Gobind Khorana 1922-2011

| 25 Comments

I just found out that Gobind Khorana died November 9 at his home in Concord MA. Khorana won the Nobel in 1968 (along with Nirenberg and Holley) for deciphering the genetic code. Before his work, nobody knew how a DNA sequence could “encode” the information necessary to make a protein macromolecule. His experiments were carried out in the classic bacterial system Escherichia coli. The realization that the genetic code in a single-celled bacterium is the exact same code used in humans is what finally convinced the biological community that all life, from trees to bacteria to elephants, shares common ancestry.

Khorana was also the first person to artificially synthesize a synthetic gene and use it to make a protein. It is not an exaggeration to say that these twin feats form the basis of all modern work on proteins.

Later, Khorana went on to use these techniques to investigate in detail the structure and mechanism of bacteriorhodopsin, which has to be one of the darn coolest proteins in the biosphere (full disclosure — I’m biased, since my lab now studies the evolution of bacteriorhodopsin). Photosynthesis evolved twice, with two very different mechanisms: plants use chlorophyll, and many bacteria use bacteriorhodopsin. While chlorophyll wins in terms of efficiency, bacteriorhodopsin is much simpler and more elegant.

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25 Comments

Wasn’t his name Har Gobind Khorana?

Joe Felsenstein said:

Wasn’t his name Har Gobind Khorana?

Yes, but he went by Gobind.

The realization that the genetic code in a single-celled bacterium is the exact same code used in humans is what finally convinced the biological community that all life, from trees to bacteria to elephants, shares common ancestry.

But that “conclusion” totally rested upon the assumption that similar effects have similar causes, and didn’t even include any consideration of the likelihood that magic was responsible for the similarities.

How can anyone even think to do science with those presuppositions?

Glen Davidson

Amazing. I can’t believe that the universal genetic code is thought of as necessarily implying universal common ancestry. Surely, it could be evidence for “convergent evolution” or, dare I even say it, a common design?

It is interesting that the genetic code, which is digital way of storing information, was discovered around the same time as the digital revolution in electronics was occurring. This ought to make some people think, but they don’t.

Theistofraud said:

Amazing. I can’t believe that the universal genetic code is thought of as necessarily implying universal common ancestry. Surely, it could be evidence for “convergent evolution” or, dare I even say it, a common design?

Only if you are so delusional as to think design is even an issue. There is too much evidence of incompetence in the “design”. I guess if you are incompetent yourself…

It is interesting that the genetic code, which is digital way of storing information, was discovered around the same time as the digital revolution in electronics was occurring. This ought to make some people think, but they don’t.

Ever heard of a coincidence, @$$hole? Besides, digital ways of storing data would be ten based, not four based. Idiot!

’ Finally convinced…” You mean before that the claims of evolution were still in doubt? This shouldn’t convince. it follows that a common design or blueprint would also have common DNA principals. Why not?

All life is so alike this creationist would want and would predict DNA would be alike in its foundations. yet not mean there is a common origin for life by way of evolution. Thats a line of reasoning and other lines of reasoning are just as good. I don’t see why this would be a conclusion from scientific investigation! Even if true.

Robert Byers said:

‘ Finally convinced…” You mean before that the claims of evolution were still in doubt? This shouldn’t convince. it follows that a common design or blueprint would also have common DNA principals. Why not?

All life is so alike this creationist would want and would predict DNA would be alike in its foundations. yet not mean there is a common origin for life by way of evolution. Thats a line of reasoning and other lines of reasoning are just as good. I don’t see why this would be a conclusion from scientific investigation! Even if true.

The creationist explanation for the origin and diversity of life is, essentially, “magic, performed by god”. If I understand you correctly, you believe this explanation should be taught as science, alongside science, in American public schools.

My question is, is there any phenomenon, artifact, or event which could not or should not be explained the same way? Why is the sky blue? There is a scientific explanation for this; should we also teach that it could be due to magic, performed by god? How was the moon formed? There is a scientific explanation for this; should we also teach that it is just as likely magic, performed by god? The explanation for why we think there was a historical figure named George Washington could be, according to your thinking, magic, performed by god. Should we teach all subjects that way? Why or why not?

dalehusband said: Ever heard of a coincidence, @$$hole? Besides, digital ways of storing data would be ten based, not four based. Idiot!

