This sure beats the daily barrage of Trump garbage reporting. Good job
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"Among the essential points of the upheaval that Woese helped initiate are 3 counterintuitive insights, 3 challenges to categorical thinking (...). The categoricals are these: species, individual, tree. Species: It’s a collective entity but a discrete one, like a club with a fixed membership list. The lines between this species and that one don’t blur. Individual: An organism is also discrete, with a unitary identity. There’s a brown dog named Rufus; there’s an elephant with extraordinary tusks; there’s a human known as (...) Darwin."
So ... as Buddhist psychology already claims for thousands of years, everything is "interconnected"?
In that case, maybe Darwin didn't come up with this idea because he was not an isolated individual, and instead entirely connected to 19th century Christian Western philosophy, which for centuries already needed to see the world from an "atomist" perspective, where each individual is considered to be entirely isolated from its environment, as the ancient Greek sense of the word "atomos" suggest (= that which cannot be divided), precisely because without this kind of in-dividualist conception, the very notion of a Last Judgment, where every single human soul is held responsible for its actions during its life on earth, and then saved or eternally condemned... can no longer be conceived of, whereas Western Christian ethics needed such a saving/condemnation as its foundation... ?
Woese showed that Darwinism was "too Christian to be true" ...?
9
How eerily similar this is to the story of Julian Jaynes.
2
Why are ALL great ideas and theories rejected at once by the scientific community? Maybe because as homo sapiens we feel threatened? Perhaps we don't want to change our rigid educations. Or perhaps it is just ego.
4
The pseudo-science behind Michael Crichton's "Jurassic Park" has been described as fantasy. How do Woese's ideas and modern genetics affect that description?
5
Very well written and interesting article. A great review of a topic I know so little about. Thank you.
22
A great piece of journalism. Pulitzer worthy.
19
But he is the most important biologist of the 20th century that you’ve never heard of. Unfortunately, Americans know basketball players and singers, not really important thinkers. Thankfully, my great-great-great-grandfather came not from Lithuania but from Mars.
9
This is why we subscribe to the NYT.
34
Ford Doolittle's articulated tree looks like the root system of trees. Tree metaphor seems quite appropriate.
4
I am disappointed by the omission of Rosalind Franklin’s contribution to the discovery of DNA in this article. Franklin’s work on the X-ray diffraction images of DNA and her formulation of DNA’s structure were fundamental to James Watson and Francis Crick’s “discovery.” Such facts are taught in the textbooks and lectures of general biology classes today. Yet if someone like Franklin, arguably a co-discoverer of DNA along with Watson and Crick, is not mentioned in a Times longread in which DNA is a lynchpin of the story, one has to wonder who else the writer might have ignored or omitted in his reporting.
36
Thank you, to the NYT and to David Quammen, for allowing this lay reader a glimpse into deep science. The writing is clear and understandable, the thinking is abstruse, reflective of a life's work cogitating on the methods life uses to extend itself. I enjoyed the article. I love the impulse that propelled the NYT to publish this excerpt. It's not the daily news, it's learning, and how we come to be what we are, clearly told. Very nice.
23
CW’s professional trajectory is exactly what happens to those who dare to change an ‘established paradigm’ in view of others who are the keepers of the pre-existing flame.
6
How beautifully-ironic that Carl Woese, himself, horizontally-fused several distinct scientific disciplines within his professional skills to provide the foundation for the discovery of Horizontal Gene Transfer.
Further, the difficult personal trajectory of Carl Weose is like many others who have caused major intellectual paradigm shifts.
11
Instead of a rather simplistic "tree " of phylogeny representing Darwinian evolution, the metaphor of the "largest" organism on earth comes to mind. In the UP of Michigan is a fungus growing in the ground that is 30 miles in diameter with shoots popping up all over. Beneath the ground this plant promotes decay and transformation of mineral and biomass into useable building blocks in collaboration with a diverse microbiological community. Other plants use these biological and mineral building blocks to also grow. All sorts of fauna from insects to moose and deer feast on this.
Underground, horizontal gene transfer and sex is stirring the pot providing diversity and opportunity for this 30 mile fungus to thrive and support all the flora and fauna above and around it.
This doesn't supplant Darwin tree, it takes in account the complexity of it's roots and emphasizes the plasticity and vigor of the DNA world. Woese realized that Archaea was needed to explain all the building blocks biology was using.
14
Thank you NYT for a lucid and extensive article by Mr. Quammen. It succeeds in not only presenting a hard-nosed, dogged scientist’s life but in introducing and delving into important research into archaea and HGT and the roots of descent. The tree of life is inosculated.
I don’t expect to understand difficult concepts in one reading of an article or even once I get my hands on “The Tangled Tree” and read that. The purpose of a difficult but well written article like this is to pique my interest, to get me checking out Wikipedia and googling new words, and maybe indulge my personal obsession with seeing a full integration of modern evolutionary theory with the complexity theory explanations of emergent complex systems.
It’s too bad the Nobel gurus do not have posthumous categories for scientists who are not fully appreciated until after their deaths like Lynn Margulis and Carl Woese. Neither should their picadillos deny them recognition.
Shout out to @Ana Luisa for numerous brilliant comments—although I believe this article was sufficiently “vulgarized” for a studious reader.
24
As a biologist and teacher, I've been following the ongoing story of the "tangled tree" for 45 years. But after reading the first third of Mr. Quammen's book of that name, I am truly gratified by his long-form framing of the story, especially with the tale of Dr. Woese's characterization of the Archaea. Anyone interested in the history of molecular biology should not miss "The Tangled Tree."; a fantastic read.
21
I seldom remember being so excited while reading an article. So many new realizations. For example, the simple rotifer (or so I thought) is anything but simple: sampling "items" from other species; discarding those that didn't offer what it wanted or needed; and incorporating what it could use. I am neither a scientist nor a philosopher, but this article aroused those potential parts of me. I will be looking for "the Tangled Tree" to read the whole, and forever thanking Mr. Quammen for reinvigorating my 79-year-old inquisitive mind.
30
Yes. Me too. And if you look at Doolittle's reticulated tree drawing as the roots (the tangled root system) of a tree, it actually becomes a very good metaphor in picture form.
6
I don't have enough background to comment on the science, other than it sounds logical. Of particular interest to me is the way your article, and what Woese was up against in his presentation of what must have been viewed as radically rebellious if not downright destructive thinking at the time, highlights the impediments to humans' understanding of their and other species as well as life in general - and not just within the sciences. A combination of ego, fear of and reluctance to change, fear of the unknown, and the fear of not fitting in... all of these attitudes and more impede growth and development in people, groups, for-profit and not-for-profit organizations, and nations. Thank you for your well-written article.
13
@Barbara I draw a different lesson, viz., that despite being done by humans, with all their frailties and egos and weaknesses and competing desires, science actually gets done, and truth actually emerges in its own time. It’s no good wishing we were different creatures; we are who we are. What is extraordinary is that we are able to do this marvelous thing. More than that it seems that we’ve somehow made our weaknesses - need for recognition, stubbornness, etc. - an instrument for our doing it. It really is quite something in my view.
12
Many of the Comments to this article indicate readers have misunderstood how Woese's work fits into evolutionary science. While horizontal gene transfer is a factor, the overwhelming driver of evolution remains as Darwin described. Bacterial evolution may be more influenced by horizontal gene transfer for a variety of differences with eukaryotes, and Woese's contribution is admirable for this insight, but it is not the revolution that some conclude.
13
A truly fascinating article. Despite his accolades, I'd not heard of Carl Woese nor his work before this. I also agree with rjon's comment below--metaphor is undervalued in much science writing and it's clearly integral in communicating the mechanisms here.
8
David Quammen is a brilliant writer and manages to successfully convey potentially challenging theories for most of us to appreciate. Thank you NYT for publishing this article. It has enlightened my understanding of the world.
43
This is the kind of content that sets the NY Times apart from other papers. Please keep it up.
65
What I got out of this article is we now have a better understanding of how evolution works. I'm not a biologist so I'm not qualified to say anything more about it.
I recently threw out my Wall Street Journal subscription and replaced it with the New York Times. At the WSJ most of the comments for an article like this would be written by evolution deniers. I looked at the comments here at the NYTimes and I was unable to find any creationists. I think that's wonderful because I never thought it was possible.
40
Great article!
7
Brilliant article. First time I've come across the HGT concept.
13
I think it is great detective work. It reminds me of the way the great geologists had to reconstruct the inherited religious sense of time, the Biblical 4,000 or so years, by a careful weighing and sifting of layers and fossils. This was 18th century work. That took courage, as it did for Darwin, because they knew they were upsetting a powerful theological order of things. Then Darwin became orthodoxy himself.
My apologies in advance, but this is almost as disturbing as finding out that the Federal Reserve created the trillions to bail out banks by electronic keystrokes. Very frightening to economic orthodoxy.
10
A wonderful article.
And very timely for me as I am about to visit Galapagos.
I have two comments.
I wish the author had told us how to prounce the name of this scientist.
And I wish, the author had talked a little bit about the "intelligent design" theory - that rejects Darwin.
Many thanks.
3
I used to work closely with Carl Woese. Carl would tell people that to pronounce his name, just remove either of the letter "e"s and read what's left.
About the second question, Carl had no time for "intelligent design". It's an assertion not a theory and untestable. The author was right not to get into it.
The article beautifully describes horizontal gene transfer (HGT), but to be clear, this is only a faster mode of evolution than simple point mutations, and works within the usual framework of "natural selection". Carl's work (including our joint work) did not replace the framework of evolution established by Alfred Russel Wallace and Charles Darwin.
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@Neil
I am a neuroscientist. When looking at the anatomical organization of, say, blood vessels to the brain and neurocircuits in the brain, I always realize that there is no intelligent design. There is lots of evidence to warrant his conclusion.
3
Excellent article!
5
@Candido Rodriguez Alfageme, Woese is pronounced as , "Oh, WOE is me!" I had the rare experience of working with Carl in the late '70s/early '80s, as a lab technician, preparing some of the films he did indeed spend countless hours staring at, comparing their spots. He certainly was unusual, brilliant and memorable. I am not at all surprised that he was nominated for the Nobel. I hope his passing was not too uncomfortable. My condolences to his family.
11
such a good read!
6
This is why I subscribed.
Amazing article!!
9
Some commenters have considered this article to be a refutation of the genius of Charles Darwin. That gave me the thought of a definition of the variable which we struggle to define: time. Time is the variable which makes Newton's discoveries more amazing than Einstein's and Archimedes' discoveries more amazing than Newton's; likewise Darwin's more amazing than Woese's. It is my opinion that building, indeed confuting a great work, is dramatically easier than starting out from essentially nothing.
7
@eclectico: I don't see it as a refutation of Darwin, but a recognition that there is another way for genetic change to occur. That change is then heritable in the way Darwin described, and changes the offspring of the organism that received the HGT. I had read occasional mentions of genes "infecting" an organism, but this was the first explanation of how it works and how it was discovered. It looks to me as if HGT is the basis for gene therapy, in which a desired gene is inserted into a virus that infects the person or animal that needs it. If that method works when you want it to, why not sometimes when it is by chance, without humans directing the process?
6
Bill Nye really ruined science writing and science education. Ever since Nye, every science writer seems to think that science has to be 'jazzed up' for people with short attention spans. The overheated prose on display here really bores me, which is sad because hidden under all the goop is some interesting science.
I can't stand science writers who don't understand that it's the science that's interesting, not all their bells and whistles.
10
@Steve Vanden-Eykel So I guess the solution is to have science writers write solely for scientists? The more specialized scientists become, of course, means that science writers must themselves become specialists writing only for other specialists—in short, they should cease being science writers and become specialized scientists.
I strongly disagree. Science writers are essentially translators and this one—David Quammen—is a very good one. Nye’s another creature, with an altogether different role to play, having little to do with translation.
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@Steve Vanden-Eykel. This article contains substantial science — especially for the masses who can become more knowledgeable through this style of writing.
10
@Steve Vanden-Eykel: Amen!
I came away from this article with a greater appreciation for the role of metaphor in science. Not analogy, as so many theorists would argue. In a world of specialization it’s the non-specialists (some, not me, would call them cross-disciplinary scholars) who are more likely to ‘discover’ new ways of looking at the world. Perhaps Coleridge caught it best when he referred to “connexions.”
6
Tree of Life
Carl Woese was a remarkable scientist who, for the first time, used phylogenetic analyses to construct a Tree of Life that he found contained three separate Domains, the Bacteria, Eukarya and his newly discovered group the Archaea. Carl was a co-author on one of the papers from my lab that described a new genus of bacteria, Polaribacter that was found in the sea ice of the Arctic as well as in Antarctica. Notably different species were found at each pole supporting the idea of a separate evolution of these species from a common marine ancestor: one species at the North Pole and another at the South Pole (Gosink, Woese and Staley, 1998 Int. J. Syst. Bacteriol. 48: pp223-235).
Carl could not have known that co-evolution is a common way in which evolution occurs. Using this approach, the current Tree of Life is now portrayed somewhat differently (See supporting Figure 1 - https://onlinelibrary.wiley.com/doi/pdf/10.1002/bies.201800036).
When evolution began in the Pre-cellular period the Euryarchaeta co-evolved with the Bacteria and the Crenarchaeota co-evolved with the Eukarya. This process likely ended when the oldest bacteria (the PVC – Planctomycetes- Verrucomicrobia – Chlamydia group) and the Eukarya developed nuclei which prevented access to the DNA of the Bacteria and the Eukarya. Thus, the archaea never became nucleated.
https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.201800036
http://rsob.royalsocietypublishing.org/content/7/6/170041
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This one man has contributed more of value to the world than every professor of the -Studies departments added in the past half century.
