Redefining the Chemistry of Life? Followup

In January 2011, I wrote a blog post on a (media-hyped) discovery of a strain of bacteria that appeared to be using arsenic instead of phosphorus in its biochemistry. In the post, I argued that this organism does not at all "redefine the chemistry of life" or find "arsenic tasty," as the study and media commentary suggested. I concluded that (at best) this organism is a facultative arsenophile, which means it seems that it can use arsenic in its biochemistry when necessary but prefers phosphorus and needs it to thrive.

In the most recent issue of Science (the journal in which the original study was published), two more papers have been published by teams who did independent research on the bacteria in question (GFAJ-1), and their findings refute the contention that GFAJ-1 is using arsenic at all. One shows that there is no evidence for arsenates being incorporated into the bacteria's nucleic acids. The other argues that GFAJ-1 is really an arsenic-resistant bacteria (a possibility I noted in my original post) that still needs phosphates to survive and thrive.

If you want my take on the research, the original post I wrote on the topic is still relevant. My original conclusion, which appears to still be valid, was as follows:

It is not an organism that has a "redefining" biochemistry, it is not an "arsenic-base" organism, it does not find "arsenic tasty"; at best it an extremophile that can possibly make use of arsenic when it is the only thing available in the environment but its preference would be phosphate.

Before I wrap this post up, I want to comment on one more thing that I quoted from Dr. Rana above. It has been suggested that this type of organism could represent an alternate way that life could emerge. Sorry, but this kind of organism does not provide a different possible pathway for life to originate. The reason why Dr. Rana says that, and I agree, is because this type of organism not only has the biochemistry of normal bacteria but has extra mechanisms that allow it to live under the harsh condition of excess arsenic. In short, it is an organism that is significantly more complex than normal bacteria that is based on phosphates alone. Arsenate is unstable, so unless you already have in place mechanisms that could stabilize the arsenates, there is no way life could form with arsenates. Origin of life in an arsenate system (vs. a phosphate system) is a significantly more complex pathway and even more improbable than the existing, phosphate-based origin of life scenarios. The same is true for all extremophiles. In fact, there have been papers written by other biologists arguing this point.

So, after time for further research and peer-review, life is still CHNOPS-based (see the original post for explanation on that) and no other alternate pathway for the origins of life is evidenced by this study. Life is still as delicate and complicated as science has consistently shown and requires an Intelligent Designer for its existence.

By His Grace,
Taylor

Redefining the Chemistry of Life?

"The way I like to think about this organism is that it's an extremophile. They've discovered a new extremophile... This is an organism that they have discovered that would prefer phosphorus but can make use of arsenic if it is present... Just because life exists under extreme conditions doesn't mean that it is more likely to originate under those conditions than more moderate conditions... Whether... high temperature, high acid, high alkalinity, high salinity, or high radiation environments, all those circumstances... will actually disrupt pre-biotic chemistry needed to generate life and this would be the same situation. Just because it exists under high arsenate conditions does not mean it could originate under those conditions." ~ Dr. Fazale "Fuz" Rana

Last month there were a bunch of headlines floating around touting a discovery made by NASA astrobiology research fellow Felisa Wolfe-Simon ("Fe Lisa" or "Iron Lisa") that she and her team published in Science. A few popular headlines were "Arsenic-eating microbe may redefine chemistry of life", "Microbe Finds Arsenic Tasty; Redefines Life", or (my favorite) "Arsenic-Eating Bacteria Opens New Possibilities for Alien Life". A few of you out there have asked me about this privately and I have given some short answers, but I have wanted to write up a more detailed comment on this work for the last month. Because December was so busy, as I am sure it was for all of you, I have not gotten to it until now. Of course, that might be a good thing because I have now had the chance to read the paper and look at some peer criticism of how this was communicated to the public. But, now that I have a little time, here it goes...

Before we get into the actual paper and discovery, I would like to talk a little about the history of thought in chemistry and biology that led to this research and Dr. Wolfe-Simon's discovery. This is going to get a little bit technical but I will do my best to explain it clearly and it is necessary to talk about this discovery.