This comment epitomizes the ignorance of Panda people. The genetic code is digital. You are astonishingly confusing digital with decimal. Do you not know that the digital processing in a computer uses just two representations, 0 and 1? It is called binary. The code of life is instead quaternary. What is meant by digital is that information is represented by discrete and not continuous values. Now, learn why you are so manifestly wrong and I am so right:

The digital code of DNA

http://www.nature.com/nature/journa[…]re01410.html

I expect a fairly contrite and profuse apology from you.

Atheistoclast said:

dalehusband said: Ever heard of a coincidence, @$$hole? Besides, digital ways of storing data would be ten based, not four based. Idiot!

This comment epitomizes the ignorance of Panda people. The genetic code is digital. You are astonishingly confusing digital with decimal. Do you not know that the digital processing in a computer uses just two representations, 0 and 1? It is called binary. The code of life is instead quaternary. What is meant by digital is that information is represented by discrete and not continuous values. Now, learn why you are so manifestly wrong and I am so right:

The digital code of DNA

http://www.nature.com/nature/journa[…]re01410.html

I expect a fairly contrite and profuse apology from you.

Absolutely not, you worthless fraud! The only thing you will ever get from me is more contempt and scorn as long as you keep coming around here with your uppity know-it-all attitude when in fact you are profoundly stupid.

Digital originally referred to human fingers (digits) which come in tens, not fours or twos. It’s because of this that we have a ten based counting system. Having computers use a binary system was the result of our primitive computer technology over half a century ago. Thus the original meaning of “digital” was expanded. If that was the “digital” revolution” you referred to earlier, that’s a step down, not an improvement.

http://www.thefreedictionary.com/digital

dalehusband said: Absolutely not, you worthless fraud! The only thing you will ever get from me is more contempt and scorn as long as you keep coming around here with your uppity know-it-all attitude when in fact you are profoundly stupid.

But I do know nearly everything there is to know.

Digital originally referred to human fingers (digits) which come in tens, not fours or twos. It’s because of this that we have a ten based counting system.

You are, I repeat, confusing decimal with digital. Now, are you going to admit that you were wrong about your denial that the genetic is in fact a digital code? Are you going to just have the decency and honesty to admit that Clast was right as he is about everything on this forum? Is it is so hard for you to face reality and recognize my knowledge and understanding?

Once, just once, I would like to see a thread on PT where every single troll comment is completely ignored, and left totally unacknowledged, like ignoring a neighbor’s nasty little barking dog. It might have the effect of depriving someone of “graduate” “credits”.

Doug,

It is necessary to remove trolls to the bathroom wall, otherwise this is what you get. I recommend a complete sweep.

I agree with mjcross, ignoring the ignorant is the best policy.

mjcross42 said:

Once, just once, I would like to see a thread on PT where every single troll comment is completely ignored, and left totally unacknowledged, like ignoring a neighbor’s nasty little barking dog. It might have the effect of depriving someone of “graduate” “credits”.

Noted. Since I already showed the true origin of the word “digital” and how its meaning was corrupted by well meaning computer experts who didn’t bother to make up a new term to apply to something not related to fingers, I rest my case. Theisto@$$hole is just blowing farts into the wind.

Robert Byers said:

‘ Finally convinced…” You mean before that the claims of evolution were still in doubt?

No, that wasn’t what was said. It was that all life shares a common ancestry. Bacteria could have had common ancestry with bacteria, separate from humans who had common ancestry with mammals, vertebrates, etc., but it turns out that bacteria and humans and everything else has common ancestry.

This shouldn’t convince. it follows that a common design or blueprint would also have common DNA principals. Why not?

Well, why? And it isn’t that they have common DNA principles, it’s that they have virtually the same genetic code. But not identical, in fact, evolution has caused them to diverge somewhat.

