Five more species of bacteria use alternate genetic codes

_{Denyse O'Leary

November 10, 2021

Genetics, Intelligent Design}

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Bringing the known number to twelve:

The genetic code that dictates how genetic information is translated into specific proteins is less rigid than scientists have long assumed, according to research published today (November 9) in eLife. In the paper, scientists report screening the genomes of more than 250,000 species of bacteria and archaea and finding five organisms that rely on an alternate genetic code, signifying branches in evolutionary history that haven’t been fully explained…
“The genetic code has been set in stone for 3 billion years,” study coauthor Yekaterina Shulgina, a Harvard University graduate student in systems biology, tells The Scientist. “The fact that some organisms have found a way to change it is really fascinating to me. Changing the genetic code requires changing ancient, important molecules like tRNAs that are so fundamental to how biology works.”
As such, the code was thought to be largely preserved across all forms of life, with scientists finding the occasional exception during the past several decades of research. In addition to finding five new alternate genetic codes, the team also verified seven others that had been discovered one-by-one in the past, bringing the total number of known exceptions in bacteria to 12.
Dan Robitzski, “Screen of 250,000 Species Reveals Tweaks to Genetic Code” at The Scientist (November 9, 2021)

Apparently, it was not set in stone. Not only was it very complex very early but it can be complex and different and still work. By now, Darwinian dogmatism is beginning to sound ridiculous.

The paper is open access.

Comments

Seekers: That is a very nice quote collection of a man giving his personal opinion and beliefs regarding the ID movement, it cannot be used as a representative of everyone who falls under the ID umbrella, but I’m sure your aware of that. Or maybe not. Just curious . . . do you think there is now a fully worked out scheme or theory of intelligent design as referred to by Dr Johnson?JVL_{November 14, 2021
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Seversky No connection between Intelligent Design and Christianity?
Of course there is a connection. Both are true. No connection between philosophical naturalism (your religion=atheism) and methodological naturalism? :) Yes there is a connection.Lieutenant Commander Data_{November 14, 2021
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Seversky, That is a very nice quote collection of a man giving his personal opinion and beliefs regarding the ID movement, it cannot be used as a representative of everyone who falls under the ID umbrella, but I’m sure your aware of that. Or maybe not.Seekers_{November 13, 2021
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No connection between Intelligent Design and Christianity? Here are a few quotes from Phillip E Johnson, regarded as the founding father of ID. One the Wedge Movement:
"The first thing you understand is that the Darwinian theory isn't true. It's falsified by all of the evidence, and the logic is terrible." "...the next question that occurs to you is, 'Well, where might you get truth?' ... I start with John 1:1, 'In the beginning was the Word.' In the beginning was intelligence, purpose, and wisdom. The Bible had that right and the materialist scientists are deluding themselves." "The next question is: Why do so many brilliant, well-informed, intelligent people fool themselves for so long with such bad thinking and bad evidence?" Johnson sees this as an issue of "turning away from" self-evident truth, the "sin question" and the need to prepare the way for acceptance of a Creator.

I have built an intellectual movement in the universities and churches that we call "The Wedge," which is devoted to scholarship and writing that furthers this program of questioning the materialistic basis of science. ... In summary, we have to educate our young people; we have to give them the armor they need. We have to think about how we're going on the offensive rather than staying on the defensive. And above all, we have to come out to the culture with the view that we are the ones who really stand for freedom of thought. You see, we don't have to fear freedom of thought because good thinking done in the right way will eventually lead back to the Church, to the truth-the truth that sets people free, even if it goes through a couple of detours on the way. And so we're the ones that stand for good science, objective reasoning, assumptions on the table, a high level of education, and freedom of conscience to think as we are capable of thinking. That's what America stands for, and that's something we stand for, and that's something the Christian Church and the Christian Gospel stand for-the truth that makes you free. Let's recapture that, while we're recapturing America

