Discovering the Tree of Life

National Science Foundation Office of Legislative and Public Affairs ^ | November 18, 2002 | NSF Press Release

[forsnax5]

NSF awards grants to discover the relationships of 1.75 million species

One of the most profound ideas to emerge in modern science is Charles Darwin's concept that all of life, from the smallest microorganism to the largest vertebrate, is connected through genetic relatedness in a vast genealogy. This "Tree of Life" summarizes all we know about biological diversity and underpins much of modern biology, yet many of its branches remain poorly known and unresolved.

To help scientists discover what Darwin described as the tree's "everbranching and beautiful ramifications," the National Science Foundation (NSF) has awarded $17 million in "Assembling the Tree of Life" grants to researchers at more than 25 institutions. Their studies range from investigations of entire pieces of DNA to assemble the bacterial branches; to the study of the origins of land plants from algae; to understanding the most diverse group of terrestrial predators, the spiders; to the diversity of fungi and parasitic roundworms; to the relationships of birds and dinosaurs.

"Despite the enormity of the task," said Quentin Wheeler, director of NSF's division of environmental biology, which funded the awards, "now is the time to reconstruct the tree of life. The conceptual, computational and technological tools are available to rapidly resolve most, if not all, major branches of the tree of life. At the same time, progress in many research areas from genomics to evolution and development is currently encumbered by the lack of a rigorous historical framework to guide research."

Scientists estimate that the 1.75 million known species are only 10 percent of the total species on earth, and that many of those species will disappear in the decades ahead. Learning about these species and their evolutionary history is epic in its scope, spanning all the life forms of an entire planet over its several billion year history, said Wheeler.

Why is assembling the tree of life so important? The tree is a picture of historical relationships that explains all similarities and differences among plants, animals and microorganisms. Because it explains biological diversity, the Tree of Life has proven useful in many fields, such as choosing experimental systems for biological research, determining which genes are common to many kinds of organisms and which are unique, tracking the origin and spread of emerging diseases and their vectors, bio-prospecting for pharmaceutical and agrochemical products, developing data bases for genetic information, and evaluating risk factors for species conservation and ecosystem restoration.

The Assembling the Tree of Life grants provide support for large multi-investigator, multi-institutional, international teams of scientists who can combine expertise and data sources, from paleontology to morphology, developmental biology, and molecular biology, says Wheeler. The awards will also involve developing software for improved visualization and analysis of extremely large data sets, and outreach and education programs in comparative phylogenetic biology and paleontology, emphasizing new training activities, informal science education, and Internet resources and dissemination.

-NSF-

For a list of the Assembling the Tree of Life grants, see: http://www.nsf.gov/bio/pubs/awards/atol_02.htm

[AndrewC]

If he's right about these internal abilities of organisms, what is there for an external agent to do?

Create the internal abilities of the organism.

[gore3000]

it is tolerably obvious that Shapiro is talking about the ability of living organisms to shape themselves in response to external events.

He does not say any such thing anywhere. Computers do not 'shape themselves' neither do information networks. These are designed. Also "the need to coordinate literally millions of biochemical events " shows quite well that random stochastic processes cannot alter or change such systems as evolutionists would have us think.

[general_re]

Create the internal abilities of the organism.

Given that "proof" is an unattainable standard, what would constitute evidence for or against such a proposition?

[AndrewC]

Given that "proof" is an unattainable standard, what would constitute evidence for or against such a proposition?

I suppose decoding a protein with this amino acid sequence "imadethesethingssmartlyinfiveyearsintheskyfindthesecret" would constitute evidence. But don't expect what I would not give someone else.

[general_re]

I suppose decoding a protein with this amino acid sequence "imadethesethingssmartlyinfiveyearsintheskyfindthesecret" would constitute evidence.

That would be rather hard to explain away, I expect ;)

But don't expect what I would not give someone else.

Sorry, not following you....

[js1138]

Actually, the Chaitin material indicates that Omega is true randomness and cannot be the result of a simple algorithm.

I don't believe the "true randomness" can be determined for a data stream.

[gore3000]

The algorithms, methods and numbers may first arrive from the theoretical physics, mathematics or information theory disciplines, without their having any particular intention to impact the theory of biological evolution.

You may be right, for one thing biology has been politicized to a great extent by evolutionists and there is not much room there for honest discussion. These are nevertheless scientific questions which need to be applied to all the sciences. The irony is that while the materialists claim that science is not allowed to consider anything which is not material as an answer, science itself, the process, is non-materialistic, and completely denies randomness. While the word algorithm comes from math, its use has been expanded to other disciplines and can be used correctly to mean 'a rule or procedure for solving a problem'. And that is what science is all about - discovering the rules and procedures of nature. Experiments in a sense are the same thing, they show the rules and procedures of these discoveries.

