My Holy Week Tweets

The following are the daily tweets I posted during this past Holy Week. The video clip is from The Gospel According to Matthew by Pasolini (1964). The music at the end of the clip if from an African mass called Missa Luba.

(Ignore the first few seconds of the video)

Saturday 4/13. Tomorrow, Palm Sunday, is the start of Holy week. As is my custom, from now until after Easter, I will engage with other Christ followers, but will not reply to anti-Christian posts or replies. This is a period of deep reflection on our Savior’s sacrifice, not one for arguments.

Palm Sunday 4/14. “Hosanna!” “Blessed is he who comes in the name of the Lord!” “Blessed is the king of Israel!” The words of the Jewish crowd as Jesus entered Jerusalem. All phrases showing they believed Him to be the Messiah. As He has proven to be, and so much more.

Monday 4/15. Jesus cleansed the Temple of the money changers & all who profaned His Father’s house. My Church is an old stone building with courtyards, chapel, lots of space. When I’m there alone, I find the calm & quiet conducive to prayer & reflection. I think Jesus would be happy there.

Tuesday 4/16. The words from Matthew, spoken by Jesus as a man “Yet not as I will, but as Thou wills” should be part of every prayer. We’re told to pray for what we need & what we want, but those words remind us that we are to accept God’s will, even if it seems a bitter cup. We too will rise.

Wednesday 4/17. “He denied it again, with an oath: I don’t know the man!” Peter’s words (Matt 26:72) break my heart, just as they broke Peter’s when the rooster crowed. To face one’s own betrayal, cowardice, & failure is bitter. Yet we do it, are forgiven, & like Peter, carry on in Christ.

Maundy Thursday 4/18. Pilate asked “What is truth?” but Jesus gave no answer, because He knew it wasnt a question. Pilate was saying we will never know the complete truth. He could not understand that the complete incarnated truth was standing in front of him. In 3 days, that truth would be proven.

Good Friday 4/19. The curtain between Heaven and Earth is torn. The ground shakes, the sky darkens. Today we are a people of sorrow, acquainted with grief. In despair, we can only pray, and wait. But He is with us, even today.

Holy Saturday 4/20. Today Peter, no longer a rock, is simply Simon. Imagine him, recalling his failure and despair of yesterday, with no idea of the coming joy. Have you been there? I have. But we know what Simon didn’t. Tomorrow brings joy and hope. Peter will rise with Jesus, and so will we.

Easter Sunday 4/21.

Shout! Run! Sing! Rejoice!


Glory Hallelujah!

He is Risen Indeed.


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Textual Analysis (Silly Alert!).

Biblical scholarship is a very difficult field of study, requiring expertise in many areas. One of the most challenging aspects of understanding the true meaning of Biblical (or any ancient) text is making sense of the wording in the context of the contemporary cultural and linguistic milieu of the period in question. As an example of the perils and trials of textual analysis, lets take this example of a future study of an obscure American text from the early 19th century.

The text is written in the form of a poem, but many authorities believe it was a song. Some scraps showing musical notation associated with parts of  the text have survived, but the fact that all attempts to actually sing the melody indicated by these notes is virtually impossible has led to strong doubts that this poem was actually ever sung. At least not to the tune as notated.

The text follows along with commentary on its analysis.

Title: The Star Spangled Banner

Oh, say can you see,
By the dawn’s early light,
What so proudly we hailed
At the twilight’s last gleaming?

Here we are being asked if we can see something in the light of the dawn. Since there is no specification of what we are being asked about, we cannot give a definitive answer. The only clue seems to be that it was something that was hailed – perhaps a taxi cab, or Julius Cesar, at the end of the shining of the twilight. So this must mean (since Julius Cesar was long dead at the time) that we are being asked if we can still see the taxi cab that brought the group of people referred to as “we” home the previous evening, and then parked outside their house in the early dawn. Generally cabs would  not have  stuck around all night outside of the house they delivered people to, so the answer must be no.

Whose broad stripes and bright stars,
Through the perilous fight,
O’er the ramparts we watched,
Were so gallantly streaming?