Yet what’s interesting is that mitochondria are closer to bacteria in their code than to the vertebrate nuclear DNA code. Evolution explains that quite nicely, so long as mitochondria are due to an endosymbiotic event. “Design” certainly doesn’t explain it. What, the “Designer” woke up one day and thought, huh, I guess I’ll stick strictly with one code for the eukaryotic nucleus, and just for kicks I’ll throw in a bacterial code into the mitochondria?

And the highly, slavishly, derivative nature of life, from DNA to morphology, is what shows that evolution occurred. Intelligence has never been so derivative, while life is derivative in just the patterns that one would predict from the levels of genetic transfer across “species.” Oddly enough, at least from a creationist standpoint, the “designer” designed “prokaryotes” as if these had transferred much DNA laterally during macroevolution, while vertebrates were designed to be almost wholly vertically derivative during chordate evolution.

How magical, indeed.

(Yes, feeding the other troll, but in order to point out the basics of evolutionary evidence to all readers.)

Glen Davidson

That’s the problem, isn’t it Glen? I agree with your motivation to offer corrective information for the benefit of would-be first-timers on PT, but what it usually does is increase the thread count beyond that which I usually seek when I’m purchasing bed linens. I’d love to jump into a thread pre-trolling and repost my request for a troll response-free thread, as an experiment. I’m not recommending it for every thread, mind you, but just once.

Anyone who doesn’t accept the genetic code as evidence for common descent is simply stating that they unreasonably reject any evidence whatsoever for common descent.

We want to distinguish common descent by evolution from magical instantaneous creation.

So we look for predictions that each scenario makes, and see which is better supported by the evidence.

Problem - magic makes any and all predictions. Same genetic code - deliberate act by inscrutable deity, magic supported. Different genetic codes - deliberate act by inscrutable deity, magic supported. Unless ID/creationists are willing to offer specific, testable, mechanistic scenarios of how ID/creationism works - and they aren’t - it can’t be either refuted OR SUPPORTED by the evidence, because it “predicts” everything.

Fortunately, though, the scientific theory of evolution does make many predictions.

Thus, we can evaluate the theory of evolution by seeing whether the evidence is consistent with what it predicts.

Certainly it is true that even a wrong theory can make some true predictions. However, if converging evidence from multiple sources keeps supporting the theory of evolution, it behooves the reasonable person to admit that the theory of evolution is favored.

(If evidence emerges that is strongly inconsistent with evolution from common ancestry via genetic variation, natural selection, and genetic drift, then it behooves a reasonable person to concede that the theory of evolution needs to be rethought. Such a situation would not “support” ID/creationism, unless ID/creationism were to offer specific, testable, mechanistic explanations. Note also that claims that things exist which are not fully explained in detail is not an argument against the theory of evolution.)

Although any type of genetic code whatsoever is equally compatible with magic, and thus ID/creationism can gain nothing from information about the genetic code, a common genetic code is far, far more supportive of evolution than multiple individual genetic codes would have been.

Another explanation is also supported - “magical intelligent design which deliberately mimics evolution”. However, there are problems with this. First of all, it is not parsimonious - if magic exactly mimics natural explanations, why introduce magic at all? Second of all, those who advocate this must do so consistently. If you advocate “intelligent designer who exactly imitates evolution”, then you must concede that only evidence favoring evolution favors this particular ID scenario.

I prefer the non-supernatural, scientific explanation, which is to me the best explanation of the data.

Atheistoclast said:

But I do know nearly everything there is to know.

You’re second-rate even as a megalomaniac. The real thing goes like this:

I don’t know as much as God does, but I do know as much as he did at my age.

– Henry Kissinger

mjcross42 said:

That’s the problem, isn’t it Glen? I agree with your motivation to offer corrective information for the benefit of would-be first-timers on PT, but what it usually does is increase the thread count beyond that which I usually seek when I’m purchasing bed linens. I’d love to jump into a thread pre-trolling and repost my request for a troll response-free thread, as an experiment. I’m not recommending it for every thread, mind you, but just once.