The product of science is thus information. Information is totally absent of material substance. Yet while materialists deny the existence of anything which is non material, they embrace science as proof that nothing outside material entities exist!

BTW - I am sure that many have thought that the sentence 'In the beginning was the Word' was somewhat allegorical or a poetic construction. My guess is that if we ever do find the algorithm of everything (which I doubt we will in this life) we will find out that the sentence is literally correct.

[AndrewC]

That would be rather hard to explain away, I expect ;)

Well, as a test I ran a comparison. This is the result.

# >ydbD
#           Length = 770
# 
#  Score = 26.9 bits (58), Expect = 2.5
#  Identities = 14/51 (27%), Positives = 25/51 (48%)
# 
# Query: 1   IMADETHESETHINGSSMARTLYINFIVEYEARSINTHESKYFINDTHESE 51
#            +  D  +++ + I GS  AR ++IN I+     S    E     +D H++E
# Sbjct: 141 VFIDSYYDNPSTIKGSINARGIFINDIIAPVVASSTNSEFMVRASDKHDTE 191
# 
# 

Now here is a result comparing MOTA flagellar protein with MTH1022.

# >MTH1022
#           Length = 279
# 
#  Score = 30.4 bits (67), Expect = 1.4
#  Identities = 26/110 (23%), Positives = 49/110 (43%), Gaps = 5/110 (4%)
# 
# Query: 136 GHMNTFEIEALMDEEIETHESEAEVPANSLALVGDSLPAFGIVAAVMGV---VHALGSAD 192
#            G+ N  E+E  M+       S       +L  + +  P  G++  V+G+     ALG   
# Sbjct: 94  GYRNRSEVEDAMERVFIVEMSNMTRGLGTLRTIIEVAPMLGLIGTVIGIWYTFRALGVNA 153
# 
# Query: 193 RPAAELGALIAHAMVGTFLGILLAYGFISPLATVLRQKSAETSKMMQCVK 242
#             PAA +   I  A++ T LG+ +A   + PL + +  +  +    ++ +K
# Sbjct: 154 DPAA-MAEGIYVALITTILGLAVAI-ILMPLYSYITGRIDDEIDKIELIK 201
# 
# 

Strange how biologists accept some things and not others.

[gore3000]

The complexity of living organisms, it seems to me, could be approximated in a similar way. -article-

While high complexity can be legitimately attributed to random events, the problem with this justification for evolution is that we know that biological systems while having a high degree of complexity, do not fit this model. Biological systems have specified complexity. The complexity is purposeful, but more important is interrelatedly complex. The possibility of such biological systems evolving was utterly destroyed with the discovery that the evolutionist's proposition of 'one gene, one protein, one function' was false. Not only does one gene make many proteins, but also many genes are required to accomplish one function. The cells themselves are not 'units', they are dependent on the functions of other cells and other cells depend on them. This results in an inextricable web of connections amongst the genes of each cell, the cell itself and the rest of the cells in an organism. The high degree of organization thus precludes any possibility of randomness being the source of the perceived complexity.

[Alamo-Girl]

Thank you for your post!

I don't believe the "true randomness" can be determined for a data stream.

According to Chaitin, that would be Omega. The Kolmogorov-Chaitin algorithmic complexity theory defines randomness within a system. But it has limitations basically because it can only define what is not random, i.e. the problem you sense. Dembski likewise argues that randomness is always subject to the possibility of a pattern being detected down the road, at which time it is no longer random.

Nevertheless, IMHO, Kolmogorov-Chaitin may present as the criteria which proves or falsifies the predictions of Intelligent Design theory. In other words, if a primordial algorithm is discovered with complexity beyond a naturalistic explanation - or in the Shapiro case at hand, if a complex algorithm is discovered at the cellular level beyond a naturalistic explanation.

From your side, the issue is argued here

From the Intelligent Design side, the issue is argued here (pdf)

For lurkers wanting an introduction to the theory: Entropy in Logic and the Theory of Algorithms

My prediction all along has been that even if Intelligent Design theory were quashed today, the advances in information theory would cause most of it to resurface quite unintentionally through the backdoor.

[gore3000]

This "filter" cannot be applied in any but the most trivial cases, because very complex outcomes can be generated by simple, iterative rules.

