements, plasmids and episomes Cold Spring Harbor, New York, Cold Spring Harbor Press.
Cohen, S. N. and J. A. Shapiro (1980). "Transposable genetic elements." Sci Am 242(2): 40-49. http://www.ncbi.nlm.nih.gov/pubmed/6246575.
Hall, R. M. and H. W. Stokes (1993). "Integrons: novel DNA elements which capture genes by site-specific recombination." Genetica 90(2-3): 115-132. http://www.ncbi.nlm.nih.gov/pubmed/8119588.
Hayes, W. (1968). The Genetics of Bacteria and their Viruses (2nd ed.). London, Blackwell.
Hedges, R. W. and A. E. Jacob (1974). "Transposition of ampicillin resistance from RP4 to other replicons." Mol Gen Genet 132(1): 31-40. http://www.ncbi.nlm.nih.gov/pubmed/4609125.
Novick, R. P. (1980). "Plasmids." Sci Am 243(6): 102-104, 106, 110 passim. http://www.ncbi.nlm.nih.gov/pubmed/6259723.
Watanabe, T. (1967). "Infectious drug resistance." Sci Am 217(6): 19-28. http://www.ncbi.nlm.nih.gov/pubmed/6061177.
I have a feeling that DakkonA is still searching for the answers to my posts that shredded
"evolution of man" into nothing but just irratonal guess work. I hope that he did not get depressed and harm himself after realizing what he think he knows, are now looking basurd due to his failure to apply his good senses when reading any book, be it bible or science book. Either this or he now could have already reconsidered his position and now picking the sensible belief over DeadRocks.
It is important to note that, when we have opposing beliefs, be it in religion, science, politics, or any subject, if both have no solid facts, we can make one belief appealing and sensible when one can show the insanity of the other opposing belief, which is almost equal to proof.
http://www.slate.com/articles/health_and_science/science/2012/09/thomas_jefferson_s_moose_how_the_founding_fathers_debunked_count_buffon_s_offensive_theory_of_new_world_degeneracy_.html
I'm still waiting for your reaction to my explanation of why an atheist crusade does harm to the cause of science education. I posted it again for you as soon as you asked.
Having personal faith in the existence of ConsciousOrigin or GOD where Consciousness came from, is not for sale. Faith is free and can make your life and our kids' lives meaningful as they begin to feel that they are accountable for every good deeds they do, for their neighbors, not part of involuntary process of evolution at all.
Richard Dawkins et al, are making money from people who are buying their books, demeaning our kids lives, making many kids feel they're just part of an involuntary process of evolution,and therefore not accountable for every evil they do driven by evolution. If "evolution of man" is the truth, then how can anyone be held responsible ? Many kids today, thinking that they just evolved from fish, can develop an attitude that stinks like fish, you know, the attitude that says, "be high for tomorrow we die because God is a lie". Teaching evolution of man is child abuse. Please rethink your positions for sanity sake. I hope it's not too late yet.
I love real good science. I have no problem discovering the REAL secrets of PhysicalNature. What I do not support is teaching "evolution of man" as if it is the truth where no one can understand the evolution of consciousness yet. Bad science poisons our kids'brains.
I hope you'll learn not to call biological evolution "involuntary process".
There is no need for a video camera to prove that sequoia trees grow from sequoia seeds. All you need to do is collect seeds from sequoia trees and plant it. However, the question of how all living things, not just the trees, originated is UNKNOWN. We can only believe as to how all started. We can only believe or not believe that GOD created trees first, not seeds, the same way GOD created Dinos, not giant eggs.
If you do not believe in GOD as the creator of all physical living things, you will end up in eternal limbo, asking yourself what comes first, giant eggs or dinos ? The evolutionists think that giant dino's eggs evolved from lizards' tini mini winny little eggs. But then, the question continues, what evolved first, lizards or eggs ?, and, as you dig deeper, you begin to question how did male and female evolved and why it is necessary fro male and female to evolve when finding a partner can be diffiuclt if not impossible ? Many ended in mental institutions trying to figure out the answer.
How did I know, you asked ? Because I dig "REAL Science" that can be tested and verified, not the voodoo science about "evolution of man" that can not be tested and verified. I can collect seqouia seeds and then plant it and watch it grow to prove that seqouia trees grow from sequoia seeds, it is as verifiable as the development of zygote into adult human, coming from mating of parents. On the other hand, there is no way I can test and observe how a dead rock turned into conscious entity to know and claim that "evolution of man" is a fact.
/snark
Please read the following if this complies with the laws of the Universe you called evolution:
A hairy thick skinned Lucy or Ape, living in the tough environment of the jungle, evolved into a soft hairless human baby that can not even survive in the malaria mosquitoe bite. Is this what you call "evolution by adaptation and natural selection" ? Don't you even notice it does not make any sense ?
Btw, why exactly do you think a human baby would be more vulnerable to malaria anyway? Just because you imagine it to be so? Further, why do you think that would be the only driving selective force?
