A fost modelul darwinian testat empiric: Întrebări și Răspunsuri

88 Responses to A fost modelul darwinian testat empiric: Întrebări și Răspunsuri

  1. andreigbs says:

    @EC

    Make sure you understand and realize the vast difference between results obtained in a strictly controlled laboratory environment where selective pressure is applied (the antibiotic drug here) vs. the natural wild where mutations are mostly harmful and there are many pressures at the same time.

    Specifically, the mutations mentioned in that paper occur at the molecular level of the drug’s target protein. There is no mutation taking place at the level of the organism’s own DNA, and so nothing gets transferred to another bacterium. Only the target protein that the antibiotic would normally act on (DNA topoisomerase, commonly known as gyrase which unwinds the DNA double-helix for transcription to occur) experiences a mutation (a substitution) at one of the amino acids that encodes for gyrase. This specific mutation affects only the bacterium in which occurs and is not transmitted to others, since it’s not part of the main DNA.

    By the way, this negatively affects the process of transcription and would normally result in this organism’s demise in the wild. However, in the lab and in the presence of antibiotics that killed all other normal variants, this mutant manages to survive. Overall though, this mutant is not „better adapted” to live a normal life. If placed in the wild, it will be eliminated.

    To me, taking all of this into consideration, it does not support random mutations driving evolution upward in the wild. And since this specific mutation occurs due to exposure to a synthetic compound (fluoroquinolone is not naturally occurring), I would be hesitant to even call it a mutation at all, and it certainly doesn’t appear random.

    We have considered „random” many things in the past until we discovered the mechanisms involved. Much like with junk DNA, which we are learning has specific roles and actions in regulating genetic expression.

    „Vrei sa ignor concluziile oamenilor de stiinta bazate pe ani de cercetare la toate academiile nationale de stiinte si laboratoarele din tarile dezvoltate, pe baza unei relatari anecdotice?”

    Sounds like an appeal to authority and consensus, coupled with a lack of personal experience in the lab. I’m only speaking from my own limited experience hands-on and what I’ve studied along the way. You are free to believe what you will.

  2. “Vrei sa ignor concluziile oamenilor de stiinta bazate pe ani de cercetare la toate academiile nationale de stiinte si laboratoarele din tarile dezvoltate, pe baza unei relatari anecdotice?”Sounds like an appeal to authority and consensus, coupled with a lack of personal experience in the lab. I’m only speaking from my own limited experience hands-on and what I’ve studied along the way. You are free to believe what you will.

    Nu. Suna ca o incredere in consensul expertilor si oamenilor de stiinta, vis-a-vis de argumentul din autoritate al amatorului care se crede savant rogue: „my own limited experience hands-on and what I’ve studied along the way”. Jobul tau nu are nimic in comun cu cercetarea ci numai cu o munca de tehnician in hospital coding iar educatia ta in biologie este bazata in mod evident pe scoala creationista.

  3. andreigbs says:

    @EC

    „Savant rogue”

    Not in the least, but by performing these kinds of experiments first-hand and knowing how they are interpreted and published enables me to critically evaluate and question the specific claims made, particularly those things you quoted and misunderstood because they are things you are not equipped nor were educated to do. That’s OK, we can still talk discuss them.

    The big picture takeaway that I would hope you understand by now (and you almost had it earlier!) is that the mutations in question are in direct response to the presence of the antibiotic. As you previously admitted, the bacteria reacts to the stress. The precise mutation in the gyrase protein is a specific response to the antibiotic. It is not a random event disconnected from the selective pressure, is it precisely as a result of that pressure. Hence, no darwinian evolution is occurring.

    The bacteria is placed in the presence of antibiotics (synthetic or otherwise) and must adapt or die on the spot. Those directed mutations enable it to survive the new environment condition, they did not take place before that pressure existed.

    Further, the induced mutations are only in specific target areas of the cell’s protein machinery, not in the overall organism’s DNA. The organism decides it would rather survive scarred for life than die. To do this, it changes the shape of the gyrase protein so that the drugs don’t recognize it and attack it, and it increases the rate at which it pumps out foreign contents through membrane porins.

    With either induced mutation, it does not become a „more fit” bacterium, it merely evades death at the expense of replication efficiency and increased energy usage of those membrane pumps. In the wild, this mutant would not survive. But in the presence of the antibiotic, when all others have died, it survives.

    Again, no random mutation or natural selection taking place. It is a stress response and targeted adaptation mechanism.

    „Jobul tau nu are nimic in comun cu cercetarea ci numai cu o munca de tehnician in hospital coding.”

    We do plenty of medical science research in creating or revising those medical codes, which is why it takes 1-2 years to develop them. It requires review of evidence-based medicine and published research. This is what I do on a daily basis, then I write the articles which educate coders on how to use the codes. If you’re interested in what I do, you are welcome to visit me here anytime. We have a lovely view of the lake and a great cafeteria I’d like to show you. But please don’t assume you know when you clearly do not.

    „educatia ta in biologie este bazata in mod evident pe scoala creationista.”

    Georgia Gwinnett College is an accredited 4-year public state college, none of my professors were creationists, and I graduated near the top of my class. As I remember, the only one who has attended a creationist school is you, taking those seminars on Origins at Andrews (please correct me if I’m wrong.)

  4. Foarte bun exemplul cu talasemia minora. Fara indoiala ca exista microevolutie si ca ea este generata de mutatii aleatorii. Dar sa nu uitam ca totusi talasemia este o tara genetica. Nu stiu daca putem extrapola la macroevolutie acest mecanism de selectie naturala prin mecanisme care personal recunosc ca sunt aleatorii.