6
It is evermore clear: what we learn and believe today is an incomplete puzzle. We want it to be whole but it never is. Tomorrow, whether we want it to, or not, another puzzle part will arrive.
17
Opponents of genetically modified organisms (GMOs) should keep in mind that we are all GMOs. The mixing of genes from different species is the normal state of affairs in nature, and their efforts to keep species "pure" and "natural" is actually unnatural, detrimental to humanity, and ultimately impossible.
18
@SSG
I have to admit that I still have to come across a proponent of GMOs (in the strict sense of the word, namely using genetics to create new species in human laboratories, and then put those new species outside in the "real world") who actually addresses the very point that its opponents are making, rather than sticking to general truths which no GMO opponents ignores or questions ... ;-)
I hope you know that creating new species isn't just what "nature" does, but what human beings have done ever since they started to raise cattle and invented agriculture?
The problem isn't that somehow only "God" should have the "moral permission" to create new species, or only non human nature. For GMOs opponents, human beings perfectly have the moral right to do so too.
What we can NOT do is to create new species in laboratories and then put them out in the fields on a large scale BEFORE scientifically testing what the impact of those specific species will be on (1) other species (2) current generations of human beings, (3) future generations of human beings, and (4) the quality of our environment as a whole.
That means that we need decades more of studies before you can take the decision to put them into our soils and water and air in a politically and scientifically responsible way.
Companies like Monsanto prefer to act in a totally irresponsible way simply because they choose to put their own short-term financial gains first.
GMOs opponents want to put AMERICA first, you see?
19
@Ana Luisa Today, science is caught between
Profit and Ethics. If I say, Smoking is the root cause for cancer, one would bring e-cigarette .
After the prevalence of e-smoking in the society for few years, if the data bank says that e-smoking also also brings cancer, the corporate comes with a GMO tobacco seed and advertise,
" Smoking 'GMO tobacco Cigarette' won't cause cancer. The genes responsible for cancer is clipped and GMO-Cigarette is the solace to the smokers of the world." Make billions through billboards, digital media ads and sell the company to the foreign band when Genetically Modified Organism has been proved as Genetically Manipulated Organism".
We are all GMOs and hence we have lost the inherent active barrier that make us to search for the seeds for external source of implanted passive barrier in the seeds,vegetables etc.
GMO food is not a panacea.
@Ana Luisa
At some point, humans discovered domestication of animals. But domestication is only a twist on the natural system of vertical heredity. As has been pointed out by famed science -fiction authors, many if not all, domesticated animals would die out, if placed into the same plane of survival with their natural relatives in the wild and without human care.
Humans have caused the extinctions of a great many species, in history but well back into the prehistoric. There were once wooly mammoths and mastodons, but it has been shown we directly or indirectly caused their extinction. There were once three species of cheetah and saber-toothed tigers, in North America. The cheetahs hunted the pronghorn antelope. Herd animals roamed by the millions, when there were only a tiny number of humans, by comparison. In more modern times, we nearly hunted the pronghorn out of existence, but it has recovered somewhat, similar the the buffalo. The pronghorns and buffalos are holdouts from the prehistoric age, along with wolves. If all the natural predators were still on the landscape, domestic cats and dogs would likely not survive very long without our help. They did not go through the same tests of evolutionary shaping like their wild cousins.
By looking into the work of Darwin and Mendeleev, I always believe that the idea of fine tuning of the periodic table of the
elements had been derived by Mendeleev from the Vertical concept of Darwin's tree. John New lands put forward his law of Octaves (periodic table)in 1864. Darwin's theory of V.G.T published in 1859. Probably, Mendeleev's source to give a fine tuning to John New Lands by making the groups of elements with similar properties into vertical columns in his table in 1869 was from the Darwin's tree.
As a biophysicist, the attempt by Woese to stretch the Darwin theory into H.G.T. could be the source from the periodic table of Mendeleev in which both periods and columns have significance and accommodate all the fundamentals of the elements in the universe.
We always see the visible parts of Darwin-tree above the ground but its deep rooted horizontal spread below the ground.
Did we miss the bus by our failure to recognize the theory of H.D.T put forth by Woese biophysicist?.Indeed, I missed him.
Yes, there are CH4(methane) releasing as well as Natural Gas consuming bacteria .
3
If ‘a human is a virus’ way to make another human’, then humans would increasingly resemble viruses more and more over millennia, but that is not the case. Therefore the effect on Darwin’s tree branches of h.g.t. must be fairly small by comparison to vertical heredity.
1
@Kelly McKee
In evolutionary biology a driving force is to get your DNA (or RNA) into the next generation. In addition to the brute force of progeny there are examples of infections altering behavior of a "higher" animal so that trip into the next generation is farther and wider.
Robert Sapolsky, a Stanford professor, has examples of this biological basis of behavior with Toxoplasmosis infection in cats making the spread of Toxo's DNA more efficient. As he says in "Being Human" (The Great Courses & in his book "Behave") we are made to order to get those microbes far and wide.
Humans ability to travel, interact and spread HIV while asymptomatic serves the virus's goal well. Our genome is full of viral shards indicating past encounters. Have these shards supplied the genetic ability to get on a plane and fly half way around the world while infectious?
11
@GTR
Rabies is yet another example of a virus's ability to change the behavior of a carrier in order to spread itself with maximum efficiency.
The rabies virus is so cunning that it managed to infest man's best friend in its most lethal form, effectively giving dogs an irresistible urge to bite and exploiting humans' close association with them, while animals such as skunks, raccoons and bats are less effective at spreading it. There are still about 55,000 annual cases of human rabies worldwide despite the vaccine.
1
@GTR
Then, Sapolsky’s theory sounds plausible, but merely suggesting other unproven theories based upon it does not substitute for scientific research on the basic theory to prove it in the first place.
Therefore, Darwin’s theory is not overturned by a lot of ‘suppose this’ and ‘suppose that’.
A wonderful and extensive look at the little bits that make everything what it is. As one who arrived into the science of molecular biology fifty plus years ago, I am enjoying the steps made to provide a look further back than "my great-grandfather had blue eyes".
Thank you NY Times for doing in depth research into areas that few might find worthwhile yet are significant in our lives.
17
KUDOS to David Quammen for a fantastically-written article that managed to inspire, educate, and challenge me!!
17
Samuel Butler, a Victorian writer and Anglo-Irish Classicist, quipped that a chicken was an egg's way to make another egg. A modern version of that observation is a human is a viruse's way to make another virus.
It takes man off the pinnacle evolution and indicates we are mere vesicles of evolution and the real work is being done by viruses and all the forms of horizontal gene transfer with some help from sex.
Are humans mere playgrounds for the real work of creating life that seems to exist in the many fantastical niches on our earth? And try to imagine the variety of niches in our universe!
21
@GTR
If that were true, then human beings would look more and more like a virus with each passing milleneum; DO WE?
@GTR
If that were true then human beings would begin to resemble viruses more and more with each passing milleneum...
@Kelly McKee: Sorry, but that's not right. Humans are the habitats, the vectors, if you will, for the virus. Humans are more than a growth medium for viruses, though. We do all sorts of things that have nothing to do with transmitting viruses.
This article is very interesting. Although there were some spots were it was hard to understand because we haven't learned about it yet. It was enjoying to read because when I grow up I want to be in the biology field. I also enjoyed this article because I did like learning about Darwin in school this year. With reading this article I did learn some new things about Darwin and his theory of evaluation.
13
@Heather Broski. Heather, your enthusiasm will be your guide and I suspect, if you enter “the biological field,” you’ll be very good at whatever you become and who you are. I’m 75 years old and there are many things in this article that I don’t understand either.
8
Very interesting article. I'm not a scientist, so I sometimes have trouble understanding all the details, but this was very clear. It's too bad that it took so long for Woese to receive the recognition he deserved. I had not heard this story before and it really casts a new light on the mysteries of life and how it functions. The truth of the universe is utterly bizarre.
7
This was such a beautiful article for a scientist like me who knows zero biology—a memorial, a scientific revelation for laymen, and a history of thought presented in a way that captures the life within universities between mentors and fellow students. I particularly appreciated the capture of the differences between technology's (engineering's) way of knowing and science's way of knowing. Few today recognize how important that difference is.
20
I think it is important to put this research in some sort of perspective. Was something discovered than changed views on evolution? Most certainly. Did it change the larger perspective of the evolutionary process? No. It did reveal an alternative pathway for genetic change.
The title implies that Darwin was wrong, which is not correct. The point made by Isaac Asimov in "The Relativity of Wrong" applies here.
"What actually happens is that once scientists get hold of a good concept they gradually refine and extend if with a greater and greater subtlety as their instruments of measurement improve. Theories are not so much wrong as incomplete."
http://hermiene.net/essays-trans/relativity_of_wrong.html
31
@uwteacher I concur with that the title, although provocative, isn’t correct. All scientific progress comes on the shoulders of those who cane before. And, any scientific theory is only the best model to explain observed reality at the time. As you say, as better instrumentation enables better insights our collective understanding improves.
What was interesting in the article was Woese’s fixation on Darwin later in life. Perhaps, it was the difference in relative recognition that drove that.
To give them both credit, UGT as a speciation driver is still subject to a ‘fitness test’ in that any UGT germ cell sequence that results in an unsuccessful phenotypical expression would not be passed along generationally. In that case, Darwin was right, even if he never understood the mechanisms.
5
On the contrary, If we look at micro cellular random displacement from these sources: natural nuclear radioactivity, horizontal genes transfer, quantum physics random effects on chemical reactions in genetic replication, modern chemicals in a polluted environment, together with any other unknown causes of genetic mutation; along with the randomness associated with sexual/asexual reproduction in the normal vertical hereditary sense, then each of these sources of genetic mutation are equivalent to the ‘roots’ of Darwin’s evolutionary tree. A tree has more than one root!
I would further add, that I hope that a widening commercial avenue of artificial genetic experimentation is not somehow justified, from out of the work of serious contributing scientists such as Professor Woese, who studied natural systems, not GMO’s!
It cannot be overemphasized, that natural life forms have survived the natural tests of the natural world over long spans of time. Yet we seem poised to adopt the opposite of the ethics best expressed by the great novel ‘Frankenstein’ by Mary Shelley, with corporations and their funding pushing us toward the abandonment of higher ethics on genetics in order to justify the artificial manipulation of genetics, led by promises of commercial profit.
5
@Kelly McKee
Kelly completely contradicts him/herself by first noting the genetic manipulations of Nature, and then blubbering that one product of Nature, Humans, is doing the same.
5
Thank you for a fascinating article. As someone with only two semesters of geo 101-102 forty-eight years ago, I am grateful it was written in an understandable and engaging way.
4
Like many science writers, David Quammen has taken to his subject too much. Carl Woese certainly made some interesting discoveries, and this book is an interesting one, but Carl Woese did not start a scientific revolution and will not be joining, let alone replacing, Charles Darwin in the pantheon of scientific gods.
Not that Charles Darwin himself will be there much longer. Carl Woese and others continue to chip away at his theory of how evolution happens. There's not much left but banal generalities that can never be disproved because they say so little.
Truth is, we know very little about how life came to be, and how we -- the pinnacle of life so far -- got here. Charles Darwin, with his pangenesis and Lamarckism, was partially discredited years ago. Luckily, mavericks like Carl Woese and Lynn Margulis help us find a new theory to replace his. Unluckily, those two scientists have died and it seems hard to replace them.
It's hard to root out established theory. Sigmund Freud's theory of the "Ich", the "Es", and the "Uber-Ich" is interesting, elegant and wrong. We have moved on from it.
Charles Darwin's theory of evolution due to repeated variation and natural selection acting over geological time is interesting, elegant and wrong. Time to move on.
Thanks to Carl Woese for helping us do that.
10
@John Smithson
Why is it so hard to just appreciate Charles Darwin in the context of his time and understanding. That saying about standing on the shoulders of giants ought to be remembered more often by moderns.
26
@lou I do appreciate Charles Darwin for his brilliant insights, careful observations, and lucid writing.
But I think we need to move on from his theory. Richard Dawkins, Daniel Dennett and others have made a religion out of Charles Darwin's theory, almost saying "Natural selection is the Creator of all things, and Charles Darwin is its prophet".
Biology needs to rid itself of dogma to progress. Carl Woese, Lynn Margulis and others have helped us do that. Those who insist on intelligent design, though I believe them mistaken, have helped too. But the puzzle remains puzzling.
Understanding the origin and nature of life will still take generations. As Max Planck said, “A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.”
You are right that we got to where we are by the efforts of those that came before us. Charles Darwin was a giant among them. But I think he was more like Sigmund Freud than Isaac Newton. Someone whose theories get mention in the history books rather than works of science.
1
@John Smithson
With all respect, I couldn't disagree more.
Dawkins and Dennett are first of all "philosophers", in the sense that that's what most of their work is all about.
Secondly, for many continental philosophers, they've done not much more than turning their own prejudices into a huge narrative, and then filling in the gaps with scientific studies - although their interpretation of those studies often isn't scientifically valid at all, but mere speculation (based on those same prejudices).
They were also "sociobiologists", a notion that suggest that they work as scientists, whereas this too is rather some kind of philosophy, based on the same typical Western 20th century prejudices rather than on sound philosophical concepts. It's the idea that Darwinism equals the survival of the fittest which equals egoism. In the end, our deepest drives would be "selfish", according to this theory, the very opposite of altruism.
In the meanwhile, however, the "father of sociobiology", Wilson, has made a U-turn (after studying ants), and most recent neurological studies indeed show that altruism is at least as much "innate" in human beings (and many other animals) as egoism.
Moreover, sociobiology was based on a selective reading of Darwin, who actually ALREADY accentuated the notion of altruism from the very beginning.