Complexity can be derived by simple rules as you claim. However, intelligent design does not claim that complexity itself is the criteria of design. The sand on the beach is complex but not designed. The proposition that something is designed requires both complexity and specificity. As an example a junkyard is complex but not designed, a Boeing 747 has specified complexity and is intelligently designed. Life has this same kind of specified complexity but to a much greater degree than a 747.

[gore3000]

I don't actually know anyone who argues that point mutations and genetic drift are responsible for everything any more.

Some posts back you said that Darwin's view of evolution was passe, but declined to give the 'new' theory. Now you claim that some of the replacements are also gone by the wayside. What you fail to tell us is again what has replaced this? While you question other theories and insist that yours is correct, you fail to tell us what your theory is. It seems like what you are doing is providing a ghostly target and each time a refutation is made you claim that it does not refute what you are thinking. Seems very much that you have no theory at all and just make it up as you go along because you know that evolution is false.

[Alamo-Girl]

Thank you so much for your post!

With regard to the first three words of the Bible "In the beginning" I would like to add that until Hubble, the science community thought the universe was steady state. Einstein's blunder, the cosmological constant, was an attempt to uphold the steady state theory.

With the Hubble constant came the Big Bang and inflationary theory - which mathematically shows that, from our space-time coordinates, the universe appears to be 15 billion (or so) years old - but from the space-time coordinate of it's inception, it would be approximately one elapsed week.

With God as the only observer and the author of the Genesis account, it works out quite nicely and I would have thought other fundamentalists would be very pleased. (I am a fundamentalist by definition because I believe the Bible is the inerrant Word of God.)

I do expect information theory to open another door - like the Hubble constant - showing complex algorithms at the roots, from cosmology to microbiology. Ultimately, I expect a primordial algorithm to be associated with the Big Bang.

Truly, I hope the evolutionist reaction to such findings will not be as dismissive as the fundamentalists' reactions to the Big Bang.

[Alamo-Girl]

Thank you for your post!

I also believe that ongoing discovery at that level will uncover patterns within biological systems that information theorists will then reduce to complex algorithms.

What appears random today (Omega) will reduce, IMHO.

[edsheppa]

arguably western science was based on [The "Design Theory"]

(Great, a digression!) I've heard some argue it but not convincingly IMO. Clearly many of the early giants were very religious fellows. They certainly talked in terms of "understanding God's design" but their science invoked only natural reasoning. And one wonders about the real religious sentiment of those like Laplace who had "no need of that hypothesis."

But what do we know about our own self-consciousness? Is this physical or non-physical - non-natural?

Unknown. However if I had to make a bet, given what I know right now and (mostly) based on the track record, I'd bet on a naturalistic explanation emerging. I expect it would be part of a larger theory of cognition. But I'd also bet that it's a good ways off.

Now, how about you? Do you think it's non-natural? What would be the nature of a non-natural explanation of consciousness? In what language would it be formulated? How would you demonstrate it convincingly to a skeptic?

It could logically be self evident to some that natural causes do not explain even the most obvious thing in ones life, i.e. consciousness.

That sounds contradictory or maybe I just don't take your meaning. How can something be logical and self evident? Self evidence requires no argument but logic does.

In any case, claims of self evidence are not per se convincing. Either the claim can be backed up by actual evidence or it falls. But even before that it must have a definite meaning and many claims of self evidence melt away right there. The self evidence claims of the Declaration falls in this category and also IMO so does non-naturalism.

(If one is not sure of his own consciousness, what can he be sure of?)

Again your meaning is unclear to me. Do you mean not sure that one is conscious or not sure that one's consciousness has a non-natural explanation? I don't see how this connects to the prior sentence.

If you look for only natural causes for everything that is what you will find.

Well yes and no. I agree that the direction determines to some extent what is found. But there are many contrary cases of serendipitous discovery. IIRC from my schoolboy days Fleming's discovery penicillin is the canonical example.

I take it you think scientists should be looking for non-natural causes too. Getting back to the questions I asked above, can you tell me how you propose to look for non-natural causes? How will you exhibit them? I assume reproducibility is out. What are the convincing criteria you will substitute? I'll tell you point blank, claiming self evidence as does AndrewC is not convincing.

Believe what you want to believe and see what you what to see

That's a cop out. Expanded rationality has been a extraordinary boon to mankind. You're turning your back on it.

[general_re]

Well, as a test I ran a comparison.