This is an intriguing thought. However, I would like to note a few complications.

1) First of all, any thread that discusses a scientific advance, including this one, tends to get very few comments, and very, very few from trolls. I suspect that this one will fill up more, but if it had been only about some aspect of bacteriorhodopsin, it would not. The original rationale for this site included refutation of creationist claims. This site can get rid of creationists very easily just by only posting technical scientific updates, and perhaps the site wishes to make that change. Also, many purely scientific sites exist, and they attract far fewer creationists.

An original rationale of this site was to dispute creationist works, and if that is to be done without the intervention of creationist comments and the inevitable replies to them, very strict monitoring will be needed.

2) By contrast, threads that specifically critique the works of creationists fill up with hundreds of comments, as creationists try to defend the work being critiqued. One could argue that they should be allowed to. Unfortunately, 100% of creationists I have encountered use unproductive techniques, which include a variety of efforts to change the subject. The general gist is that they implicitly admit that they can’t defend, or in most cases, understand, the work being critiqued, but that they are obsessively unable to tolerate others pointing out its flaws. It often if not always comes up that they don’t even understand or agree with the creationist argument they are defending. They will simply “say anything to deny that anything any creationist ever said could ever have been wrong”.

3) Threads that talk about social or political developments tend to be intermediate in comment numbers. Again, the same principle applies. If you’re talking about court cases or political campaigns that involve creationism, very strict monitoring would be needed to keep creationists from commenting.

I’m not at all sure that “2)” and “3)” can be tastefully or even ethically done without allowing free play of comments, even if the the extent of annoyance.

I realize that you are talking about replies to trolls, but I think that the result of that would merely be opportunistic takeover of threads by creationists, to the extent that the original point of the post seemed to have been successfully refuted by creationist arguments.

RIP Gobind. Bacteriorhodopsin is a neat protein but don’t forget how fantastic are the proteins in plants such as the phytochromes besides chlorophyl.

I was wondering if anyone knows what happens to DNA out in space does the RNA act different or the so called junk DNA or the ATCG or any other peculiararity or that nothing happens different at all.

Marilyn said:

I was wondering if anyone knows what happens to DNA out in space does the RNA act different or the so called junk DNA or the ATCG or any other peculiararity or that nothing happens different at all.

Your question is under-specified. Do you mean DNA molecules just floating around in space by themselves, or DNA that is encased in humans who happen to be in space in protective habitats like the space station, or what?

I was thinking about how ordinary it really is to infer derivation (in relation to comments on this thread), and how oddly IDiots deny it, so I Googled one of Stephen Meyer’s references to it. He also mentions it in his book Signature in the Cell, but I didn’t want to write that out. So here’s Meyer noting how we infer derivation, only he weirdly calls it detection of “design”:

STEVE: No. You just put words into my mouth. I was saying that the scientists in many fields -– you and I were talking about plagiarism before we came on the air -– it’s possible now with programs to detect papers that students turn in that have been plagiarized. Well that’s a form of inferring to design. Kind of sneaky malevolent design, but when you see a string of characters that match up from two different strings, highly improbable arrangement, that match, we call that a specification and you have improbability in specification, we design people say that indicates intelligence. Well, that’s a form of reasoning that is not only – let me finish…

http://www.pbs.org/thinktank/transcript1246.html

Only in the loosest and most question-begging sense (in what way is it “design”?) is this detecting “design.” It’s detecting derivation, and if we can assume derivation in his case, why not in the case of life?

Life doesn’t “look designed” except in a very amorphous and agency-biased manner, but it looks derived through and through, and all reasonable tests for such derivation support that inference. Behe accepts that (without accepting that it is the limits of known mechanisms of derivation and adaptation that give us the best indication of evolution), while Meyer apparently is more of a traditional creationist, nevertheless trotting out the fact that we can detect derivation readily (with changes, certainly, in the case of human judgment) without understanding how that speaks volumes for evolutionary evidence.

Follow the evidence they say, and then mold the evidence to fit their presuppositions, not accepting what is obvious from that evidence.