Life as we know it has six major elements that are crucial for it: carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur. You might see these abbreviated as CHNOPS because they are commonly talked about as a group in reference to life. These particular elements are among the most abundant in the universe and have unique chemical properties that allow them to assemble into complex, stable molecules that can then further aggregate into complex, stable super-systems (DNA and RNA would be examples of these) to create an organism. Most scientists today believe that life must have these elements to exist. There are, however, a few that believe life could possibly be built on an alternative biochemistry. For example, it has been suggested that silicon could replace carbon or, in the case of this discovery, arsenic could replace phosphorus.

Why these particular replacements? Well that has to do with the chemistry of the elements in the Periodic Table (PT). The PT is one of the greatest achievements of science (I say that even though I am a physicist, not a chemist) and one of the reasons I say that is because of its construction. One can look at the PT and get a lot of information about the elements just by the position of those elements in the table. For example, elements in the same column have similar chemical properties. The closer they are, the more similar the chemistry. That is what is important for our purposes here. Take a look at the cutout from the PT on the left. Carbon's chemical symbol is C, silicon's is Si, and silicon is right below carbon in the PT, which shows us that there are chemically similar. Phosphorus' chemical symbol is P, arsenic's chemical symbol is As, and arsenic is right below phosphorus in the PT, which, again, tells us that they too are chemically similar. Some scientists think that the chemistry may be similar enough to represent possibilities for alternate biochemistries other than CHNOPS. Perhaps one could replace Si for C, thus the biochemistry would be SiHNOPS or perhaps As could replace P creating a CHNOAsS biochemistry. It is this kind of thinking that motivated the study.

Before we go further to the pertinent study, a few words need to be said about phosphorus and arsenic since they are the important elements for this particular discovery. In nature phosphorus primarily exists as phosphates (an ion with four oxygen atoms bound to a phosphorus atom). In this form, phosphorus plays an extremely important role in biochemistry. It is crucial to a number of biochemical functions (like regulating protein activity and the formation of the cell membrane) and biomolecules (like DNA, RNA, and metabolites). It has been generally thought that it is phosphorus' unique qualities that allow it to play an integral role in all of these functions but, as described above, arsenic is chemically very similar to phosphorus. Could arsenates (similar to phosphates) serve the above functions?

Arsenic does form into arsenates (an ion with four oxygen atoms bound to an arsenic atom) but they are toxic. Since arsenates are so similar to phosphates, organisms can incorporate them into biomolecules but since they are different from phosphates, the bonds in those biomolecules created with arsenates (instead of phosphates) will become unstable and break down, creating havoc in the metabolic system of the organism. So arsenate is similar enough to phosphate to be allowed into the cell but dissimilar enough that, once incorporated, the cell starts to break down. If this happens on a large enough scale the organism will die. So, life should not be capable of existing in an arsenate system.

This brings us to this discovery by Dr. Wolfe-Simon and her team. First, I would like to say that this is very impressive work. These scientists should be commended for this discovery and they should be proud of themselves for opening up the door to what will probably be years of fascinating research on this organism and others like it. That being said, the discovery as portrayed to the media and the general public is overblown. This newly discovered organism is not an "arsenic-based" organism, it does not find "arsenic tasty", and it is not really as "alien" as it is made out to be.

So, what did they discover? Well, Dr. Wolfe-Simon and her team went to Mono Lake in CA to search for bacteria that use arsenic. They chose Mono Lake because it has an extraordinarily high phosphorus and arsenic content so any bacteria found there would at least have to be able to deal with arsenic. They discovered a strain of bacteria, that they labeled GFAJ-1, which appears to be able to use arsenates and phosphates to grow. They then wanted to see if it could survive only with arsenates. In order to test this, they took GFAJ-1 from the lake (where the environment has high levels of phosphorus and arsenic) into their lab and put it in an environment with no phosphates and lots of arsenates. They did this to try to force the bacteria to use only arsenates, if it could, since phosphates were not available at all. They found that GFAJ-1 did survive and appeared to be incorporating arsenates into its biochemistry. Now, since the bacteria was formed in the lake with phosphorus and arsenic, they have not yet proven that it can completely substitute arsenates for phosphates because the bacteria still had plenty of phosphates to run critical systems. They did, however, show that it appears that at least some of the cells functions were using arsenates instead of phosphates, which was thought to be impossible. Through a process known as fractionation they found evidence that the arsenates were being used by GFAJ-1 in proteins, nucleic acids (DNA and RNA), and metabolites. The bacteria was even able to grow and reproduce under these conditions. Conventional biochemical knowledge says that GFAJ-1 should have died because the arsenates should have destabilized almost its entire metabolic system. With all this data, however, the conclusion that this bacteria appears to be able to do what was thought impossible--incorporate arsenates into its biochemistry, stabilize the arsenates (through a yet-to-be-determined mechanism), and survive--seems plausible (though it is also possible that this bacteria could simply be strongly resistant to arsenates).