Well, as a check of your test, I went to the journals for the relevant excerpt. Hopefully the graphic will show up for you, but if not, I'll grab it and put it somewhere where it will. I count 55 residues, of which 23 are common to both motA in A. aeolicus and MTH1022 in M. thermoautotrophicum, or 42%. Which beats both your comparisons handily ;)

---

Conformational Change in the Stator of the Bacterial Flagellar Motor

Seiji Kojima and David F. Blair*

Department of Biology, University of Utah, Salt Lake City, Utah 84112

---

The occurrence of significant conformational change in the stator has implications not only for the present-day mechanism but also for the evolution of the flagellar motor. A membrane complex that undergoes proton-driven conformational changes could perform useful work in contexts other than (and simpler than) the flagellar motor, and ancestral forms of the MotA/MotB complex might have arisen independently of any part of the rotor. We queried the sequence database using the sequence of the best-conserved part of MotA (the segment containing membrane segments 3 and 4) from Aquifex aeolicus, a species whose lineage is deeply branched from other bacteria. In addition to the expected MotA homologues, the search returned a protein sequence from the archaeal species Methanobacterium thermoautotrophicum (protein MTH1022) that shows significant sequence similarity not only to MotA but also to the protein ExbB (Figure 9). ExbB is a cytoplasmic-membrane protein that functions in conjunction with ExbD, TonB, and outer-membrane receptors to drive active transport of certain essential nutrients across the outer membrane of Gram-negative bacteria. The energy for this transport comes from the proton gradient across the inner membrane. Thus, MotA and ExbB are both components of systems that tap the proton gradient to do work some distance away (at either the rotor-stator interface or the outer membrane; Figure 9).

---

Figure 9 Correspondences between the MotA/MotB and ExbB/ExbD complexes. (A) Functions of the complexes. Both use the membrane proton gradient as a source of energy to drive processes occurring outside of the membrane (either the application of force to the flagellar rotor, or active transport of nutrients across the outer membrane). As shown here very diagrammatically, the complexes are hypothesized to do work by undergoing conformational changes as protons move on and off critical Asp residues in MotB and ExbD, respectively. (B) Membrane topologies. The ExbB/ExbD complex also contains the protein TonB, which has a single membrane segment with topology (N-terminus in) like that of segment 1 of MotA. Pro and Asp residues important for function and conserved in both systems are shown. (C) Alignment of a ca. 50-residue segment from selected MotA and ExbB sequences. Shown below are approximate positions of membrane segments (segments 3 and 4 of MotA, or segments 2 and 3 of ExbB). The arrow indicates a Pro residue that is conserved in both systems and known to be important for function of MotA (Pro173 in MotA of E. coli). V. chol., Vibrio cholerae; D. rad., Deinococcus radiodurans; M. ther., Methanobacterium thermoautotrophicum; A. ael., Aquifex aeolicus; D. vulg., Desulfovibrio vulgaris. Using the M. thermoautotrophicum MTH1022 sequence fragment to query the database of finished and unfinished bacterial genomes (National Center for Biotechnology Information, 5/21/01), pairwise BLAST E-values for these alignments are for V. cholerae [ExbB], 1E-6; for D. radiodurans [ExbB], 9E-5; for A. aeolicus [MotA], 0.004; and for D. vulgaris [MotA], 0.002.

---

Other features also point to a connection between the Mot and Exb systems. MotA functions in a complex with MotB, which as noted contains the critical residue Asp32 near the cytoplasmic end of its single membrane segment. ExbB functions in a complex with ExbD, which likewise has a single membrane segment with a critical Asp residue near its cytoplasmic end (Asp25 in ExbD of E. coli; ref 59). Although ExbB has only three membrane segments in contrast to the four in MotA, the membrane segments that show sequence similarity have the same topology. The protein TonB is also present in the complex with ExbB and ExbD (59, 60) and would provide an additional membrane segment to round out the topological correspondence (Figure 9). ExbB contains a well-conserved Pro residue (Pro141 in E. coli ExbB) that is the counterpart of Pro173 of MotA. Although MotB and ExbD do not share close sequence similarity apart from the critical Asp residue, in certain positions in the membrane segment the residues most common in MotB proteins are also common in ExbD proteins. Finally, like the MotA/MotB complex the ExbB/ExbD complex contains multiple copies of each protein (61). Together, these facts make a reasonable case for an evolutionary connection between the Mot proteins of the flagellar motor and the Exb proteins of outer-membrane transport (and by extension the TolQ/TolR proteins, which are related to ExbB/ExbD but whose functions are less understood).

