Replies to Cosmic Ancestry, 2012
Convictions are more dangerous foes of truth than lies — Friedrich Nietzsche
8:56 AM: Brig, I noticed that you have a lot of material on your blog about horizontal DNA transfer. In one diagram of how this occurs across phyla, all the arrows go from smaller to larger organisms. But I wrote a blog about transfer in the opposite direction, which you may find of interest:
Inter-Kingdom Horizontal DNA Transfer in all directions: Infectious bacteria evolve by acquiring protein domains from eukaryotic hosts, Posted: 11/06/2012 http://www.huffingtonpost.com/james-a-shapiro/interkingdom-horizontal-d_b_2081420.html
Thanks again for contacting me and putting me in touch with your site, Jim
James Shapiro is featured in a What'sNEW article about a blogstorm, 9 Dec 2012.
Viruses and Other Gene Transfer Mechanisms is a related local webpage.
9:12 AM: Dear Michael -- I have read the new report and commented at [the link below]. The report is lengthy and full of data. I hope I have understood it sufficiently. Any guidance? In any case, I would like to know
your thoughts.... Thanks. Best regards, Brig
...The evolution of aerobic citrate metabolism among cloned bacteria., What'sNEW, 19 Sep 2012.
From: Mike Behe | 24 Sep | 10:12 AM: Hi, Brig. ...I did read Lenski's report and it's pretty much as I thought it would be -- a pre-existing citrate transporter got placed next to a preexisting promoter that works in the presence of oxygen, so -- voila -- citrate can be imported in the presence of oxygen. We call that "microevolution" -- nothing new was made. Best wishes. Mike
Michael J. Behe | Department of Biology | Lehigh University
10:22 AM: Dear Michael --
Have you seen this story? Have you commented, and where? From my hasty reading, only a very few substitutions produced a new enzymatic function. Best regards, Brig Klyce...
Kasavajhala V. S. K. Prasad1, Bao-Hua Song et al., "A Gain-of-Function Polymorphism Controlling Complex Traits and Fitness in Nature" [abstract], doi:10.1126/science.1221636, p1081-1084 v337, Science, 31 Aug 2012.
From: Mike Behe | 7 Sep | 2:12 PM: Hi, Brig. Sorry to take a while getting back to you. The paper does not impress me much. The enzyme had a very similar activity on methionine, and with mutation could use ile and val better. However, if you look at Fig 3B, the original enzyme already had activity toward valine, which was increased several fold by the mutation. Interesting, but nothing to write home about. Best wishes. Mike
An analysis of long-running evolution experiments..., our What'sNEW article of 29 Apr 2011, comments on Behe's system that classifies loss-, modification-, or gain-of-function mutations.
7:27 AM: Dear Brig Klyce, I have been following your website for some years now and I always find it an interesting source of articles. I'm not a "panspermist", but I keep an open mind regarding these matters.
However, I have to comment on two of your recent articles. One is refers to the evolution of muscle cells:
http://www.panspermia.org/whatsnew69.htm#12020628 ...the other refers to synapses in sponges: http://www.panspermia.org/whatsnew70.htm#120723
In both cases your argument is that these genes are present but not building muscles nor synapses, and therefore the present paradigm is at a loss to explain their appearence in the genome, therefore favouring Panspermia as the only alternative answer. I think, and forgive me saying so, that you are beying somewhat desinginious here.
In both cases (the genes that are responsible for building muscles and for building synapses) ARE beying used/expressed. In the first case, they appear to be related to regulation of waterflow (and they are clearly beying expressed, therefore used). In the second case we don't know what they are doing, but they are clearly beying expressed, therefore used somehow in a different context. Your remark to the first case "Genes that exist before the appearance of the features they encode, and identical features that appear to evolve independently, several times, are baffling for darwinism" is therefore unwarrented and, there I say, somewhat dishonest. The same for "In the darwinian scheme, they are entirely out of order. Genes are supposed to be composed incrementally, under selection pressure. But in sponges, with no nervous systems, what selection pressure could compose the genes for nervous systems?"