As to Freud: contrary to Darwin, his theories have NEVER been proven. And Woese didn't refute Darwin, he merely makes Darwin's tree a bit more complex ...
4
What a spellbinding and superb piece of writing - I was slack-jawed all through my dinner.
This is why I subscribe to the Grey Lady.
6
As we search outer space for signs of life as we know it on Earth the definition of life as we know it on Earth continues to evolve and expand. Alfred Wallace independently developed and discovered a theory of evolution by natural selection along with Charles Darwin. Both men were given credit at the time for their insight. But neither man knew about genes nor DNA.
3
Darwin did NOT create the "Tree of Life." He merely provided the first reasonable approximation of the nature of the tree.
4
Great article. Interesting on many levels. Well written. But something I wanted to know from the very start: How do you pronounce Woese's name?
3
@Allen Drachir
Actually it's very badly written. Luckily for the writer it contains so much interesting material that it is likely to survive its authorship.
1
@Allen Drachir it is pronounced woes as in woe is me.
https://www.youtube.com/watch?v=dnnYy8QlQy8
1
Could archaea have originated outside of earth?
2
@Shtarka, we'll never know. Also, a panspermia origin of life from extraterrestrial microbes could simply kick the abiogenesis origin of life from the primordial soup of Earth to the primordial soup of an extrasolar planet. It wouldn't disprove abiogenesis altogether.
1
@Shtarka
That doesn't seem to be impossible. Here's what was discovered recently:
"In March 2015, complex DNA and RNA nucleotides, including uracil, cytosine and thymine, were reportedly formed in the laboratory under outer space conditions, using starter chemicals, such as pyrimidine, an organic compound commonly found in meteorites. Pyrimidine, like polycyclic aromatic hydrocarbons (PAHs), is one of the most carbon-rich compounds found in the Universe and may have been formed in red giants or in interstellar dust and gas clouds."
If complex genetic material can be formed in outer space conditions, it's not impossible, at least in theory, that bacteria and archaea maybe exist outside of our planet too. And as archaea can survive in extreme conditions, maybe they "landed" on our planet together with some meteor ... ? That being said, for the moment nothing excludes the possibility that they were "born" here, or that at least planet earth's bacteria and archaea were born on earth (all while having other planets where similar forms of life existed or exist too ... ?).
To be continued ... ;-)
https://www.nasa.gov/content/nasa-ames-reproduces-the-building-blocks-of...
1
Never mind. I re-read the sentence. Meaning we didn’t know about the existence of the creatures until 41 years ago. Not meaning they didn’t exist until 41 years ago. Sorry - a little confusing.
2
Darwin’s Tree Intact After ‘Scrambling’
There are groups of scientists today who would love to steal the mantle of Einstein, in their respective fields of science. Einstein’s relativity theories, by contrast, while transformational were so good at solving longstanding puzzles in physics that they were largely shown to be true during his lifetime. First and foremost, it was shown that relativity mathematics reduced down to that of Newtonian physics and were therefore consistent with known factual science.
The advent of photon physics is a good example to bring up here. In a beam of light, even the purest ones of those such as from lasers, there is always the individual photon, but then there is the behavior of the aggregate whole, which behaves as a classical beam of light. Similarly, in Darwin’s analogy tree model, there are perhaps branchlets, but then there are branches! The branchlets don’t go very far, the branches become established and last through time.
Today’s discourse on the trillions of combinations of chromosomic DNA that is possible, loves to focus on micro cellular random displacement; but those random displacements can effectively cancel out as ‘noise’ - they don’t lead very far. Instead organisms must survive by being shaped in their environment over time. There is literally nothing in more recent work that changes that basic premise, of the larger branch pathways overcoming based upon the ability to survive.
Yeah, this ten thousand word (my knowing about half of them) may be an explanation of life, but can it compete with
"So God created every kind of magnificent marine creature, every kind of living marine crawler with which the waters swarmed, and every kind of flying creature. And God saw how good it was."
The problem is that the second explanation is winning, especially in this country. Current work on lateral transference is being done by recent McAuthur Prize Laurette Victoria Orphan at Cal Tech, on extremophiles in the deep ocean lava jets. They seem to share organelles wantonly, as development is not by traditional survival of the fittest, but by aggregations that somehow become functional.
While knowledge is exploding, the dominant political force in this country is the tapping of primitive emotion that eschews complex thinking, not even at the level of this fascinating research.
Thank's N.Y. Times. Keep trying to challenge your readershp
12
@Call Me Al
Dear Al (you asked for it ... ;-)),
1. The Bible isn't a scientific document at all, so there cannot possibly be any "competition" between it and science, from a rational point of view. Darwin's tree of life may be the result of random forces in the universe, or have been designed by a God who created the universe in the first place. Science will never be able to prove anything when it comes to the existence or non existence of God, precisely because by definition, he is "unknowable" ... . That's also why most Nobel Prize winners are actually religious people: there is no incompatibility here at all. For a more detailed philosophical explanation, see Bruno Latour's "Rejoicing or the Torments of Religious speech".
2. Certain politicians and certain religious leaders have always tried to make their followers believe that there is incompatibility between religion and science and that they should ignore scientifically proven facts that if taken seriously might get those politicians/leaders into trouble, personally. The best way to reduce their impact on ordinary citizens is to remember that there's no incompatibility at all, rather than to cultivate the myth that both are about the same subject and "in competition".
3. Darwin's "survival of the fittest" was never about individuals, but about competition among species. AND he has always shown that INSIDE a species, individuals who collaborate have a better chance to survive than those who try to compete ...
7
@Mor
I think you missed the point. This article is about Carl Woese and only incidentally about Horizontal Genetic Transfer and Archaea. And what a fascinating article it is! Quammen masterfully explains the science while simultaneously revealing the complex and haunted character of Woese. Complaining that Quammen clutters up his explication of the science with annoying biographical references is like complaining that the technical manual to your 3-D printer does a poor job of character development, or that the Bible would be so much better if it were not marred by theological material.
10
1. Technical manuals are supposed to be understandable for non technicians, so include graphs and definitions explaining technical terms in a clear, simple way. This article doesn't do so at all.
2. Technical manuals indeed don't contain character development, whereas that's exactly what this article tries to do, all while simultaneously trying to explain a scientific discovery to the average NYT reader (= without microbiology degree). The result is poor character development AND a poor quality as technical manual.
3. If the focus here was supposed to be character development rather than science, the subtitle of this article is profoundly misleading, in that case the "we" here does NOT include the average reader of this piece, but only microbiologists.
Conclusion: the fundamental problem with this MSM article is that its title and first paragraphs make you believe, as reader, that you'll discover a crucial scientific discovery about life, made decades ago already, but once you realize you indeed never heard about Archaea, two or three roots of life, and horizontal gene transmission, and would really want to know what this is all about, you get long paragraphs about character development instead. And that's disappointing, especially in times like these, when vulgarization of crucial scientific discoveries is completely ignored by most MSM, with political consequences that are more dangerous than ever ...
2
The one biology course I took
left me wondering what in the world RNA did.
I did not believe then that Darwin had really
answered the questions and I did not and still
do not believe that Science has all the answers.
Yet Biologist tinker with DNA/RNA
seemingly without any worry about
un-forseen consequences...
Meanwhile, I would like to know how in the
world Viruses ever came into being on earth.
My Grandchild's Biology book - far more demanding
and complicated than my memorising 206 Bones -
has pictures of Viruses that make them look
like Aliens for and in all the world.
3
In his infamous lecture "On Protein Synthesis" delivered in 1957 (published 1958), Francis Crick permanently changed the logic of biology - as Horace Judson described it in his most wonderful book, The Eighth Day of Creation. Crick's is arguably one of the most important scientific papers ever written; he proposed at least 3 revolutionary ideas: Biotic Codes, tRNA, The Sequence Hypothesis etc.
As Judson noted, "one paper from the period that an amateur of science, or a professional for that matter, can read today for instruction and pleasure ....The manner was deceptive. Like a gymnast who never seems to take a deep breath, Crick made the most agile leaps with nary a grunt to disturb the conversational tone."
And this is where Crick penned the most prescient prediction : "Biologists should realize that before long we shall have a subject which might be called "protein taxonomy"- the study of amino acid sequences of proteins of an organism and the comparison of them between species . . . these sequences are the most delicate expression possible of the phenotype of an organism and . . . vast amounts of evolutionary information may be hidden away within them".
4
I'm disappointed that David Quammen elides the important contribution of Lynn Margulis to endosymbiosis theory that Carl Woese expanded upon and for which he discovered the genetic basis. In 1967 Margulis (as Lynn Sagan, she was married to Carl Sagan at the time) published "On the Origin of Mitosing Cells," which proposed the hypothesis that eukaryotic cells gained organelles such as the nucleus, mitochondria, and chloroplasts, by phagocytic bacteria engulfing other bacteria and making them symbiotic within the larger cell. This was a radical hypothesis at the time, but has since been proved correct. Was Woese aware of Margulis work in 1969 or did he independently approach the hypothesis via a different route, that of horizontal gene transfer? Margulis should have won a Nobel Prize for her work, but was not celebrated as she should have been. It would have been thorough to have addressed this question, and give an important female Biologist her due recognition.
13
@Steven Keirstead In his book David Quammen talks a lot about Lynn Margulis. I think you would be satisfied that he gives her her due there. This article consists of edited excerpts from the book. It's not an abstract or summary.
Lynn Margulis was an interesting person and a thoughtful and original scientist. But she had her faults too. Among other things, she believed that the terrorist attack on the New York World Trade Center on September 11, 2001 was faked.
I don't think there was any conspiracy to deny Lynn Margulis the recognition she was due.
9
Elegant article on this complex scientist. I was lucky to spend many hours in Carl Woese’s lab while a young scientist at nearby Argonne (DOE) while writing computer programs to “read genomes” — my own first foray from computer science and AI into molecular biology. Carl helped me understand the “words” buried in DNA, like the several letters where the ribosome binds in front of a series of codons, and challenged me to drive my reader with those words. He prompted me into a long computational genomics career. I am grateful.
20
For all those out there who like me felt disappointed when reading here that Woese had discovered something fundamental and then failed to see what more precisely because of the many anecdotes and lack of definitions in this article: fortunately Wikipedia writers have more pedagogical/vulgarizing talent than the author of this piece, so after having read their article about Archaea, here's an attempt to try to summarize Woese's discovery:
- 4 billion years ago, for the first time there was water on planet earth
- hundreds of billions of years later, the first living organisms were "born". They had only one single cell, so are called "unicellular organism". As they're very small, they're also called "microbes".
- before Woese, those microbes were called bacteria (viruses don't have a cell structure, so aren't independent life forms) or prokaryotes, the predecessors of eukaryotes, unicellular organisms that have a nucleus, contrary to bacteria
- eukaryotes then got together, forming multicellular organisms such as plants and later on mammals
- Woese discovered that some bacteria actually had much more in common with eukaryotes than others, especially genetically, and put them in a new category, called "Archaea"
- eukaryotes and archaea have a common ancestor X, and X and bacteria have a common ancestor Y
- contrary to what Darwin thought, the genome of microbes doesn't evolve in a linear way, as different "species" existing simultaneously intermingle.
Is that it ... ?
7
@Ana LuisaIt It would be better to write, 'contrary to what Darwin's theory of evolution required' rather than what you wrote.
3
@memyselfandi
The author of this article seems to disagree with you:
"(...) young Charles Darwin, just back from the Beagle voyage and scribbling reckless thoughts in a notebook, drew a small sketch of the first evolutionary tree. Above it he wrote: “I think.”
This tree was hypothetical, its branches labeled with letters, not actual species, but what it meant to Darwin was: I think all creatures have arisen from a single source, diverging and changing somehow over time.
He didn’t yet have a theory of the evolutionary process — the concept of natural selection would come later — but his sketch at least gave him an image of evolutionary history and its results. From that he could work backward, attempting to deduce the mechanism."
Darwin’s Tree Intact After ‘Scrambling’
There are groups of scientists today who would love to steal the mantle of Einstein, in their respective fields of science. Einstein’s relativity theories, by contrast, while transformational were so good at solving longstanding puzzles in physics that they were largely shown to be true during his lifetime. First and foremost, it was shown that relativity mathematics reduced down to that of Newtonian physics and were therefore consistent with known factual science.
The advent of photon physics is a good example to bring up here. In a beam of light, even the purest ones of those such as from lasers, there is always the individual photon, but then there is the behavior of the aggregate whole, which behaves as a classical beam of light. Similarly, in Darwin’s analogy tree model, there are perhaps branchlets, but then there are branches! The branchlets don’t go very far, the branches become established and last through time.
Today’s discourse on the trillions of combinations of chromosomic DNA that is possible, loves to focus on micro cellular random displacement; but those random displacements can effectively cancel out as ‘noise’ - they don’t lead very far. Instead organisms must survive by being shaped in their environment over time. There is literally nothing in more recent work that changes that basic premise, of the larger branch pathways overcoming based upon the ability to survive.
8
@Kelly McKee
This indeed doesn't allow us to abandon Darwin's basic idea of the evolution of life on earth in a way that corresponds to a tree structure.
But the vertical evolution of life isn't less random than sideway displacements, so why would you propose to reject them as "noise", when it comes to understanding and reconstructing the tree of life?
And when it comes to "larger branch pathways": the discovery of Archaea actually shows a third form of life lying at the very basis of life on earth, and these are precisely the species that evolve through horizontal exchanges of genes. They've survived MUCH longer already than mammals, for instance, so why would you discard this type of evolution as "noise", IF "the ability to survive" is the criterium you propose in order to evaluate the importance of a specific gene transmission mechanism?