[gore3000]

I can't recall anyone actually attacking Christianity, but there have certainly been objections to literal interpretations of the Bible.

All atheists use that method of attacking Christianity. As pointed out they know that a direct attack is less effective than a flank attack.

Well, there's this thing about beginnings. You want life to be created by existing life, so you're kind of fudging the "first life" thing. Or maybe God is not alive? And the fact that "evolution" doesn't include "abiogenesis" is just simply that evolution describes change, not beginnings.

Hard to discern your intended meaning. However, on this very thread the evolutionists are all defending abiogenesis tooth and nail. The opponents of evolution are all against it. I don't believe in such great coincidence. More importantly, the evolutionists claim that their beliefs are based on science. Abiogenesis as has been shown already has been totally discredited by science. Therefore evolutionist's insistence on abiogenesis shows that their guiding principle is not science.

This is a really odd proposal. I can see you arguing for ALL species being created, or for all "kinds" being created, but what would ONE species do for you? As to the question itself (why not one?), because that would make no sense to either side of the discussion.

You are answering my question with a question. Thus your answer is an evasion. If evolution were adhered to as science, then evolutionists should have no problem making such a concession. But man is the ultimate goal of evolution because it is the goal of evolution to 'refute' Christianity. In fact they have brought themselves much grief on this account alone. Why get into a fight against all if the goal is a scientific one instead of a teleological one?

If an Intelligent Designer designed anything at all, then everything could have been designed. If everything was designed, then nothing is related. If nothing is related, then all of our biological inferences are imaginary. ID simply creates more problems than it solves. Stick with God.

The above shows that evolution is an ideology, an ideology whose purpose is to completely eradicate God's hand from nature. Just what I am asserting. It also shows again that in spite of overwhelming evidence for the ID position, the evolutionists reject it out of hand in favor of 'hopeful monsters'. Showing again that evolution is not about science, but about atheism.

More of the same rant.

Not quite and your only 'refutation' is a personal attack. Science is not ideological but evolutionists are, that is why they cannot give an inch. They cannot allow God into anything because their purpose is the promotion of atheism. Let me note that Darwin himself asserted that a single example that could not be explained by evolution would completely destroy the theory. This does not seem to be the mentality or type of thinking of a scientist, but the mindset of an ideologue which has an axe to grind. This axe is the attack on Christianity which his atheism required.

[AndrewC]

Which beats both your comparisons handily ;)

Well actually no. It beats the message handily but is a subset of the longer sequence comparison of the E.coli(mota) and the MTH1022. The mota selection in your comparison is also from a different bug but essentially the comparison looks better because a smaller range was extracted. The point made is that, taking the whole range into consideration, the expectations are of similar order.

[Junior]

All atheists use that method of attacking Christianity.

Ah, spoken like a true, closed-minded fanatic. So, why do humans have genes for tails?

[PatrickHenry]

I meant the word faith to mean "something that is believed with strong conviction." That implies "without doubt or question" and thus usually is associated with religious belief. Perhaps it would have suited you better if I had said:

That is the problem, isn't it? Both sides reach a point of strong conviction - one in a hypothesis and the other in theology.

All hypotheses, IMHO, should be subject to testing and especially, to falsification - or else they risk becoming ideology. I would that the criteria for falsification of the theory of biological evolution were specified and published (if they are, I haven't found them thus far.)

Better. Much better. Now you have it right -- both sides reach a point where they won't budge. To a casual observer, it seems that they are not only equally stubborn, but equally unmoveable. But that would be error, because as I said, the hypothesis can be disproved, and he who holds a discredited hypothesis will drop it when the evidence becomes undeniable. That's how science moves forward. So the stubbornness of the scientist is: "I'm sticking with my theory until it's proven wrong." The stubbornness of the theologean has no until associated with it.

As for the criteria for falsifying evolution, it's mentioned from time to time in our threads, but you're not a constant player here, so you've missed it. The theory explains the data (fossils, DNA, etc) as a natural development over time. Any clear evidence of development out of sequence would blow the theory away. The usual example is a fossil of a mammal which is unmistakably from a time long before mammals could have developed. An even neater example -- which never appeared -- would have been the discovery that man's DNA was clearly unrelated to that of every other terrestrial animal. The discovery of DNA was a grand test of Darwin's theory. Such unique DNA for mankind would have shown that: (a) we descended from extra-terrestrial voyagers who were castaways on this world; or (b) we were specially created, apart from the other life on this world. Although people continue to argue for "a" or for "b", there is no scientific evidence to do so. But there might have been.