The Genesis project

A new paper on planetary seeding was published recently in Astrophysics and Space Science, and there is an interview with the author, Claudius Gros, at Science magazine.

Through the most of Earth’s history, life had existed in microbial form. Only about half a billion years ago complex multi-cellular life appeared, leading to the evolution of higher organisms we see today. This could happen because Earth was in its habitable zone all this time. If it wasn’t, complex life would not have time to evolve. Gros proposes that if we seed other planets, even if they are only transiently habitable, life will have the chance to evolve to complex forms there, because it will start off from the “Cambiran explosion”.

Gros proposes that we will seed other planets in about 50-100 years using probes with artificial intelligence (AI) needed to synthesize microbes adapted for a particular planet that the probe approaches. In our view, this scenario is too optimistic. Even if AI will be at hand in 50-100 years, it may not help. The space journey would take many thousands (if not millions) of years. The more elaborate the technology involved, the more chances are that something will go wrong with it if left unattended during such periods of time. To be fail-safe, the space probes should be as simple as possible.

A more realistic project is to seed star-forming regions rather than planets, as proposed by Michael Mautner back in 1997 (it is surprising, by the way, that Gros never mentions Mautner, who has been persuing the program of planetary seeding for more than 30 years). No AI is required in this case, and, furthermore, it may in fact turn out to be more efficient, as star-forming regions produce up to a few thousand stars (with their planetary systems), so, with the same effort, you may end up with several seeded planets, instead of just one.

Comments to the New Scientist article

New Scientist printed a feature about our study. We appreciate the author had tried to get to the bottom of the thing. Nonetheless, there are some points we feel we should comment on.

First, 37 is certainly not an answer to life and everything. It’s a mystery for us why it catches so much attention (not only by this author), while the most essential part is typically looked over. Also, after reading the feature one might have an impression that because the patterns are non-random, we argue that they are artificial. Non-randomness alone is by no means a sign of artificiality.

“It was clear right away that the code has a non-random structure,” says Makukov.

To clarify: as the code was cracked (in 1960s), it was clear right away that it has a non-random structure. It is not that everyone thought that the code is random until recently.

As to what – or who – planted the message, Makukov stresses that he doesn’t know. 

Little green men?  Pink fluffy fairies! 😉

The reddit Science AMA

It was a nice experience to have an AMA session at /r/science.

Most contributors were able to balance between skepticism and open-mindedness. It was not surprise for us to see a certain portion of pseudoskeptics who invariably invoke allegories all of which boil down to the same mantra “this is nonsense because this cannot be otherwise”. But it was surprise for us to learn that absolutely any topic in Science AMA series gets 83-93% upvoters, regardless of how many points a thread gets. In other words, whatever the subject is, there is always about the same proportion of people who dislike it.

Links to a couple of threads:
If you wish to claim that any order you detect comes from artificial sources, you first have to eliminate order that comes from known sources.” (A very long but instructive discussion with an anonymous structural biologist. Many appreciations to him for this discussion).
The onus is on you to prove that ideas of notations and zero are incompatible with evolution

Why the genetic code is not universal

A fresh post by Matthew Cobb at Jerry Coyne’s blog explains in lay terms why the genetic code is not universal. Keep in mind that the explanation is simplified, and only one presumable mechanism (codon capture) responsible for non-universality is mentioned, while there are a few more distinct mechanisms that have been proposed (e.g., ambiguous intermediate). Also, intriguing to learn that Cobb has just finished the book “Life’s Greatest Secret: The Story of the Race to Crack the Genetic Code”.

Note that what Cobb describes has happened during evolution after the Last Universal Common Ancestor (LUCA – first cells on Earth from which all terrestrial life evolved), so all of that is absolutely compatible with the seeded-Earth hypothesis and with the message in the universal genetic code.

