Three Things Biologists Rarely Know About Biology
| April 18, 2018 | Posted by johnnyb under Biology, Evolution |
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.
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- 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.
- 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.
- 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.
45 Responses to Three Things Biologists Rarely Know About Biology
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@johnnyb
If you are going to make claims like these, you had better have references, and lots of them.
1. I can take a guess as to what you are referring to but you make a number of misstatements along the way,
“Most biologists are trained to think of mutations as being “undirected” if they aren’t 100% on-target. ” No they aren’t. They are taught that mutations occur without respect to the needs of the organism.
“However, there are systems which reduce the mutational search space by well over 99%.”
That’s a pretty good trick if it works. Are you thinking of Susan Rosenberg’s work? References?
2. Endosymbiosis. Can you show examples of gaining or losing a symbiont? References? How many examples? If you want to claim this plays a significant role there had better be a lot.
3. Non-genetic inputs. Prions are a pretty poor example of positive evolution. They are misfolded proteins that are toxic. And I doubt they are heritable. You pass on the tendency to develop prions but not the prions themselves. References?
Presence or absence of pheromones can certainly trigger large scale changes, such as sex reversal in fish. But they aren’t going to be a pathway for evolution. Those are programmed responses necessary to create a new morphology, a program that is likely the product of design. How do you evolve a process to create a female fish when there is none? One of the males makes the change. How does that work? There is no reproduction until you get it right. But it’s never been done before and there are a lot of steps. That happens by evolution or by design?References?
Maybe biologists haven’t heard of these mechanisms because they aren’t significant or heritable. Or because they aren’t as described here.
I think you should consider the possibility that biologists know more about these topics than you do. Take the first example
I guess you are talking about somatic hypermutation when you are talking about “directed” mutations, but these are somatic (so irrelevant to evolution) and not directed.
I think johnnyb’s point is that although these things are known by biologists as a whole, individual biologists don’t know them. Of course, there are a lot of things individual biologists don’t know about biology.
The directed mutations point is something that I think is interesting in its own right, except is isn’t directed mutation, as johnnyb basically admits. I think it might be better not to resort to what looks like sophistry. Perhaps say that “evolution that looks like directed mutation is pervasive”. That way you can get to explaining some fascinating biology without looking like you have an agenda.
As to:
Otherwise known as Darwinian Cognitive Dissonance Disorder (DCDD).
Yes folks, it is a mental disease. But there is hope:
A big question is, how many biologists can even afford to know what is going on here? Consider what happened to Gunter Bechly: “Erased” paleontologist Bechly gets support from Science and Health Council
Aren’t they safer as Aren’t I good? girls?
ba77 – Brian Miller’s education is in physics, not psychiatry. 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?
caleb:
They are taught that all mutations are undirected- the result of chance alone.
There are mutations which occur that do benefit the organism.
If you want to read about the evidence for directed mutations read “Evolution: A View from the 21st Century” by James Shapiro
Well Bob, since to experts you appealed to experts we will go:
The following found that ALL people, especially including atheists, (i.e. people who have voiced a predisposition to believe that they are not really people at all but are really neuronal illusions 🙂 ), have a tendency to believe in God and also have an innate, deep-seated, ability to ‘detect design’:
The following video and studies found that the belief in God and/or Design is a ‘knee jerk’ reaction even for atheists. Moreover, in the video it is shown that atheists have to mentally work suppressing their innate design inference!
It is not that Atheists do not see Design in nature, it is that they, for whatever severely misguided reason, live in denial of the Design that they themselves see.
I hold the preceding studies (and quote) to be confirming evidence for Romans 1:19-20
Of further note: The following studies found that this ‘knee jerk’ instinct to believe in God and/or Design is with us from childhood:
As to the fact that the Atheist’s suffer mentally and physically as a result of suppressing their natural belief in God, I cite this book from Professor Andrew Sims former President of the Royal College of Psychiatrists
And the detrimental physical effects on the health of Atheists is found to b rather pronounced in the following study.