5
@Ana Luisa
Thx for replying. Self replication, is the fundamental pathway for life, otherwise species of higher organisms could not exist. Therefore, at some point, self replication became crucial for living organisms. It is apparent in life all around, as Darwin observed.
Therefore, to continue with our logic, we should develop a percentage of reproduction via vertical heredity vs. other means. We should observe that this percentage is a much larger figure, back through time. When life was pure microbe, however, that percentage might change, until at the beginning, it was perhaps more equally divided between replication pathways.
The article states that the ‘strange’ microbes are exceedingly rare today. If they are rare, then it is a safe assumption that the h.g.t. pathways are much less commonplace than vertical hereditary ones through most of the intervening time. Therefore it is a safe assumption, although not full proof, that the percentage of vertical pathways is much more prevalent in evolutionary change in life’s history. Thus the branches of Darwin’s tree remain intact.
When a mass extinction occurred, such as when the dinosaurs perished, mammals over great time evolved to fill the void left behind. All such change requires a catalyst for genetic mutation to occur, somehow. Only Darwin’s evolution idea offers sufficient explanation for how this could occur, together with enough proof. Over time, genetic change unconducive to life would disappear.
1
Darwin’s Tree Intact After ‘Scrambling’
There are groups of scientists today who would love to steal the mantle of Einstein, in their respective fields of science. Einstein’s relativity theories, by contrast, while transformational were so good at solving longstanding puzzles in physics that they were largely shown to be true during his lifetime. First and foremost, it was shown that relativity mathematics reduced down to that of Newtonian physics and were therefore consistent with known factual science.
The advent of photon physics is a good example to bring up here. In a beam of light, even the purest ones of those such as from lasers, there is always the individual photon, but then there is the behavior of the aggregate whole, which behaves as a classical beam of light. Similarly, in Darwin’s analogy tree model, there are perhaps branchlets, but then there are branches! The branchlets don’t go very far, the branches become established and last through time.
Today’s discourse on the trillions of combinations of chromosomic DNA that is possible, loves to focus on micro cellular random displacement; but those random displacements can effectively cancel out as ‘noise’ - they don’t lead very far. Instead organisms must survive by being shaped in their environment over time. There is literally nothing in more recent work that changes that basic premise, of the larger branch pathways overcoming based upon the ability to survive.
In his infamous lecture "On Protein Synthesis" delivered in 1957, Francis Crick permanently changed the logic of biology (as Horace Judson described it). As Horace Judson acknowledged in his 8th Day of Creation, This paper published in 1958. As Judson noted, "one paper from the period that an amateur of science, or a professional for that matter, can read today for instruction and pleasure ....The manner was deceptive. Like a gymnast who never seems to take a deep breath, Crick made the most agile leaps with nary a grunt to disturb the conversational tone."
It is arguably one of the most important scientific papers ever written, because he proposed at least 3 revolutionary ideas: Biotic Codes, tRNA, The Sequence Hypothesis etc.
And this is where Crick penned the most prescient prediction : "Biologists should realize that before long we shall have a subject which might be called "protein taxonomy"- the study of amino acid sequences of proteins of an organism and the comparison of them between species . . . these sequences are the most delicate expression possible of the phenotype of an organism and . . . vast amounts of evolutionary information may be hidden away within them".
1
Evolution based on natural selection? I see your science and I raise you faith. Admittedly, I’ll never be able to present any evidence to support my claims, but we’ll also never know how many fossil remnants have been lost to the ocean.
Blaise Pascal couldn’t have been that great of a mathematician.
Aside from its being a crystal-clear exposition of some fairly arcane science, this essay possesses the magical property – if first clipped to end precisely on the line “because, according to a friend, he didn’t want to shake Bill Clinton’s hand” – of arguably being one of the the longest and most complex jokes in the history of man.
HGT, indeed.
3
You are brilliant!
Hilarious!
One thing that we should learn from Carl Woese's work is that science is never settled. Whatever we think we know is always subject to be upended by future discoveries, insights and theories.
It's a shame that the climate alarmists seem not to understand this.
4
@Yggdrasil
You will note that the overall concepts of selection and inheritance were not dumped. The concept of the "Relativity of Wrong" applies here.
In the same way, the essential facts of climate change are not in dispute, except by those committed to a contrarian position.
7
No, that's not what you can conclude from this article.
Yes, there are "scientific revolutions" or paradigm shifts, where lots of things that we held to be true for centuries all of a sudden are proven to be wrong. But those things were merely PREMISSES on which the previous paradigm were based, not proven facts. A scientific paradigm shift normally takes over (= explains and proves to be true) all the previously proven facts, but (1) manages to explain many other facts too, and (2) proves that some of the premisses were wrong, and by doing so forces us to adopt a whole new way of thinking.
Example: Newton versus Einstein. Newton's laws were based on the premisse of a "homogeneous" universe and time and space as "absolute". Einstein showed that Newton's gravity law for instance was perfectly correct, BUT that once you go to a VERY large/small scale of reality, you need other types of laws, contrary to what Newton SUPPOSED (but had never proven, as at that time physics didn't have access to these scales of reality). So Einstein has proven that Newton was RIGHT, but only here on earth and for a scale of reality corresponding to our daily life, whereas once you look at the universe itself, you have to conclude that time and space are relative.
What Woese does here isn't a paradigm shift though, it's merely complicating Darwin's tree of life a bit more (adding some branches and a root).
So no, rejecting Newton/Darwin/proven science is NOT a rational position ... ;-)
14
@Ana Luisa
There are people who want Darwin to be wrong, and will argue about it forever, because they "believe" in some fantasy world and a "creator." Their real targets are not just Darwin, but "science" in general, and also people like Dawkins and Dennett, etc, who articulate and discuss Darwin for the masses, and argue against "creationist" theories. I believe that your sensible and rational reply is part of what has to be said in reply to those people, but we also cannot ignore the problem that these people are not going to be convinced by rational argument. They were not argued into their current "beliefs" by rational people, and they are not going to give up those irrational contentions and positions when faced with rational arguments.
I took biology 40 years ago
would definitely fail today as it is so much more complicated and confused than it was back then
amazing what we can learn when we think
6
Darwin’s Tree Intact After ‘Scrambling’
There are groups of scientists today who would love to steal the mantle of Einstein, in their respective fields of science. Einstein’s relativity theories, by contrast, while transformational were so good at solving longstanding puzzles in physics that they were largely shown to be true during his lifetime. First and foremost, it was shown that relativity mathematics reduced down to that of Newtonian physics and were therefore consistent with known factual science.
The advent of photon physics is a good example to bring up here. In a beam of light, even the purest ones of those such as from lasers, there is always the individual photon, but then there is the behavior of the aggregate whole, which behaves as a classical beam of light. Similarly, in Darwin’s analogy tree model, there are perhaps branchlets, but then there are branches! The branchlets don’t go very far, the branches become established and last through time.
Today’s discourse on the trillions of combinations of chromosomic DNA that is possible, loves to focus on micro cellular random displacement; but those random displacements can effectively cancel out as ‘noise’ - they don’t lead very far. Instead organisms must survive by being shaped in their environment over time. There is literally nothing in more recent work that changes that basic premise, of the larger branch pathways overcoming based upon the ability to survive.
You are entitled to your opinion, however please keep in mind that it is not necessary for anyone to believe in a scientific theory in order for it to be true. For example, you may not believe Einstein’s theories about matter and energy, but an atomic bomb designed on these principles will explode when detonated. Science is based on research and evidence, not faith or belief.
8
The "tape reader" that Brenner was referring to was not an audio tape or videotape, but the punched paper tape that was used to communicate with the early computers. The programs and data were input on punched paper tape, and the output was punched by the computer.
I do agree that today the 3-D printer is the analogy that communicates. David Quammen used the analogy that was familiar in his growing-up years.
5
Scientists speak of different forms of life when they cannot yet define what life is; only it's characteristics. Somewhere out there is an almighty God who created everything. Because people do not have the intellectual ability to grasp the concept of God they deny that He exists and try to explain the extreme complexity of living things with nonsense such as thinking that we human beings evolved from single cell organisms.
2
Science - as philosophers of science have explained for a long time now - doesn't answer "Why?" questions, it answers "How?" questions.
How did a planet without any mammals change into a planet with mammals, for instance?
Proven answer: through natural evolution and selection.
But WHY was the result of this evolution the existence of mammals and not something else? And why was there natural evolution in the first place?
No scientist will ever be able to answer these questions because that's not what a scientific method is designed (or able) to do.
I don't believe that there's a God out there, but that's not because I would fail to "grasp the concept of God". It's because I don't think that it's very likely that something like that would exist.
Here's where I do agree with you though: atheists (scientists or not - but most scientists, even today, are actually religious people ... ) often claim that it is irrational/unscientific to believe that there must be a God, even though NO scientist has EVER been able to proof that he doesn't exist. From a rational/scientific point of view however, absence of proof is not enough at all to claim proof of absence. And as the concept of God indeed includes the characteristic "unknowable", you're right to remember that "scientifically proving God" is an oxymoron.
That being said, ALL available evidence shows that man evolved from single cell organisms. And nothing shows that God rejects that idea as "nonsense" ... ;-)
2
@Aaron Adams Actually NASA came up with an excellent definition of life: "A self-sustaining chemical system capable of Darwinian evolution." God's existence or lack there of isn't a proper subject for science, as these hypotheticals cannot be tested by experiment or observation, unlike subjects in Biology.
3
@Aaron Adams
Science is our best attempt at an evidence-based explanation for how the world works.
Religion is just the unsubstantiated beliefs that people have inherited. It really does not work a an explanation for how the world works. See:
God is not a Good Theory (Sean Carroll)
https://www.youtube.com/results?search_query=God+is+a+bad+theory
2
Like the climate change article last week, this one will not be popular with people who understand what it is talking about. In the interests of making a good story with human interest, it oversimplifies, omits, and overstates. The NY Times can do better.
2
Woese died hoping for a clear and concise scientific legacy as Darwin enjoyed. I fear however that Woese might be the greater thinker and will one day reap the benefits of his work only to have some lab rat whippersnapper oblirate his sideways thinking with evidence that it was upside-down or a backward process instead. Legacy being only as reliable as the moment you catch lightning in a jar. Unfortuntly?
1
Great piece to read. We need this kind of piece nowadays.Thank you. Darwin boarded The Beagle which sailed from Plymouth England in 1831 to describe the fauna and geology of South America as well as the South Pacific islands, New Zealand, Australia, Mauritius and Madagascar. In his book The Voyage of the Beagle, he showed his humanity and the dreadful thought that species somehow had progenitor and geology was dynamic. It took him years gather data until he published The Origin of Species in 1859. In chapter four titled Natural Selection or Survival of the Fittest of the latter book showed a diagram that include line F depicting Woese's theory.
5
The first third of this article suffers from some editing problems that make it confusing. Early in the article, a major breakthrough is retold that a new branch called archaea was discovered and said to be a third kingdom, different from the two previously kingdoms of bacteria and eukarya. Darwin’s evolutionary tree idea is then shot down because of this, since there can’t be 3 separate branches. But then it says that eukarya branches from archaea, which seems to contradict the idea of 3 branches, and validate the idea of the tree - just in a different order with archaea first.
I do like this article overall, but the introduction is edited haphazardly and so the premise does not follow logically. It could be fixed with a some editing in the first third of the article. The last 2/3 of the article is fine.
4
What incredible hype. All the biology in the article has been in introductory text books for at least 20 years. I was especially struck by the line, Woese is “… the most important biologist of the 20th century that you’ve never heard of.” Really? Check the list of Nobel Laureates in Physiology and Medicine.
1
@William Barklow
Even though I have a Bachelor degree in Medicine and finishing a PhD in human sciences, I had never heard about Woese and his stunning discoveries.
The task of MSM is to "vulgarize" scientific discoveries, if not only scientists will know the truth, whereas "we the people" may vote for politicians proposing policies based on things that have proven to be false for decades already, and as a consequence, that cannot possibly work.
And when you know that today, a whopping 38% of the American people believes that Darwinism should be ignored and that instead we should assume that human beings in their present form exist for only 10,000 years, it becomes clear that there's still a LOT of vulgarizing to do ... ;-)
That being said, this is unfortunately clearly not the purpose of this article, as serious vulgarization leaves out all the anecdotal evidence and psychological speculation and replaces it with a clear definition of the basic concepts of a specific scientific field, an understandable overview of what has been discovered, and a clear discussion of its impact on how we thing about reality. So I doubt that this will actually change a lot of minds ...
3
@William Barklow
Not hype. How do you suppose the biology in those text books got there?
3
Outstanding – kudos...
Now, just go find us the neurogeneticist who’s going to fundamentally change the way we think about evolution and the culmination of life...
May be challenging – at this point, she’s probably still be a doctoral student...
Perhaps, going forward, she’ll strike up conversation with Doudna...
1
Interesting material but presented in too arcane a manner.
2
Terrific article. The kind of writing that makes the NYTimes what it is.
6
Fascinating, but one quibble. The article says, "(E)vidence of H.G.T. has even been found in mammals — an opossum from South America, a tenrec from Madagascar, a frog from West Africa." Since when is a frog a mammal?
5
@Michael Ireton, yes, I noticed that error too. Quammen should have written "vertebrates" to correctly group his two mammal and one amphibian examples of HGT. "Tetrapods" would have worked too, but I doubt many non-biologists know what that term means.
3
During the nineties, the critiquing of natural selection reached a feverish pitch and set off the so-called "Darwin Wars." A number of scientists who attacked natural selection were wrongly branded as creationists. It reminds me of today's political debates. Those who criticize Obama, Obamacare, excesses of the liberal media, and feminists and those who defend cops, the criminal justice system, prison guards, and high-minded conservatives are all taken as Trumpists by countless champions of political correctness.