Did they show that this life is "alien" or discover something that "redefines" the chemistry of life? No, they did not. Let me explain why. Assuming they are right that GFAJ-1 really is incorporating arsenates into its biochemistry: 

• First, even though the organism was able to survive under the extreme arsenate-rich and phosphate-poor environment, it was far from thriving like it did in Mono Lake where phosphate was readily available. The bacteria grew very slowly, reproduced at a proverbial snail's pace, and had a very distorted growth morphology. What is going on here is not completely clear yet, but these issues in the growth of the bacteria show that it probably has some kind of machinery in place to stabilize arsenates yet would prefer phosphates. So while the bacteria can survive in an arsenate-rich environment, it certainly prefers phosphates and will only thrive with phosphates.
• Second, there has been no long-term experiment done to see how long this bacteria can survive under these conditions. The bacteria began with phosphates since it was taken from Mono Lake. As it reproduced in the lab those phosphates were divided up to run critical systems. It is highly possible, as some critics has suggested, that colony could die off after it has spread its phosphate supply too thin. 
• Third, this finding is not proof that there is any bacteria naturally doing this. It only shows that it this bacteria seems to have a mechanism that allows it to use arsenate when it has to. It could potentially do it naturally (no one is sure how long it can) but this is certainly not proof that there are lifeforms regularly doing this.
• Fourth, the team had to create an arsenic-rich, phosphorus-poor environment. Finding a natural environment like this where biochemistry would have to be completely redefined is highly unlikely. Why? Because phosphorus is much more abundant in our universe than arsenic. In the earth's crust there is 667 times more phosphorus than arsenic. In the rest of our known universe there is 2500 times for phosphorus than arsenic. These abundances show that it is highly improbable that there would ever be a naturally occurring environment anywhere in the universe with all arsenic and no phosphorus that would cause life's chemistry to be redefined in a way similar to GFAJ-1.

What is the bottom-line? If it is not "alien" and does not "redefine" life's chemistry, what kind of organism is it? As I quoted from Dr. Rana above, it is (at best) an extremophile--organisms that can grow and survive under extreme conditions like high temperatures, high acidity, or, in this case, environments with high amounts of toxic arsenates. To get a little more specific, it could be a facultative arsenophile, which means it seems that it can use arsenic when necessary. Organisms are either obligatory or facultative. The former means they require a particular set of conditions to live. The latter means that the organism can make use of something if it is present under extreme conditions but do not prefer it. For example, e. coli is a facultative anaerobe, meaning that it would prefer an environment with oxygen but can, if necessary, survive in an oxygen-poor environment. In this case, GFAJ-1 being a facultative arsenophile means that it seems to make use of arsenic under extreme conditions. It is not an organism that has a "redefining" biochemistry, it is not an "arsenic-base" organism, it does not find "arsenic tasty;" at best it an extremophile that can possibly make use of arsenic when it is the only thing available in the environment but its preference would be phosphate.

Before I wrap this post up, I want to comment on one more thing that I quoted from Dr. Rana above. It has been suggested that this type of organism could represent an alternate way that life could emerge. Sorry, but this kind of organism does not provide a different possible pathway for life to originate. The reason why Dr. Rana says that, and I agree, is because this type of organism not only has the biochemistry of normal bacteria but has extra mechanisms that allow it to live under the harsh condition of excess arsenic. In short, it is an organism that is significantly more complex than normal bacteria that is based on phosphates alone. Arsenate is unstable, so unless you already have in place mechanisms that could stabilize the arsenates, there is no way life could form with arsenates. Origin of life in an arsenate system (vs. a phosphate system) is a significantly more complex pathway and even more improbable than the existing, phosphate-based origin of life scenarios. The same is true for all extremophiles. In fact, there have been papers written by other biologists arguing this point.