  5. Pe de alta parte, argumentul d-lui Edi cu pojarul si varicela care au decimat milioane de amerindieni ca nu aveau imunitate mi se pare ca nu e prea riguros, sau poate ca nu inteleg eu bine. Fiindca nimeni nu are imunitate la aceste boli. Nici noi europenii nu avem. Si la noi se moare de pojar la greu si cateva zeci de copii tocmai au murit in ultimul an de pojar. Nu mi se pare un argument valid ca aztecii au murit de pojar sau de varicela.

  6. Unii spun ca separatia intre microevolutie si macroevolutie e neintemeiata si arbitrara. Dupa parerea mea, ceea ce ar putea separa cele doua concepte ar fi complexitatea ireductibila. Inca nu stim sigur daca exista sau nu complexitate ireductibila. Pe mine insa, tipul de constiinta umana, limajul articulat, gandirea abstracta, constiinta mortii etc, toate acestea ma duc cu gandul la un salt, la o cezura intre om si restul animalelor. Vorbim prea adesea in cifre si afirmam ca intre genomul cimpanzeului si al omului e o diferenta de doar 2 procente. Nu prea inteleg cum anume se fac aceste calcule, ma indoiesc de valabilitatea lor atata timp cat nici macar nu stim ce face fiecare gena sau fiecare portiune de genom in parte. Nu stiu cum s-au facut aceste calcule dar ele imi par pure abstractiuni. Diferenta intre om si cimpanzeu e atat de mare incat a vorbi aici de procente mi se pare o eroare. Sa luam chiar si banalul fapt de rade. Numai oamenii rad, animalele nu rad. Si nici nu plang. Astea sunt diferente banale, nu mai vorbesc de cele enumerate mai sus gen constiinta, gandirea abstracta, limbajul articulat. Nu stim inca daca toate astea se pot explica prin selectia naturala. E posibil sa se poata explica, dar nu stim.

  7. Ca sa parafrazez titlul unei carti a filozofului ateu Daniel Dennett, nu stiu daca de la bacterie la Bach este o linie continua. Si ca tot am spus de Bach, merita ascultat asta.

  8. andreigbs says:

    @AndreiVoiculesc

    „Dar sa nu uitam ca totusi talasemia este o tara genetica.”

    Yes, a result of a negative genetic mutation which can result in anemia, enlarged spleen, weak bones, slows children’s growth, and can cause death.

    All very bad things, and adding a malarial infection doesn’t make it better. In fact, to this day scientists are hesitant to say what the actual mechanism in thalassemia minor is that confers some protection against malaria. Note that people with this genetic disorder are not immune, they just experience fewer to no symptoms (specifically in minor thal.)

    Despite this perceived „advantage,” the global malaria situation today is serious and actually becoming worse according to the WHO (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2620631/).

    However, plenty of research indicates that naturally acquired immunity (NAI) against malaria (and other diseases, since you mentioned the Aztecs) protects millions of people. This type of natural immunity is being studied at the moment in the hopes of creating an effective vaccine against infections.

    Contrary to what EC believes, there is a certain amount of immunity protection that is inherited passively, from both or either parents, and especially from mother to child. That immunity can also result simply from previous exposure to malaria (or other diseases) and building up natural antibodies against it, then giving that passive immunity to offspring. This is being studied.

    Simply put, we do not yet know nearly enough to say with any degree of certainty what exactly is going on. The best we can do is observe, experiment, and try to come up with explanations that are testable and make sense. If we knew it all, we’d have no disease of any kind and doctors would be out of work.

  9. andreigbs says:

    @AndreiVoiculesc

    Scuze ca nu prea vorbesc romaneste destul de bine ca sa ma exprim asa cum as dori, de aceea scriu aproape totul in engleza.

    Hai sa ne uitam putin aici:

    „Vorbim prea adesea in cifre si afirmam ca intre genomul cimpanzeului si al omului e o diferenta de doar 2 procente.”

    Mai intai, sunt deacord cu tine ca asta e o diferenta pur abstractiva. Diferenta reala e de la cer la pamant.

    Problema este, insa, ca aceasta cifra, chiar abstracta fiind, este eronata chiar din anul 2005, cand cercetatori de la NIH au constatat ca diferenta genetica intre genele (nu intregul genom) care codeaza proteine la cimp si la om este de cel putin de 6% (https://www.genome.gov/15515096/2005-release-new-genome-comparison-finds-chimps-humans-very-similar-at-dna-level/).

    Daca comparam intregul genom, inclusiv toate secventele ADN care (aparent) nu codeaze proteine, diferenta este mult mai mare. In plus, peste 50 de gene extrem de importante la om nici nu apar la cimp.

    Asa deci, de vreo 13 ani incoace s-au mai facut alte comparatii genetice demonstrand din ce in ce mai multe diferente intre cele doua genomuri.

    .

  10. Asta cu 2% diferenta intre om si cimpanzeu e clar ca nu avem cum sa calculam la momentul asta, fiindca nu stim exact ce rol au toate fragmentele din ADN-un nostru sau al cimpanzeului. Asa ca o simpla insiruire de baze azotate e posibil sa fie 98% comun, dar e o pacaleala fiindca asta nu spune nimic. E vorba de cum interactioneaza unele cu altele, nu simpla insiruire.

  11. andreigbs says:

    @AV

    „E vorba de cum interactioneaza unele cu altele, nu simpla insiruire.”

    Tocmai! Mai sunt si alte motive, si asta pentru ca viata este mult mai complexa decat matematica, statistica, sau jocuri cu gene pe computer.

    Este imposibil sa deslusim cum si de ce ne deferintiem noi, oamenii, de cimpi doar facand o analiza moleculara de genetica la computer.

  12. AV,

    Vezi aici un articol in Science:

    Using a technique known as whole exome sequencing, researchers—including Tsimshian scientists Barbara Petzelt and Joycelynn Mitchell—sifted through the DNA for genes related to immune response. They then sequenced DNA samples from 25 Tsimshian living near Prince Rupert today. Comparing the two sets of genes, the team discovered several immune-related gene variants that were rare among the living. For example, a variant of a gene known as a HLA-DQA1, which codes for proteins that sort healthy cells from invading viruses and bacteria, was found in nearly 100% of ancient individuals, but in only 36% of modern ones.

