04 March 2021

Perfecte camouflage van citroenvlinder misleidt ObsIdentify (NIA) software

ObsIdentify is helaas niet zeker:
 Breed pijlkruid - Sagittaria latifolia (12.1%) 25 feb

het resultaat: Breed Pijlkruid (12,1%)!

Ik had de beste foto uit een serie van een Citroenvlinder aangeboden aan ObsIdentify (NIA) beeldherkennings software in waarneming.nl. Ik was verbaasd over het resultaat: geen vlinder, maar Breed Pijlkruid, een plant! 

De de onzekere voorspellingen waren allemaal planten (zie screenshot). De Citroenvlinder lijkt op Breed Pijlkruid?! NB: de foto's zijn scherp; onscherpe heb ik niet gebruikt; de foto's zijn met een goede macrolens gemaakt (SONY 90mm macro); zo dichtbij mogelijk, en zijn bijgesneden zoals steeds wordt aanbevolen; er is niet mee 'geknoeid'.

Het enige wat ik kan bedenken: camouflage! De Citroenvlinder lijkt op een blad! Een blad met nerven. Wat me al eerder opgevallen was, dat Citroenvlinders een voorkeur hebben om uit te rusten op onze gevlekte klimop. Hoe komen ze op het idee? Weten ze dat ze daar het minst opvallen? Maar dan moeten ze weten hoe ze er zelf uit zien! Een vlinder met een correct zelfbeeld? Zelfbewustzijn? Ik heb een theorie. Door predatie van vogels worden individuen geselecteerd die gewoon een erfelijk vastgelegde voorkeur hebben voor bladeren als de gevlekte klimop. Ze hoeven dus helemaal niet 'te weten' hoe ze er zelf uitzien.

Als controle heb ik nog 10 foto's van dezelfde vlinder aangeboden waarbij driemaal Citroenvlinder werd herkend maar met een percentage van slechts 50% (2x) en 33,4% (1x). Breed pijlkruid, Erwt, Klimop, Kaukasische klimop en Oosterse wingerd kwamen voorbij in de antwoorden met allemaal percentages lager dan 25%. Dus: onzeker. OK. Behalve 1 foto: Klimop - Hedera helix met zekerheid 96.2%


ObsIdentify voorspelt Klimop - Hedera helix met zekerheid 96.2%


Ik heb nog geprobeerd de vlinder beter te isoleren door de achtergrond zwart maken, maar dat hielp niet.

Ik moet toegeven: als je niet weet dat hij er zit, en hij stil zit, dan zie je hem niet. Complimenten voor de camouflage van de Citroenvlinder! Hij is de software te slim af!

Na een aantal dagen heeft een (menselijke) moderator de Citroenvlinder goedgekeurd. Dank U wel!

O ja, 25 februari is extreem vroeg in het jaar voor een Citroenvlinder! Maar dat had U zelf natuurlijk ook al door!


Vorig blog over ObsIdentify:


Update: heeft U problemen met invoeren van een comment mail me:



26 February 2021

SARS-CoV-2 was designed says Intelligent Design Theorist Michael Behe

Michael Behe (©Discovery Institute)
'exquisitely and purposively arranged'


Intelligent Design Theorist Michael Behe, author of Darwin's Black Box [2], was asked in the early days of the covid-19 pandemic to comment on the pandemic. He wrote a short blog.
"So, do I think viruses were designed? Yes, I most certainly do! The viruses of which we are aware — including the coronaviruses, Ebola, and HIV — are exquisitely, purposively arranged, which is the clear signature of intelligent design. [1].

Let's first try to understand what it means that viruses are designed and discuss later the evil designer. Behe tells us that viruses in general are designed including 'coronaviruses'. But coronaviruses consist of 4 genera with 21 species. Are they all designed? Behe does not go into details. The details are important because viruses differ in their potential to cause local outbreaks, epidemics or pandemics in animals or in humans. Behe tells us that they all are 'exquisitely, purposively arranged'. But 'purposively arranged' for what purpose? To infect bats or humans? How does he know? Should we conclude that SARS-CoV-2 was more 'exquisitely designed' than SARS-CoV-1 because the SARS-COV-2 caused a pandemic and SARS-CoV-1 only an epidemic? Apparently, there are unexplained differences in exquisiteness. The concepts 'exquisitely', 'purposively' are too vague to have scientific meaning. But Behe uses the concepts nonetheless without any specifications. If SARS-CoV-2 is so 'exquisitely and purposively' designed, would he be thrilled to be infected by this beautiful virus? [14].