So apparently, this taxi cab which is the subject of the first stanza was covered in stripes and decorated with stars, which sounds bizarre (almost all NYC taxicabs were painted yellow for unknown reasons or significance), but then again, so is the idea that people would hail a taxi cab with pride. Maybe there was something special about the cab. The perilous fight is easy. Ever try to get a taxi in midtown NY at the height of the rush hour? It probably wasn’t any easier back then. There is no possible clue to what ramparts they watched over (assuming that the omission of the “v” in “over” has some reason). And it appears that the stripes and stars in the first line were streaming, which makes the appearance of this taxi cab even more bizarre. And why the word “gallantly”, unless it refers to the driver who managed to get them home?

And the rockets’ red glare,
The bombs bursting in air,
Gave proof through the night
That our flag was still there.

This is really a stumbling block. Its either allegorical (I mean Manhattan can be rough, but rockets and bombs didn’t generally glare and burst in the streets) or this entire incident occurred on July 4th, which actually also fits the last line, since flags were also displayed on that national holiday. The third line is hopelessly obscure. The issue of proof is completely outside of anything related to the rest of the piece.

O say, does that star-spangled
Banner yet wave
O’er the land of the free
And the home of the brave

This last stanza seems to hold some important keys, since it contains the title of the piece (the star spangled banner). Again, as in the first stanza it asks a question, which seems impossible to answer or even understand. Banners are flags (see previous stanza) but what does this have to do with our taxi cab? “Star spangled” is clearly an idiom whose meaning is lost to history, although it might relate to the stars painted on the taxi (see above). The last two lines are extremely difficult. It appears that this banner may or may not be waving over two places, whose descriptions are… well much too general to give any clues about their precise location. The land of the free could be almost anywhere, depending on who exactly (humans? Animals?) are the free creatures referred to. As for home of the brave, well that could be the subjects (“we”), since they did venture out into the night of July 4th in New York City, found a bizarrely decorated taxi, and made it home in one piece. In conclusion, this text is most likely an insignificant personal record of a wild night in New York on a national holiday that clearly involved considerable loss of cognitive function on the part of the writer, probably due to intoxication.


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My Academic Genealogy

Becoming a scientist involves, among other things, personal transmission of knowledge and methodology from academic scientists to their students and trainees. Every scientist has spent time as an apprentice in the laboratory of a senior academic advisor or mentor, from whom they learned the tools and tricks of the trade. The budding scientist learns how to write a paper, how to make collaborations, how to hold a pipette, how to survive long periods of experimental failure, how to set up apparatus, and on and on. When students finally graduate with a doctoral degree, they go out into the world, and, eventually—with time, hard work and success—they become professors and begin to train their own students. And the cycle repeats, creating a long chain of teachers and students.

Every scientist can be said to be the product not only of his/her advisor but of all those scientists along the chain, creating a sort of genealogy of advisors and students, analogous to parents and children.  Its possible to produce the “academic genealogy” of any scientist by tracing the mentors of mentors as far as possible. I recently did this for myself using a web site called The Academic Family Tree. I will present the results going from myself backwards in time:

My mentor Charlotte Russell was Professor of Biochemistry at City University of New York, where she worked on heme biochemistry, as well as protein purification and natural product biochemistry.

Her mentor David Shemin (1911 – 1991) was Professor of Biochemistry at Columbia University. He worked on Heme biosynthesis and the biochemistry of red blood cell formation.

His mentor Robert M. Herbst (1904 – 1992) was Professor of Biochemistry and Molecular Biology at Northwestern University. He worked on reactions and synthesis of amino acids and peptides, the synthesis and chemistry of polynitrogen heterocyclic systems, and the chemistry of medicinal compounds.
His mentor Treat Baldwin Johnson (1875 – 1947) was a Professor at Yale who worked on pyrimidine chemistry.

His mentor Henry Lord Wheeler (1867-1914) was Professor at Yale and a pioneering organic chemist and biochemist. His research focused on pyrimidines. He developed a test for the presence of uracil and cytosine. He was a founding editor of the Journal of Biological Chemistry.

His mentor Horace Lemuel Wells (1855 – 1924) was professor of analytical chemistry and metallurgy at Yale. Wells dealt with inorganic chemistry and mineral analysis, especially with the salts of the halogens.

His mentor Oscar Dana Allen (1836 – 1913) was a professor at Yale, who investigated the chemistry of cesium and rubidium and made the first accurate determination of the atomic weight of cesium.