    That finding suggests that the immune-related genes of the ancient Tsimshian were well-adapted to local diseases but not to novel infections like smallpox and measles, the team reports today in Nature Communications. Because European-borne epidemics altered the disease landscape, survivors were less likely to carry variants like HLA-DQA1, which were less able to cope with the new diseases (precisely how is still a mystery). “Those ancient genetic variants that were once adaptive were no longer adaptive after European contact,” Malhi says.

    Measuring differences between the ancient and modern DNA, Malhi and colleagues calculated a rough date for the genetic shift, about 175 years ago. At that time, smallpox epidemics raged throughout the Americas, including in Prince Rupert Harbor. Those with the most susceptible immune system genes were killed. Based on the new findings and historical accounts, the team says that close to 80% of the community died in the decades following initial European contact.

  13. Asa ca o simpla insiruire de baze azotate e posibil sa fie 98% comun, dar e o pacaleala fiindca asta nu spune nimic. E vorba de cum interactioneaza unele cu altele, nu simpla insiruire

    Nu vad unde este pacaleala. Nimeni nu sustine ca deosebirea intre om si cimpanzeu se reduce la 2% substitutii dedectabile in prezent. Insa comparand omul cu celelalte primate observam cea mai mare apropiere moleculara de cimp. Este normal ca studiile ulterioare sa avanseze de aici mai departe. Apoi exista raportul foslilelor care sugereaza rerlatia habilis, ergaster, erectus, sapiens, desi pot exista verigi lipsa, si descendenta genului homo din hominide, care au stramos comun cu cimpanzeul. Un procent de 2% difernta moleculara dupa 10 milioane ani este ce putem astepta intr-o estimare conservatoare. Care este rolul fiecarei gene si al relatiilor intre ele sau al programului de exprimare, e ceva ce vom cauta sa intelegem in urmatoarele 300 de ani. Nu e motiv sa ne oprim si sa ne intoarcem la dualismmul corp/suflet.

  14. Andrei,

    Problema este, insa, ca aceasta cifra, chiar abstracta fiind, este eronata chiar din anul 2005, cand cercetatori de la NIH au constatat ca diferenta genetica intre genele (nu intregul genom) care codeaza proteine la cimp si la om este de cel putin de 6% (https://www.genome.gov/15515096/2005-release-new-genome-comparison-finds-chimps-humans-very-similar-at-dna-level/).

    Asta pentru ca genele care codeaza sunt supuse selectiei naturale. Este prezis de teoria evolutiei ca diferenta este mai mare in genele care codeaza, dar asta nu afecteaza procentul in totalitate.

    Daca comparam intregul genom, inclusiv toate secventele ADN care (aparent) nu codeaze proteine, diferenta este mult mai mare. In plus, peste 50 de gene extrem de importante la om nici nu apar la cimp.

    Te contrazici. Spui mai intai ca diferenta este mai mare in genele care codeaza si apoi ca este mai mare daca luam in evidenta pe cele care nu codeaza. Dimpotriva, diferenta este mai mica in genele care nu codeaza, pentru ca acestea indica ceasul molecular. Am spus-o, si o repet: genele supuse selectiei pozitive au o rata de substitutie mai mare decat ritmul mutatiilor in general.

    Cele 50 de gene noi intra bine in procentul de 2%. Aici intervin traspozonii, transpozonii replicativi, si dublarile de gene + mutatii.

    Cuvantul „aparent” in: „toate secventele ADN care (aparent) nu codeaze proteine”, dovedeste o ignoranta surprinzatoare pentru cineva educat in biologie. ADN-ul codeaza numai in grupe de cate trei litere numite codoni. ADN-ul care nu codeaza il recunoastem dupa faptul ca nu este in grupe de cate trei cu „semne de punctuatie” la inceputul si sfarsitul secventei, formate tot din codoni. Poate ca o parte din el are functie de reglare a genelor codatoare, dar in nici un caz nu codeaza.

  15. Andrei,

    Este ironic ca ma patronizezei cu 4 ani la Gwinnett College in timp ce imi reprosezi „argumentul din autoritate” pentru ca iau in serios expertiza celor care au adus o contributie in domeniu.

    Mai intai, argumentul din autoritate implica ignorarea expertilor in domeniu in favoarea opiniei celor care vin dintr-u alt domeniu de cunoastere. In nici un caz a lua in considerare consensul celor care fac biologia, nu doar o invata sau o predau, nu este argument din autoritate.

    Insa daca tu ignori ce ai invatat la College, si ce sustin oamenii de stiinta care au avut o contributie la dezvoltarea biologiei evolutionare in ultimul secol, de ce ne ceri noua sa luam in considerare scoala pe care ai facut-o, mai ales ca tu insuti sustii ca ai rezerve fata de ce ai invatat. Bunul simt si ratiunea imi spun ca este mai probabil sa nu fi inteles ce ai invatat, chiar daca ai trecut exmenele cu nota optima. Am trecut si eu prin Georgia State, si pot sa spun ca nu ma surprinde.

    OTOH, nu am auzit ca AMA sa fi facut studii care contrazic evolutia. Din cate stiu, toate studiile in bacteriologie sunt bazate pe paradigma selectiei naturale, ca dealtfel intreaga stiinta medicala.

    In ce priveste Andrews, am invatat exact ce sustii tu, si le-am aratat ca nu tine apa, de aceea lucrez acum ca voluntar.

