People systematically overlook subtractive changes. People tend to solve design challenges by adding extra elements even when taking something away would be simpler and more advantageous, according to an article in Nature today [1].
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| It took decades to think of removing pedals, rather than adding stabilisers [2]. |
In January I blogged about the highly transmissible British variant [3]. This variant suffered from no less than 3 deletions [4]. Two occurred in the Spike protein. The British variant did not seem to be handicapped very much. On the contrary. At the time I didn't pay attention to the remarkable fact that deletions contributed to a positive effect. It didn't struck me as odd.
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| three deletions highlighted from [3]. |
Now I see that those deletions have a beneficial effect for the virus. (Not for us!). Nucleotide deletions in a specific part of Spike protein of SARS-CoV-2 may alter antigenicity. That means they normally provoke an immune response in the body. In this case that immune response is weaker. Specifically, deletion of amino acids 69 and 70 in the British variant B.1.1.7 resulted in a substantial higher infectivity of the virus. So, these the deletion of these amino acid seem to improve SARS-CoV-2 fitness. Deletion of amino acid 144 in B.1.1.7 variant and amino acids 242-244 in B.1.351 variant have also been associated with reduced binding capacity of certain neutralizing antibodies, and thus have a beneficial effect for the virus [5].
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| How can this LEGO structure be stabilised? [2] |
When confronted with this LEGO structure with a blue supporting block in the left corner (see picture), and asked to stabilize the structure, most people add three supporting blocks in the remaining corners, but some simply removed the blue block. A simple and perfect solution. See video [2].
Evolution, found the same solution by trial and error. By removing a few amino acids, the virus has been improved.
I found the examples from everyday life helpful and inspiring. If you liked them too, please forward this blog post to your friends!
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| Fingerless Gloves (source) |
Fingerless gloves: surprising result when you delete parts of the age-old design of a glove! Fingerless gloves are useful where dexterity is required that gloves would restrict. Cigarette smokers and church organists sometimes use fingerless gloves.
Notes
- People systematically overlook subtractive changes, Nature 8 April 2021
- Less is more: Why our brains struggle to subtract, youtube 7 April 2021
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Finding the highly transmissible British SARS-CoV-2 B.1.1.7 variant in
the USA, blog 7 Jan 2021
- Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape, Science 12 Mar 2021
- SARS-CoV-2 Variants vs. Vaccines, American Society for Microbiology, March 3, 2021.
- "The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the Spike protein " 18 Mar 2021
Possible important/interesting News update:
ReplyDeleteUnexpected novel Merbecovirus discoveries in agricultural sequencing datasets from Wuhan, China
https://arxiv.org/abs/2104.01533
Thank you. This is a remarkable publication. Apparently, the authors were able to search agricultural databases from Wuhan, China and found viruses that are not supposed to be present in crop species. They conclude: contamination! This is certainly relevant for the precise origin of SARS-CoV-2.
ReplyDeleteI would not publicise these findings. The Chinese are certainly alarmed and start a thorough clean up of their databases. Or simply close them all of them. Thereby killing all future investigations of Chinese sequences. I'll wait and see...
https://nautil.us/blog/covid-experts-were-putting-out-campfires-but-the-forest-fire-rages
ReplyDeleteAre we really?
"Common wisdom tells us that deletions in human texts cause loss of information."
ReplyDeleteThis common sense idea is the core of all ID criticisms of darwinian evolution, viz Behe's First Rule of Adaptive Evolution, as stated in Darwin Devolves, his latest book : Break or blunt any gene whose loss would increase the number of offspring.
Such mutations are easy to come by. And viruses know the rule: less is more!
"Evolution found the same solution by trial and error. By removing a few amino acids, the virus has been improved."
ReplyDeleteI think the point here is not the trial and error
although "it serves to acknowledge plainly our ignorance of the cause of each particular variation"
So, I think the point is that the virus has improved- that it has reached a beneficial effect: beneficial, given the (proteine) chemistry of our cells and our immune system (rather than that of chimps f.e. )
Viral mutations is evolution in action: differential reproduction (including recombination, though without sex!). Or to wit: it is chemistry all the way down. And all the way up!
Harry P: thanks for your thoughts. To start with this one: "Or to wit: it is chemistry all the way down. And all the way up!".
