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Three Things Biologists Rarely Know About Biology

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I’ve talked to a number of biologists, and it seems like there are a number of important facts that are left out of a standard biological education.

The following things seem to be either skipped or glossed over in biology education. These are based on my interactions with biology majors, grad students, and even post docs. Nearly everyone either has either forgotten them (which means their professors just mentioned them in passing) or they were never covered in the first place.

    1. The pervasiveness of directed mutation. Most biologists do not realize that directed mutations even exist, much less the extent to which they exist. This is due both to a lack of knowledge about the mutational systems which are known, as well as to a lack of understanding of what it means for something to be directed. Most biologists are trained to think of mutations as being “undirected” if they aren’t 100% on-target. However, there are systems which reduce the mutational search space by well over 99%. Within the tiny space remaining, the search may be random, but it is directed because (a) it is triggered by a need of the organism, and (b) it skips a significant chunk of the genome which is not likely to carry the result.
    2. The significance in symbiosis in evolution. Most biologists are only trained to see mutations as being significant in evolution. That any change in form or interbreedability must be due to mutation. The one exception is at the beginning of Eukarya, they permit themselves to believe in endosymbiosis. However, as numerous areas of biology have shown, gaining or losing a symbiont can actually generate significant morphological change in a single generation.
    3. The importance of non-genetic inputs to the resulting morphology. Many differences in form, including heritable ones, can result from non-genetic inputs. The simplest of these is prions, where the shape of a protein affects the shape of later generated proteins. If a similar protein has a different conformation, it can alter the conformation of later proteins. This can cause phenotypic changes which are heritable, but are not in any way genetic.

In fact, the field of Ecological Developmental Biology has a number of examples of #2 and #3. Organisms can change morphologies merely due to the presence of pheromones in the environment. If those triggers persist after several generations, oftentimes the trait will the “stick” even without the environmental driver!

Anyway, I’ve found that evolution has essentially blinded numerous biologists and funneled them all into an understanding of evolution which is directly counter to how organisms are experimentally understood to change. Certainly there are many great biologists who understand these issues. However, I might go as far as to say that a majority of biologists are poorly informed on these points.

Comments
ET & AK Antibiotic resistance and sickle cell are trade-off mutations hence fail as examples of beneficial mutation. The other two fail as well as shown and you're left with no such thing as "beneficial mutation". Did you conveniently forget what the argument was?!? What's the point of continuing the discussion if you won't admit clear evidence? Typical Darwinist nonsense.Nonlin.org
April 23, 2018
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Allan Keith:
That is how evolution works.
Except there isn't any evidence that evolution works the way you need it to.ET
April 23, 2018
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Nonlin,
Apolipoprotein AI-Milano and LRP5 are at best insufficiently studied, but the fact they can only be found in small populations goes to show they are not universally beneficial and in fact are trade-offs like everything else.
They have to start somewhere. That is how evolution works.Allan Keith
April 23, 2018
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As seen, antibiotic resistance fails as does sickle cell
Fails at what?ET
April 23, 2018
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ET@35 Allan Keith@28 and 36 As seen, antibiotic resistance fails as does sickle cell. You must acknowledge! Apolipoprotein AI-Milano and LRP5 are at best insufficiently studied, but the fact they can only be found in small populations goes to show they are not universally beneficial and in fact are trade-offs like everything else. Apo-A1 promisses have fizzled: http://blogs.sciencemag.org/pipeline/archives/2016/11/16/the-long-saga-of-apo-a1-milano Wikipedia: "Mutations in LRP5 cause polycystic liver disease" You both must acknowledge you have nothing. And do your research before replying with more nonsense.Nonlin.org
April 23, 2018
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es58, I use google doc. and Libre Office.bornagain77
April 22, 2018
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Well Bob (and weave), having to convince a person, who holds a worldview that tells him that he might not actually exist as a real person, but may very well be be a neuronal illusion, that his worldview leads to cognitive dissonance is a bit like trying to convince someone who is under the belief he is Napoleon, that he is not the Napoleon, :) But your delusional thinking is particularly acute, because you are in double denial. You are in denial of the denial inherent in your atheistic materialism. As touched upon here
Right here on the pages of UD, Bob (and weave) O’Hara and Allan Keith have repeatedly strenuously objected to being called ‘neuronal illusions’, and claimed that, (despite the fact they were shown that many leading atheists themselves claim to be illusions), https://uncommondescent.com/intelligent-design/progressives-eating-their-own/#comment-656813
bornagain77
April 22, 2018
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HUH??? Cite Professor Andrew Sims former President of the Royal College of Psychiatrists about the detrimental effects of atheism on mental and physical health and Bob (and weave) responds with,,, “I guess that means that you aren’t a psychiatrist, and can’t cite any psychiatrists to beck up a diagnosis of mental illness.”,,, DUH!!!