  16. Titluri publicate de AMA – cautare „natural selection”

    Natural Selection and the Origin and Evolution of Weeping in Man
    Natural Selection and the Form of the Human Female Breast
    The Buttocks and Natural Selection
    Natural Selection and Man’s Relative Hairlessness

    Din nefericire:

    Is it possible to bridge the divide between intelligent design and evolutionary theory? “I believe that individuals who have a deep faith can also respect the value of science, including what is known and unknown,” says Philip Pizzo, MD, dean of the Stanford School of Medicine. “However, when faith denies scientific data, a serious risk emerges which, in my opinion, extends beyond evolution or creationism, since it moves closer to theocracy and moral judgments that can challenge tolerance, open-mindedness and free thinking — and freedom itself.”

    Unlike Pizzo, many doctors and medical researchers have remained silent on the evolution controversy. The American Medical Association, for example, has taken no position on the intelligent design movement, even though virtually every other science organization in the United States has issued a statement of concern. And last October, when the New England Journal of Medicine published an anti-I.D. perspective, the feedback was overwhelmingly negative.

    “We got more letters about that piece than about any other article we published in recent years,” says journal deputy editor Robert S. Schwartz, MD, author of the controversial editorial. “Almost all of the letters were signed by people with ‘MD’ after their names. About two-thirds opposed me, many of them personally, calling me the anti-Christ and so forth.”

    Aici e cazul sa vorbim intr-adevar despre argumentul din autoritate. Dealtfel, cand argumentul este „anti-Christ”, imi aduc aminte de cativa medici pe care ii cunosc (din biserica) si care sustin ca sucul de morcovi si baia de sezut vindeca cancerul. Ma intereseaza ce spune stiinta medicala, nu idiosincrasii individuale.

  17. JAMA Aug 2012

    Diversity Matters
    The Importance of Comparative Studies and the Potential for Synergy Between Neuroscience and Evolutionary Biology
    Bruce A. Carlson, PhD

    Many neuroscientists study primates because of their relatively close evolutionary relationship to humans (ie, anthropocentric model systems approach)… The implicit assumption of the anthropocentric approach is that degree of evolutionary relatedness reflects degree of similarity; thus, in studying the brain of as close a relative to humans as possible, one is studying a brain that is as similar to humans as possible… This approach seeks to identify how natural selection acts as a driving force shaping the evolution of brain structures, perception, cognition, and behavior to adapt organisms to their environments.

  18. Pe scurt, gasesc 0 suport pentru ID/YEC in JAMA si destule studii bazate pe TE.

  19. andreigbs says:

    My dear Edi, I’ve warned you about this before: you tend to rush and misread, or misquote, or misunderstand, or all of the above, and your entire argument then goes astray. We end up arguing past each other, which is fruitless. I think you may possibly be a little under the weather, which would explain your somewhat cloudy judgment. Or you can blame it on my lousy romanian 🙂

    First things first:

    „Asta pentru ca genele care codeaza sunt supuse selectiei naturale.”

    Nope, natural selection never operates at the gene level, only on what is expressed phenotypically by the organism. (If it operates at all!)

    Next, a misunderstanding:

    „Te contrazici. Spui mai intai ca diferenta este mai mare in genele care codeaza si apoi ca este mai mare daca luam in evidenta pe cele care nu codeaza.”

    There is no contradiction, only your misunderstanding based (hopefully) on my language gap. Just to make sure you understood first: the fact is that the difference between the coding regions in the genomes of man and chimp are 6% different, not 2%.

    OK? 6%, not 2% and only looking at coding regions (the codons that make amino acids). And that was in 2005! Let’s catch up to the times, shall we?

    If we include the non-coding regions of the genome as well, that difference increases markedly. Estimates are from 14-16% difference. So in fact, the overall genetic similarity between man and chimp is somewhere around 84-86%. Studies are ongoing and this figure will likely change.

    On to:

    „Cuvantul „aparent” in: „toate secventele ADN care (aparent) nu codeaze proteine”, dovedeste o ignoranta surprinzatoare pentru cineva educat in biologie.”

    Perhaps it was my language gap again, let me try to clear it up. A sequence of DNA (or RNA) does not imply only the 3-base codons. I was talking about the entire sequence, or strand if you prefer, of DNA which is lined up base to base to base to base to base without interruption when we look at a DRA/RNA strand.

    Your „correction” is once again unwarranted.

    Now for some common ground:

    „pentru ca iau in serios expertiza celor care au adus o contributie in domeniu.”

    Fantastic, and so do I! And I enjoy reading science publications, since I learn something new every time. But that does not mean that every paper ever published is correct or that you should never question the material presented. I’ve never asked you, or anyone, to ditch your belief in the experts and embrace my position or any other. In fact, I said you are free to believe what you will. I maintain that.

    And then this:

    „de ce ne ceri noua sa luam in considerare scoala pe care ai facut-o?”

    Actually I didn’t, rather it was in response to your condescension suggesting that I had attended a creationist institution for my degree. But what’s truly ironic, by the way, is that there is no other biology graduate commenting here except me, and I’m taking heat from a bunch of actual amateurs. Anyway, moving on…

    „Bunul simt si ratiunea imi spun ca este mai probabil sa nu fi inteles ce ai invatat.”

    Nay, I understand quite well and I apply scientific principles in critically evaluating between good science and bad science because there is plenty of both. Experience and evidence here tells me you believe all science is good science, which is naive at best.

    This brings us to the AMA reference and their current neutral stance on I.D., compared to many other science outlets that disparage I.D., creationism, and basically anything else that dares to question the Darwinian paradigm.

    This is where the real problem is: that establishment academia would rather suppress, vilify and attack all messengers that point out the lack of evidence in the labs and the lack of evidence in the real world to support the idea that naturalistic evolution is the ONLY possible explanation for the complexity of life, instead of encouraging debate and discovery. The only option allowed is to squeeze and cram everything through Darwin’s nose.