All too many subscribe to the belief that "if you're not with me, you're against me." Both in science and politics the feeble-minded masses onlurecognize two choices. If only they could count to three.
2
Thank you NYTimes for introducing me to two wonderful human beings: Carl R. Woese and David Quammen.
3
Sounds like an attack on greatness David...ie an attack on Darwin.
Yes Darwin was no means perfect, he omitted research and was proven wrong on several things but nobody can dispute his ground breaking book the origins of species.
Maybe next to Newton's book, the greatest scientific published book in the modern era.
Your article drones on and on re esoteric, minute detail of things that nobody could understand unless you were a scientist looking to diss Darwin.
I am glad to report you failed as least in my opinion.
2
Completely mind boggling. I am astounded.
6
Thank you New York Times for being able and willing to give David Quamman the space needed to tell this extraordinary story both about the individual scientist and about the science, all new to me.
I had made a decision to begin this week by avoiding commenting, even reading articles about you know who and his corrupt enablers and to replace that by searching for articles in Science and other departments and commenting there as appropriate. I am being well rewarded and recommend to other readers that they might try this.
Only-NeverInSweden.blogspot.com
Citizen US SE
10
@Larry Lundgren Your interesting comment perspectives will be missed regarding "you know who" (who knows little) and his followers who prefer to know as little as possible.
But, in the context of this article, we here in the USA need to continue to work against horizontal ignorance transfer. The infective (and invective) pool of ignorance that can intrude into our body politic grows daily. The potential result is a stunted nation.
1
I had very mixed feelings reading this essay.
At first, I was truly amazed reading about a discovery made decades ago already and that changes our notion of the "tree of life", and felt so happy and privileged to be able to get to know such fundamental scientific progress just by reading the NYT.
As I continued reading, however, I became very disappointed. Here we are again, with a high-quality newspaper taking the lofty initiative of vulgarizing revolutionary science ... and then leaving out everything that is necessary to be able to achieve such a goal, and making up for such a dramatic gap with some biographical anecdotes and - even worse, but what seems to be a favorite occupation of historians - "psychologizing" (= speculating about which negative emotions someone the author does not know might have had).
THIS, dear NYT, is one of the reasons why the US has a science-hating conservative party and president. We urgently need REAL vulgarizing articles. That means rejecting the idea that science isn't exciting enough to just stick to it and that we need anecdotes in order to make it palatable for the reader - science IS an adventure in itself, so no distraction needed here.
Most of all, we need DEFINITIONS. What's the difference between eukaryotes and bacteria? Long ago, I got an undergraduate degree in medicine, so I still vaguely remember that one has a nucleus, the other not. But then what are archaea more precisely? What is so revolutionary here, CONCRETELY ... ?
8
Articles like this demonstrate why the NY Times is such a great publication. I've learned so much about science, art, food, real estate, forgotten people and things I would otherwise have never known. Each day brings practical goodies, as well as mind-tingling food for abstract thought. Even if the Times didn't make money - they recently reported a profit - only a fool who doesn't read would call it a failure.
5
Just a minor comment: Woese studied physics, moved to biophysics, and worked in microbiology / molecular biology. He should be called a physicist, maybe a biophysicist, but certainly not a microbiologist.
@What'sNew To me, it would seem wiser not to quibble about the name of his specific discipline, and rather to acknowledge his interdisciplinary drive as a theoretical scientist.
7
This was great to read. Thank you.
4
Entire paragraphs of this brilliant article reminded me of Lamarck. You know, lateral transfer of RNA, etc.
3
@former financial executive, that's not a good interpretation of the history of this science. Darwin, Wallace, Lamarck, and other scientists before 1953 had no idea that DNA and RNA held genetic information.
2
Sixty plus years ago when I was 16 I earned 90 cents an hour after school washing agar from petri dishes for Carl Woese. He was an easy boss to work for. He was interested in many things. He taught himself to play the piano, trumpet, and ukele. In the intervals between irradiating bacteria he would play the trumpet and he taught me to play the ukele a little. He talked about work published on electrodes planted in the “pleasure center” of a rat’s brain. Such a rat would press a lever indefinitely for a little electrical jolt to that center rather than do anything else. It disturbed Carl to think, If the same were true of people, what that might say about life’s purposes for human beings. He was also interested in ESP. The Carl Woese I knew then was eager to teach and discuss, at least one on one. After college when I left the east coast to teach in a one-room school in Montana, I visited Carl and his wife. We mused about the crazy behavior of a fish in their aquarium, and Carl sent me off with this microscope from medical school to use with my students. He was not crotchety then.
Academics can be petty, stupid, and cruel. How would any of us respond if our best work were rejected and we were called such names as “nut case.” Few of us would respond with grace.
His claim that microbiology should be organized as much of biology is--- asking big questions and stressing phylogentic evolution ---is a directive well taken, His work n horizontal evolution is eye-opening.
26
Another reminder that Nietzsche wasn’t actually crazy when he proclaimed that Empiricism is dead. Surf’s up, dude.
1
I do YDNA analysis for older men who want to know who they genetically descended from on their paternal side. A lot of SNP / STR analysis and triangulation to get their male “vertical” phylogeny correct. I usually charge $1/Yr and go back 500 years. But now I can offer a Deluxe package and go back 3.5 billion years. I am going to be rich!
3
Thank you for publishing this article, NYT and thank you Daveid Quammen for writing.
2
Great article! Just wish the Times would replace the creationist-sounding term “creature” with the scientific term “organism.” There is no need to dumb down a scientific article by using “creature,” like the article is some fantastical tale of the weird. No scientist says “creature.” We say “organism.” Readers will understand this term. Stop perpetuating creationism in science articles.
5
They lived in "sewage"? Primordial "sewage"? What's that?
If ever a 1977 hed writer and copy ed needed to distinguish b/w predate and pre-date, that was it.
2
Very good article.
3
Has the author of this article ever heard of the paleo-biologist
Stephen Jay Gould???
He described evolution not as a tree but a series of bushes!
6
@seeing with open eyes
Gould may have got the "bushes" imagery from the Menorah. Although Doolittle's tree has more "bushes" than the Menorah has candles.
Cool! Don't forget Lynn Marulis when it comes to "sideways heredity": https://evolution.berkeley.edu/evolibrary/article/history_24
4
Great article! NYTimes should stop using "creature," which smacks of creationism, and start using "organism," which is the proper scientific term. You don't need to dumb it down. People know what an organism is, or they will figure it out from the context. It comes off as somewhat patronizing, actually. Do you think you will scare your readers if you say "organism"?
1
We ourselves — we humans — probably come from creatures that, as recently as 41 years ago, were not known to exist.
Typo, or are we in a time warp? ; )
The NYT once again shows us what a real world class newspaper looks like. My main point is this research was paid for by G E, public funding via NASA, and a university system over one mans life time. I wonder given our current "show me the money" mentality if this work is even possible now. Public or private funding, I can't see G E or any other company doing this, the share holders would revolt. This is the great shame, and given the present rise of the "science deniers" those of us who believe in reason, must make our voice heard.
2
Fascinating..reposted it within our organizations networks
3
I am reminded of a recent video I saw (?nytimes) of bacteria snatching pieces of dna from their enviroment like a frog might use their tongue to get an insect. Pretty cool stuff. Good article.
4
I'd like to know who scrambled Darwin's Brain to the point he believed that mutations and death could somehow cause Dinosaurs to magically turn into BIRDS and fly away. Or cow like creatures to turn into whales because they hung out by the ocean. LOL
Evolution is nothing more than a fairy tale for adults and a religion for Atheists to hang their hat.
@Common Sense
Lol ... I suppose you also laugh away the idea that the earth turns around the sun because anyone with a little bit of common sense can open the window and then see that the sun is moving from left to right, whereas it's merely common sense to remember that we all feel that the earth below our feet does not move, if not we'd fall off our chairs ... ? ;-)
3
@Common Sense, You would do well to take a Biology course or a few to clear up your misconceptions of what evidence Charles Darwin used for his Theory of Evolution, and what was contributed by later scientists who were building upon his work. I am wondering if you even read this article, as your attack on Darwin has nothing to do with Carl Woese's work.
Darwin knew nothing of DA or mutations, yet by studying DNA, we have far more and better evidence for evolution than Darwin could have ever conceived. FYI, wales evolved from carnivores, not bovines.
6
@Common Sense
No, evolution is currently the best evidence-based explanation for how the diversity of life arose.
You really need to learn something about science. Your post is nonsense.
4
Actually, it‘s not Darwin’s tree, it’s Gods. I know no one writing such a braggadocios headline could believe such a thing, but let me lay another profound insight on ya: Dicking with this tree is what brought the flood. Now, I am almost positive you don’t believe that either, but science should tread lightly. The next judgment is by fire, science gets it, and they call it the heat-death. Only like everything else, they confuse the time-line, and add a few too many zeros. Yes, the next judgment will be by fire, will melt mountains, rid the world of man’s “foot-print,” and of those that think God, smh. Tick-tock, if you don’t Know the Truth, you better get on your knees and ask God to reveal it.
@Brad
"heat death" does not mean death by fire. it means entropy has reached it's maximum and there is no more free energy. Look it up, dude.
3
How could one write this and not mention Margulis?
5
One small negative comment to begin: "...comparing such molecules could reveal phylogeny. The new branch of science is called molecular phylogenetics. Wrinkle your nose at that fancy phrase, if you will, ..." There's absolutely no need to apologize for using legitimate terminology; neither embarrassment nor condescension look good in a magazine piece about science.
As a retired professor (but not in one of the sciences) I enjoyed reading the comments from people who are revising their fall-semester syllabi to include this article. Thank you! Students need to have some exposure to the reality that vision, equipment-building, data collection, analysis, interpretation, and communication all involve different kinds of hard thinking, tedious physical work, and thrilling breakthroughs. Being good at all of these is close to impossible for a good, or even great, researcher, so collaboration is key. I would love to peek in on the brains of undergrads to see the flash of comprehension as they read and discuss this.
4
A very well written article, with clear explanations of intricate concepts, and wonderful portrays of the inner works of science, and of the protagonist. The narrative illuminates the subjects brightly. I just ordered the book. What a nice article by Quammen, the author of my one of my favorite books ever, ‘’The Song of the Dodo’’
9
Carl Woese was my thesis adviser. The description of him is quite accurate. More play should have been given to Mitchell Sogin whom has passed on the torch of this extraordinary technique to determine evolutionary history. Every Summer for the last 40 years, Mitch has given an intense sequencing course at the Marine Biology Laboratory in Wood's Hole. 100s, if not 1000s, of graduate students, post docs and professors on leave, have taken this course and magnified the use phylogenetic relationships for determining symbiotic relationships and adding detail to the tree of life.
13
Carl Woese was one of the heroes of molecular biology, a non-biologist who made one of the greatest discoveries in the history of biology. When I was a graduate student in the 1970s doing some of the same kinds of RNA experiments with scary amounts of radioactivity as his lab's, I read Woese's papers but I didn't really get them. His obsession with 16S rRNA seemed to border on the pathological. But then he announced the discovery of a new domain of life and the method to his madness was revealed to those of us who couldn't comprehend the genius of his project.
Mr. Quammen's article a wonderful piece of science writing on a somewhat arcane topic that deserves broader understanding. It is unfortunate that even today many high school and college biology students are not exposed to the concept of the three domains of life and the impact of Woese's contributions. As with Steve from Ithaca, I have some minor quibbles with the article. I agree with Steve that the ribosome is nothing like a 3D printer. The tape reader is the better metaphor. The picture that accompanies the article indicates it was taken in 1961. The blackboard in the picture appears to have a list of 18 triplet codons next to the the amino acids they encode. I don't believe that many codons were known in 1961. Could the date on this picture be wrong? I would have liked to see a more complete explanation for why Woese chose the Goldilocks molecule 16S rRNA as the subject of his sequence determinations.
16
@Dave is right about the state of codon knowledge in 1961. I well remember when Marshall Nirenberg succeeded in the first decoding -- using UUU. Went to his lecture at my university -- must have been '62 or '63. It was awhile before other codons were worked out. Nirenberg's work was so elegant that even we undergrads knew he would get a Nobel. What an exciting time it was to be in college, much like what the 1920s and 1930s must have been in physics. Astonishing new results every few days. A century of experimental results suddenly making sense. I even switched my major to biology for a year (then back to physics).
2
@Dave
After looking at the photo a little longer, I can see how it might really be from 1961. It is difficult to make out the amino acid abbreviations next to the column of RNA triplets on the left side of the black board, but the last two at the bottom appear to be tyr (tyrosine) and val (valine), each followed by triplets that are not the correct codons for these amino acids. It appears that Woese, while at G.E., was trying to deduce the genetic code from theoretical first principles, as a physicist would. Unfortunately, he failed, as has everyone else who has tried.
1
As someone who has worked a bit in this field, has met/seen Woese a few times, and knows some of the other principals in this article, I think that it's wonderfully written. We should keep in mind what it is and isn't. It is not a textbook description of the science, and in fact, it's a condensation of what are probably several chapters in Quammen's book that was released today. The article can't be expected to completely explain these complex topics to neophytes. There will be more complete descriptions in the book of the science and of the scientists involved in this human endeavor. Some may find it too gossipy, but Woese was a fascinating character and no plaster saint. I think the article succeeds in whetting the appetite for the book in readers who want to know more, and I have a copy on order myself.
33
A few minor points. It's probably in the book, but the article doesn't mention the influential 1965 paper by Emile Zuckerkandl and the great chemist Linus Pauling that gave the rationales for using DNA, RNA, and protein sequences to infer evolutionary history. There was already a cottage industry of using the amino acid sequences of cytochrome c to classify animals when Woese wrote his letter to Crick. However, lots of microbes don't have cytochrome c, and Woese sussed out that 16S rRNA (and its relative in eukaryotes) was found in all cells and evolved slowly, prerequisites for building a universal "tree" of life.