You mean a group of fish, that evolved from oORGANICS at point "A" of time, had undergone a mysterious magical niche or had undergone an unfamiliar tough environment, decided not to swim away from danger, in a WIDE OCEAN, and died out, while their mutants turned into super iguana, and the millions of mutants that also mutated into iguana, also died out ? Does that rational science to you ? How come the fish is still a fish, while those mutants that is supposed to be the fittest to compete, who evolved from a fish, all died out while fish still survives ?
And let us pretend that your wishful thinking is a fact, what about those that evolved from ORGANICS at next point of time ie, "B, C, D, to Z points of time" which would evolved billions of TREES ? We should have billions of evolving successors of those who died out who became extinct, if organics DID NOT STOP evolving ? We should have missing links running around now, alive. Why dig for the dead, if evolution is true ? It does not make any sense. The teaching of nonesense can make life pointless and meaningless, and can hurt our kids future, which can
In Science, "conclusions" are based on solid facts that are discovered. The absence of solid facts does not incapacitate anyone to believe for any reason, logical or not. There is a difference between KNOWING because of facts, and BELIEVING for a reason for lack of facts.
NO ONE knows the FIRST CAUSE of PhysicalUniverse including Consciousness. This does not mean that just because we don't know, we can no longer believe in search of our FirstCause. This is really a discussion of what belief makes sense for lack of solid fact. Unlike many evolutionists who claim they have facts&evidence, I never claim mine is based on fact. Mine is about faith.
Now, let's compare what belief makes sense about FirstCause as follows:
I believe that my invisible unprobable Consciousness, who is the independent observer of the reality within and around me came from a Conscious Origin or GOD.
On the other hand, Science thinks that the UNCONSCIOUS matter, dusts, or rocks, blown by BigBang away further and further apart, expanding the Universe in tremendous speed they say, mysteriously collapsed and rejoined to end ALIVE and CONSCIOUS through billions of years.
ConsciousOrigin makes more sense than clueless unconscious involuntary matter,dust,or rocks turning into conscious being free to volunteer defying its involuntary process. Please don't ignore your GOD-given intelligence, it did not come from DeadStones.
"In conclusion, James A. Shapiro's “Evolution—A New View from the 21st Century” prepares the ground for the next great synthesis in biological evolution. This new synthesis should be able to deal with the inherent tendency of biological systems to increase their complexities at all levels of biological organization (from DNA sequences and single proteins up to multicellular organisms and ecological communities) and to associate/merge into larger assemblies. This 21st century synthesis will include our recent understanding of life as a phenomenon supported by knowledge embodied in sentient chemical systems, where biocommunication is inherently linked to life as well as to biological evolution. Sentience, subjectivity, cognition, communication, and intelligence appear to be inherently associated with both life and biological evolution"
http://ukpmc.ac.uk/articles/PMC3204118;jsessionid=b9bVDIMofQbbrNjUV7Mf.16
Decision-making is a well-established scientific phenomenon in cell biology. The control of the cell cycle, for example, depends upon a host of decision-based "checkpoints" (http://www.huffingtonpost.com/james-a-shapiro/living-cells-complex-syst_b_1204827.html). The August 2010 issue of Nature was devoted to "Decision-making in the Immune System." Do you reject all this science as well? That would be a purely philosophical rather than scientific choice.
BTW, you have not responded to my comments in response to your two statements. (That is, as far as I know; you may have posted them lower down in the chain.) Please do.
Science never claim that they understand fully about consciousness. Until now, consciousness is still one of science unsolved biggest mysteries. So, it is too early for you to conclude that Consciousness is just the property of the brain. I do not conclude. like you do. I just believe that Consciousness is our soul coming from GOD, not from physical nature. I believe only our physical brains and bodies belong to physical nature. Our consciousness is UNPHYSICAL, not part of the physical world, that is why it is independent from the brain, free to be aware of brain's thoughts, even free to reject brain's thoughts to believe in the UNKNOWN beyond the physical. How can a physical cause produce unphysical effect such as faith in GOD beyond physics ? The hint of GOD is everywhere, it is up to you to ignore it.
You are always free to think that you are nothing but an involuntary chemical process of the brain, just like a leaf floating on a river, not in control, not knowing where its currents can bring you to, feeling free to be anything because the river is to blame. Your call.
That is, in fact, a conclusion. If it was not, you would not be trying it use it to somehow disprove all of science.
Wolves and Dogs belong to same species, the wolves are just much violent and aggresive. It is no different than describing a savage man from the jungle and civilized man from the city, both are same species.
What I meant when I asked for close links are real CLOSE LINKS between different species of millions of species, not just humans, such as close links of gerrafis, rhinos, elephants, whales, humming birds, porcupines, etc etc. Why not even a single one we can see alive and well if organics DID NOT STOP EVOLVING ? Why would the billions of close links for Dinos would be even extinct if organics continues to evolve into viruses and bacterias to evolve into Dinos thru billions of years ? Clearly, "evolution of man" defies Physics because the physical cause and effects are all missing.