Since these genes are beying expressed and used, and in one case we know they are beying used for water regulation, then none of these remarks on your part are valid. They are clearly functional and utilized by the organisms, albeit in a different context. Therefore they are obviously under selective pressure to evolve. None of these examples are for Panspermia neither are they baffling for the current paradigm. I don't know why you have made such remarks and included these articles on your website. I like to think that you are an honest individual, but when you use this kind of arguments I can't shake the feeling that you are beying intentionaly misleading to your readers. Please don't fall into the same fallacies as ID/creationism proponents.
Please forgive me if I sound rough, but english is not my mother language and I'm just trying to be clear in my argument.
On another note, a few months ago I noticed that NASA has approved funding for an aerobiology experiment using Ion Torrent for sequencing high altitude air samples. You could try to find the announcement at NASA's astrobiology webpage. I though this would be interesting for you, since you have been involved in a similar project. Since I didn't see any comment on that on your website I assumed you are not aware of that project. I hope you find that interesting. ...Best wishes, Pedro
from Klyce / 18:35: and from Pereira / 25 July, 2:43 AM: Dear Brig klyce, thank you for your reply. I was a bit afraid that my email to you sounded somewhat harsh, even though that was not my intention. I was just trying to put my case as clear as possible and I'm happy that you realized that.
Dear Pedro -- Many thanks for your thoughtful email. I am gratified if someone is paying attention.
You're welcome! You can rest assured many people pay attention to your website. They may not be convinced by the case for Panspermia, but many keep an open mind and it is always refreshing to see some interesting articles that bring some of the problems in science to the fore.
I try to keep my What'sNEW articles brief, so sometimes I omit details. Also, I am actively promoting a scientific point-of-view, against an opposing point-of-view that is actively promoted by a much larger and more powerful lobby, so I state my cases in the bluntest terms. However, I plead "not guilty" to your suggestion that I was disingenuous in the two articles you mention, or ever. (Occasionally I make mistakes, and when they come to my attention, I acknowledge them.)
That is good to hear. When people don't know each other personaly it is always difficult to fully evaluate one's purpose and outlook.
You are correct to note that some genes for advanced features may also have other uses in more primitive species. Sometimes the two uses are eventually separated by gene duplication and subfunctionalization. In those cases, my use of the word "genes" is shorthand for "exons-that-become-genes", but the point is valid. If those exons exist before the features they encode, darwinism cannot explain them.
I agree. The question of the origin of the genes, however, is a different matter, one that is not solved yet. But that is not really the point of my criticism. The point is that "the features they encode" in this case are present in the organisms. More bellow.
In other cases genes may serve more than one purpose and never undergo subfunctionalization. An enzyme that catalyzes a tricky reaction can also double as a viral coat protein for example. As a coat protein, that molecule may be under selection pressure as a coat protein, but not as an enzyme. Similarly for the genes you mention that are being "expressed and used" (in water regulation, for example) I ask, what selection pressure gives them their modern function?
That is difficult to say. This is essentially an "historical problem". It is dependent on historical contingency. There are genes that in a more "primitive" organims have functions as water regulators (I don't remember the details, probably they are part of some protein complex in the cell membrane). What happened so that they eventually become part of muscles? That is what researchers want to answer. But these are all dependent on events that happened hundreds of millions of years ago. We can only learn about how things work at a molecular level and then hypothesise about what could have happened, maybe reconstructing (or more specifically, "de-constructing") the process. But what were the pressures? Difficult to say. This is a question that you should ask someone more versed in animal evolution (I work in microbial metagenomics/high-throughput sequencing), since they have more insight into this then I do. But I don't see a problem here in terms of darwinism. Notice that even if you assume that the necessary changes in regulatory programs could not have evolved purely by chance and had to be delivered "already made" you would still need the same selective pressures to fix them in the populations and evolve the muscle system. So the answer for "what selection pressure gives them their modern function" is the same answer needed to explain why where those programs selected after they arrived from space. The question of how genes evolve by mutation acted upon by selection vs arrival of pre-made genes from space is a somewhat different issue when it comes to my criticism of these two articles.
Of course there are genes that participate in complex functions that are very little different from their ancient predecessors that served in simpler functions. Regulatory genes have given them new assignments in complex functions. Darwinists pretend that this regulatory programming needs little in the way of explanation. This is an issue on which I have not much commented. I probably should.
Yes, it is a bigger problem then many people recognize, although I don't hold answers. I keep an open mind, even though I think Panspermia in it's "Hard" version/Cosmic Ancestry is not convincing at this stage.