I was specifically asking about this comment by you @4:
Otherwise known as Darwinian Cognitive Dissonance Disorder (DCDD). Yes folks, it is a mental disease.
Sims doesn't say he's describing a mental disease, still less a Cognitive Dissonance Disorder. He is also not talking about Darwinism.Bob O'H
April 22, 2018
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Ba77@21 what format do you store your notes in spreadsheets onenote that you can do easily find and retrieve them , database?es58
April 21, 2018
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Nonlin,
That’s ET’s quote. Ask him.
I know. I was responding to your subsequent request of him. I seldom agree with ET, but in this case he is correct.Allan Keith
April 21, 2018
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No, it isn't all linked. There are mutations tat benefit the organism. Period. Allan Keith brought up another beneficial mutation in 28. Look it upET
April 21, 2018
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ET@30 Moving the goalposts? It's all linked and you brought up "fittest" @26. Allan Keith @28 That's ET's quote. Ask him.Nonlin.org
April 21, 2018
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rna, You have to get into the weeds for the specifics with Dr. Behe on that one.,,, He had three classifications. Loss of Function, Modification of Function and Gain of Function. Myself, glancing over your list, and since antibiotic resistance is now shown to be ancient, I would safely assume all those examples to be classified as 'modification of (preexisting) function'.
(Ancient) Cave bacteria resistant to antibiotics – April 2012 Excerpt: Antibiotic-resistant bacteria cut off from the outside world for more than four million years have been found in a deep cave. The discovery is surprising because drug resistance is widely believed to be the result of too much treatment.,,, “Our study shows that antibiotic resistance is hard-wired into bacteria. It could be billions of years old, but we have only been trying to understand it for the last 70 years,” said Dr Gerry Wright, from McMaster University in Canada, who has analysed the microbes. http://www.scotsman.com/news/health/cave-bacteria-resistant-to-antibiotics-1-2229183# Antibiotic resistance genes are essentially everywhere – May 8, 2014 Excerpt: The largest metagenomic search for antibiotic resistance genes in the DNA sequences of microbial communities from around the globe has found that bacteria carrying those vexing genes turn up everywhere in nature that scientists look for them,, http://www.sciencedaily.com/releases/2014/05/140508121347.htm
The main point being, Darwinists originally thought they had stunning proof for evolution in action with antibiotic resistant bacteria. And indeed Darwinists taught it as supposedly undeniable proof for Darwinian evolution for decades to gullible students. But the fact of the matter is that 'antibiotic resistance is hard-wired into bacteria', and Darwinists were found to be falsely using an evidence that actually points to the elegant Design of bacteria as a pseudo-proof for their pseudoscientific theory. As Dr Wells pointed out in his book "ICONS of Evolution", and in his subsequent book "Zombie Science", this tendency of Darwinists to use false evidence for their theory is the norm rather than the exception.bornagain77
April 20, 2018
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bornagain #22 your list is a bit one-sided. ampicillin resistance: a specialized enzyme called b-lactamase inactivating ampicillin kanamycin/neomycin: a specialized phosphotransferase enzyme that chemically modifies kanamycin and neomycin so they become ineffective tetracyclin: specialized ribosome binding proteins such as TetO that actively remove tetracycline from the ribosome chloramphenicol: a specialized enzyme that transfers an acetyl group to chloramphenicol thereby inactivating it ... in many other cases specialized enzymes modify ribosomal rnas by adding methyl groups So one wonders why Behe so exclusively focused on those mechanisms where he did not need to mention that they are carried out by specialized proteins that have an often exclusive role in actively conferring antibiotic resistance. I am conviced that he knows them because they are often used as genetic markers in genetic engineering experiments.rna
April 20, 2018
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Yes, Jack, it is of interest but not in the way that you think. There is a huge difference between mere evolution and Darwinism (not an insult by the way). Darwinism is evolution by means of blind and mindless processes. Dr Behe made it clear in his ignored testimony tat there is a difference and that ID only argues against evolution by means of blind and mindless processes 9which is an untestable position). It seems the norm that evos equivocate and then play the victim. PatheticET
April 20, 2018
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Nonlin- Stop moving the goalposts. Thank youET
April 20, 2018
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Off topic, but maybe of interest: https://blogs.scientificamerican.com/observations/on-darwinism/ I don't have any place to post new material, so I just posted this here. Sorry.jdk
April 20, 2018
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Nonlin,
Can you summarize the evidence for: “There are mutations which occur that do benefit the organism.” if any? References are fine for support, but should not replace a strong argument.
Apolipoprotein AI-Milano LRP5Allan Keith
April 20, 2018
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ET,
What? Those mutations definitely benefit the organisms that have them when antibiotics are present. That was my claim: There are mutations which occur that do benefit the organism.