And then there is a problem of timing of the origin. SARS-CoV-2 appeared in December 2019 in Wuhan, China. Was it designed at that time and place? To discuss this, we need a quote from Behe's article:

"Viral mutations can change the shape of the skeleton key at random. Most of the time the process doesn’t work but, every once in a while, the virus hits the jackpot."[1].

But this is a clear description of random mutation and natural selection! He continues: "In some cases, a viral key that had bound to a wild-animal protein mutates and becomes able to bind to a similar human protein" [1]. Here, he describes zoonosis, a jump from animal to human. But again, he describes it as a process of random mutation and natural selection. Winning the jackpot is luck, not design. Conclusion: SARS-CoV-2 originated by random mutation and natural selection. Behe does not notice the contradiction. 

It becomes even more interesting. SARS-CoV-2 has a unique 12 base / 4 amino acid insert at the contact site of the virus with the human receptor [6]. It is not present in other corona viruses. Since the beginning of the pandemic conspiracy theories spread on social media claiming that the virus was bio-engineered by China [7]. That is an intelligent design theory contradicting its natural origin. Behe ignores it. Why? It would be the perfect opportunity for ID theorists to apply their 'inference-to-design-methodology' to the origin of SARS-CoV-2 [8]. That method was designed to distinguish between natural and designed objects. Apart from Behe, William Dembski would be the right person to do it [9]. He could for once and for all give the definitive answer and silence all other conspiracy theorists. As far as I know no ID-er has done it so far. A missed opportunity. Why? Could it be that ID-ists already have an explanation: the virus was designed (by God). Could it be because ID-ists share the belief that SARS-CoV-2 doesn't have a natural origin? However, some ID-ists accept a natural origin [15].


Storm analogy

Behe: 

"...while of course the virus is dangerous, the situation can be compared to a strong storm on the ocean. The waves may be huge and the surface roiling, but the deeper waters continue as they always have, essentially undisturbed. In a similar way, although superficially it changes very rapidly, some researchers think that the coronavirus2 and many other virus types3 have remained basically the same for tens of millions of years" [1],[10].

Basically the same? SARS-CoV-2 stayed basically the same for millions of years and then suddenly caused a pandemic! When one particular virus "hits the jackpot" (Behe's words), how helpful it is to say it is basically the same? It does not help the scientific understanding of what causes a pandemic. I do not understand why Behe quotes two pre-pandemic publications [11],[12] if he wants to explain the origin of a new pandemic. The coronavirus group was created some tens of millions of years ago and did not change basically? So, there was no evolution? But the virus hit the jackpot! In his own words, the purpose of the storm metaphor is "most viruses do not affect humans and may well have a positive, necessary role to play in nature of which we are currently unaware". But even if true, is irrelevant and an inadequate respons. We are discussing SARS-CoV-2, and not other viruses. We are discussing a pandemic, not harmless viruses.

The most important question for virologists is: can we predict an outbreak that could cause a pandemic? What information do we need? How can we be prepared? Behe's reaction: the virus stays basically the same, and there are good viruses too! Both remarks are irrelevant. He should have payed attention to 'hitting the jackpot'. He has the right biochemical knowledge to do that.

The two articles Behe uses to support his basically the same claim are both pre-pandemic (his note 2 is dated 2013 [11] and his note 3 is dated 05 December 2018 [12].) So,  March 2020 he uses pre-pandemic publications to show that SARS-CoV-2 is basically the same!


Evil by Design

Continuing the first quote:

"Well, then does that mean the designer is evil and wants people to suffer? No, not necessarily. I’m a biochemist, not a philosopher. Nonetheless, I see no reason why a designer even of such things as viruses should be classified as bad on that basis alone." [1].

Behe introduces the topic 'evil' in a discussion of the SARS-CoV-2 pandemic. This is nothing less than the infamous theological problem of evil [13] which is an argument against the existence of a benevolent God. Behe does not tell us what additional facts are required in order to classify the Designer as evil. What could be added? Please note, that Behe refrains from saying: 'the Designer is morally good'. Why? Anyway, Behe did not solve the problem of evil.

Behe has problems with a Darwinian evolutionary process of random variation and natural selection, a mindless process of trial and error. However, he has no problem with an Intelligent Designer who exquisitely (!) and purposively  (!) designed pathogenic viruses and bacteria such as malaria, Ebola, HIV and the current SARS-CoV-2 virus. At the time he could not know that there are now 28 million SARS-CoV-2/covid-19 cases and more than half a million deaths in the US alone and 2,5 million deaths worldwide [3], but I am sure that he did not change his mind about the moral character of the designer. What could change his mind? [16]. Behe thinks that the person who designed SARS-CoV-2 is not necessarily evil. A bioterrorist is defined as someone who uses biological agents, such as pathogenic organisms, for terrorist purposes. A bioterrorist is not necessarily evil? Then what would make a bioterrorist evil?