ReplyDeleteI think this is an attractive misunderstanding of what an organism is (often heard in ID circles).
Example: just as it would be foolish to say of a book: it has no content, it has no story to tell, it has no information, it has no meaning because ... it is chemistry all the way down. And all the way up! That would be stupid. A printed letter in the book is indeed chemistry because it is just 100% ink. And the paper is also 100% molecules. Also: an organism is made exclusively of molecules and nothing more. But, how do you explain female and male organisms? Where does the femaleness and maleness property come from? Molecules all the down and up? But there are no male and female molecules! Do molecules have sex? There you have it!
So to say it friendly: "Or to wit: it is chemistry all the way down. And all the way up!" is a meaningless distraction, or honestly: just irrelevant bullshit! :-)
Harry P: "Break or blunt any gene whose loss would increase the number of offspring"
ReplyDeleteThe S gene of SARS-COV-2 has deletions, but does this count as 'break or blunt'? The S gene is certainly not dysfunctional, loss-of-function, broken, or weakened. The virus is flourishing. It is a deletion that escapes immune attacks. Quite a positive thing ... for the virus.
(continued) no loss or degradation, but gain-of-function by deletion!
ReplyDeleteBS or bovine manure?
ReplyDeleteWe're talking viruses here - not sex-differences.
(You are just moving the goalsposts).
I never said that a book is just chemistry because it amounts to printed ink. (You simply jump to a wrong analogy)
Genetic sequencing is key to tracking, and fighting, Covid-19.
(and all other viruses, for that matter )
I can only repeat what I said:
ReplyDelete"So, I think the point is that the virus has improved"
Meaning the point here is NOT the trial and error
Though "it serves to acknowledge plainly our ignorance of the cause of each particular variation"
Unless we solve that problem (i.e. our ignorance), we "will never be able to say anything substantive about function.
"https://sandwalk.blogspot.com/2021/04/bold-predictions-for-human-genomics-by.html#comment-form
Harry, I responded to your "Viral mutations is evolution in action: differential reproduction (including recombination, though without sex!). Or to wit: it is chemistry all the way down. And all the way up!"
ReplyDeleteechoing the often repeated mantra of ID-ists Michael Behe that there is only biochemistry and that you don't need selection and evolution to explain organisms.
In order to explain it to a non-biologist I introduced the explanation with an analogy (text on paper) and then the explanation itself. It explains why you can never reduce an organism to pure chemistry and never explain an organism without evolution. These are profound principles, if you understand these, you have learned a profound insight which prevents misunderstandings the rest of your life. Think thoroughly about it until you understand why it is so important. If you are not interested in these topics, then have a nice day!@#$^
Gert,
ReplyDelete1. you are dead wrong about Behe. Like most ID-ists he doesn't deny that there is 'selection' and even 'evolution'. Behe simply maintains that darwinian evolution amounts to devolution, see above.
2. instead of lecturing me, you should explain that 'differential reproduction' entails more than differences in reproduction (recombination) of dna sequences (in populations over generations)
Differential reproduction of what else than dna sequences?
3.
Your accusation of reductionisme misses the mark. Please, read all my responses. The quote is Darwin's. He's right. The central issue in evolutionary biology, or in evolution theory at large (which is mainly 'verbal guesswork') is our present ignorance about how to get from sequences to function (see also the sandwalk discussion)
sequence and function is an analogous problem in language btw
Harry, on 9 April you wrote: "Or to wit: it is chemistry all the way down. And all the way up!".
ReplyDeleteWhat do you mean by that?
Okay, good you asked!
ReplyDelete'all the way up and down' is my variation on the infamous turtle quip - with Phil Anderson (1972) in mind
In OoS, Darwin writes, "Any variation that is not inherited is unimportant to us."
In other words, evolution is about genes, viz the differential reproduction of DNA sequences, which is chemistry all the way down.
"But the number and diversity of inheritable deviations of structure, both those of slight and those of considerable physiological importance, is endless", Darwin continues.
So evolution also boils down to all the chemistry up, all the way upwards to the "phenotypic effects," as biologists would say.