His mentor Samuel William Johnson (1830 – 1909), traveled to Germany to study under Von Liebig. He became Professor of Agricultural Chemistry at Yale. He devised apparatus for the determination of carbon dioxide and improved the Kjeldahl method for determining nitrogen in proteins.

His mentor Justus von Liebig (1803 – 1873) was the founder of organic chemistry and made major contributions to agricultural and biological chemistry. He invented the Liebig condenser (still used today). After his studies in Paris with Gay-Lussac, he returned to Germany, where he become Professor at the University of Giessen.

His mentor Joseph Louis Gay-Lussac (1778–1850) is known for his discovery that water is made of two parts hydrogen and one part oxygen, and for Gay-Lussac’s law of  gasses. He also worked on measurement of alcoholic content in beverages.

His mentor Claude Louis Berthollet (1748 -1822) is known for his scientific contributions to the theory of chemical equilibria, for his contribution to modern chemical nomenclature, and work on bleaching agents.

Antoine Lavoisier (1743-1794) is widely considered to be the “father of modern chemistry” and central to the 18th-century chemical revolution. He identified oxygen and hydrogen, did research on combustion and stoichiometry, and had a major influence on both the history of chemistry and the history of biology.

 So I am 12 academic generations removed from the father of chemistry, Antoine Lavoisier. Pretty neat.

This was nice to see, but not surprising. It’s likely that most current scientists can trace their academic genealogy to early illustrious giants. What it means is that all scientists are standing on the shoulders of those who came before us in a very personal way.

But on another level, it’s nice to think that perhaps some word of wisdom conveyed from Lavoisier to Berthollet might have been passed down through these generations and repeated to me from Charlotte Russell, and from me to many others. Because it didn’t end with me. I have trained ten grad students and eleven post docs. And most of them have trained others. I have academic “children” and “grandchildren” as well as twelve generations of “ancestors.” This means that scientific conferences are actually family reunions of thousands of academic “cousins.”

I did a quick check, and I am happy to see that I am (academically) related to Francis Collins, Linus Pauling, and many more modern scientists, with Von Liebig as a common ancestor who trained dozens of European and American chemists and biochemists.  Welcome to the family!



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Biblical Inerrancy and Biblical Science

I recently read the draft of a brilliant paper by one of the leaders in the science-and-faith field, my friend Denis Lamoureux. Denis is well known for his outspoken views and the fact that he is in possession of not one, nor two, but three doctoral level degrees, one in dentistry, one in evolutionary biology, and one in theology. In this paper (which I read as a draft, but which will be published shortly), Denis writes about one of his favorite subjects, the scientific consensus about the nature of the world in the ancient near east (ANE).

Reading his draft article gave me some ideas about the use of the word “inerrancy” as applied to Old Testament descriptions of cosmology, biology, and geology. What follows is a rough summary of those ideas.

At any period of history, there tends to be a general consensus about what is true about the world, whether based on basic observations or more scholarly efforts in logic and experimentation. This doesn’t mean everyone agrees or holds the same views as the consensus—we need only examine the present day to find millions of people who believe all sorts of nonscientific and extraordinary things. Likely this has always been true. But at least among the intellectual and cultural elite, scientific understanding about how the world works tends to spread and take root in the culture, and often the entire civilized world. This was no less true in the ANE than in Classical Greece, medieval or Enlightenment Europe, or today.

There is little question that the Biblical treatment of scientific knowledge reflects the scientific consensus of the ANE, including Egypt, Mesopotamia and probably other ANE cultures as well—with some regional variations, of course. Most of the details of that consensus have been since proven to be false or, at best, incomplete.

This fact has fueled a long-standing controversy about the issue of Biblical inerrancy. The thinking goes, if God inspired the writing of the Bible, why would He allow the human writers to get it wrong? God surely knows the truth: there is no firmament in the sky, and the Sun doesn’t circle the Earth. Why wouldn’t an omniscient God correct those mistakes?

One approach to this thorny issue has been various flavors of concordance, meaning attempts to interpret the words of Scripture in a way that would show that they weren’t really wrong, because instead of referring to actual physical reality, they were either allegorical or metaphorical, or somehow meant to imply something other than what they say.