NYT on Genomic SETI: DNA vs. genetic code

There is a 2007 article in The New York Times, where Dennis Overbye discusses “genomic SETI”. Overbye was inspired by Japanese researchers who, shortly before, managed to embed the famous formula “E=mc2” and the year of its publication “1905” into bacterial genome (though, in fact, embedding non-biological information into genomes was performed as early as in 1986 and 1988, to name a few). Dennis Overbye hypothesizes that some kind of a message might already reside in DNA of terrestrial organisms, if life on Earth was seeded by a preceding galactic civilization, as proposed by Francis Crick and Leslie Orgel (though, again, Crick and Orgel proposed that Earth was seeded with living cells, not with DNA, as Overbye writes; seeding DNA makes no sense – it will simply decay outside the cell).

Overbye comes to the conclusion that there are two disadvantages to genomic SETI. The first one is that DNA mutates:

The sad truth is, as others will tell you, this is a bit like writing love letters in the sand. “I don’t buy it,” said Seth Shostak, an astronomer at the SETI Institute in Mountain View, Calif., pointing out that DNA is famously mutable. “Just ask Chuck Darwin,” he added in an e-mail message.

Apart from that it’s not clear what Darwin has to do with that (he had no idea about DNA, not to mention its mutability and role in heredity), this seems reasonable. Even though DNA is now considered to be the most reliable information storage that can safely keep information for tens and hundreds of thousands of years, it is still not that durable as needed for messaging in cosmic seeding, where intact message must be replicated with DNA for billions of years until intelligent beings (if any) evolve. This does not imply that it is definitely impossible to use DNA as billion-years storage; but no one knows how to do that.

The second problem is more subtle:

Gill Bejerano, a geneticist at the University of California, … pointed out that the problem with raising this question is that people who look will see messages in the genome even if they aren’t there — the way people have claimed in recent years to have found secret codes in the Bible.

Well, in this opinion the search for a message in genome is just that – take a genome and search for anything interesting. That’s not the way science works. You have first to develop the methodology for data analysis, based on the initial assumption(s). Without this component, any science will reduce to numerology and Bible codes. Of course, there still might be false positives, and typically all researchers tend to see patterns in data that seem to confirm their hypotheses, but this happens normally in any research.

At all events, both problems essentially dissolve if one turns from genomes to the genetic code. First, unlike DNA, the genetic code does not mutate (a few minor variations notwithstanding). Second, unlike genomes which are huge and diverse, the genetic code is small and universal. You simply don’t have much freedom here to see a lot of messages that are not actually there.

Attacking a straw man

The “straw man” is a type of argumentation where someone distorts the original statement of an opponent, or even attributes a false statement to him, and then debunks it. There is a nice example of a straw man argumentation among some bloggers concerning our Icarus paper. Here is one of them. The author writes:

[The paper] rests on a false comparison of two options:
1. Created by random chance
2. Created by space aliens
This is set up so that if the first is unlikely, the second “must” be right.
The setting is rigged because these two aren’t all the possibilities. There is at least one more:
3. Created by a non-random natural process (e.g. evolved)
To declare any one the ‘preferred’ choice they’d have to investigate all three possibilities, then compare what was found. But they don’t: they only look at the first then declare the second as the ‘winner’ without ever looking at the third.

The straw man here is that we tested exactly options 1 and 3. To quote Appendix B from the paper:

We tested both versions of the null hypothesis (“the patterns are due to chance alone” and “the patterns are due to chance coupled with presumable evolutionary pathways”).

Then we go on to describe how we take certain evolutionary pathways into account. Even if the paper is read perfunctorily, it is impossible to miss such a big chunk of text. So we are forced to conclude that the straw man here comes not from inadvertence, but from mere unfamiliarity with the notion of evolution. Non-random evolution does not imply deterministic process, as perhaps those guys believe. It implies a stochastic process acted upon by non-random forces (which are represented in our statistical test with corresponding filters applied to randomly generated codes).