    I suspect this may be why you keep your „theistic” qualifier to a minimum: your associations with the atheist evolutionists here might then be at risk.

    I would suggest we discuss ideas or papers, if you want to discuss at all. Fair? Attempting to associate me with Bible-belt flat-earthers, anti-vaxxers or other fringe groups as a reason to dismiss or avoid my questioning of bad science when I point it out to you is not the right way forward.

    Again, my invitation for you to come visit remains open. If you don’t like our cafe here, we can walk over to Eataly for some fresh hot coffee. Lavazza coffee, to be exact. They also have cold Peroni if you prefer. 🙂

  20. polihronu says:

    “But what’s truly ironic, by the way, is that there is no other biology graduate commenting here except me, and I’m taking heat from a bunch of actual amateurs.”

    Sa nu uitam ca amatorii astia ti-au aratat deja, cu virf si indesat, ca ti se intimpla sa nu pricepi articole din specialitatea ta.

    “establishment academia would rather suppress, vilify and attack all messengers that point out the lack of evidence in the labs and the lack of evidence in the real world to support the idea that naturalistic evolution is the ONLY possible explanation for the complexity of life”

    Is there evidence for anything else than evolution? Cu fraze ca asta nu faci decit sa demonstrezi, din nou, ca esti doar un sfertodoct confiscat de dogma.

  21. andreigbs says:

    @EC

    I almost forgot:

    „ma patronizezei cu 4 ani la Gwinnett College”

    I should clarify that it took me 6 years to complete my biology degree, not 4. I was working full-time at Kaiser Permanente and it was difficult to find the classes I needed to take in the right order, available only in the evenings after work. Oftentimes I’d have to take an extra class in the sciences until the right biology one became available the next semester. Still, after spending 40 hrs/week at work and another 20 hrs in classes/labs, it made me appreciate Sabbath time all the more.

  22. Andrei,

    Asta pentru ca genele care codeaza sunt supuse selectiei naturale.”

    Nope, natural selection never operates at the gene level, only on what is expressed phenotypically by the organism. (If it operates at all!)

    Red herring.

    Next, a misunderstanding:

    “Te contrazici. Spui mai intai ca diferenta este mai mare in genele care codeaza si apoi ca este mai mare daca luam in evidenta pe cele care nu codeaza.”

    There is no contradiction, only your misunderstanding based (hopefully) on my language gap. Just to make sure you understood first: the fact is that the difference between the coding regions in the genomes of man and chimp are 6% different, not 2%.

    OK? 6%, not 2% and only looking at coding regions (the codons that make amino acids). And that was in 2005! Let’s catch up to the times, shall we?

    If we include the non-coding regions of the genome as well, that difference increases markedly. Estimates are from 14-16% difference. So in fact, the overall genetic similarity between man and chimp is somewhere around 84-86%. Studies are ongoing and this figure will likely change.

    Nope. The substitution rate is higher in coding DNA because of positive selection. So, aprox. 2% is the substitution rate for all the DNA, while 6% is the SR for coding DNA.

    On to:

    “Cuvantul „aparent” in: „toate secventele ADN care (aparent) nu codeaze proteine”, dovedeste o ignoranta surprinzatoare pentru cineva educat in biologie.”

    Perhaps it was my language gap again, let me try to clear it up. A sequence of DNA (or RNA) does not imply only the 3-base codons. I was talking about the entire sequence, or strand if you prefer, of DNA which is lined up base to base to base to base to base without interruption when we look at a DRA/RNA strand.

    As far as I understand English, in your sentence, apparently means allegedly. And me, the dilettante says that „base to base to base to base to base without interruption” is non-coding unless it is a sequence of codons starting with ATG and ending with TAA. So, beyond any communication gap, there’s a structural difference between coding and non-coding DNA. If you meant functional/non-functional, it would be a different story, but you didn’t say it.

    As regards your conspiracy theory, as you said, I took the ID/YEC/Origins classes 600 and I cant tell where is the conspiracy. It is a theocratic coup going on in the US and Eastern Europe and one does not have to be an atheist to be against.

    I will be happy to learn the taste of Lavazza or Peroni, when I am better. Right know, I am experiencing first hand the evolution of viruses.

  23. Congrats. Now, did you start college as an YEC? It is an important question.

    I first learned TE when I was 16, while doing amateurish marine biology in Constanta. My guru was the founder of oceanology in Romania, and I am still proud to have been his favorite disciple, in both diving and science. I converted to YEC by faith only. I discovered, while being a pastor with GCC, the monsters that lurk beneath YEC. I appreciate the Sabbath too.

  24. andreigbs says:

    @EC

    The fact that natural selection does not operate at the gene level is no „red herring,” but is another example of you ignoring the facts that may disturb your overall position.

    „The substitution rate is higher in coding DNA because of positive selection. So, aprox. 2% is the substitution rate for all the DNA, while 6% is the SR for coding DNA.”

    Positive selection is just a fancy term for Darwinian evolution, and refers to selection promoting the spread of beneficial alleles. We were talking strictly about the genetic differences we observed when lining up the genomes of chimp and man. There is no rate of substitution present when we are analyzing the two side by side, there is only the comparison of coding regions and non-coding regions.

    (And when we talk about coding/non-coding, we generally assume coding=proteins, or functional and non-coding=no proteins, non-functional. There are functional portions of the genome that do not code for proteins specifically. They are promoter regions or have other regulatory functions. But in general, the coding=proteins is understood and accepted.)

    The difference in coding regions is 6.4%. We determined this by ignoring the non-coding regions. But when we compare the DNA strands to include non-coding regions as well, the two strands begin to diverge early and often, with bases mismatching and the difference in the genomes growing to approx 14-16%. I don’t care about molecular clocks or claims of positive selection which are unfounded. The two genomes do not align.