So what has Dr. Wolfe-Simon's done? She and her team have done some excellent research and made a fascinating discovery but they have not redefined anything or discovered something alien. What they have done is open the door for much more research in this area. There are still a lot of questions to be answered about this bacteria. Is GFAJ-1 really using the arsenates or just surviving as best it can in such an environment? If so, how are the arsenates stabilized? What do the molecules that incorporate arsenate look like? Could a DNA molecule with arsenate instead of phosphate be made in the lab?

By His Grace,
Taylor

Synthetic Life and the Delicateness of Life

"It shows you how accurate it has to be, one letter out of a million..." ~ Dr. Craig Venter

Many of you heard about the very impressive step that Craig Venter and his team at the J. Craig Venter Institute have made in the quest to create artificial life. It was in the headlines about two months ago. If you did not hear about it, just do a Google search for "A step to artificial life: Manmade DNA powers cell" and a good number of results from many different news agencies will come up. I have wanted to write about this incredible scientific advance for a while but have not been able to find the time until now.

The above statement by Dr. Venter, I think, has great implications for the design debate going on in the scientific community (though he probably did not mean for it to). I will get into that, but first I would like to summarize what he and his team did because it is very impressive work that should be applauded for it has almost limitless potential for possible agricultural, commercial, biomedical, and environmental applications.

First things first: what did Venter and his team do? They truly have created a cell completely powered by synthetic DNA and it was an achievement he and his team have been working on for the past fifteen years. What did they do? For the details one would have to have read the paper that was published in the journal Science, so allow me to break it down for you as best I can.

Let me start with a basic overview. In this research they were working with two different kinds of bacteria, Mycoplasma mycoides (M. mycoides) and Mycoplasma capricolum (M. capricolum). They chose these bacteria because of their relatively small genome size (about one million genetic letters which is about 1,000 genes) and the rapid growth rate of M. capricolum (less time wasted growing bacteria). First, they sequenced the entire genome of M. mycoides. A genome consists of many DNA molecules and the DNA molecules are a collection of genetic letters (abbreviated A, G, C, and T), which hold the genetic information about the organism. Sequencing a genome means determining the order of all the genetic letters, thus creating the "blueprint" for the organism. Second, they synthesized/created a synthetic version of the M. mycoides genome starting with the four basic chemicals of DNA (corresponding to the genetic letters). Third, they implanted the synthetic M. mycoides genome into a M. capricolum bacterium. That genome replaced the host's native genome and took over the operation of the bacterium, essentially changing the M. capricolum bacterium into a (synthetic) M. mycoides bacterium.

Even though I only described three major steps, the process is not simple at all. Allow me elaborate on some of the difficult points.

• Sequencing the entire genome of M. mycoides, even a small genome like this one, is very difficult. They had to take the genome and fragment it (separate it into chunks) and then take each fragment and further fragment them until the whole genome was broken down into its individual letters. (A recent advance in graphene could potentially speed up this process considerably.)
• Synthesizing the genome is even more difficult. They essentially did the above process in reverse. They created small fragments (about 1,000 genetic letters) of the genome, took those fragments and put them together to make larger fragments, then took those larger fragments, and so forth until they had a complete genome. To do this they needed a very good strategy. They looked at the entire sequence (all one million letters), determined the best points to break it up into 1,000-letter fragments, made sure the fragments overlapped slightly (so they could piece them together), and then started creating the fragments and assembling them. To assemble the fragments they used yeast as a kind of "factory" to combine sets of ten 1,000-letter fragments into fragments of 10,000 genetic letters, then combine those 10,000-letter fragments into 100,000-letter fragments, and then, finally, combine those into the one million-letter genome. (Using the yeast as a "factory" is far more complicated than what I just explained because they had to incorporate DNA sequences that caused the yeast to recognize the DNA as its own and they had to do this without altering the M. mycoides genome. They also had to introduce DNA sequences to allow them to do quality control checks after every step to make sure each stage was executed without error.) This is an incredibly ingenious, complicated, and delicate strategy for synthesizing DNA sequences.
• Their strategy for implanting the synthetic genome into a M. capricolum bacterium was equally ingenious and difficult. One of the big hurdles were enzymes known as restriction endonucleases (RE). These are enzymes found in bacteria and archaea that serve as a defense mechanism against the introduction foreign DNA into the cells of the organism (which is exactly what Venter's team was trying to do). These enzymes cleave to specific locations of the DNA helix and cut the DNA at those locations, destroying the foreign DNA. One might then ask, "What about the natural DNA in the host organism? Why is it not destroyed?" Well, natural DNA has a protection system against the RE called the methylase system. This system "methylates" the host's natural DNA by adding a modification enzyme to the RE cleavage sites, which protects it from the RE. In order to get around this, Venter's team developed a strain of M. capricolum with the RE disabled, thus making the M. capricolum susceptible to the (foreign) M. mycoides genome they needed to implant. Then, after implanting it, the synthetic M. mycoides genome produced its own RE that destroyed the host's M. capricolum genome, thus allowing the M. mycoides genome to take over the operation of the M. capricolum bacterium completely. This transformed the M. capricolum bacterium into a synthetic M. mycoides bacterium, which was able to grow into a whole colony of synthetic bacteria.