Would you give up something beneficial? Yet the bacteria give up AB-resistance after the stimulus is removed. Same goes for Sickle-cell trait - these are clearly trade-offs that most modern carriers would gladly give up. Definitely not the Darwinist fairy tale of "beneficial mutations that spread throughout the population resulting in the transmutation of species". Get it? Also, there's no such thing as "fitness" or "natural selection" for that matter: http://nonlin.org/natural-selection/.Nonlin.org
April 20, 2018
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Yes, bornagain77, I am aware that "beneficial" can mean "loss of function/ loss of specificity". What is beneficial is all relative. And that the fittest bacteria is still a bacteria. The fittest clown fish is still a clown fish. The fittest of any population is still the same species as that population. There isn't any known mechanism capable of going beyond that.ET
April 19, 2018
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Sickle-cell trait is a benefit for the humans who have it and live in malaria zones.ET
April 19, 2018
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What? Those mutations definitely benefit the organisms that have them when antibiotics are present. That was my claim: There are mutations which occur that do benefit the organism.ET
April 19, 2018
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ET@20 "The mutations that confer an advantage for bacteria which are being subjected to antibiotics, come to mind." But those mutations disappear from the population when the stimulus is removed. They are trade-off, not beneficial mutations. Anything else?Nonlin.org
April 19, 2018
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ET, I'm pretty sure that you are aware of the caveat that Dr. Behe and others have pointed out: "Break or blunt any functional coded element whose loss would yield a net fitness gain."
“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/ List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria: Table 1 excerpt: Actinonin - Loss of enzyme activity Ampicillin - SOS response halting cell division Azithromycin - Loss of a regulatory protein Chloramphenicol - Reduced formation of a porin or a regulatory protein Ciprofloxacin - Loss of a porin or loss of a regulatory protein Erythromycin - Reduced affinity to 23S rRNA or loss of a regulatory protein Fluoroquinolones - Loss of affinity to gyrase Imioenem - Reduced formation of a porin Kanamycin - Reduced formation of a transport protein Nalidixic Acid - Loss or inactivation of a regulatory protein Rifampin - Loss of affinity to RNA polymerase Streptomycin - Reduced affinity to 16S rRNA or reduction of transport activity Tetracycline - Reduced formation of a porin or a regulatory protein Zittermicin A - Loss of proton motive force http://www.trueorigin.org/bacteria01.asp Thank Goodness the NCSE Is Wrong: Fitness Costs Are Important to Evolutionary Microbiology Excerpt: it (an antibiotic resistant bacterium) reproduces slower than it did before it was changed. This effect is widely recognized, and is called the fitness cost of antibiotic resistance. It is the existence of these costs and other examples of the limits of evolution that call into question the neo-Darwinian story of macroevolution. http://www.evolutionnews.org/2010/03/thank_goodness_the_ncse_is_wro.html Helping an Internet Debater Defend Intelligent Design - Casey Luskin - May 3, 2014 Excerpt: antibiotic resistance entails very small-scale degrees of biological change.,,, antibiotic resistant bacteria tend to "revert" to their prior forms after the antibacterial drug is removed. This is due to a "fitness cost," which suggests that mutations that allow antibiotic resistance are breaking down the normal, efficient operations of a bacterial cell, and are less "advantageous. http://www.evolutionnews.org/2014/05/helping_an_inte085171.html Is Antibiotic Resistance evidence for evolution? - 'The Fitness Test' - video https://www.youtube.com/watch?v=rYaU4moNEBU A Tale of Two Falsifications of Evolution - September 2011 Excerpt: “Scientists were surprised at how fast bacteria developed resistance to the miracle antibiotic drugs when they were developed less than a century ago. Now scientists at McMaster University have found that resistance has been around for at least 30,000 years.” http://crev.info/content/110904-a_tale_of_two_falsifications_of_evolution (Ancient) Cave bacteria resistant to antibiotics - April 2012 Excerpt: Antibiotic-resistant bacteria cut off from the outside world for more than four million years have been found in a deep cave. The discovery is surprising because drug resistance is widely believed to be the result of too much treatment.,,, “Our study shows that antibiotic resistance is hard-wired into bacteria. It could be billions of years old, but we have only been trying to understand it for the last 70 years,” said Dr Gerry Wright, from McMaster University in Canada, who has analysed the microbes. http://www.scotsman.com/news/health/cave-bacteria-resistant-to-antibiotics-1-2229183# Antibiotic resistance genes are essentially everywhere - May 8, 2014 Excerpt: The largest metagenomic search for antibiotic resistance genes in the DNA sequences of microbial communities from around the globe has found that bacteria carrying those vexing genes turn up everywhere in nature that scientists look for them,, http://www.sciencedaily.com/releases/2014/05/140508121347.htm
bornagain77
April 19, 2018
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Nonlin.org 'Maybe I’m not the first to ask… How do you manage to write so much and with so many links? Thanks" I've kept semi-organized notes for the past 10 years or so.bornagain77
April 19, 2018
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Nonlin- The mutations that confer an advantage for bacteria which are being subjected to antibiotics, come to mind.ET
April 19, 2018
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ET@7 Can you summarize the evidence for: "There are mutations which occur that do benefit the organism." if any? References are fine for support, but should not replace a strong argument. bornagain77, Maybe I'm not the first to ask... How do you manage to write so much and with so many links? Thanks.Nonlin.org
April 19, 2018
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too funny,,, if just more citations are provided then Darwinists might start to take ID more seriously! :) The problem is not that there is not already abundant evidence against Darwinian claims. The problem is that Darwinian evolution is basically, especially when compared to other fields of science, an unfalsifiable pseudoscience that is impervious to empirical falsification.