I would never intentionally mislead anyone. I do intentionally try to lead my readers to open their eyes about evolution. My main question is, is evolutionary progress in a quarantined system possible? Closed-system tests in biology do not prove it. Nor in computers. Third-best for my question are historical reconstructions using gene sequences. The examples we are discussing are all in this category. I would perhaps be a bit more cautious if closed tests in biology or computers showed any promise for darwinism.
I'm aware of your views regarding those matters. As I said, I've been following your website for a few years now. We can discuss these things later if you wish, I like discussing these issues since Astrobiology is extremely important a topic for me but I find it difficult to find coleagues that even care!
Anyway, all I'm criticizing is that the way you put your comments regarding these articles are misleading (unintentionaly I'm sure) for readers not very well versed in biology. Those that are well versed will interpret your comments the same way I did, that is, that you are failing to realize that the features these genes encode are already there. These are not "muscle genes" or "synapses genes", they are genes that encode molecules that can be used in different contexts for different functions, a bit like LEGO (in simplistic terms). Maybe you should reformulate your comments, because as they are I'm afraid biologists will interpret your comments the same way I did and think you are as good as the local ID/creationist thug. This will harm Panspermia more than aid it.
Thank you again for your close reading. I welcome your attention. Best regards, Brig
You are welcome. Feel free to contact me for further discussions if you feel like it. ...Best wishes, Pedro
from Klyce / 10:38 AM: Dear Pedro -- many thanks for your kind words and careful comments. In fact, I do align with some advocates of ID by agreeing with their criticisms of darwinism (but not their alternative explanation (if they even have one.))
You seem pretty sure that LEGO, or something like it, can solve the problem. But I urge you to look at the lack of direct evidence (demonstrations) and the weakness of the case from historical resonstruction, as we are discussing.
Meanwhile I should perhaps slow down on my criticism of old genes for new features, and instead ask for evidence that regulatory genes can evolve to assemble new features from old components. (Many regulatory genes come from transposons that are acquired by some kind of HGT, maybe from viruses.) ...Very best regards, Brig
Surprisingly, the genome of the Poriferan demosponge....is the What'sNEW article of 23 Jul 2012, that prompted this Reply.
"Here we show that a muscle protein core set....", What'sNEW 28 Jun 2012, is also referenced in this Reply.
7:13 AM: Dear Brig: Early successes of NASA's Kepler Mission (logically inferring that in a Universe of infinite Earth-like exoplanets "we are not alone") launch a new age on Earth with new frontiers in astrobiology.
The search for parent planets of humankind (SPPH) will likely focus on planets showing evidence of global water equilibrium, extant, in progress, or in prospect on all planets with intelligent life.
Earth's destiny as a parent planet of intelligent life has origins in catalysts such as the Kepler Mission, the global commons movement, ethnicity revisited, the merger of astronomy and biology (astrobiology), discovery thus far of over 2000 exoplanets, Astrobiology Research Trust - and in universal forelaws of empathy and compassion seated within the genome of humankind and all intelligent life. www.forelawsonboard.net/NewAge.html
In forelawsship on board, Robert E. Cobb | www.forelawsonboard.net
11:26 AM: Dear Armen -- ...I congratulate you on your work and the interest it has attracted. ...You would notice from my page containing the links, and elsewhere on my website about panspermia, that I believe there are two major aspects of the origin-of-life problem, namely, hardware and software. Virtually all of the work done today, including yours, deals only with the hardware side. And progress there is very slow. Meanwhle, I beleve the software side is harder. It should have an advantage, because those experiments can be done in computers. But the experiments do not succeed.
11:57 AM: Dear Brig,... In my understanding, the transition from nonlife to life can be described as an appearance of replicating entities in an energy flow. In other words, an energy flow should be somehow utilized for generation of rather complex entities capable of self-replication. Surprisingly, our computer simulation of 2003 seems to show how this could work. I discuss this point in the article of 2009. I attach both articles [links to online versions are below], and you can directly jump to the page 15 of the 2009 article, section "Multifarious energetics of the Zn world", and then consult the 2003 article, if needed.