Even if you got lost in the above explanation, you probably are beginning to realize now how incredibly complicated and difficult this scientific advance was. It took dozens of scientists fifteen years to be able to get this far and there were many setbacks along the way. One setback, the one Venter was commenting on in the above quote, was the result of a mutation (a "typo") that altered one genetic letter out of the million-letter genome. This typo set them back several weeks and completely disabled their synthetic M. capricolum bacterium. The mutation of one genetic letter out of a million caused the organism to be unable to operate and die.

What does mean for the design debate (I mentioned this in the very beginning of this post)? 

1. This advancement shows how complicated and delicate life is and that the work of an incredibly intelligent mind (or a team of incredibly intelligent minds, in this case) is required in order for life to originate. It has shown empirically that to transform life (representing the evolutionary process) or to create life from scratch (representing the origins of life process) requires the intervention of an intelligent agent (if one genetic letter is wrong, as mentioned above, the whole genome is useless). Work like this does not eliminate a need for God; quite the opposite, for it demonstrates how precarious life is and that God is required for life. 
2. This work also demonstrates life's minimum complexity and shows that, even in its lowest possible state, life is extremely complex (far more complex than any naturalistic evolutionary model can account for). 
3. This work creates a completely new category of arguments for design in the universe. The already existing categories of arguments made by scientists that support design are the following: 1) inference to the best explanation, which basically looks at all the models that could account for life and seeks to show that the naturalistic evolutionary models are inferior in their explanation of the facts and 2) argument from design, which basically looks at the apparent design in the universe, notes the similarities to independent human designs, and then argues by analogy that life must be designed. This work introduces a third form of argumentation, which argues that we know now from empirical experience that the making of life requires intelligent ingenuity.

From my Christian point of view this work is very exciting not only because is it just really cool science, not only because it opens up science to a not-too-far-off world of possible applications (bacteria that can create hydrogen for clean fuel, bacteria that can create cheap pharmaceuticals, or even bacteria that can consume oil), but also because it shows in a compelling way, I think, that life requires a Mind--Intelligent Designer--to exist and cannot be the result of random, natural processes. 

By His Grace,

Taylor

Planetary Habitable Zones

"For the host stars with effective temperatures lower than 4,600 K, the ultraviolet habitable zones are closer than the habitable zones. For the host stars with effective temperatures higher than 7,137 K, the ultraviolet habitable zones are farther than the habitable zones. For a hot subdwarf as a host star, the distance of the ultraviolet habitable zone is about ten times more than that of the habitable zone, which is not suitable for the existence of life." ~ "Habitable zones and UV habitable zones around host stars" by Jianpo Guo, Fenghui Zhang, Xianfei Zhang,  and Zhanwen Han