Biblical literalists, including YECs, dismiss such arguments, based on the difficulty of knowing how to interpret Scripture. Of course Scriptural interpretation is always being done (by everybody) and we are able to distinguish between different kinds of Biblical texts (poetry, history parable, etc.). Still, the problem with concordance is that it doesn’t really address the central question of why God would allow something false to be written in His Book.

But where does that leave us? If we acknowledge that there are incorrect scientific statements in the Bible, we are admitting that inerrancy is a myth. That acknowledgment then brings into question everything in the Bible and weakens the basis of our faith. Or does it?

Let’s imagine that a group of scientists of Christian faith decided to rewrite the Bible today, in a revised modern version that would correct all the scientific errors of the original and produce a truly inerrant version. We would add our knowledge of the universe: the laws of physics, evolution, microbiology, and so on.

But would such a revision really be scientifically inerrant? Would it be true? Not likely. We now know that scientific truth is subject to rapid and dramatic change, and I am sure no one would doubt that our current version of the true nature of cosmological and biological origins and mechanisms would appear terribly errant to readers 5000 years in the future.

So we are left with the unanswered question posed by Pilate in John 18:38 “What is Truth?”

My point is that describing the complete scientific truth about our universe (which inerrancy would require) is impossible for any human at any time. This is a fact we now know, and clearly it has always been known by God, which is why He did not attempt to correct the erroneous information that the inspired Biblical writers committed to paper. On this view, it is a mistake to even discuss any scientific treatment as being either errant or inerrant outside of its historical context. Does anyone attack Darwin for not knowing about genes? Or Pasteur for ignoring viruses? Why didn’t Galileo discuss Black holes? And so on.

It has struck me that when God appeared on earth, hundreds of years after the composition of Genesis, He spoke of many things and taught many lessons, but He said nothing about science. Jesus could have corrected some of the earlier errors about nature. After all, the science of that time had progressed thanks to Greek philosophy, and some of that new knowledge probably had spread to Judea. But no such modernization of the original text was ever recorded among the sayings of Jesus. When He spoke of fulfilling the law, Jesus was talking about moral and behavioral statements, not the understanding of nature or how the world was built.

The theological statements of Scripture are inerrant. The scientific and nature-based statements of Scripture are errant because they must be, since we cannot know the final truth of any part of them. Therefore, I propose that when we discuss Biblical inerrancy, we remove any scientific descriptions of the world (including the details of its creation) from the discussion and focus on the universal and timeless truths of God’s Word.

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After I rejected the strong atheism of my upbringing, I spent many years wondering what the truth was about the existence of God. I investigated several theistic and spiritual systems. At one point I became fascinated with Jewish mysticism; I read several books on Buddhism; I listened to relatives who had delved deeply into Indian religion; I learned transcendental meditation. (I even peeked into Scientology – and I fled.)

All of this convinced me that there really was something that existed beyond the material world studied by science. I called this something “spirituality”. I began thinking that maybe the idea of “God” was the immaterial manifestation of this spiritual reality. But I was also getting the sense that if that was true, God was a very distant and unknowable entity. Both the Kabballah and the sayings of the Buddha seemed to confirm this.

I found myself standing on the shores of a sea of mystery, certain that the waters hid treasures of beauty and goodness, but with no way to see them for myself.

And then, prompted by a friend, I read the Gospels. I had read some of them before in school, but only as an exercise to reinforce my atheistic scorn at the stupidity of Christianity. Back then I was focused on the magic, the contradictions, the naiveté of the ignorant who believed in scientifically impossible events like the resurrection.

When I read the Gospels the second time, my mind was open, freed of the ideological certainty of atheism. I still saw the contradictions, but now they appeared as evidence for truth, the kind of differences one would expect in true eyewitness accounts. I still saw the magic, but now it confirmed for me my new-found conviction that science is not the only pathway to truth. And now I saw the figure of Jesus Christ, and reading His words, I realized that God must have seen me standing on the shore, staring helplessly at the waves. Jesus Christ rose from those waters and held out His hand to me.

“So you want to see God?” He asked me. “Here I am.”

The above is a poetic image, but something very similar actually happened to me, in a dream about a frightening cliff, and in another about a beautiful garden. Jesus was there in both, showing me a new reality, helping me find the gate. Jesus Christ was real, He was the incarnation of God, and He was calling me.