If we understand our own times, we will know that we should affirm the reality of God by challenging the domination of materialism and naturalism in the world of the mind. With the assistance of many friends I have developed a strategy for doing this, ... We call our strategy the "wedge"
...
"We are taking an intuition most people have [the belief in God] and making it a scientific and academic enterprise. We are removing the most important cultural roadblock to accepting the role of God as creator."[51] "Our strategy has been to change the subject a bit, so that we can get the issue of intelligent design, which really means the reality of God, before the academic world and into the schools."[44] "This isn't really, and never has been, a debate about science. It's about religion and philosophy."[45] "So the question is: 'How to win?' That's when I began to develop what you now see full-fledged in the 'wedge' strategy: 'Stick with the most important thing' —the mechanism and the building up of information. Get the Bible and the Book of Genesis out of the debate because you do not want to raise the so-called Bible-science dichotomy. Phrase the argument in such a way that you can get it heard in the secular academy and in a way that tends to unify the religious dissenters. That means concentrating on, 'Do you need a Creator to do the creating, or can nature do it on its own?' and refusing to get sidetracked onto other issues, which people are always trying to do."[15]
As for ID as science, Johnson did write later
I also don’t think that there is really a theory of intelligent design at the present time to propose as a comparable alternative to the Darwinian theory, which is, whatever errors it might contain, a fully worked out scheme. There is no intelligent design theory that’s comparable. Working out a positive theory is the job of the scientific people that we have affiliated with the movement. Some of them are quite convinced that it’s doable, but that’s for them to prove…No product is ready for competition in the educational world.
Seversky_{November 13, 2021
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Does anyone else get the feeling that when you read CD and Sev, you are fighting against the Black Knight in the Holy Grail? How many more legs/arms/teeth do you have to stand on? Everything seems to be ad hoc to try to fix the myriad of holes in the materialist boat.zweston_{November 13, 2021
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Sev@24 "That said, there is clearly a vast amount we don’t know yet about this Universe. Maybe there is hope in the unknown." Hope of what? That science will find a way to support a materialist process origin for everything we see? What a blind faith statement!... And one that leads to no real hope ultimately either.zweston_{November 13, 2021
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Seversky
We can posit some vast alien intelligence behind it all but that just pushes the question of origins back one stage so asking who designed the designer is a perfectly legitimate question.
Of course it is a legitimate question. However not for ID. Intelligent design theory seeks only to determine whether or not an object was designed. Why would anyone think that the onus is on ID to provide for ultimate answers? If someone proves that a certain chemical explains some phenomenon, is the answer to the question "but what caused the universe to exist?" also a mandatory follow-up?Origenes_{November 13, 2021
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Intelligent Design traces back to before Christianity was founded. Why do ID's opponents think their ignorance is an argument?ET_{November 13, 2021
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seversky:
We have no idea why or how the Universe has come to be as it is.
Then there isn't any treason to exclude Intelligent Design from science classrooms.
We can posit some vast alien intelligence behind it all but that just pushes the question of origins back one stage so asking who designed the designer is a perfectly legitimate question.
Is that what archaeologists and forensic scientists do? Or are you just desperate?ET_{November 13, 2021
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Methodological materialism is a restriction , a limitation that is necessary to do science . Ok. Unfortunately the Science of origins didn't even begin to progress while other sciences have developed like never before .Why is that? Why didn't scientists realize how a cell came about? A scientist limited by methodological materialism can think at only one explanation: We have to dig more, to try harder ... In objective reality there are at least 2 explanations : first, if randomness is true then scientists have a fundamentally wrong aproach and second, if a Superior Mind is involved then the power of our processor (our brain) is too "low" for the job . In the last 100 years is nothing new in the Science of origins (even the technologies and tools of biology science labs progressed like crazy) .Why? Because the scientists are bound(by the Methodological materialism) to accept a wrong presupposition(never observed in reality) that a code can emerge from random processes. This is an example of unprovable belief . And they are blocked.Lieutenant Commander Data_{November 13, 2021
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The confusion by many that ID is intertwined with Christianity is deliberate misinformation done knowingly to undermine it. Because it is misinformation, it is as I said above a non-sequitur. Opponents of ID including many Christians will deliberately tie ID with creationists knowing the average person assumes this means Young Earth Creationists. And this means bogus science. So ID is tied to bogus science in the eyes of most. And thus discredited. Now ChuckDarwin knows this is not true but yet persists in making fake claims and snarky remarks. He will not address science or logic. He is AOL on anything relevant. Don’t expect any epiphany (sorry to use a Christian term) for him or any other here disputing ID. They already understand what it is about but are emotionally tied to a position that contradicts ID but they cannot support their positions with logic or evidence. They constantly rely on making false claims about ID. It’s difficult to understand such people but the world if full of them. It’s almost as if the world was designed that way.jerry_{November 13, 2021
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ChuckDarwin, this is the case for Christianity: 1) there is a creator of the universe - supported by ID and accepted by Paul Davies - they are in agreement 2) Christ is God or sent by God to accomplish something - ID says zero about that. ID does not contradict that. However, ID does not contradict a lot of things. 3) Christ started a Church - obvious from early writings by adherents- nothing to do with ID So how is ID tied to Christianity when it says nothing about 2) and 3).jerry_{November 13, 2021
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Jerry & ChuckDarwin
ChuckDarwin: This statement explicitly ties ID to Christianity:
[Paul Davies:] The intelligent design movement has inevitably seized on the Goldilocks enigma as evidence of divine providence….