I'm afraid that the ribosome is actually more like a tape reader than a 3D printer. The "folding instructions" for a protein are essentially inherent in its linear sequence, and it folds spontaneously as it spools out of the ribosome. Finally, Woese fought the idea that eukaryotes were directly derived from Archaea, and would have hated the Lokiarchaeota concept, which I believe is correct and is one of the most exciting area of science today. No doubt I'll have further quibbles as I read the book, but from the reviews I've read it sounds like it gets things right.
The discovery of the Archaea/16S tree was the most important one in evolutionary biology in the last 50-100 years, and I'm glad that this article has introduced it to and struck a chord in so many readers
22
@Steve
Interesting comment, thanks.
Here's where I disagree though: what you call "neophytes" are actually 99,99% of the people reading the NYT and already so interested in science that they try to read NYT articles about science.
Why would any newspaper publish articles about an important scientific discovery written in such a way that only 0.01% of its readers can understand what's that discovery actually is (= those already working in that particular scientific field - in other words those who already know this) ... ?
If you add to that the fact that the US has the largest carbon footprint per capita in the world and is now led by a political party that undermines science and people's interest in science on a daily basis, imho you cannot but be amazed when you see that the only MSM newspapers still accepting to write about science, do so in a way that makes those articles incomprehensible for 99% of its readers.
And yes, from a LITERARY point of view this is a well-written article. And from a HISTORY point of view it contains data that may interest those who would like to get the know Woese as a person.
But from a SCIENTIFIC point of view, it could easily have been made readable, just by inserting (in the marges, IF this is an excerpt from a book) a couple of definitions and graphs. The NYT could even merely have taken them over from Wikipedia ... (I've done so myself in a comment here yesterday, but apparently the NYT refuses to publish even that ...).
2
@Ana Luisa Hello and thanks for your comments.
I just got the book today, and skimming through it, I don't think it would make you much happier. It is very much focused on the history and the personalities of the scientists. The description of the science itself is pretty breezy, with some cool metaphors and a few more illustrations, but nobody is going to pass a college molecular biology class after reading it.
I think the 0.01% number is an overstatement. I think that a lot more people got the gist that comparing 16S rRNA among organisms led to the recognition of a third kind of life perhaps more closely related to us than bacteria. The business about HGT is is more difficult, and to my thinking, it's importance is overstated for non-microorganisms, where it is the exception rather than the rule.
Certainly, from some of the comments here, people were misunderstanding some of the science, but as you mentioned this article is more historical than scientific. An article in Scientific American (where there have been articles on this) would have more about the science, but of course way fewer people would read it.
I think the concepts relating to climate change are less esoteric than those for evolutionary molecular biology and Losing Earth, the long-form article in the NYT Magazine a few weeks ago, covered it well and my non-scientist wife understood nearly all of it.
Interesting article. I think it’s a bit overdone as to his contributions though. Identifying Archea was a big deal, but I just can’t get too stirred up about horizontal gene transfer in higher species. Viruses have been inserting their DNA into other life forms for eons and while that is not unimportant, the vast majority of evolutionary change and descent comes from vertical transmission.
7
@Robert D. Carl, III, True, however, horizontal transmission of genes by viruses has enabled some important traits to emerge, such as neurons being able to make connections necessary to establish memories in brains, the formation of placentas in most mammals, and more traits that as yet remain undiscovered. Only after a trait finds its way into a lineage, whether by de novo mutation, or by conjugation, transformation, or transduction, can it be transmitted vertically to the progeny.
3
I would further add, that I hope that a widening commercial avenue of artificial genetic experimentation is not somehow justified, from out of the work of serious contributing scientists such as Professor Woese, who studied natural systems, not GMO’s!
It cannot be overemphasized, that natural life forms have survived the natural tests of the natural world over long spans of time. Yet we seem poised to adopt the opposite of the ethics best expressed by the great novel ‘Frankenstein’ by Mary Shelley, with corporations and their funding pushing us toward the abandonment of higher ethics on genetics in order to justify the artificial manipulation of genetics, led by promises of commercial profit.
15
@Kelly McKee
The GMO process is simply conjugation, transformation, or transduction conducted by humans. It is very useful in producing organisms that have characteristics that are useful such as drought tolerance in some plants that naturally lack that, among many examples. The idea of creating "Frankensteins" (beyond being literally incorrect, Frankenstein was the person not the monster) is highly unlikely, except perhaps in micro-organisms. The genetics of higher organisms is sufficiently complex and sophisticated that introduction of most genes from other species (as well as most mutations) simply does not work.
1
I think it is important to point out that Darwins theory of evolution is not wrong when applied to larger living systems. HGT is not contradictory, it is complementary. Just like there is still value in Newtonian Physics despite Relativity, and in Relativity despite Quantum Physics. It's normally not necessary to say such obvious things, but in a laymans journal like the NYT it's probably useful.
On the micro level, the transition between chemical reaction and "life" is not a hard boundary, but rather a chaotic mess which only looks regular when under rules of statistics and thermodynamics.
Moving up the scale in size and complexity, life becomes so specialized and optimized - that direct cross-species exchanges cannot survive, except for some very minor changes taking place via virus. Even in that case, it can just be considered as a source of mutation - not something outside of the tree model.
20
Another fascinating (and mind-blowing) read in the sciences from the Times. Not quite sure what has changed, if anything, regarding which topics get published, but I sure hope it continues. Between this article and the recent "What the Mystery of the Tick-Borne Meat Allergy Could Reveal", the Times has set a new bar for science writing, explaining incredibly complex topics to an audience that may not have an extensive background in the sciences, a Herculean task. Bravo to both the authors and the Times. Well done!
24
Darwin’s Tree Intact After ‘Scrambling’
Einstein’s relativity theories, while transformational, were so good at solving longstanding puzzles in physics that they were largely shown to be true during his lifetime. First and foremost, it was shown that relativity mathematics reduced down to that of Newtonian physics and were therefore consistent with known factual science. This level of scientific advancement has not been equally shown to have occurred here; and yet the author seems to idolize Prof. Moise to that degree.
Perhaps the advent of photon physics is a good analogy to use here, however. In a beam of light, even the purest ones such as those from lasers, there is always the individual photon. But then there is the behavior of the aggregate whole, which behaves as a classical beam of light. Similarly, in Darwin’s analogy of a tree, there are perhaps branchlets, but then there are branches! The branchlets don’t go very far, the branches become established and last through time.
Today’s discourse on the trillions of combinations of chromosomic DNA that is possible, loves to focus on micro cellular random displacement; but those random displacements can effectively cancel out as ‘noise’ - they don’t lead very far. Instead organisms must survive by being shaped in their environment over time. There is nothing in more recent work in microbiology that seems to change the fundamental premise, of large branch pathways overcoming based upon the ability to survive.
1
This is a very tight statement and a wonderfully written summary of a man and his work. It is also an interesting - and admittedly controversial - acknowledgement that we are all GMO's.
How ironic.
9
@Charles. No, we're not. GMOs - in common parlance - are created by human agency, hubristic, fallible and ignorant. In the non-capitalised (branded) meaning of the term, we are all genetic organisms modifying according to rules and accidents that we don't understand with several billion years head start on us. Artificially modifying life forms and releasing them on an unsuspecting and unprepared nature is very long term experiment with unknowable consequences.
1
Very impressive and well written article. Amazed the writer understood the issues and the science.
As an engineer and product manager of DNA sequencers in the 1990s I was on the periphery of this world. Egos abound, as do the same petty jealousies and frailties of humanity in any field, be it digging ditches or molecular biology. Oh, the stories I herad about the inventor of PCR, from people who worked with him, they would curl your hair.
8
@Garrett Clay Check out David Quammen's body of work. It is worth it.
The beauty of science is that it can change as new information is available. Eventually the hope of evolution will be completely abandoned and scientists will rejoice that only a Creator could endow such complexity, beauty, and resilience.
2
@Jim Robertson
That's not what Woese shows ... ;-)
What he shows is that Darwinian evolution isn't merely happening in a linear way, as Darwin thought (based on numerous examples that prove linear evolution), but sometimes ALSO happens "sideways", as Woese discovered by studying a new kind of microorganisms.
That' a CONFIRMATION of the very essence of Darwinism, when it comes to the evolution of species, not a refuting of it, or proof of the opposite theory (= no evolution, everything created at once - also called Creationism).
As to your "beauty" argument: that's a philosophical argument, not a scientific argument. And it's easy to refute: as Oscar Wilde already wrote, beauty is in the eyes of the beholder ... . What is beautiful for us is something totally different than what is beautiful for a cat, for instance. Secondly, there's absolutely no reason why a Darwinian evolution would NOT be able to lead to what humans tend to call beautiful ... .
Finally, Woese has just shown that the study of Archaea precisely ADDS to our understanding of how a Darwinian type of evolution could lead to such complexity, as now we know that even the branches of the evolutionary tree can intermingle ... .
But don't despair: there's absolutely no philosophical or scientific argument against the idea of a Creator deciding to create planet earth's ecosystem ... through the implementation of Darwinism as evolutionary mechanism. So Darwinism doesn't necessarily lead to atheism at all.
26
@Jim Robertson, The beauty of science is that it increases our understanding about everything. Religion doesn't do that. If we are here because God created us from dust on the ground, it's a nice story but does not increase our understanding of where we really came from. There is no understanding in religion, only satisfaction, comfort and certainty. Those states of mind are pleasant and agreeable but they add nothing to understanding.
23
@Charles Justice
Imho it's precisely because of this non-scientific prejudices about religion that Creationism is so popular these days.
The Bible indeed doesn't provide any scientific information about the world, simply because it was written by people living in an age where science didn't exist yet.
But to imagine that religion means "satisfaction, comfort and certainty" is only possible if you never met (or read) authentically religious people.
Doubting whether God actually exists or not is something that all truly religious people have to face from time to time. And deciding to live your life with compassion isn't always that "comfortable".
Furthermore, there's also no reason at all why religious people would by definition feel any "satisfaction" when rejecting science, as most Nobel prize winners are actually religious people too.
Finally, there is NO scientific proof of the absence of a God at all, so deciding to live your life as if there isn't is as much a decision based on uncertainty as is the decision to build your life around the notion of a living God.
It's when pro-science people start to reject religion for non-scientific, simplistic reasons, that we risk to alienate religious people who didn't have the chance yet to have a real taste of what scientific activity is like, rather then to invite them to come and have a look for themselves...
1
These would be some really nice ideas if the theory of evolution were true but unfortunately for evolutionists it is not. There are huge gaps in the fossil record that have never been explained but even more glaring than that is evolutionists have never been able to explain how the human eye evolved.
1
@Charley Larson
To your satisfaction, or ability to understand perhaps. By the way, why did you focus on the human eye? Why not a dog's eye or an eagle's eye. Or do you not care about those species.
@Charley Larson. Well, Charlie, wrong on both counts. These notions were dismissed long ago. Come up with something new.
@Charley Larson
Theories in science are never true or false. They either explain the data, in which case they stand, or they don't explain the data, in which case they are either rejected or modified.
Evolution explains huge amounts of data in the living world. Nothing else ever came close.
You exaggerate. The continuity of the fossil record in far larger than the gaps.
As for the human eye, if you research the evolutionary literature you'l learn it is quite well understood. What's interesting are the errors in physical optics. For example, the sensors point the wrong way. The blind spot caused by bunching the optic nerves. A college student majoring in physics would not make such mistakes.
Much more interesting are the data we haven't yet explained. Why has homosexuality persisted widely in mammals? It cannot help the struggle for survival. The same goes for permanent breasts in females of homo sapiens. They only appear in other species when required for lactation. Check it out at the zoo!
Like most good theories, there's always more!
3
Why is this surprising? The fact that some human cells, which have been affected by viruses/ bacteria, can create cancer with new/ different DNA in subsystems of humans (ie only some cells/ organs areas and not the whole), why couldn't similar "infections" create cross DNA "contamination" why may or may not benefit the "host". I appreciate the discovery of this but I am not sure it is surprising.
@Donald LaCoy
If I understood well, the surprising there here isn't that a virus can insert his genome into the cell of an animal which then affects that cell's functioning, it's that the combination of two cells with a different genome can lead to a new, third cell, with a genome that has never existed before AND that is perfectly autonomous and viable.
Cancer cells or HIV infected cells kill the human body, so they can't create a whole new lineage.
So it's the fact that in the case of Archaea there is no "host", and yet different types of genomes can communicate AND create whole new phylogenetic groups that completely changes Darwin's linear idea of evolution of species.
At the same time, the discovery of Archaea means that the origins of life are also more complicated that what microbiologists thought in the 1970s, as instead of first having bacteria and then, through endosymbiosis, eukaryotes (so basically two types of cells, first one without nucleus containing/protecting the cell's genome, and then one with a nucleus), we have to take a third type into account, the Archaea, which are actually closer to human genome than that of bacteria, whereas Archaea and eukaryotes have a common ancestor X, which itself has an ancestor in common with bacteria.
So now, we have a whole new, additional factor explaining both the origins of life on earth, and the incredible amount of different species that have existed in the past and exist today, compared to Darwinism.
16
@Donald LaCoy. You're right, Donald. There was no reason why the microbiology community around the world should have been surprised. It was obvious, right? If you so casually think it's obvious, maybe it's because of 3000 well-crafted words that made it understandable.
Are there any other ho-hum paradigm-changing scientific discoveries you'd like to share with us? Especially a few we don't yet know about?