Well, let’s take a deep breath. I was at the time, as I had been long before and remain today, a scientist. And by most objective measures, a fairly successful one. I know that dreams are images produced by neurophysiological and psychological factors, and, like so many subjective experiences, they can be easily explained  as materialistic phenomena. So perhaps I had those dreams (and other subjective experiences) because I wanted to (as I have since been told many times).

That explanation was the one I had used as a young man to dismiss several similar experiences that I couldn’t readily make sense of at the time. But now I rejected it, as I rejected atheism as a failed worldview.

I thought of the widespread belief among scientists of the late 19th century that there wasn’t much else to learn about the physics of the universe, and the idea that the origin of life would be a simple problem of chemistry to solve. What replaced all these beliefs was not something simpler and more elegant, but theories that are far more complex and perhaps even semi-mystical, bringing into question our reliance on pure materialism as the universal truth of nature. I expect the same to happen with the current popular notion that consciousness is nothing but an illusion,

To say that dreams are just neurological impulses is like saying a Kandinsky painting is just paint and canvass, a Beethoven symphony is just sound waves, and love is just a trick of hormones. One could as easily say that the ideal gas law or the Schrödinger equation are just letters and symbols with an equal sign in the middle. And what you’re looking at now is merely the geometrical arrangement of two-dimensional symbols against a white background – “reading” is an illusion.

Which brings me back to my reading of the gospels. The figure of Jesus was powerful and produced a sense of awe in my soul. But perhaps even more important to me were the mortal characters in the story. Acts of the Apostles, which I read for the first time, brought these people into sharp focus. Peter, the man who denied Christ and abandoned him at the end, and Paul, the archenemy of the new faith, sprang off the pages as real people, not the subjects of a mythological propaganda piece. I was quite used to the stories of Soviet heroes from my childhood – they were so perfect that even as a child, I suspected that there might be just a touch of exaggeration there. But Peter was weak before he became strong; Paul was headstrong and vicious before he became virtuous (if still headstrong).

It was the resurrection of Jesus Christ that produced the transformations of these men. It was the same event that brought them together and called out to so many people of the time. It was the event that led within less than 100 years to the growth of a new religion to over a million believers – despite persecution, the murders of their leaders, and the destruction of Jerusalem, the original center of the new faith.

There was no doubt in my mind as I finished Acts that the resurrection was the central point of Christianity, that it defined who Jesus was and who we are. Because I saw myself in Peter, and even more so in Paul. Not because of the great work they did after the resurrection, but because of Peter’s weakness and Paul’s intransigence. And as I finally came to accept Christ as my Lord and Savior (the details of which, along with those of my dreams I have written about elsewhere), I saw that I and all of suffering humanity are perfectly reflected in the transformed lives of these apostles.

But how can a scientist believe in miracles? That question has been asked and answered numerous times, and I have not much wisdom to add. I rejected scientism a long time ago, even while still an atheist, so I have no problem understanding that science has limits, and that miracles, by definition, are not addressable by science. Even my father, a communist, atheist, strict materialist, and also a physical chemist, told me that the scientific method is not able to address all questions in life and nature.

Science has been my lifelong passion, but I have always been enamored of history, and while I never considered making it an official professional relationship, my attachment to the lure of historical scholarship has also been a lifelong affair. Everything I have read about the history of Christianity confirms my subjective belief in the reality of Christ’s resurrection and divinity. Again, this case has been presented by many, and I can only add that I found it convincing from the time I understood the historical reality of the first century.

I believe in the resurrection of Christ because I believe in God, and in Jesus Christ as the incarnation of God on earth, and I believe in the redemption of human beings like Peter, Paul, Mary Magdalene, myself, and you. If there was no resurrection, there would have been no Christianity, and history would have been entirely different, probably without science, hope, or moral progress. As C.S. Lewis so famously said, “I believe in Christianity as I believe that the Sun has risen, not only because I see it but because by it, I see everything else.”

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Merry Christmas to All!

And a happy and blessed new year. I will be back in January with new posts on various topics, including the origin of life, the question of purpose, how to be happy, and similar light stuff. And before we know it, Spring will be here. Peace and blessings.