Darwinian evolution is a pseudoscience (Popper and Lakatos) - March 2018 https://uncommondescent.com/intelligent-design/coursera-vid-by-darwinism-is-wrong-prof-banned-from-youtube/#comment-655046 Moreover, the falsification criteria that were set forth by Charles Darwin himself have all been met by Michael Behe, by Douglas Axe, by Stephen Meyer, and by Lee Spetner. Yet, despite each of Darwin’s own falsification criteria being met, Darwinists STILL refuse to accept empirical falsification of their theory (which is still yet more proof that we are dealing with a pseudoscience instead of a real science.) https://uncommondescent.com/intelligent-design/ohia-only-human-intelligence-allowed/#comment-655865 Since falsifiability/testability is considered the gold standard by which to judge whether a theory is scientific or not, I want to delve a little more into falsifiability/testability. (and apply it to the basic precepts of the reductive materialism that undergirds Darwinian thought) - April 2018 https://uncommondescent.com/intelligent-design/ohia-only-human-intelligence-allowed/#comment-655886
Moreover, although the Darwinist firmly believes he is on the terra firma of science, the fact of the matter is that Darwinists are adrift in an ocean of fantasy and imagination with no discernible anchor for reality to grab on to:
Basically the atheist claims he is merely a ‘neuronal illusion’ (Coyne, Dennett), who has the illusion of free will (Harris), who has illusory perceptions of reality (Hoffman), who, since he has no real time empirical evidence substantiating his grandiose claims for Darwinian evolution, must make up illusory “just so stories” with the illusory, and impotent, ‘designer substitute’ of natural selection (Behe, Gould, Sternberg), so as to ‘explain away’ the appearance (i.e. illusion) of design (Crick, Dawkins), and who must make up illusory meanings and purposes for his life since the reality of the nihilism inherent in his atheistic worldview is too much for him to bear, and who must also hold morality to be subjective and illusory since he has rejected God. Bottom line, nothing is real in the atheist’s worldview, least of all, morality, meaning and purposes for life. https://uncommondescent.com/intelligent-design/the-ubiquitin-system-functional-complexity-and-semiosis-joined-together/#comment-655355
It would be hard to fathom a worldview more antagonistic to modern science than Atheistic Materialism has turned out to be. Verses
2 Corinthians 10:5 Casting down imaginations, and every high thing that exalteth itself against the knowledge of God, and bringing into captivity every thought to the obedience of Christ; Matthew 7:24-27 “Everyone then who hears these words of mine and does them will be like a wise man who built his house on the rock. And the rain fell, and the floods came, and the winds blew and beat on that house, but it did not fall, because it had been founded on the rock. And everyone who hears these words of mine and does not do them will be like a foolish man who built his house on the sand. And the rain fell, and the floods came, and the winds blew and beat against that house, and it fell, and great was the fall of it.”
bornagain77
April 19, 2018
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I’m curious to know what psychiatric qualifications you have that make you feel competent to diagnose psychiatric conditions in others. Are you, for example, a member of the American Psychiatric Association? Now there's professional field rife with long term political scandal. Most members of said organization are philosophical materialists who believe psychiatric conditions in total are the signs and symptoms of organic brain disease. Without ever having any proof and without ever having found a cure for a single category. A group which for decades included homosexuality in its diagnostic manual, and miraculously found a political cure for that organic disease in 1974.groovamos
April 19, 2018
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caleb:
Wild claims need clear evidence.
He didn't make any wild claims. caleb:
If you are going to say that you have knowledge of biology that other biologists lack, you had better be able to substantiate it by references to the primary literature or quotes from books.
He didn't say he had knowledge of biology that other biologists lack. He's not even a biologist afiak.Mung
April 19, 2018
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