If you throw a coin into the air, you will expect it to drop down into the ground which complies Physics.
Physics is not about throwing "Evolution of Man" into the air and, when it is about to hit the ground, all the physical effects, I mean the Close Links, disappears.
No, they do not.
"the wolves are just much violent and aggresive." Which is because... drum roll please... natural selection by humans for those wolves which had these characterisitcs.
"It is no different than describing a savage man from the jungle and civilized man from the city, both are same species." Untrue. First, you have a gross deficiency in your characterization of low-technology societies as "savages". Second, there is no meaningful genetic distinction here aside from culture.
"Why would the billions of close links for Dinos would be even extinct if organics DID NOT STOP EVOLVING ?"
Trying to decipher your question... if a beneficial mutation resulted in a better organism which competed with the previous one, it would eventually cause the previous version to die out.
And from there your post dissolves into confusing jumbles of words.
While I generally agree with you in your opposition to Coasal's Creationist ideas, he is correct about dogs and wolves. They are members of the same species and freely interbreed. People who are wrong about many important issues do not have to be wrong about everything.
You can not see gradations because animal and human species did not evolved, but created. The Holy Spirit created human bodies in many different races spread all over planet earth, where some races became extinct, I believe. Anyways, Inuits and Papua Guinea Natives belongs to same species.
The billions of close links I am referring to, that should NOT be ALL dead, where at least we can see some ALIVE and WELL, since organics did not stop evolving, are between different species such as from bacteria to fish, from fish to iguana, from iguana to lizards to rats to Dinos or to monkeys or hairy apes then to chinese. I am talking about billions of CLOSE LINKS from billions of stages of evolution, as close as a difference of a day, or a week, or a year of evolution, etc etc, in the same manner you can see CLOSE difference of developing zygote or sequoia seed to maturity which can readily be observed because all their links of stages of growth are ALL ALIVE.
"The billions of close links I am referring to, that should NOT be ALL dead, where at least we can see some ALIVE and WELL" See: lungfish, lamprey eel, C. elegans... Every species that is alive is a representative of an ancestral species. These are the close links. It would be against the laws of the universe, however, if species existed that stayed completely, 100% unchanged over hundreds of millions of years. What you are asking for could not exist.
http://www.amnh.org/exhibitions/past/darwin
All of these will provide Huffington Post readers of Shapiro's blogs much better information on evolution in the 21st Century than what they have been reading from his blogs, other articles and papers, and especially, his book.
"I highly recommend Richard Dawkins' "The Greatest Show on Earth" and Carl Zimmer's "The Tangled Bank" as the two best introductions to modern evolutionary biiology for the general public; Zimmer's especially so since it really is a "textbook" and may cover more on evolutionary biology than does Dawkins' book. I also highly recommend............................."
I read many of those books, and they left me with many more questions than answers. Dr Shapiro's theory addresses and answers those questions that those other books just completely avoided or speculated, or glossed over....
.
Your analogy is not even close. Plant's growth is natural as human zygote's growth where you can readily observe growth of seed to maturity. You can observe all stages of growth from seed to maturity now because all links are alive and readily available to see. You can see a week old germinating seed of sequoia, a year old, a 100 yrs old, etc, or you can see a zygote developing into fetus, baby, or a senior, etc, now as the links are alive in many stages of growth. On the other hand, billions of close links of all species, not just humans, from unconscious organic compounds to fish to chinese, are all MISSING, that you have to dig the dead to prove your evolution.
Ask yourself, if living things or organics are evolving, why are all billions of close links from billions of stages of evolution, are all DEAD ? If organic DID NOT STOP evolving, we should see close links alive now the same way we can see babies,todlers,teens, same way we can see all stages of sequoia growth. There's NONE so far. "Evolution of Man" defies Physics because your physical causes&effects are all missing. Go Figure.
The idea that we should be able to see every single evolutionary stage either living or preserved in the fossil record is just a foolish Creationist talking point.
Consider this. Creationists assert that every single human being on this planet descended from a pair of human beings. We see great variety amongst the human races. Why do we not see every possible gradation from, for example, Inuit to Papua New Guinea natives alive to today? Even Creationists will accept that all breeds of domestic dogs originated from wolves. Why then do we not see every gradation from wolf to Chihuahua, from wolf to poodle, from wolf to dachshund and from wolf to EVERY breed of dog in the world today?
"if living things or organics are evolving, why are all billions of close links from billions of stages of evolution, are all DEAD"
There are finite resources in the world. Not everything that ever existed can continue to exist, especially if something better comes along that can out-compete it for the same resources. And of course, you are ignoring the plenty of examples of life which is representative of these stages.
When you write things like "set up a video camera and document a single population of seeds growing into a big sequoia," I begin to doubt the quality of your thinking. Great oaks do from little acorns grow, and each sequoia would have come from a single seed.