In The Edge of Evolution (2007) he wrote about malaria:

"Malaria was intentionally designed. The molecular machinery with which the parasite invades red blood cells is an exquisitely purposeful arrangement of parts. (...) What sort of designer is that? What sort of "fine-tuning" leads to untold human misery? To countless mothers mourning countless children? Did a hateful, malign being make intelligent life in order to torture it? One who relishes cries of pain? Maybe. Maybe not." (p.237) [2]

Again, he prefers that an Intelligent Designer designed the most horrible pathogenic bacteria and viruses, to accepting they are the result of a blind, purposeless, random, natural process. Think about this: one cannot blame a virus, but one can and must blame a person. Especially, if that person is a God who is said to be merciful and compassionate and the foundation of morality. 

Was it really necessary to create 24 families of pathogenic viruses with more than 260 virus species that infect humans? [17]. Why that abundance?  In total, there are about 1,400 known species of human pathogens (including viruses, bacteria, fungi, protozoa and helminths) [18]. A little bit overdone. God wasn't satisfied with only 1 or 2 pathogenic species? It must have been great fun to create such overwhelming pathogenic biodiversity.


Have a nice day

Years ago I was worried by an unsettling statement of anthropologist Jonathan Marks:

"The scientist says: Science has explained many things about the universe. Your life has no meaning. Have a nice day." [5]

I tried to find a good answer. Yes, I know that 'the meaning of life' is outside the domain of science. But still it worried me. Many years passed by before it occurred to me that religion (Christianity) had no comforting truths to offer to a sensible and sensitive person. On the contrary: God created Malaria, Ebola, HIV, SARS-CoV-2. Have a nice day. I would rather accept reality as it is and try to find cures for those illnesses, then believing that those horrible diseases are created by a morally good God and leave it at that. Have a nice day!



Updates

5 March: Comments are welcome. Because of problems, I disabled moderation, but I cannot disable the google image test. If you still have problems at adding a comment, please mail the comment to:

6 March: replaced heading 'Evil' by: 'Evil by Design'

14 March: some editing, moved a passage, added and replaced a sentence, but the conclusion is the same. 

16 March: added paragraph with notes 17 and 18.

Notes

  1. Michale Behe Evolution, Design, and COVID-19, March 10, 2020.
  2. Darwin's Black Box review; The Edge of evolution review.
  3. worldometers (US) worldometers (world) 24 Feb 2021
  4. See my review of that book on my WDW website. 
  5. Jonathan Marks (2003) "What it means to be 98% chimpanzee. - Apes, people, and their genes.".  As a reply here I collected a list of 'comforting religious truths' (enough for a future blog!).
  6. I blogged about the PRRA insert here.
  7. Just type 'sars-cov-2 engineered' in the search field of youtube!!!
  8. Did Intelligent Design Just Miss Its Corona Moment?, American Scientist July 16, 2020
  9. Mathematician William Dembski (1999) Intelligent Design. The bridge between science and theology , invented the design inference (Specified complexity). See my review of that book.
  10. Behe's refers to two mainstream publications based on evolution by random mutation and natural selection! See below: [11], [12]
  11. Wertheim, J. O. et al. 2013. A case for the ancient origin of coronaviruses. Journal of Virology 87:7039-7045.
  12. Simmonds, P., Aiewsakun, P. and Katzourakis, A. 2019. Prisoners of war — host adaptation and its constraints on virus evolutionNature Reviews Microbiology 17:321-328. published 5 December 2018. That is in the year that the pandemic started! Remarkably, the article says: "...rates of sequence change that are orders of magnitude greater than those of the hosts they infect. They display evolution in real time as they acquire antiviral drug resistance, mediate persistent infection through escape from T and B cell immune system responses to infection or, at the experimental level, rapidly adapt to different cell culture conditions, new receptors and new hosts." So, Behe quotes an article that demonstrates evolution! This is an important article about archaeo-virology and paleo-virology. 
  13. See for 'the theological problem of evil' for example my review of Swinburne's Is There a God?  and God, Hitler and the Free Will Defense on my WDW website. Website of Stanford Encyclopedia of Philosophy: Problem of Evil.
  14. this sentence added on Sunday 28 Feb 2021
  15. Jonathan Wells admits that SARS-CoV-2 could have evolved, so was not intelligently designed. Michael Egnor writes: "intelligent design of the COVID-19 virus seems unlikely." Both contradict Michael Behe. [2 Mar 2021]
  16. "It is estimated that viral infections contribute to approximately 6.6% of global mortality." Would that change his mind? (source) Added 5 Mar 2021.
  17. See table with humans pathogenic viruses in wikipedia. See a list of all viruses (wikipedia). Added: 16 March 21.
  18. Microbiology by numbers, Nature Reviews Microbiology 12 Aug 2011. Added: 16 March 21.