The "habitable zone" is something that is crucial in the conversation about life on other planets. The habitable zone is the intersection of two cosmological regions that must both be favorable to life: one within a solar system (circumstellar habitable zone) and the other within the host galaxy (galactic habitable zone). The galactic habitable zone defines a region that is close enough to the galactic core to provide a sufficiently high level of heavy elements to form rocky planets (like Earth) and yet far enough away so that high-frequency radiation does not harm or destroy life. The circumstellar habitable zone is usually defined as the region around a star where liquid water can exist on a planet. Recent research, however, has added a new constraint to the circumstellar habitable zone. This new constraint is an ultraviolet (UV) habitable zone. This region is a band around a star where any planets in it will receive enough UV radiation energy to drive the chemical reactions related to life’s origins (assuming a naturalistic evolution model) and yet not too much, which would result in the destruction of DNA. DNA would never be able to survive on a planet that is too close to its host star because of too much radiation, and it would never be able to form on a planet that is too far from its host star because of not enough radiation.

The paper cited above shows that in the vast majority of stars the liquid water habitable zone and the UV habitable zone do not intersect. "Effective temperatures" that the paper refers to are the temperatures of black bodies that would emit the same total amount of electromagnetic radiation as the stars being studied. Basically around any stars with effective temperatures below 4,600 K the UV habitable zone is too close to the star for liquid water to exist (it would all evaporate), and around any stars with effective temperatures above 7,137 K the UV habitable zone is too far from the star for liquid water to exist (it would all freeze). Around such stars there is no possibility for life as we know it. In fact, requiring a planet to fall within both zones (the liquid water and the UV zone) eliminates 80% of all stars as possible candidates for life-supporting planets. This adds to the growing body of evidence that Earth is uniquely fined-tuned for life as we know it.

By His Grace,
Taylor

Refreshing Objectivity

"No one has publicly disagreed with my interpretation of the Apex fossils. But privately, some would prefer I were mistaken, since they (and I, too) would prefer a simpler evolutionary story, one that told us these oldest fossil organisms were capable only of primitive ways of living and that advanced metabolic lifestyles evolved much later. But the evidence seems strong, and what one might 'prefer' shouldn’t matter." J. William Schopf, The Cradle of Life

William Schopf is a professor of paleontology at UCLA. About 15 years ago Schopf and his team found microfossils (now known as the Apex fossils) in the Pilbara Supergroup (the oldest rocks structures on earth) and they have turned out to be the oldest fossils for life on earth. This discovery created a problem for naturalistic evolution, as Schopf expresses above. The reason his discovery was such a problem is that it seemed to show that life appeared suddenly on earth and very complex (as complex as the simple life on the planet today). There in lies the problem because from a naturalistic evolutionary perspective that cannot be the case.

Over the past 15 years Schopf's discovery has been debated heavily amongst origins of life researchers. The hottest opposition was brought against Schopf and his team by a UK team of biologists led by Martin Brasier, a professor of palaeobiology at Oxford. From about 2001 to 2003 Brasier debated with Schopf and attempted to prove that what Schopf and his team found was only the result of unusual chemical processes. The debate was eventually won by Schopf when two other independent teams confirmed his findings.

While the debate over the biological origins of these fossils ended there has been continued debate over their complexity until now. Recently a paper (written by an interdisciplinary team from Australia and Japan) was publish in the journal Astrobiology that has caused further troubles for naturalistic evolution because it reveals the complexity of these fossils. This team used a new 3D image reconstruction technique to analyze the fossils from the Pilbara Supergroup. This new technique allowed them to see that these fossils were much bigger and Schopf's team had thought--about 15 microns which is the size of human cells and much bigger than the simple bacteria that exists today (simple bacteria today measure about 1 micron). They also discovered that these organisms were highly complex with double-membraned cell walls, spheroids contained in the membranes that look like cell nuclei, and "flange-like" appendages that were constant in shape, proportion, and dimension (possibly flagellum like many current bacteria have).

All this is to say that I appreciate Schopf's honesty and objectivity about his discoveries. The evidence in his discovery and recent discoveries shows that the earth's earliest life was highly complex with internal structure, complex membranes, and appendages. It is evidence that is not compatible with naturalistic evolution but is what one would expect from a Creator. He would have preferred the story be different because it cannot be reckoned with naturalistic evolutionary models, but he would not hide behind what he wished to be true. He shows refreshing objectivity that is sadly lacking in many current scientists.

By His Grace,

Taylor