    You can maintain the myth that the overall difference is 1-2% (wrong since at least 2007 http://science.sciencemag.org/content/316/5833/1836.ful), but it appears as yet another example of being unable to distinguish between good and bad science.

    „Now, did you start college as an YEC? It is an important question.”

    I started college back in 1998 at Georgia State. My first cellular biology course was one of about 150 students. It wasn’t just a culture shock coming from AAA, but also a huge chasm to overcome because the level of academic proficiency expected was not something AAA had prepared me for. By midterms I was considering dropping the class because it was so difficult, but after speaking with my professor and him telling me that he had noticed my potential and that I just needed to put it to use, I decided to do just that. I finished that class with an A and changed my major from music to biology. It only later occurred to me that he probably didn’t even know my name, he just encouraged me because of my grade thinking I might do better.

    I was just a church-going teenager at the time, and the theory of evolution turned my understanding of the natural world upside down initially. In a way, I was hoping that, by learning the mechanisms and how the theory explains or predicts things, I would become convinced by all of the evidence that my professors promised me would be demonstrated.

    So I learned everything I could, hoping that the irrefutable evidence would appear. In each class, it was said the real evidence is in the next courses, until I got to those courses and found out the evidence is far shakier than they had let me to believe.

    In those higher courses, they focused on very specific biological and biochemical mechanisms that operate on very precise conditions and feedback loops, and they respond in very specific, directed ways. Nothing is left to chance, or randomness, and many of my professors didn’t even mention evolution or random mutations over deep time as being the explanation for their appearance.

    It dawned on me somewhere along the way that the evidence for evolution they had promised me would be there instead became evidence that life and living systems are so complex, so ordered, so fragile and yet so resilient, so specific and interconnected, so full of limitless intelligent information that there is no way for it to have appeared one day, billions of years ago, just once, for no reason, and out of nothing.

    I only stayed at Georgia State for 3 semesters, then I stopped attending and decided it was time to spend my energy elsewhere. It wasn’t until 2009 that I finally scratched the itch to go back to school for my first love, biology. I had completed an A.S. degree from 2006-2008 but wanted to give biology another try.

    In 2009, I started the biology program at Georgia Gwinnett College. With every science class completed, I increasingly felt that the purpose of my teachers (most of them) was to instruct me by memorizing and repeating the mantras of random mutations and natural selection as the sole reason for life on earth. The problem was that the laboratory portion of science courses offered no evidence that anything was random or occurring by chance.

    We learned in class how bad mutations are and how almost anything can cause them, then we were supposed to repeat the mantra: random mutations and natural selection. If you think about, both „mechanisms” lead mostly to death. Mutations mostly kill, and so does natural selection.

    By the time I graduated in 2015, I had gotten to the point where I had considered all of the supposed evidence, I had read so many studies and evaluated them critically for shortcomings, and I saw that while the theory and the ideology said one thing, results and experiments said something else entirely.

    What’s worse is that questioning its veracity is not allowed but actually gets you into trouble. To me, that’s not true science. It is an ideology that doesn’t tolerate dissent and seeks to stifle dialogue or any debate of its accuracy because they know it cannot withstand close inspection or be demonstrated with empirical observations in the lab. If they could have proven it with laboratory evidence, there would be thousands of published experiments where we could see how a bacterium becomes a better one, or gains a new function, or turns into an eukaryote.

    How fantastically cool would that be? Being able to see it under a microscope, going from a unicellular structure with no defined nucleus to becoming a multicellular organism, organizing its DNA tightly around histones, compressing it into chromosomes and enveloping it into a nucleus.

    Don’t you think if we could have observed it happening in the last 200-300 years that we’ve had decent microscopes, it would have been already published and touted everywhere as real evidence of evolution? But it doesn’t exist, and never will, in spite of the lofty claims made. You just have to take it by faith.

  25. polihronu says:

    Oh, the stupidity!

  26. It wasn’t just a culture shock coming from AAA, but also a huge chasm to overcome because the level of academic proficiency expected was not something AAA had prepared me for.

    See, this is your SDA problem and, even more, American problem. HS education in the US is a joke, especially in GA. And, btw, I was a student at GA state and was culture-shocked by the low level in science and math. Actually, it was like repeating the 11th-12th grade. I struggled with cognitive dissonance when I became SDA, not when I went to university or college.

    To make it short, you need to ger out of the echo-chamber.

    As for the „gene level” thing, natural selection operates at the level of gene, phenotype, population. However, ultimately, it is the DNA that matters when we talk about molecular differences between man and chimp.

    Another problem with your argument is that if, we estimate a greater difference based not on observable measurement but on Bayesian probability as a function of the molecular clock in geological time, (which I agree with), you must accept phylogenetics, which you don’t. So, please argue from a YEC position only.

  27. andreigbs says:

    @EC

    „See, this is your SDA problem and, even more, American problem. HS education in the US is a joke, especially in GA.”

    One thing my Dad is always reminding me of: generalizations are almost always bad.

    Of the 50 U.S. states, Georgia ranks 18th best in high school education, while just for comparison, Illinois is a distant 31st. (https://www.usnews.com/education/best-high-schools/articles/how-states-compare)

    And even though education in the U.S. (as compared to Europe, China or Japan) isn’t quite as rigorous, America still tops the list of „best countries in science,” by a wide margin, so there goes that argument (https://www.scientificamerican.com/article/global-science-best-countries-science-scorecard/?WT.mc_id=SA_printmag_2012-10).

    I’m not embarrassed to admit I may have struggled initially, but the wake-up call didn’t go unanswered. I didn’t get 2 college degrees just by showing up 😉

    Once more, just for being stubborn: natural selection can only occur (if at all) at the population level. Never at the individual level, since it takes two to tange, and definitely not at the gene level.

    We weren’t talking about molecular differences between man and chimp; we were talking specifically about genetic differences, DNA differences, and those are currently at 6%.