23 February 2021

How to investigate the origin of SARS-CoV-2 yourself

The real pleasure of doing science is finding new things yourself. I show you in this blog how you can make discoveries yourself. A few days ago I blogged about the video of Dr. Wilson. The good thing about his approach is that he helps us to find out basic facts about the origin of SARS-CoV-2 ourselves. In his video he gives a few hints how to do it, but does not give the full details. Here he shows how you can enter bat viral sequences in the NCBI software:

NC_045512, MG772933, MG772934

and the fourth: RaTG13. These are the identifiers of human SARS-CoV-2 RNA viral sequence and of the evolutionarily closely related bat viral sequences. Everybody can compare them. You don't need to be a professional virologist. You don't need any training. It is free access. You don't need an account.  Just a few mouse clicks as shown in this video:

video 1 min 36 sec

What the video shows: start with this NCBI virus screen. The Virus field should be empty because we are using only Accessions. Accessions are identifiers of specific sequences.

enter them in the Accession field and Submit.

For a start, I want to focus in the Spike protein. So, click on the  [Protein (70)] tab. Sort the Protein column. Select the surface glycoprotein, spike protein, spike glycoprotein by hitting 4 check boxes:

4 Spike protein accessions are selected


After hitting the Align button the real magic happens. The result is an alignment of the 4 protein sequences of the Spike protein. Optionally, hit the Sequence ID button to get the standard SARS-COV-2 sequence on top. In the video I show how to find the famous PRRA sequence. The PRRA sequence is very important and it is said to have caused the pandemic outbreak of SARS-COV-2 in humans [1]. The PRRA sequence sits in the middle of the Spike protein. The Spike protein gets the virus into human cells. It's an evolutionary innovation.

I guessed that PRRA must be somewhere in the middle of the 1273 AA Spike sequence, between position 600 en 700.

and there it is: the famous PRRA insertion!
 

A little bit sliding to the left and right, and there it is: on position 682! PRRA ! Sensation! That is the pleasure of discovering things yourself: PRRA is present in the SARS-COV-2 Spike protein and not in the 3 most closely related bat Spike protein sequences. It is an insertion relative to the other sequences. The alignment tool made it perfectly clear. If scientists told you it is there, it would not impress you very much. But seeing is believing. The gap in the other 3 sequences is not a real gap. It is a virtual gap necessary to align the rest of the sequence. There can be no real gap in a RNA or DNA string.

We are talking here about an insertion of only 4 amino acids: P R R A or 3 x 4 = 12 bases. Is that really a big evolutionary problem? Is all the fuss about 4 amino acids?

Please don't overlook the fact that the SARS-COV-2 Spike protein can be aligned with bat sequences! That means they are evolutionary similar enough that the Alignment tool succeeds in aligning them. Yes, there are many differences, but they are all single amino acids substitutions. So, they do not cause a complete failure of the alignment. Dr. Wilson points out that we don't expect these single amino acid substitutions if those bat viruses were used to create the SARS-CoV-2 virus in the lab. In fact, the engineered virus should be nearly 100% identical to an existing bat virus, except for the PRRA site. But that is not what we see. It would be pointless to create hundreds of pointless mutations. Conclusion: SARS-CoV-2 virus is not engineered.

Possible reply: but the putative engineers didn't use those bat sequences, but others! My reply: but where are they? Nobody have found them. The fact that nobody has found bat viral sequences 99,9% identical to SARS-CoV-2 is a problem for both hypothesis, the natural and the unnatural. Evolutionary biologists did not find the missing link, and 'Intelligent Design theorists' did not come up with the sequences that were used to create SARS-CoV-2.

Finally, we are comparing sequences with the first-ever sequenced SARS-CoV-2 in Dec 2019 in Wuhan in a human. Not with the highly mutated sequences of today. The bat sequences are older. The hunt is for bat viral sequences more recent or more similar to SARS-CoV-2. This blog will certainly not be the final blog about the origin of SARS-CoV-2!

I recommend readers of this blog to view the video of Dr. Wilson again (8 min) to have a better understanding of his arguments for the hypothesis that the SARS-CoV-2 virus has a natural origin. It doesn't make sense to repeat all his arguments here.


Notes

  1. The sequence at Spike S1/S2 site enables cleavage by furin and phospho-regulation in SARS-CoV2 but not in SARS-CoV1 or MERS-CoV, Nature, 9 Oct 2020.

 

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