Glen Davidson

Ben said:

Robert Byers said:

‘ Finally convinced…” You mean before that the claims of evolution were still in doubt? This shouldn’t convince. it follows that a common design or blueprint would also have common DNA principals. Why not?

All life is so alike this creationist would want and would predict DNA would be alike in its foundations. yet not mean there is a common origin for life by way of evolution. Thats a line of reasoning and other lines of reasoning are just as good. I don’t see why this would be a conclusion from scientific investigation! Even if true.

The creationist explanation for the origin and diversity of life is, essentially, “magic, performed by god”. If I understand you correctly, you believe this explanation should be taught as science, alongside science, in American public schools.

My question is, is there any phenomenon, artifact, or event which could not or should not be explained the same way? Why is the sky blue? There is a scientific explanation for this; should we also teach that it could be due to magic, performed by god? How was the moon formed? There is a scientific explanation for this; should we also teach that it is just as likely magic, performed by god? The explanation for why we think there was a historical figure named George Washington could be, according to your thinking, magic, performed by god. Should we teach all subjects that way? Why or why not?

This was about DNA. All creationists want is the truth and that taught everywhere. if we disagree then equal time for ideas of equal worth. the people can decide that and creationism will do fine.

https://me.yahoo.com/a/JxVN0eQFqtmg[…]X_Zhn8#57cad said:

Robert Byers said:

‘ Finally convinced…” You mean before that the claims of evolution were still in doubt?

No, that wasn’t what was said. It was that all life shares a common ancestry. Bacteria could have had common ancestry with bacteria, separate from humans who had common ancestry with mammals, vertebrates, etc., but it turns out that bacteria and humans and everything else has common ancestry.

This shouldn’t convince. it follows that a common design or blueprint would also have common DNA principals. Why not?

Well, why? And it isn’t that they have common DNA principles, it’s that they have virtually the same genetic code. But not identical, in fact, evolution has caused them to diverge somewhat.

Yet what’s interesting is that mitochondria are closer to bacteria in their code than to the vertebrate nuclear DNA code. Evolution explains that quite nicely, so long as mitochondria are due to an endosymbiotic event. “Design” certainly doesn’t explain it. What, the “Designer” woke up one day and thought, huh, I guess I’ll stick strictly with one code for the eukaryotic nucleus, and just for kicks I’ll throw in a bacterial code into the mitochondria?

And the highly, slavishly, derivative nature of life, from DNA to morphology, is what shows that evolution occurred. Intelligence has never been so derivative, while life is derivative in just the patterns that one would predict from the levels of genetic transfer across “species.” Oddly enough, at least from a creationist standpoint, the “designer” designed “prokaryotes” as if these had transferred much DNA laterally during macroevolution, while vertebrates were designed to be almost wholly vertically derivative during chordate evolution.

How magical, indeed.

(Yes, feeding the other troll, but in order to point out the basics of evolutionary evidence to all readers.)

Glen Davidson

Okay. Your saying the DNA thing unified all life. not just in the big divisions. That was the discovery.

Still however it fits and follows that a great thinking designer would make all life with a common genetic code at deep levels. What else would one do? Its what a creationist would want and even predict. A common DNA code doesn’t make a common designer unlikely.

I can’t get into the case you bring up for whats likely.

Richard B. Hoppe said:

Marilyn said:

I was wondering if anyone knows what happens to DNA out in space does the RNA act different or the so called junk DNA or the ATCG or any other peculiarity or that nothing happens different at all.

Your question is under-specified. Do you mean DNA molecules just floating around in space by themselves, or DNA that is encased in humans who happen to be in space in protective habitats like the space station, or what?

In a test tube on board a space ship and all what you say. If possible, also was that the reason that the Columbia went into space, to find out about these things, but the mission ended so terrible. I’m wondering if DNA needs Earths surrounding to form any kind of species that is on Earth also how the subject corresponds to extra terrestrial existence.

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This page contains a single entry by Douglas Theobald published on November 21, 2011 2:08 PM.

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