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My Favorite Enzyme Part 3 (Final)

OK readers, here we go. Now that you have the basics, let’s get back to the hero of this series, my favorite enzyme, Aminoacyl tRNA Synthetase (usually referred to as aaRS, not Syzase). Remember that the task of the enzyme is to join the right tRNA with the right (cognate) amino acid. The tRNAs each carry one amino acid to the ribosome where their cargo (the amino acid) is added to the growing protein chain in the correct order. This happens because the tRNAs, using their anticodon triplets, bind in turn to the codons on the mRNA, which have been copied from the master code sheet, the DNA.

Amino acids and tRNAs cannot recognize each other because they are parts of different chemical systems, so there is no way that the correct amino acid (matching the tRNA anti codon) could ever get matched with its tRNA without help. It would be like an English-only speaker having a conversation with an Italian-only speaker. They need a translator. And the helper/translator is aaRS. That’s why I consider this enzyme to be at the heart of the entire translation process.

How does the enzyme do this? First, each enzyme has a binding site for its specific amino acid. So alanine aaRS has an alanine binding site. It also has a binding site for each of the 4 tRNAs that carry one of the 4 anticodons for alanine. Once this very large enzyme has alanine bound in one site and an alanine tRNA bound on the other site, the protein conformation (the protein’s shape) shifts in a way so that the end of the tRNA and one end of the amino acid are close. The enzyme then catalyzes a chemical reaction (requiring energy) between the two molecules, and the result is a strong chemical bond between tRNA and amino acid. The process is illustrated in the following figures.



Imagine the interpreter saying “Mr. Smith, let me introduce Mr. Russo; Signor Russo, le presento il Signor Smith.” And the two men shake hands. Only in the chemical case they don’t let go; they are bound.


So the enzyme has done its job. It has taken its amino acid and matched it with the right tRNA so that the amino acid will be put in exactly the right place determined by the DNA sequence. Once this is done, the new bonded tRNA-amino acid complex can leave its binding sites, and as a tightly bound couple navigate its way to the ribosome, where the two molecules will part company, the tRNA to go back to finding another aaRS (or maybe the same one), and the amino acid to live the rest of its life as part of a protein.

But wait, we aren’t done. If this were the whole story, it would be amazing and exciting, but there’s more. You see, the entire process of translation really needs to be very accurate. If the wrong amino acids get attached to the wrong tRNA, the protein sequence will not be what it’s supposed to be, and the protein might not work. In fact, the entire translation process, including the work of the aaRS, is extremely accurate, with one mistake in over 10,000 trials. To reach that level of accuracy, the binding and matching I described above just won’t cut it. Many amino acids are very similar to many other amino acids (just ask a biochem grad student), and mistakes can definitely be made. A leucine might just fit into the binding site on an isoleucine aaRS, and that wouldn’t be good. And alanine is only slightly bigger than a glycine, and it would take an amazingly well engineered binding site to be able to distinguish the right from the wrong amino acid with 99.999% success.

So the enzyme has some tricks to make sure it hasn’t screwed up. Once the amino acid and tRNA are bound, the happy couple are shunted to another site on the enzyme called the editing site. This site is shaped in a way that will allow almost any amino acid and tRNA to get in, except the right ones. That particular amino acid tRNA just doesn’t fit. It’s especially good at admitting smaller amino acids while excluding the right one. So if everything is correct, the amino acid tRNA does not (cannot) bind in the editing binding site, and it breaks free from the enzyme to go on its merry way toward the ribosome. But if a mismatch or some other error had taken place, and the mistakenly bound couple does fit into the editing site, it’s cut into pieces by the action of the enzyme and never gets close to the ribosome.

So not only does my favorite enzyme recognize the proper amino acids and from 1 to 6 proper tRNAs, and not only does it provide the energy and mechanical means to link the two together, it also makes sure it got it right and deals a death blow to any erroneous products. Pretty neat, eh?

And I should mention that every cell in every living thing on this planet has the same system and has had it as far back as LUCA. In fact, we have no idea what came before and how the present universal system evolved, since it’s this system that is the biochemical key to evolution. But we can discuss this another time. For now I hope you will agree that aminoacyl tRNA Synthetase should be everyone’s favorite enzyme.


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