Jerry: The explanation by ChuckDarwin is a non sequitur.
I am with Jerry on this: ID is not and should not be tied to Christianity. While it is true that many intelligent design proponents are Christians (which is their world-view right), not all are. I for one am not a Christian. It is straightforward: to believe in intelligent design is not necessarily to believe in Christianity. In support of ChuckDarwin, Paul Davies might make the claim that this is the case. But if so, Davies is mistaken.Origenes_{November 13, 2021
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This statement explicitly ties ID to Christianity
The explanation by ChuckDarwin is a non sequitur. Nothing is related to Christ and it’s hard to say anything is Christ oriented when nothing is said about Him. All ChuckDarwin is saying is that the creator had/has an objective. That is consistent with Christianity but not Christianity per se. It could be consistent with other conceptions of the creator too. As I said ChuckDarwin is an ID adherent. He just has trouble using logic and reasoning.jerry_{November 13, 2021
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Davidl1 @26 You are welcome. Intelligent Design is simply the science of design detection — how to recognize patterns arranged by an intelligent cause for a purpose — nothing more and nothing less. Intelligent design defined. What ID points to is a very interesting question, however it is beyond the scope of ID itself.Origenes_{November 13, 2021
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Origenes, thanks for the explanation / definitions. My understanding (maybe incorrect) was that people like Benjamin Franklin were considered deists. He believed that humans were intentionally created, and given the ability to reason, by God, but he rejected theism. I think that ID points to a belief in a creator who intentionally created the universe and living things in the universe. That doesn't necessarily mean a benign or involved creator, just a creator (or creators, etc). Believing anything more (e.g. religion) or less (e.g. that living things were the result of unguided processes) takes some rationalization. (not necessarily wrong, but not a conclusion based on ID).davidl1_{November 12, 2021
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With regards to the origin of life, we have a good idea what the promoters of non-intelligent abiogenesis are up against. https://www.youtube.com/watch?v=W1_KEVaCyaA https://www.youtube.com/watch?v=zU7Lww-sBPg –Ramram_{November 12, 2021
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We have no idea why or how the Universe has come to be as it is. Matter, energy and the laws by which they are ordered may be sufficient to account for what we observe but we have no idea why they are as they are. We can posit some vast alien intelligence behind it all but that just pushes the question of origins back one stage so asking who designed the designer is a perfectly legitimate question. Beyond the relatively benign conditions in this thin envelope of atmosphere that surrounds our little planet, the Universe is implacably hostile to life such as ours. Even here we are far from being safe and secure. I suspect that our ancestors were dimly aware of that and the hope that someone, somewhere might be looking out for them became belief over time. It's not necessarily wrong but the phrase "grasping at straws" comes to mind. That said, there is clearly a vast amount we don't know yet about this Universe. Maybe there is hope in the unknown.Seversky_{November 12, 2021
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Davidl1
To me, the view that is as close as possible to self-evident, is that the universe and the things in it (including living things) are here by intent. That doesn’t rule out religion, but it certainly doesn’t depend on it.
An obvious explanation of the self-evident intent, you speak of, is a God. Matter and energy is no option since it has no intent whatsoever. So, I agree intent doesn't rule out religion, quite the contrary in fact. But indeed it doesn't necessarily point to religion, an alien could have seeded the earth with life.
My understanding is that Deists reject the idea of a personal God, but that doesn’t preclude belief in creation of life.
Meyer calls the belief in an impersonal God "pantheism." It can explain the creation of life. However, as Meyer argues, pantheism cannot explain the fine-tuning/ creation of the universe:
Eastern pantheists assert “atman is brahman,” meaning “the soul of the self” or “the soul of the world,” is “the soul of the One,” where the unified but impersonal oneness of all things represents the ground of all being—all that is ultimately real. Though a pantheistic worldview affirms the existence of a god, it fails to explain the origin of the universe for much the same reason that naturalism does. The god of pantheism exists within, and is coextensive with, the physical universe. Thus, god as conceived by pantheists cannot act to bring the physical universe into being from nothing physical, since such a god does not exist independently of the physical universe. If at some finite point in the past the physical universe did not exist, then a pantheistic god would not have existed either. If the pantheistic god did not exist before the universe began, it could not cause the universe to begin to exist.
Origenes_{November 12, 2021
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Davidl1 Here are some definitions from the book 'Return of the God Hypothesis' by Stephen Meyer:
“Naturalism” (or materialism) views matter and energy and the laws of nature as the prime realities. “Pantheism” asserts an impersonal deity present in matter and energy as the prime reality. “Theism” affirms a personal, intelligent, transcendent God who also acts within the creation. And “deism” affirms a personal, transcendent, intelligent God who does not act within the created order after its initial origin.
Origenes_{November 12, 2021