I have concluded that the origin-of-life from nonlife is impossible, and that therefore, life must come from the eternal past. This requires amending the big bang theory, but that happens all the time
anyway. May I ask you not to ignore this alternative? Thanks. Best Regards, Brig
In fact, this alternative is never ignored completely by scientists. However, this alternative is not quite comfortable because then one should explain how life may have emerged in the eternal past. It is not easy. The earth geology provides, at least, a reasonable framework for chemical simulations. This framework can be even guiding, as we show in our PNAS paper. In the same time, we know nothing about the ethernal past, so that there is no starting point for speculations or modeling. With best regards, Armen
Armen Y. Mulkidjanian, PD Dr.Dr.Sc. | University of Osnabrück | School of Physics and School of Biology/Chemistry | Osnabrück, Germany
Armen Y Mulkidjanian, "On the origin of life in the Zinc world: 1. Photosynthesizing, porous edifices built of hydrothermally precipitated zinc sulfide as cradles of life on Earth" [html], doi:10.1186/1745-6150-4-26, n26 4, Biology Direct, online 24 Aug 2009.
Armen Y Mulkidjanian et al., "Survival of the fittest before the beginning of life: selection of the first oligonucleotide-like polymers by UV light" [html], doi:10.1186/1745-6150-4-26, n3 v12, BMC Evol Biol., online 28 May 2003.
The RNA World... is the local webpage about origin-of-life theories, with a link to another of Mulkidjanian's articles, posted 21 Feb 2012.
5:09 AM: Hi Brig. Elsewhere, long long time ago in far far away Galaxy, I read this quote. I couldn't better explain but … It sounds familiar to me … Ciao, Gabriel Manzotti | Monza
"I love you sons of bitches. You're all I read any more. You're the only ones who'll talk all about the really terrific changes going on, the only ones crazy enough to know that life is a space voyage, and not a short one, either, but one that'll last for billions of years. You're the only ones with guts enough to really care about the future, who really notice what machines do to us, what wars do to us, what cities do to us, what big, simple ideas do to us, what tremendous misunderstanding, mistakes, accidents, catastrophes do to us. You're the only ones zany enough to agonize over time and distance without limit, over mysteries that will never die, over the fact that we are right now determining whether the space voyage for the next billion years or so is going to be Heaven or Hell."
— Kurt Vonnegut, "God Bless You, Mr. Rosewater"
11:28 AM: Dear Brig Klyce, ...In studying panspermia and cosmic ancestry, it seems to me that some questions can be answered with some degree of confidence and other questions remain difficult to resolve.
I'm not hung up over the question of bacterial life traveling between planets, and it seems reasonable to suppose that bacterial life existing in cometary bodies in dormant form is the transport mechanism that mediates the distribution of life throughout the galaxy. It seems that given enough time and a population of comets at higher temperatures in the past, where liquid water could have existed (and don't we know from the presence of clay minerals in comets now that there must have been liquid water?), life finds a way. There also seems to be even more room for transport at the gene level by non-living cells.
But naturally one has to turn to the question of the origin of life in the galaxy/universe. Does Fred Hoyle's metaphor of the 747 assembling itself spontaneously hold water as an accurate metaphor? Can any amount of time solve the problem of abiogenesis?
from: Brig Klyce | 12 Jan | 6:03 PM: Me, I think not. Origin-of-life research has considered every imaginable possibility, and has demonstrated little or nothing.
I'm troubled by this question. My tendency has been to think that on some planet or comet, somewhere, there was a primordial soup and perhaps an "RNA world" or a clay/organic world or some as yet unknown precursor chemistry where life could have progressed through pre-cellular evolutionary stages. In other words, I'd like to believe in the possibility of a completely non-creationist origin of life story, just displaced from Earth to allow more time.
But now I'm not so sure. What if Hoyle is essentially right, that there simply is no pathway from organic soup to life, no matter how much more time you add to the mix (even in a static universe, having given up the 13.7 bya Big Bang theory).
I once asked Fred how long it would take for life to originate. He answered, 10 to the 17th power years. I'm sure he was pulling my leg. I was being deferential and did not followup.
I am wondering how your ideas have progressed over time. In some places on the Cosmic Ancestry web site, you seem to suggest that life may have always existed. In some places, Hoyle said that it must have been created by someone, somewhere. But if so then who or what created the intelligence that created life? It seems that these questions lead either to and infinite regress of extraterrestrial creator gods, or a traditional creator of some sort.