2
@Ana Luisa Thank you, that was so clear that even I, with zero knowledge of biology, just learned something!
A very nice article for me. I have heard of the archaea, but have not attempted to learn much about them. I had not heard of Dr. Woese AFAIR.
What really struck me (because of my own interests) is the discussion of his “New Biology” article.
I read that as a call to focus more on BASIC research in biology, rather than the current overwhelming emphasis on applied bioMEDICAL ressarch.
We are currently infatuated with introducing new therapeutics that will reprogram the organism, in spite of not understanding much about how the organism maintains its physical structure over the lifespan. This ignorance leaves us open to unknown and potentially dangerous adverse effects from such novel therapies.
A major problem with focusing on basic research, in our culture, is that it doesn’t necessarily or obviously offer large financial returns.
18
I'm disappointed to see no mention of Lynn Margulis' seminal 1966 paper (published in 1967 as Lynn Sagan, as she was married to Carl Sagan at the time) that introduced the endosymbiosis theory for the evolution of eukaryotes from prokaryotes, from phagocytic bacteria and some food bacteria they failed to kill, which Carl Woese and others helped confirm. We now know that a couple billion years ago the last common ancestors of modern plants and animals "ate" alphaproteobacteria type bacteria that became symbiotic mitochondria, and later engulfed cyanobacteria that became plant's symbiotic chloroplasts. Her microscopy work was seminal, and dovetails nicely with Woese' genetic studies, but is also too often ignored in the history of science.
72
Apologies for misspelling Lynn Margulis and David Quammen in previous comment.
It's my understanding, from reviews of this book, that Quamen DOES give Lyn Margolis her due in her own section in this book.
1
@Steven Keirstead Lynn Margulis (or Sagan) was not mentioned in this article, but she gets a lot of ink in the book The Tangled Tree. Carl Woese may be the star of the book (and the sole star of this article) but I'd say Lynn Margulis got a leading role too. Probably more mention of her than anyone other than Carl Woese.
3
Learning about the hard-fought and brilliant discoveries of so many geniuses who labored in obscurity makes the worldview of the powerful Creationist movement in the US seem so small and sad. Small because creationists are revulsed by the complexity, nuance, and ambiguity of the real world. And sad because they pass on this intolerance for scientific thought to their children.
40
I don't think Creationists are "revulsed by the complexity, nuance and ambiguity of the real world".
Creationism (just like the anti-climate science "movement") is uniquely American. You (almost) don't find it among other conservatives in the West. In that case, you cannot but suppose that there must be something wrong with the way science is taught here, no?
Science, as an activity, is merely a cultivation of the natural curiosity about ourselves and the world with which we're all born. It's based on the fact that nobody likes to be asked to accept something as true before you understand just what it is, and why it is considered to be true. It's based on the natural questioning mind, which you can see delightfully at work in any young child. It is by definition a "rebellious" activity, motivated by what Plato called a "terrible love of the truth".
But how many science teachers still have - let alone transmit - this terrible love of the truth ... ? How many just try to impose scientific RESULTS onto their students, who are then supposed to learn them by heart - whether they understood those results or not?
And then we're not even talking yet about the militant atheism that some science teachers adhere to, and that makes them feel morally superior to religious people even though nobody has ever scientifically proven that God doesn't exist.
In a way, this article does the same thing: no clear explanation of basic ideas, and a focus on people rather than "the truth" ...
1
Beautiful essay honouring a wonderful man. No more apt phrase was quoted in the obituary encapsulates the reception of these discoveries ( in Science 2013 (339: ): “I point at the moon
and they focus on my finger!” At that time, too many in mol biol amd microbiol lacked the education (let alone a wider reading and curiosity) to even understand his goals and the core concepts.
A couple of corrections/additions. An actual species are individuals, admixture etc via LGT does not obviate the individuality of the segment of (populational) lineage. (Read Michael Ghiselin). Species are the products of the tokogenic processes of organismal descent. The species CATEGORY is ontologically distinct from the genomic tier, in the genealogical hierarchy. Species exist - we keep on discovering now ones (albeit as biodiversity vanishes).
10
I apologize for bringing politics into this immensely enjoyable and apolitical discussion, but we live in an age where everyone who works in the sciences or enjoys them should, I think, consider themselves as soldiers, honor-bound to defend our scientific disciplines against the ravages of Trump and all his minions. Compare and contrast the lives of two difficult men, Carl Woese and Donald Trump. They are polar opposites in every value that people in the sciences have in common.
I liked this article so much in part because it is a refuge from having to think about politics for a brief moment. But escaping into challenging and enjoyable scientific questions is not going to advance scientific values or human knowledge.
30
How in the world can the topic of Trump have any relevance to this fascinating, well told tale. I take it back, it is extremely relevant.
1
Exactly.
But that means that we URGENTLY need articles CLEARLY explaining scientific discoveries, in terms understandable for any ordinary citizen.
As soon as you don't define any basic concept of the scientific field you're reporting on (as is unfortunately the case with this piece too), you're already loosing 99% of ordinary citizens trying to read this and wanting to UNDERSTAND - whereas the passion to understand is precisely something scientists and most ordinary citizens share.
For the other 1% (people who are scientists, like me), those who aren't microbiologists but are used to regularly reading scientific vulgarizing articles outside of their own scientific field, you know that sometimes authors of those pieces actually aren't that good in vulgarizing, so omit the first crucial step (definitions). Because of your own work though, you know what method to use in order to fill in the blanks yourself and try to reconstruct those definitions by studying the semantic context in which the author is using those notions. That requires some time/investment/patience, but sometimes it's possible.
Doing so becomes completely impossible, however, if you have to suspend your attention during long paragraphs about the supposed psychology of a scientist, or anecdotal data about his own personal life. Then you create SO much confusion, that no real understanding, EVEN for a fellow scientist, is still possible.
And that's sad, from both a scientific and political point of view...
Extraordinary writing, as I've come to expect from The Times. The story is fascinating and the writing is compelling. Thank you Mr. Quammen.
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The fluidity of life forces is now fact. The variability of our genome is such a marvelous discovery. The potential for change in our care is profound. Static is out.
11
I want to congratulate David Quammen on such a great piece of writing. You've taken complex subjects--biology, scientific process, human nature--and illuminated them wonderfully. I'm inspired. I would pay a higher subscription price if I knew I was getting more writing like this.
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Hear! Hear!
Completely agree. I just sent to a dozen people. So clear and understandable for the layperson, a gift.
2
@JJ
In that case ... could you please summarize the very essence of what this piece is trying to say, in language that is understandable for people who aren't microbiologists ... ?
Thanking you in advance.
(And yes, there's a bit of irony in this question, because I suspect that you won't be able to summarize this in your own words. I'd even guess that if you're not a microbiologist, you didn't even understand what is so revolutionary here ... as all the main definitions that would allow us to understand, are cruelly lacking:
- what's the difference between viruses and bacteria?
- what's the difference between bacteria and archaea?
- what's the relationship/link between archaea and human beings?
- why is it that Woese rejects an opinion that today many people have come to accept as self-evident, namely that the human genome is the "Holy Grail" of microbiology and the most important subject to study in order to understand human health (and as we even often read in comments these days, even mental health)?
Without clear discussions of these questions, and clear answers, an essay like this may be very well written (nobody can deny that), but WHAT does it achieve for the - more than ever oh so necessary - vulgarization of science?
Very little, I'm afraid ...
But maybe someone here can prove me wrong ... ?
What a wonderful story. The human aspect of the science here holds such important lessons - lessons that can be transferred to other disciplines of life.
5
Wonderful article and book! I'm already revising the curriculum of my freshman biology class, which starts in 7 days, to expand on my heretofore light discussion of HGT as an evolutionary force, along with the better-known processes of mutation, natural selection, sexual selection, genetic drift, etc. The Tangled Tree will join Your Inner Fish and The Log from the Sea of Cortez as highly recommended reading for my students. They will also be encouraged to consider the implications of CRISPR technology for humans and other species. These assignments will hopefully broaden their perspectives and help them address astonishing and unpredictable challenges in the Anthropocene era.
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@Jon S. I hope your students appreciate you as you sound excited and engaged about the new school year. When you point to the moon, if only one does not focus on your finger it is worth it.
1
Absolutely the most interesting and important biology article I have read in many years about a process that seems obvious once someone who senses its possibility, shows its real and then brings it to our attention. I was a zoology major in the 50's but I never heard of Woese until now. Life is a little more complex than I thought and I have to catch up on a lot of reading about the new understandings. Thank you,NYT.
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Thanks David Quammen. This is an inspiring and poignant essay on the nature of scientific questioning, and the boldness of one who followed his unorthodox vision, and for a moment, opened the heavens for a further, tiny glimpse.
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Thank you. I am saddened that knowledge is so little prized today that your article is the first to arrive within my horizons, that of the non-specialist, the man on the street. Not only tells what it does but it shows how the most relevant information is passed over by the usual media, for years!
Thanks to David Quammen and kudos, exceptional work. Thanks to the NYT for the wisdom to publish it.
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Thanks for this. My college freshman students will start their semester by reading it and reporting what they did or didn't understand, not just the science but the human aspects of how science is done.
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In Physics, Einstein did not come to his theories in isolation. It took the works of the likes of Newton and Maxwell (they in their turn relied on the works of those before them) before him. Someday, somebody will produce a "unified theory". That theory will again be revised.
In Biology, The day you hear someone say they have the absolute answer as to the evolution of life on this planet, is the day somebody else will go to work to add more to the story.
Math, Physics, Chemistry, Biology and human culture in combination make up the tangled lens through which we view this Universe. What sort of lens will be needed to view a different universe? 'Cause you know there is a good probability there are more out there. RAW
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@richard wiesner
You may overestimate what scientists claim they owe to their predecessors - mots folks think Newton was speaking ironically or with deliberate cruelty.
"What Des-Cartes [sic] did was a good step. You have added much several ways, & especially in taking the colours of thin plates into philosophical consideration. If I have seen further it is by standing on the shoulders [sic] of Giants." ~ Newton
And Einstein did not truly rely on those two esteemed predecessors - he was trying to solve problems presented by empirical data and observation with their theories - Newton's additive frames of reference and Maxwell's relative movement
2
As a non-scientist but someone interested in learning a bit of everything what struck me about this article was how connected life is on so many levels. It seems that the more we learn the more we see how much a part of everything we are. I hope that knowledge keeps us from destroying things in our greed and belief in our separateness and dominance and right.
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OK, so Darwin might have been wrong about how many origins there were. Evolution is a process and nothing about how many origins there were disputes his theory of variant generation and natural selection. Darwin is a genius because he got the process correct, not because he predicted how many origins of life there were.
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@CBH Thanks, CBH. In order for a gene transferred laterally to survive in progeny it has to provide an advantage in a niche. Isn't that natural selection?
1
WOW! A huge thank you to the NYT for providing space for this hugely important story. And an even bigger thanks to David Quammen for being able to describe so clearly such incredibly complex ideas.
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An excellent informative and interesting article. Progress has been made in horizontal gene transfers in hierarchy/heterarchy studies, since Woese's time.
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@Mor
Well, if it bothers you so much and you aren't satisfied with skipping over such odious passages, then start writing the books you want to see published. Not that any of this seemed like gossip to me. And some of these passages were ones I found particularly delicious--in ways that allowed me to enjoy this full, well-rounded literary and scientific meal even more.
You know, it is very possible to simultaneously be a person who enjoys such "human interest" bits, when woven in with purpose or used as a clever literary and story telling device, while also being the kind of person who doesn't need them to facilitate her understanding of the material at hand. And if they do make someone want to read further--well, then, what in the world is wrong with that?
In short, nothing like rules and calls for purity--always such a blast. Woohoo!
16
Here's the problem: if you're not a microbiologist, you need very clear and understandable definitions of the basic technical concepts in this field in order to minimally understand the meaning of the scientific discovery this essay is trying to describe.
If an essay doesn't provide those definitions (as is the case here, unfortunately), the only possibility left that might allow you to at least understand a little bit what's going on, is to deduct the meaning of those concepts through studying the context in which the author is using them.
If, however, you constantly "dilute" that context by switching to a totally different kind of subject and scientific fields (history and psychology), it becomes truly impossible to grasp the scientific meaning of the discovery that this piece is all about.
And if you don't understand it, you can't comment it (as most comments here show, nobody indeed discusses the very content, when it comes to the microbiological part of this essay, except for a few college professors working in this field 24/7).
Concretely, that means that one of the VERY few articles about science published in a MSM, is actually inaccessible for 99,9% of ordinary citizens.
In that case, just remembering how great we, the few privileged people who love science enough to at least try to read this, believe science is, will never be enough to get science-based and science-promoting policies in DC again.
We need people to want to read further BECAUSE of the science.
3
As a microbiologist who taught medical microbiology at university, I fully appreciated this article. I was of course, familiar with Woese's work, and utilized it in teaching. However until now, I really knew very little about the brilliant man who contributed so greatly to my field of study. Thank you for this article.
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@Diana
With all respect, but this is precisely what I regret about this essay.
All that it does is providing some historical data about the man behind an apparently gigantic scientific discovery, which is only understandable and interesting if you're already a microbiologist yourself.
The rest of us FINALLY see an article about a tremendously important scientific discovery in a mainstream newspaper, so hope to learn what that discovery is, in clear terms, so that we can share in the passion of understanding and the joy of discovering something new about the world, and then - probably today even more importantly - help spread the news ... only to observe that basic technical notions aren't defined here, so we actually can't grasp the meaning of this discovery at all ... .
Knowing whether a scientist who made a huge discovery personally liked explaining stuff to others or not certainly isn't entirely uninteresting, but not the reason why we wanted to read this in the first place ...