Verse:
I don’t have time to respond in detail at the moment, but thought I would point to a few resources:
(1) I did a video many years ago summarizing some really interesting new areas in mutation studies:
https://www.youtube.com/watch?v=YJwWhhpua_o&list=PLED30A9B8304C8C21
(2) You might also check out the series I did for UD many years ago on directed mutation:
Responding to Merlin
(3) On symbiosis, check out this evolution of a cecal valve due to a new novel symbiotic association:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2290806/
To see the blindness of biologists to the effects of symbiosis, check out this quote by Lynn Margulis from her book Symbiotic Planet:
(4) As for the importance of non-genetic inputs to morphology, what I really had in mind was Jonathan Wells’ work, but I didn’t then (and don’t now) have the time to look it up. If someone wants to link to it I would appreciate it. I don’t even think it originated with Wells, but he has made it more prominent.
This has been publicized in the popular press since 1986 or before, when I read about it. This type of intentional cover up in the textbooks should be a major scandal in any field of study; for some reason biology is tolerant of this type of thing. Here is a piece from 1990: https://www.newscientist.com/article/mg12717342-900-science-can-bacteria-direct-their-own-evolution/
Bob:
And? Does that mean that unlike psychiatrists and psychologists he can actually back up his claims?
Or do you actually think that being a psychiatrist means something?
ba77 @ 8 – OK, so I guess that means that you aren’t a psychiatrist, and can’t cite any psychiatrists to beck up a diagnosis of mental illness.
ET @ 11 – ba77 was making a diagnosis of mental illness. Being a psychiatrist means that at least one has experience in dealing with mental health issues.
Bob:
The same can be said about being a parent. 😎
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 guess I could cite Bob’s response itself as confirming evidence that atheists suffer acutely from Darwinian Cognitive Dissonance Disorder (DCDD). 🙂
But anyways here are Prof. Sims credentials:
@johnnyb and others
If you want to be taken seriously you need to provide real references to research papers, or books by biologists like Shapiro. (Did he claim that the search space is reduced by 99%? Where did that come from?) Quotes from your own youtube videos don’t cut it. (I will take a look though.)
Two examples of symbiotic change are not overwhelming. And I still need a reference. The Drosophila one I already know about. The Drosophila symbiont in question is Wolbachia. It has coopted an essential process in germ cells–it’s more like a parasitic disease than symbiosis in most cases.
The reason for the sterility is because Wolbachia causes incompatibility between infected males and non-infected males, and other things as well. Read Wikipedia at the very least, for heavens sake, before claiming speciation. https://en.wikipedia.org/wiki/Wolbachia
My goal here is not to diss you. It is to raise the level of discussion. Wild claims need clear evidence. 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.
And my comments are aimed not just at you but at many other posters. Take it as friendly criticism from a biologist. Raise your game.
caleb:
He didn’t make any wild claims.
caleb:
He didn’t say he had knowledge of biology that other biologists lack. He’s not even a biologist afiak.
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.
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.
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:
It would be hard to fathom a worldview more antagonistic to modern science than Atheistic Materialism has turned out to be.
Verses
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-
The mutations that confer an advantage for bacteria which are being subjected to antibiotics, come to mind.
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.
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.”
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?
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.
Sickle-cell trait is a benefit for the humans who have it and live in malaria zones.
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,
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,
Apolipoprotein AI-Milano
LRP5
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.
Nonlin- Stop moving the goalposts.
Thank you
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. Pathetic
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, 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’.
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.
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.
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 up
Nonlin,
I know. I was responding to your subsequent request of him. I seldom agree with ET, but in this case he is correct.
Ba77@21 what format do you store your notes in spreadsheets onenote that you can do easily find and retrieve them , database?
I was specifically asking about this comment by you @4:
Sims doesn’t say he’s describing a mental disease, still less a Cognitive Dissonance Disorder. He is also not talking about Darwinism.
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
es58, I use google doc. and Libre Office.
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/pi.....-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.
Fails at what?
Nonlin,
They have to start somewhere. That is how evolution works.
Allan Keith:
Except there isn’t any evidence that evolution works the way you need it to.
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.