    You can stick to your molecular clock and geologic time, nobody is taking those away from you. It doesn’t mean they’re true, however.

    Since I’m a free agent and haven’t officially joined any camp or movement (I’m not a SDA member currently), I can argue however I wish using the available information. The problem is not my mode of attack of this fallacy dubbed „Evolution,” rather the feeble attempts to prove my reasoning or facts wrong. I know the pressure points. The theory, apart from being able to explain the appearance of life, is vacuous in even attempting explaining how life diversifies.

    It only stands because it is constantly sheltered, propped up by ideologues.

  28. America still tops the list of “best countries in science,” by a wide margin, so there goes that argument

    What is the wide margin when you leave out Europe and Japan?

    But this is not the issue. Adrian and you actually do reject the empirical testing of measurable predictions in favor of a sort of 17th century vulgar empiricism.

    O sa continui in romana ca sa inteleaga toata lumea. Ai spus ca teoria gravitatiei poate fi testata la nivelul experientei comune.

    Teoria lui Newton: G=MXM/R^2. Singurul mod de a testa aceasta teorie este facand predictii matematice asupra miscarii planetelor in sistemul solar. Mai mult, ai nevoie de calculus pentru a face si verifica asceste predictii. La nivelul experientei comune, ni se pare normal ca corpuri de greutate diferita sa cada cu viteze diferite, ceea ce este fals, desi e „confirmat” in experienta comuna.

    TE este bazata pe teste empirice care constau in predictii masurabile confirmate prin observatii si experiment. Restul e astronomie ptolemeica.

  29. I didn’t say „individual” I said „phenotype” – pheno-type as opposed to geno-type.

  30. andreigbs says:

    @EC

    The margin remains wide enough and we enjoy the fruits of others’ labor.

    „Ai spus ca teoria gravitatiei poate fi testata la nivelul experientei comune.”

    I did? When? I don’t remember talking about gravity with you, but nice attempt at deflecting 😉

    BTW, you forgot the one very important requirement as to WHEN or WHY objects of different masses move at the same speed.

    Hai sa continui si eu in romana ca sa inteleaga toata lumea 😉

    Testele empirice inca nu au demonstrat nici macar o singura instanta in care o celula de viata, sau o populatie de celule daca vrei, sa fi evoluat in celule de viata mai complexa sau mai buna decat cum a fost ea la inceput.

    Iar de aici pana a fi asa de increzator ca viata cum o vedem acum s-a dezvoltat in timp de miliarde de an, prin mutatii aleatorii dintr-o bacterie pana la om, e cale foarte lunga lipsita de orice fel de validare empirica.

    Asa ca eu a-s lasa-o mai moale cu predictii masurabile si alte studii, care de fapt marea majoritate nici nu sunt repetabile de catre altii, ca sa nu mai spun ca nu-s aplicabile in natura larga unde sunt o mie si una de variabile necontrolabile.

    Ce propune TE deocamdata ramane fara demonstrari empirice; este doar teorie, filozofie, si ideologie impusa cu forta.

  31. andreigbs says:

    @EC

    One last thing:

    I found it amusing that you deem „17th century empiricism” as vulgar, yet in the same breath have no problem accepting Newton’s discoveries of calculus and gravity, both in the 17th century.

    Perhaps the real reason you look down on this empiricism is because when it is actually put into practice, we discovered that notions such as the once-popular „spontaneous generation” was actually a farce. That was, oh let’s see, Redi in 1668?

    And since then, btw, scientists have consistently and spectacularly failed at any and all forms of abiogenesis.

    Might this be why you shun actual empiricism? Because when used and interpreted properly it actually disproves evolution’s claims? If so, it’s really OK; you’re neither the first nor the last to do so, and it doesn’t mean we can’t be friends 🙂

    I hope you get better soon, so we can go get that coffee.

  32. MATEI IOAN-OCTAVIAN says:

    Gbs
    Once more, just for being stubborn: natural selection can only occur (if at all) at the population level. Never at the individual level, since it takes two to tange, and definitely not at the gene level.

    What is the definition of natural selection and why can’t occur at the gene level?

  33. andreigbs says:

    @Matei

    Hi there! This might be a long discussion 🙂

    Most Darwinians claim it is the process by which organisms that are better adapted to their environment tend to survive and produce more offspring. But this is disputed even today, contrary to EC’s confidence that „all is well.” (See http://www.pnas.org/content/early/2018/03/22/1722232115.short for more)

    Darwin himself mused: „It may be said that natural selection is daily and hourly scrutinizing, throughout the world, every variation, even the slightest; rejecting that which is bad preserving and adding up all that is good; silently and insensibly working, whenever and wherever opportunity offers, at the improvement of each organic being in relation to its organic and inorganic conditions of life.”

    To me, it sounds like he personified NS as some intelligent, sentient being that knows when a change is going to be good or bad (as compared to what?) for an organism and rejects all bad changes. That’s ludicrous.

    The short version is that natural selection (NS) cannot see anything at the genetic level to select or distinguish as advantageous, since it doesn’t know beforehand what will be advantageous later. It is not psychic or all-knowing 😉

    We need to realize that this supposed mechanism is in fact blind, it has no planned direction, will, purpose, or goal. We ascribe far too much power to it, and only by looking at things in hindsight from the outside as spectators to Nature.

    It would be different if NS could predict genetic changes reliably, something like „Gene XYZ2 will mutate at the 122nd base, and this new adaptive function will result and overtake the competition.”

    But no evolutionist would be caught dead making such a prediction. They only explain the event (any event!) AFTER it’s happened, being sure to credit NS for making it possible.

    NS is said to be acting on populations that have experienced and fixed (or have a high allele frequency of) beneficial mutation(s), such that it provides an advantage resulting in more offspring (as if fitness always = more offspring!), or by being able to survive calamities that may decimate others who don’t have that advantageous mutation.