So I hope that one or the other microbiologist here can do for a moment what someone like Paul Krugman manages to do for his own scientific field (economics) on a daily basis: explaining the very essence of a discovery in plain English, using clear concepts and well-defined words.
Because if you can't even do this in MSM articles about science, how can we ever expect taxpayers to want to fund science or vote for politicians defending science-based policies ... ?
Just askin' ...
A wonderful article, and one that helps me much in my effort to understand a little of the changes of thinking since I was taught about the two kingdoms in the 1950's. I hadn't known of Woese. His focus on deep understanding is wonderful to me in a world in which most people including many scientists are more focused on practical or economic results. I'm reminded of the story about Rutherford, whose lab, after he had been recognized as a prominent scientist, was visited by Queen Victoria. Supposedly she, having been told what he was working on, said something like "Very interesting, but of what use is it"? To which he replied "Madam, of what use is a baby?" His work, of course, formed the basis of all modern electronics.
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@Thomas
That story is about Clerk Maxwell, and his explanations of electricity and magnetism.
4
@Thomas you are a bit mixed up. It was Faraday who supposedly said "Of what use is a baby," about his work in electromagnetism. Rutherford's work was the basis of nuclear physics, not electronics.
1
There is a lot to like about this article. The ability of Woese, Fox, and Sogin to discover a new kingdom of life from rRNA sequencing is almost unimaginable in today's genome era. But the implication that Darwin and bifurcating trees has been overturned is misleading. Many evolutionary biologists make this argument, but others argue that there are many gene families that support the more conventional view. Just because Woese had an outlandish idea that was right (Archaea) does not mean that all his controversial ideas will stand the test of time.
13
I've always believed that the Woese story is the strongest argument against academic administrators (deans, provosts, etc) in the sciences who are bean counters and too business-oriented. Over the years, I've known administrators who were able to read a colleague's work--well outside of their own discipline--and understand that it was inherently interesting and valuable, even if the author was not a polished self-promoter. Or, able to ask intelligent questions until they could understand the work and evaluate it. I've also known administrators who relied solely on numbers of papers, dollar amount of grants, etc. in evaluating a colleague and were totally incapable of understanding material outside their own sub-discipline. The greatest American universities endeavor to hire brilliant faculty and then get out of their way. All too often, unfortunately, modern universities focus too much on chasing big grant dollars and piles of published manuscripts and too little on taking risks for quality, lasting work. I hope university administrators will read this article and realize that the best work is not always done by the smoothest talker and biggest schmoozer.
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@Patricia Maurice-- Amen sister.
1
Listen to Jerry Seinfeld talk about the exact same dynamic in writing a comedy series and creating a live audience show, all the while having to deal with corporate TV suits who wanted to inject and direct and decide what was to be approved or disapproved. Jerry and Larry David would simply close the door in their faces and continue on as brilliant comics and comedic writers--in spite of the TV network administrators.
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@Patricia Maurice
As I recall when UCIrvine was first established the goal was to "hire brilliant faculty and get out of their way." I was privileged to be a student during that era.
2
A wonderful article. I am a Neurobiology Prof. at Yale and knew the rudiments of this story. Yet I learned so much history and gained a great new perspective from this article. I am now even more addicted to the Times than before.
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I was struck by the description of HGT between bacteria or viruses and eukaryotes in nature. Human-made genetically engineered plants, animals, and microbes are apparently no more "artificial" than ones created using selective breeding. In both cases we are just controlling the direction of processes that already occur in nature.
But because many people don't know about HGT, and don't understand either genetic engineering or selective breeding, we have spent almost 30 years battling about GMOs!
26
actually, there is research - that shows various Cancers are reprogramming cells to produce the ingredients they need to multiply and H.G.T. would easily fit into the overall theory of what is going on.
7
Thank you NYT for reminding me why I subscribe to this wonderful journal! Brilliant, enlightening, and life-affirming. Bravo!
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@Eric
Seconded, Eric. The same thought kept recurring throughout my reading of the article.
5
To Mor of California,
You are right. There is something wrong with education. It's that the quality of education is uneven in this country, and it is precisely the human element, or gossip as you see it, that may draw a person in.
At introduction few people have the ability to appreciate the beauty of abstract knowledge or philosophical speculation, and why should this beauty of discovery be restricted to a few?
A high school student deemed the article, "a good summer prokect", while a high school teacher enthused that her, "students will love it."
An introduction to the scientist may be in order to appreciate the science. My introduction to physics was sparked by the lectures of Richard Feynman, and his dynamic personality and style was the foundation. Stephen Hawking' s lectures and essays as well as other authors bibliographies have continued to feed my interest. Why should the appreciation of science, particularly the 'hard' sciences, be limited to those with a natural flair?
It's a wonderful article, one I'm sure my granddaughter's teachers, at a STEM Magnet school will find interesting. It's articles like this that inspired my subscription, as well as the reader's comments. To all of you, including Mor, thank you.
52
Wonderful article about an innovative researcher. For those not enjoying the human element it is the Woese's of the world that go against the tide to bring their innovation to the world. Praise his courage as well as his science.
37
Lovely article. It was fun to hear about the complex man behind the papers I struggled with in grad school. It is true that molecular biology tends to morph into biomedical engineering, but there are still lots of very good people around asking deep questions. Re the human genome project: brute force, profoundly boring and repetitive, but it had to be done when it was done. Because humans pay the taxes that fund basic research and because in the end it had to be interesting. I was surprised to learn that they have mammalian frogs in west Africa.
10
If you look closely - or with fresh eyes - at Darwin's drawing you might say that it resembles more bush than a tree. The tree interpretation is I think a 'read backwards' from Darwin's supporters; in the case of Ernst Haeckel, for example, the tree is explicitly a tree in that it has a single trunk (with humans at the top.) Equally, the older religious metaphor of 'tree of life' probably doesn't help either. Yes, the roots are common to all species, but what Darwin was trying to show was differentiation, albeit with some characteristics of 'progress' (up to branches, certainly via increasing complexity) but not the unilinear progress towards the 'top of tree' towards humans as often suggested by later interpreters.
22
A wonderful article. Thank you.
Woese was a hero of science when I took Biology many years ago. And the transfer of genes - for example between bacteria, sometimes by viruses, sometimes by bacteria mating with each other! - was all the rage then too.
I'm glad it and he are back - possibly to be reinterpreted in light of so much new information. Will read the book with great interest.
30
This fascinating story illuminates several problems in the sciences:
- Some scientists are poor communicators and have a hard time explaining their work even to colleagues, not to mention people in other fields--which can mean that scientists doing really important work don't get enough funding or support.
- People view scientists as innovators when they are just as conventional as everyone else--as is evident when someone comes along with a theory or approach that blows conventional knowledge out of the water. Hence the too-common story of a scientific community of (mostly) men who immediately reject an idea or approach or finding that later turns out to be prescient and true as nutty and false.
- People who see the universe in an entirely different way are rare, and it's a good thing that we have public and private colleges and universities where those people can work. Whatever failings those institutions have, their role in supporting research--which may lead everywhere or nowhere--is crucial.
107
people who see the world in a different, unique, new way are scary; they might get ideas.
9
I’m willing to bet the farm that the vast majority of outside the box scientific theories are no good and die their deserved deaths. The problem is, how do we recognize the handful that are good? There has to be a mechanism in place for winnowing the wheat from the chaff. And I think this is called open scientific research sharing.
4
This is why I read the times, bravo. A good read for a novice. Now if we can just employ scientists to assure our species survival.
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@hb If Trump allows scientists to help and he heeds their advice
Completely fascinating, equally informative and beautifully written.
Thank you.
It's for half hours like the one I just spent -- deep inside ANY prismatically revealed subject -- that I subscribe to the NY Times.
164
It's not clear to me how you get to the existence of a third kingdom from fragments of rRNA although I haven't read Woese's papers. I found this story stimulating, except for the knocking of Darwin, because I had some of the flaws described for Woese. I published the sequence of human beta-actin (with Klaus Weber) and cloned the gene to determine its sequence. We observed the remarkable conservation of the protein from yeast to humans. It is strictly a eukaryotic gene/protein. So I was very surprised to read that Guljamow et al. found a strain of the cyanobacterium Microcystis aeruginosa that had acquired an actin gene probably from the intestinal track of a marine invertebrate. I doubt that they were looking for this or that they were influenced by Woese. They cite Russell Dolittle's 2002 review of HGT.
18
@John Leavitt The ribosomal RNA sequences Woese and Fox found for Archaea are radically different from those of Bacteria, and by analyzing mutations in the rRNA sequences among many species of prokaryotes (a term that includes both Archaea and Bacteria) they developed a phylogenetic tree, which was later refined, though essentially confirmed, by them and by other scientists. Archaea also have many biochemical differences from Bacteria, and both biochemical differences and similarities to Eukaryotes (which Lynn Margulis, then named Lynn Sagan - at the time Carl Sagan's wife, had proposed in 1966 evolved by endosymbiosis: ancestral bacteria that engulfed other bacteria that became mitochondria, and others that also engulfed cyanobacteria that became chloroplasts found in algae and plants).
11
Terrific essay, my students will love this.
14
Although there are a few minor glitches here, mentioned by others (CO2, previous awareness of HGT), this is a wonderful article. It's rare to see a science writer capture the process and the feeling so accurately.
68
I had the pleasure of knowing Dr. Woese when I was a graduate student at Urbana in the 1970’s. It is a real pleasure to read this appreciation of a remarkable man. In spite of the way he sometimes came across as tongue-tied, I saw him as one of the best teachers I ever encountered. His graduate seminar class was always the highlight of my week. He was also acutely aware of the posturing, jealousy, and arrogance of some of the characters who populated molecular biology in those days, something we discussed at length in comments about a term paper I wrote for him. These are fond memories for me.
165
The 1960 'insight' from Brenner and Crick is incremental, rather than revolutionary. In 1957, Crick gave a talk in which he postulated a continuous RNA template with instructions specifying the sequence of amino acids in a protein: "...the template would consist of perhaps a single chain of RNA." (Crick, FHC. 1958. Symp Soc Exp Biol. 12: 138-163; quote from p. 156.). What was new in 1960 was that this was not part of the structure of the 'microsomal particle' (not yet given the name 'ribosome') and so the tape and the tape reader (or the program and the computer...) were distinct.
12
This is a very interesting way of looking at things and it really changes to paradigm that we are so used to. I understood most of it and from what I gathered, this is amazing work. But that's just me, a lowly high-schooler I was asked to pick an interesting article for a summer project and this certainly fit into said category. It's interesting to me based on the fact that I knew the rudimentary facts about Darwin's hypotheses but this really expanded upon my knowledge. Bravo.
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@William McDermott
A lowly high schooler – not so William.
The fact that you show the curiosity to read this and apparently have interests beyond social media distractions speaks well of you.
Everyone starts at their own beginning and makes their own way. Each journey is unique, and it is often true that some of the most obscure and unfathomable of these journeys have the greatest impact.
Stay curious and questioning.
7
I am sure there was much of value in this essay but I began it with skepticism because the author asserted the impossible about metabolism of the Archea. No trick of evolution can make the reaction of carbon dioxide to yield methane and free energy proceed. It ALWAYS goes the other way, even 3.5 billion years ago. Hydrogen sulfide can support metabolism in ocean vent organisms because there are reducing equivalents available. Not with CO2. Otherwise, very interesting presentation.
9
@Alan Magid
Note that the comment about CO2 is from the 1977 article. Admittedly, it could have been pointed out that this is not current belief.
19
@Alan Magid Methanogens use hydrogen gas (H2) to reduce CO2 to methane and produce free energy.
10
What an wonderful article! It takes an abstract topic, makes it immediately apparent why we readers should care, and then takes the time and space required to explain the technical details. Grace, humor, precision - this article makes me glad to subscribe to the Times.
202
Wonderful article, very well written, telling both the scientific and the human stories elegantly. And it did that most important thing: it taught me something I didn't know.
205
An interesting and important article. But I find the intrusion of “human interest” bits annoying and unnecessary. If I want to read a scientist’s biography, there are plenty of books and articles in this genre. Popular science should be about science. The issue of lateral gene transfer and the “shape” of evolutionary development are exciting and interesting in themselves. They don’t need to be spiced up with superficial character sketches that I skipped anyway as I was reading the article. Unfortunately a lot of people are unable to appreciate the beauty of abstract knowledge or philosophical speculation and require gossip to make it palatable. There must be something wrong with public education in this country if you need to be introduced to the scientist in order to appreciate the science.
25
@Mor
This seems to me to be another argument for ritual purity. If one appreciates the science of multiple influences then this article in a popular press would want a more complex presentation...which is what have.
10
That science is done by people is an important point that too many people fail to appreciate. Your last sentence is absolutely correct, but the other dimension was for too long absent. Franklin failed to be included in the Watson and Crick paper that explained the structure of DNA and led to their Nobel prize because of Watson and Crick's (flawed) humanity, even as they had acquired Franklin's data and insights through that same flawed humanity and her's.
I as a biologist have known and appreciated the science that Woese contributed long before this article, and it found its way into elementary textbooks long ago. Now I know the history better through having learned about the personalities involved, especially that of Woese.
One caveat with how Quammen expressed genetic isolation of species. Genetic recombination across species lines was been long known prior to Woese's work. Related species of animals, plants, fungi, and bacteria have been known to share genes through various mechanisms for many decades, including ordinary hybridization. It is the degree of horizontal gene transfer influencing genomic composition that was the big surprise, not its existence.
81
I would disagree about DQ’s style. David Quamen has for decades been the best explainer of science in American writing. While the human part is not essential to understanding of the principle at hand, it is hugely insightful for those of us groping through some other vague path of (hopefully) discovery.
52