Another second genetic code

Recently a paper was published in Science which reported that in human genome some codons, apart from coding amino acids, also serve as binding signals for certain proteins that control gene activity. Well, this is another instance of overlapping of the genetic code with yet another code (regulatory code, in this case). The funny thing is that both the press release and the news outlets are writing that “scientists have discovered a second code hiding within DNA”. Yes, Edward, a second code… Well, the sixth second code, to be exact 🙂

The following excerpt from the 2011 paper by Edward Trifonov makes it clear:

According to the media sympathetic to science and enthusiastic about sensational discoveries, the “Second Genetic Code” as it was called by New York Times was discovered by Ya-Ming Hou and Paul Schimmel and published in Nature in 1988. It was about recognition of tRNAs by respective aminoacyl-tRNA synthetases. Thirteen years later New Scientist announced the second Second Genetic Code, discovered by Jenuwein and Allis and published in Science. This time it was about histone modifications. Five years later, New York Times, again, reported about “a second code in DNA in addition to the genetic code”. This was already the third Second Genetic Code, discovered by Segal et al, suggesting now nucleosome positioning rules. One, surely, would raise eyebrows having learned that there is also the fourth Second Genetic Code — on interaction specificities between proteins and DNA, and the fifth Second Genetic Code, the name given by Nature magazine to the set of rules governing gene splicing. Bewildered reader, naturally, would say “I’m done with seconds, can I have a third?”

Discovery News note

The Discovery News opus, supposed to be about our Icarus paper, is in fact not.

They go on to argue that their detailed analysis that the human genome (map here) displays a thorough precision-type orderliness in the mapping between DNA’s nucleotides and amino acids.

Human genome? The word “human” occurs indeed a couple of times in the Icarus paper, but we failed to find the phrase “human genome” there. What a nice example of human-centered chauvinism 🙂

It is fun to trace how mass media play the game of broken phone. Referring to the Discovery News note, the guys at the Huffington Post write the following: “The scientists are suggesting that an advanced alien civilization “seeded” our galaxy eons ago with an ET signal that eventually found its way to Earth, implanting a genetic code into humans, reports” Translating this passage, Russian mass media go even  further, saying that “…alien civilization “originated” our galaxy billions of years ago by means of a signal that reached the Earth and implanted a genetic code into humans, reports” Salvador Dalí with his surrealism fades in comparison.

Biological SETI inevitably smacks head-on into an idea that is completely antithetical to science: the concept of intelligent design (ID)

Another way to put it is that we all should immediately contact Craig Venter and ask him to remove his email and other watermarks from genomes of Mycoplasma laboratorium, because it is completely antithetical to science and smacks head-on into (or simply smacks of) ID.

This interpretation leads them to a farfetched conclusion: that the genetic code, “appears that it was invented outside the solar system already several billions years ago.”

Now, compare it to the complete sentence from the paper: “Whatever the actual reason behind the decimal system in the code, it appears that it was invented outside the Solar System already several billions years ago.” Well, we admit that our English is not perfect. But does that sentence indeed sound ambiguously so that one might say the word “invented” here is about the genetic code, rather than about the decimal system?

Merry Christmas, Discovery News! 😉

Simplification of the genetic code

During the past decade the most popular exercise that biochemists performed with the genetic code was its expansion via incorporation of unnatural amino acids. Only last year they tried to reverse the task and to simplify, rather than complexify, the genetic code by excluding certain amino acids from it. A few days ago an article appeared in ACS Synthetic Biology which describes the code where four amino acids (Asn, Cys, Trp and Tyr) were excluded and their codons were reallocated to amino acid serine (Ser), which thus has 13 codons in this code:

While expansion of the genetic code with unnatural amino acids is normally performed within living cells, the simplification of the code like that shown above is achieved, certainly, in a cell-free extract. Living cells will not survive radical modification of all its proteins (however, another recent experiment has shown that E. coli might live in fact with one of the amino acids – tryptophan – eliminated from the proteome).