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Origines, My understanding is that Deists reject the idea of a personal God, but that doesn't preclude belief in creation of life. I think the arguments that support intelligent design in life are very similar to the arguments that support intelligent design in the universe. Fine tuning is everywhere in life. Does that conflict with deism? To me, the view that is as close as possible to self-evident, is that the universe and the things in it (including living things) are here by intent. That doesn't rule out religion, but it certainly doesn't depend on it. I would think that would be consistent with deism.davidl1_{November 12, 2021
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Davidl1
Personally I think ID points directly to deism.
WRT a fine-tuned universe, ID and deism have no quarrel. However deism holds that there was no designing intelligence involved with the advent of organisms — the deist typically accepts Darwinism. ID has a very different take on that.Origenes_{November 12, 2021
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Personally I think ID points directly to deism. There may be other things pointing to Christianity, but that's completely outside the scope of ID. ID is compatible with Christianity (and deism and pretty much any variant of theism as far as I know), but it's not a Christian worldview.davidl1_{November 12, 2021
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The fact that Davies is a deist explains why he has no problem whatsoever pointing out that materialism has no explanation for the laws of nature; creating them is part of the limited job of a deistic God. Davidl1 @16
... he acknowledges that fine tuning is a problem. I think he’s one of the few people who are objective enough to trust regardless of which side you believe.
Same thing here. That's no 'acknowledgment' by Davies. Fine tuning is not a problem for a deist, on the contrary.Origenes_{November 12, 2021
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Chuck... you are unbelievable... forget about Paul Davies ... you have missed the point again... Look at the video i posted above, and LISTEN TO WHAT CRAIG VENTER IS SAYING !!!martin_r_{November 12, 2021
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CD, Thanks for the response. I think divine providence also applies to non-Christian worldviews that accept a deity that intervenes in human affairs and/or is responsible for the universe. ID is certainly not a Christian worldview, so I'm skeptical that Davies thinks it is. I've always enjoyed Paul Davies books / articles. He's not personally ID-friendly, but a lot of what he writes is ID-friendly. This was the first time I've heard anybody say he is an ID supporter. I read something by him where he discussed the failures of materialistic OOL explanations, and I think that's what got me interested in his ideas.davidl1_{November 12, 2021
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This statement explicitly ties ID to Christianity:
The intelligent design movement has inevitably seized on the Goldilocks enigma as evidence of divine providence....
Davies then describes divine providence as it appears in classic Christianity. The link is unmistakable. I've been a long-time fan of Davies, so I get a little piqued when the ID folks try to claim him as their own, especially where he has rejected their worldview. No deist denies some type of cosmic organization and design. However, deism explicitly rejects theistic religions such as Christianity, etc. which form the underpinnings of ID.chuckdarwin_{November 12, 2021
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I never considered Davies to be an ID-supporter, but I think he provides a lot of information that is lends itself to an ID interpretation. He acknowledges that the commonly accepted materialist mechanisms for development of life are inadequate, and he acknowledges that fine tuning is a problem. I think he's one of the few people who are objective enough to trust regardless of which side you believe. Was there something in the article specifically that indicates that he considers ID to be a Christian worldview? The only references I saw to Christianity were showing parallels between science and Christianity.davidl1_{November 12, 2021
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Notice that although variations may be random, [natural] selection is far from random, so that it is not true to say, as is sometimes quipped, that Darwinism attributes the organized complexity of the biosphere to nothing more than random chance.
This is not an endorsement of Darwinism. Notice the weasel words in this quote This just says that natural selection is not random. It doesn’t say it does anything important relevant to Evolution. Two things: 1) Darwinism or micro evolution is not about the Evolution debate. It’s about genetics. 2) micro evolution done a zillion times does not produce macro evolution. So Darwin was right about genetics but wrong about Evolution. ChuckDarwin is batting a thousand on support for ID. Everything he says supports ID. Question: is he a plant by Barry?jerry_{November 12, 2021
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As to Paul Davies, he’s a very open-minded man who is certainly an ID-supporter as such; however, he’s convinced that the ‘intelligence’ that crafted life here on earth came from outer space. As a mathematician, he can see through the horrible defects of neo-Darwinism ideology.
Actually, Davies is a theoretical physicist, not a mathematician, and a deist. He is not a fellow traveler with ID (i.e. "sort of a (sic) ID-supporter") and in fact has labeled it as "outdated and simplistic." He views the intelligent design movement for what it is--a Christian worldview. https://www.theguardian.com/commentisfree/2007/jun/26/spaceexploration.comment Moreover, Davies supports natural selection as the biological mechanism to explain evolution From his book Cosmic Jackpot:
Notice that although variations may be random, [natural] selection is far from random, so that it is not true to say, as is sometimes quipped, that Darwinism attributes the organized complexity of the biosphere to nothing more than random chance.
chuckdarwin_{November 12, 2021
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