    Let’s think about it though.

    Darwinians claim that random beneficial mutations happen all the time, even right now, giving some organisms an advantage to be used at a later time. They cannot say that mutations, or any genetic change, are in response to environmental pressures as this would be directed adaptation and completely the opposite of Evolution. Yet, we actually see this in the lab on a regular basis.

    What we don’t see is the supposedly „happening every day” random beneficial mutations in action in the lab, and we’ve been looking for over 100 years.

    But they continue to claim that random mutations are potentially beneficial despite the proven fact that most mutations are actually harmful. Only very minor mutations don’t kill the organism outright, and very small negative mutations add up over time in subsequent generations which result in population decline. In most cases, mutations cause disease, malformations or other disadvantages and these organisms usually don’t survive to reproduce or can’t find a willing partner to reproduce with.

    Random mutations have never produced a new organ, such as wing or an eye or a spleen.

    All mutations first take place at the genetic level. One DNA base may be substituted for another, or it may be deleted or moved elsewhere, or an extra base or two are inserted. These mutations are caused by different kinds of factors, including UV damage, toxic agents, mistakes during the transcription process, and they affect the protein makeup of the organism which dictate its function and appearance.

    As long as the very minor genetic mutation(s) don’t change the appearance, ability, or behavior of the organism, it stands an equal chance of reproduction because NS can’t see anything beneficial or different to select for. Only when a mutation causes an outward expression of a new or different trait (for example, an albino organism) could NS have a plausible opportunity to act.

    If you’ve watched any nature documentary, the method by which all animals reproduce and the way populations are maintained is strictly thru sexual selection which has nothing in common with natural selection. Sexual selectiont is directed, purposeful, very picky, not at all random, and mutants are usually ignored or kicked out of the group.

    So in practice, NS isn’t doing much if anything even at the population level.

  34. MATEI IOAN-OCTAVIAN says:

    gbs

    „To me, it sounds like he personified NS as some intelligent, sentient being that knows when a change is going to be good or bad (as compared to what?) for an organism and rejects all bad changes. That..”

    that’s is the reason that Darwin use Spencer’s ” survival of the fittes” in later editions. (there is a letter in wich Wallace suggest this

    now… in the „gene eye view” of evolution the unit of selection must have heredity, variability and multiplication(for Dawkins is not only the DNA gene, but the meme also). NS is the diferential survivor of those entitys in a finite world.

    Evolution is the change in the gene frequency in the gene pool… that’s why we say the gene is the unit of selection

    if you say that the population is the unit of selection( group seltection) mean that NS is the diferential survivor of populations, but as far as i know authors say that even if this kind of selection exists don’t have the power to shape populations because the variation among population is smaller then among individuals.

    „Random mutations have never produced a new organ, such as wing or an eye or a spleen.”

    and they never will… no one clam this. this sounds like that monkey typing argument

  35. polihronu says:

    „You just have to take it by faith.”

    Si daca ar fi adevarat (nu e), esti plin de ridicol – pentru ca tu esti cel care ne oferi ca alternativa doar ‘faptele credintei’. Critici evolutia pentru ca nu ar fi „stiinta adevarata”, dar o faci in numele non-stiintei care sint creationismele de orice fel. Rusine.

  36. andreigbs says:

    @Matei

    „that’s is the reason that Darwin use Spencer’s ” survival of the fittes” in later editions. (there is a letter in wich Wallace suggest this.”

    Problems exist with this slogan too. How do you define „fittest”? For evolution’s purposes, fittest means „has the most offspring.” But it’s not the only definition, since actual fitness is much more than how many offspring you can have. Wallace and Darwin didn’t see eye to eye on many things, natural selection especially. It’s been problematic since day one.

    Then again, this slogan looks like it could be changing soon, to „survival of the laziest.” (https://phys.org/news/2018-08-evolution-favor-survival-laziest.html)

    If NS is used to explain everything that ever happens in Nature, then it truly explains nothing.

    There is no „gene eye view” of evolution, because evolution has no stated purpose or goal or direction. And just so you’re aware, serious scientists distance themselves from zealous idealogues like Dawkins. The man is an embarrassment.

    „Evolution is the change in the gene frequency in the gene pool.”

    No, my friend. It sounds nice but is devoid of substance. Evolution is supposed to be the change in the inherited traits (expressed!) of a population from generation to generation. Traits are the expression of genes that are copied and passed on to offspring during reproduction.

    For evolution into higher or different species, you need NEW and meaningful information. That information then needs to be put into action: it needs to produce a new trait, and that new trait needs to be an advantage. Until then, NS has no way to see or select it. It must be expressed sufficiently that it actually confers an advantage to that population.

    If NS is always getting rid of the unfit, or the disadvantaged, then why is there so much redundant DNA found in organisms? If that genetic information offers no advantage and actually costs the organism energy to have to copy it every time it reproduces (a clear disadvantage), then we would expect NS to have removed those useless genes from the gene pool. After all, it has had plenty of time over the supposed hundreds of millions of years.

  37. MATEI IOAN-OCTAVIAN says:

    Then again, this slogan looks like it could be changing soon, to „survival of the laziest.”

  38. MATEI IOAN-OCTAVIAN says:

    „Then again, this slogan looks like it could be changing soon, to „survival of the laziest.”

    they are just playing with words…

    „There is no „gene eye view” of evolution, because evolution has no stated purpose or goal or direction. ”

    non sequitur… I don’t see the conection ..

    „No, my friend. It sounds nice but is devoid of substance. Evolution is supposed to be the change in the inherited traits (expressed!) of a population from generation to generation. Traits are the expression of genes that are copied and passed on to offspring during reproduction”

    from the population genetics pov evolution is about gene frequency..

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