I have concluded, after long thought, that life must come from eternity. I hope I do more than suggest this. I have even said that cosmology should be made to conform to this principle, rather than biology conforming to the big bang. I doubt that Hoyle was a creationist in any sense. Infinite regress is avoidable, but complete, sure knowledge is probably not possible. Definitely not, in my undestanding of Goedel.
I suppose these questions are so beyond our current state of knowledge, that we can only speculate, but even so, what limits do we currently have on these speculations? What can be ruled out at this time, and what is still a possibility?
I'm not trying to rule out anything, but to have the strong version of panspermia ruled IN, as a theory with merits, worth considering.
I'm also very interested in "psi" -- there is a lot of good work that has in many minds demonstrated that telepathy and remote viewing are real phenomena. These ideas are not, in my view, explainable by a physical mechanism but are hints and clues that mind is fundamental, perhaps more fundamental, than matter. Evidence for psychokinesis hints to ways in which the power of attention and intention acts on the material world. A friend suggested to me that it is worth considering whether mind can have acted as a self-organizing principle to get life started. He actually felt that it was more reasonable to suppose that mind over matter explains the origin of life on Earth than that life came from space. I disagree with that, but I think it's reasonable that patterns in the mind preexisted physical life, and maybe are a way of overcoming the statistical hurdles associated with abiogenesis. I'm tempted to propose an origin for life in the distant past somewhere in the universe that involves mind over matter over the course of billions of years. However, at this point I suppose it's just explaining one mystery with another mystery. But, I thought I'd ask if you had given any thought to this.
I am a strict materialist. Nothing comes from nothing. But why are we trying to explain the origin of life, when we have never witnessed it. We take it on faith in a very flimsy new theory (the big bang).
My other question is where you stand regarding directed panspermia. Most of your focus seems to be on genes and maybe endospores being the primary unit of transport between planetary biospheres. But, if higher-level civilizations are supposed to exist with capability to travel throughout the universe, or at least send probes or drones, then maybe life forms perhaps larger than bacteria could possibly have been transported or delivered to the Earth. Perhaps it's simply more acceptable to reason about bacterial transport since the putative extraterrestrial visitors would inevitably raise the spectre of UFOs.
Directed panspermia seems possible, but costly and unnecessary. I touch on this issue on my page titled "How Is It Possible?"
Any response you might provide will be considered private and off-the-record unless you specify otherwise. :)
Heck, tell everyone! Point them to Cosmic Ancestry! Thanks for your interest.
6:29 PM: Happy New Year, Brig. If you feel like taking a break from reporting on microbiological bench-lab research, here's a development from the other end of the biological spectrum, in case you missed it.
The November 2011 issue of The Atlantic magazine carried a profile of Edward O. Wilson, essentially a promotional piece for his upcoming book, "The Social Conquest of Earth." In the book, Wilson challenges the traditional evolutionary model of social behavior. That model, called "kin selection," says that complex societies evolve by natural selection in situations where an individual assisting, or otherwise sacrificing for, a close relative promotes the reproductive advantage of their shared genes. The article comments, "Wilson believes that this whole theory has been a wrong turn intellectually and that this bedrock concept, with major implications for understanding our own nature, is overdue for radical revision."
So what radical alternative does Wilson propose?
First, he points out that complex social behaviors do not depend on the participants being closely genetically related. He give examples. According to the article, he and his collaborators conclude that, rather than relatedness being the key factor, "a very small number of species simply seem to be genetically 'spring loaded,' or 'strongly predisposed' to the development of eusociality in conditions where natural selection favors it."
Later in the article, the operative genes are called "trigger genes." And later the article paraphrases Wilson as attributing sociality to an accumulation of such pre-adaptations.
So, if Wilson is right, then the evolution of societies; whether insect, human, or other; depends on spring-loaded, pre-adaptive trigger genes. In other words, genes that happen fortuitously to be present already when circumstances arise such that they become beneficial. Why they remain preserved prior to that time, who knows?
The new book will provide a more thoroughgoing explanation, I'm sure, such as distinguishing between prosocial and eusocial behaviors, but the evolution of social behavior per se seems to be a case of social genes predating societies. An analog to metazoan genes predating metazoans? ...Best, Ken
Metazoan Genes Older Than Metazoa? is a related local webpage.