Endless indeed. Especially when we talk about "infinitesimal" "variations" and phenotypic effects that affect the genotype. Especially, as you know, the phenotype of our species is quite "extended" to use Dawkin’s phrase. (Since Francis Galton this is aka the Nature-Nurture problem, and very typical of our evolution in contrast to that of chimpanzees, for example).
Thanks to AI-based models e.g. DOI: 10.1038 / s42256-021-00325-y) we are learning more and more about the chemistry all the way down. But our knowledge of the chemistry all the way up could continue to fall seriously short.
That might even be the case if you believe that Feynman is right: “So what is this mind of ours: what are these atoms with consciousness? Potatoes from last week! (What do you care what other people think, 244).
Potatoes or no potatoes, that’s the question.
So I hope you get the irony.
PS
ReplyDeleteOf course there's a lot more to say- well worth a whole blog!
But allow me to add just one important note. It's not just because of the new models (and data-analysis techniques) that we are rapidly gaining new knowledge about the chemistry all the way down, but of course, it is also because of new techniques - genetic engineering, synthetic biology etc- that enable us to accumulate new data and do experiments, test hypotheses etc, in an unprecedented way.
Harry said: "In other words, evolution is about genes, viz the differential reproduction of DNA sequences, which is chemistry all the way down."
ReplyDeleteand:
"So evolution also boils down to all the chemistry up, all the way upwards..."
You are echoing Michael Behe (need a quote?). It amounts to: we can do science without the theory of evolution, all you need is chemistry. Progress is only made by (bio)chemistry. Darwinism did not contribute anything to that progress.
But that brings us back to pre-Darwinian times!
Example: Behe has nothing sensible to tell about SARS-CoV-2 other than that it is irreducible complex, so must have been designed! Well, that sets us back 150 years in time! Well, that is progress :-(
Secondly, your comment proves that you didn't get my remarks about female and male molecules (Saturday, April 10, 2021 at 9:49:00 AM GMT+2) :-(
'any variation that is not inherited', boils all the way down to chemistry. What else, would you say?
ReplyDeleteAnd that means ultimately: all the way down to elementary particles, to QM and the SM, viz the most successful reduction of complexity we presently have- even though possible new particles don’t quite fit in the scheme…...
So much for your Behe ‘argument’.
Is my example (see DOI) setting us back 150 years?
Or the research I referred to in my PS?
Indeed, Darwinism did not contribute anything to this unprecedented progress, let alone to the accumulation of new data. No wonder you never answered Monday, April 12, 2021 at 12:29:00 PM GMT+2
(Same holds, a fortiori, for (paleogenetic and - proteomic) research on the survival of Homo sapiens and the untimely demise of the Neanderthal and Denisova (f.e. NOVA1 research), as compared to all Darwinian stories about the evolution of our big brains, our typical flat face (chin, big nose, loss of beak), loss of baculum, of hair, or our bipedality (over 20 ‘explanations’ and counting) , our ‘invention’ (Darwin’s words) of fire- and cooking.
Does darwinism have anything more to say about the origin, or evolution, of sexual reproduction than what genetics and or biochemistry already told us (e.g. about viral genes, placenta and genomic imprinting etc etc )
There you have it! You just keep struggling with (my) irony.
Just as molecules don't have 'sex', potatoes have little to do with our mind - but molecules all the more, according to people like Feynman.
But molecules is the only thing you get when you stick to 'any variation that is not inherited'’. Everything else turns out to be just stories and models, just interpretations of what darwin said. A lot of semantics (see Welch, 2017, to mention but one example we've discussed)
Of course, there is a lot more not-inherited variation than met the eyes of Darwin some 150 years ago. That might even be true if you believe that Feynman is right. Or as I wrote: our knowledge of the chemistry all the way up could continue to fall seriously short.
And that’s the key question (that also Darwin may have had in the back of his mind when he reached his ‘remarkable conclusion’ in DoM).
Harry, stop throwing in Darwin, Behe and everything else!
ReplyDeleteStop with quote mining! Think! Think about this question: either 'chemistry ALL THE WAY DOWN' means anything useful, or it is totally irrelevant. Again: THINK before you answer this question: if you examine all the molecules in a female do you find in the end female molecules that explain this individual is a female?
Gert,
ReplyDeletethanks for your suggestions. They nicely round off your contribution to our discussion.